Add first working version of enzo

Source spack-env.sh to execute spack bootstrap. Then source
spack-env.sh again to get module functionality.

.codecov.yml

@@ -1,36 +0,0 @@
-coverage:
-  precision: 2
-  round: nearest
-  range: 60...90
-  status:
-    project:
-      default: true
-      llnl:
-        threshold: 0.5
-        paths:
-          - lib/spack/llnl
-      commands:
-        threshold: 0.5
-        paths:
-          - lib/spack/spack/cmd
-      build_systems:
-        threshold: 0.5
-        paths:
-          - lib/spack/spack/build_systems
-      modules:
-        threshold: 0.5
-        paths:
-          - lib/spack/spack/modules
-      core:
-        threshold: 0.5
-        paths:
-          - "!lib/spack/llnl"
-          - "!lib/spack/spack/cmd"
-
-ignore:
-  - lib/spack/spack/test/.*
-  - lib/spack/env/.*
-  - lib/spack/docs/.*
-  - lib/spack/external/.*
-
-comment: off

.flake8

@@ -1,8 +1,8 @@
 # -*- conf -*-
-# flake8 settings for Spack core files.
+# flake8 settings for Spack.
 #
-# These exceptions ar for Spack core files. We're slightly more lenient
-# with packages.  See .flake8_packages for that.
+# Below we describe which flake8 checks Spack ignores and what the
+# rationale is.
 #
 # Let people line things up nicely:
 # - E129: visually indented line with same indent as next logical line
@@ -11,11 +11,16 @@
 # - E272: multiple spaces before keyword
 #
 # Let people use terse Python features:
-# - E731: lambda expressions
+# - E731 : lambda expressions
 #
-# These are required to get the package.py files to test clean:
+# Spack allows wildcard imports:
+# - F403: disable wildcard import
+#
+# These are required to get the package.py files to test clean.
+# - F405: `name` may be undefined, or undefined from star imports: `module`
+# - F821: undefined name `name` (needed for cmake, configure, etc.)
 # - F999: syntax error in doctest
 #
 [flake8]
-ignore = E129,E221,E241,E272,E731,F999
+ignore = E129,E221,E241,E272,E731,F403,F405,F821,F999
 max-line-length = 79

.flake8_packages

@@ -1,22 +0,0 @@
-# -*- conf -*-
-# flake8 settings for Spack package files.
-#
-# This should include all the same exceptions that we use for core files.
-#
-# In Spack packages, we also allow the single `from spack import *`
-# wildcard import and dependencies can set globals for their
-# dependents. So we add exceptions for checks related to undefined names.
-#
-# Note that we also add *per-line* exemptions for certain patters in the
-# `spack flake8` command.  This is where F403 for `from spack import *`
-# is added (beause we *only* allow that wildcard).
-#
-# See .flake8 for regular exceptions.
-#
-# Redefinition exceptions:
-# - F405: `name` may be undefined, or undefined from star imports: `module`
-# - F821: undefined name `name` (needed for cmake, configure, etc.)
-#
-[flake8]
-ignore = E129,E221,E241,E272,E731,F999,F405,F821
-max-line-length = 79

.gitignore

@@ -8,9 +8,8 @@
 *~
 .DS_Store
 .idea
-# Ignore everything in /etc/spack except /etc/spack/defaults
-/etc/spack/*
-!/etc/spack/defaults
+/etc/spack/licenses
+/etc/spack/*.yaml
 /etc/spackconfig
 /share/spack/dotkit
 /share/spack/modules
@@ -23,5 +22,3 @@
 .#*
 /.cache
 /bin/spackc
-*.in.log
-*.out.log

.mailmap

@@ -3,7 +3,6 @@ Adam Moody            <moody20@llnl.gov>                Adam T. Moody
 Alfredo Gimenez       <gimenez1@llnl.gov>               Alfredo Gimenez         <alfredo.gimenez@gmail.com>
 Alfredo Gimenez       <gimenez1@llnl.gov>               Alfredo Adolfo Gimenez  <alfredo.gimenez@gmail.com>
 Andrew Williams       <williamsa89@cardiff.ac.uk>       Andrew Williams         <andrew@alshain.org.uk>
-Axel Huebl            <a.huebl@hzdr.de>                 Axel Huebl              <axel.huebl@plasma.ninja>
 Ben Boeckel           <ben.boeckel@kitware.com>         Ben Boeckel             <mathstuf@gmail.com>
 Ben Boeckel           <ben.boeckel@kitware.com>         Ben Boeckel             <mathstuf@users.noreply.github.com>
 Benedikt Hegner       <hegner@cern.ch>                  Benedikt Hegner         <benedikt.hegner@cern.ch>
@@ -49,7 +48,6 @@ Robert D. French      <frenchrd@ornl.gov>               Robert D. French
 Robert D. French      <frenchrd@ornl.gov>               Robert.French           <frenchrd@ornl.gov>
 Robert D. French      <frenchrd@ornl.gov>               robertdfrench           <frenchrd@ornl.gov>
 Saravan Pantham       <saravan.pantham@gmail.com>       Saravan Pantham         <pantham1@surface86.llnl.gov>
-Sergey Kosukhin       <sergey.kosukhin@mpimet.mpg.de>   Sergey Kosukhin         <skosukhin@gmail.com>
 Stephen Herbein       <sherbein@udel.edu>               Stephen Herbein         <stephen272@gmail.com>
 Todd Gamblin          <tgamblin@llnl.gov>               George Todd Gamblin     <gamblin2@llnl.gov>
 Todd Gamblin          <tgamblin@llnl.gov>               Todd Gamblin            <gamblin2@llnl.gov>

.travis.yml

@@ -1,107 +1,40 @@
 #=============================================================================
 # Project settings
 #=============================================================================
+language: python
+
 # Only build master and develop on push; do not build every branch.
 branches:
   only:
     - master
     - develop
-    - /^releases\/.*$/
 
 #=============================================================================
 # Build matrix
 #=============================================================================
-jobs:
-  fast_finish: true
+python:
+  - 2.6
+  - 2.7
+
+env:
+  - TEST_SUITE=unit
+  - TEST_SUITE=flake8
+  - TEST_SUITE=doc
+
+matrix:
+  # Flake8 and Sphinx no longer support Python 2.6, and one run is enough.
+  exclude:
+  - python: 2.6
+    env: TEST_SUITE=flake8
+  - python: 2.6
+    env: TEST_SUITE=doc
+  # Explicitly include an OS X build with homebrew's python.
+  # Works around Python issues on Travis for OSX, described here:
+  # http://blog.fizyk.net.pl/blog/running-python-tests-on-traviss-osx-workers.html
   include:
-    - stage: 'flake8 + documentation'
-      python: '2.7'
-      os: linux
-      language: python
-      env: TEST_SUITE=flake8
-    - stage: 'flake8 + documentation'
-      python: '2.7'
-      os: linux
-      language: python
-      env: TEST_SUITE=doc
-    - stage: 'unit tests'
-      python: '2.6'
-      os: linux
-      language: python
-      env: TEST_SUITE=unit
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=unit, COVERAGE=true ]
-    - python: '3.3'
-      os: linux
-      language: python
-      env: TEST_SUITE=unit
-    - python: '3.4'
-      os: linux
-      language: python
-      env: TEST_SUITE=unit
-    - python: '3.5'
-      os: linux
-      language: python
-      env: TEST_SUITE=unit
-    - python: '3.6'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=unit, COVERAGE=true ]
-    - stage: 'unit tests - osx'
-      os: osx
-      language: generic
-      env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7, COVERAGE=true ]
-# mpich (AutotoolsPackage)
-    - stage: 'build tests'
-      python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=mpich' ]
-# astyle (MakefilePackage)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=astyle' ]
-# tut (WafPackage)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=tut' ]
-# py-setuptools (PythonPackage)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=py-setuptools' ]
-# perl-dbi (PerlPackage)
-#    - python: '2.7'
-#      os: linux
-#      language: python
-#      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=perl-dbi' ]
-# openjpeg (CMakePackage + external cmake)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=openjpeg' ]
-# r-rcpp (RPackage + external R)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=r-rcpp' ]
-# mpich (AutotoolsPackage)
-    - python: '3.6'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=mpich' ]
-
-stages:
-  - 'flake8 + documentation'
-  - 'unit tests'
-  - 'build tests'
-  - name: 'unit tests - osx'
-    if: type IN (cron)
-
+  - os: osx
+    language: generic
+    env: TEST_SUITE=unit
 
 #=============================================================================
 # Environment
@@ -114,36 +47,23 @@ addons:
   apt:
     packages:
       - gfortran
-      - mercurial
       - graphviz
-      - gnupg2
-      - cmake
-      - r-base
-      - r-base-core
-      - r-base-dev
-      - perl
-      - perl-base
-
-cache: pip
+      - libyaml-dev
 
 # Work around Travis's lack of support for Python on OSX
 before_install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions python > /dev/null || brew install python; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then rm /usr/local/include/c++ ; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions gcc    > /dev/null || brew install gcc;    fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions gnupg2 > /dev/null || brew install gnupg2; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then virtualenv venv; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then source venv/bin/activate; fi
 
 # Install various dependencies
 install:
-  - pip install --upgrade pip
-  - pip install --upgrade six
-  - pip install --upgrade setuptools
-  - pip install --upgrade codecov
+  - pip install --upgrade coveralls
   - pip install --upgrade flake8
-  - if [[ "$TEST_SUITE" == "doc" ]]; then pip install --upgrade -r lib/spack/docs/requirements.txt; fi
+  - pip install --upgrade sphinx
+  - pip install --upgrade mercurial
 
 before_script:
   # Need this for the git tests to succeed.
@@ -153,15 +73,13 @@ before_script:
   # Need this to be able to compute the list of changed files
   - git fetch origin develop:develop
 
-  # Set up external dependencies for build tests, because the take too long to compile
-  - if [[ "$TEST_SUITE" == "build" ]]; then cp share/spack/qa/configuration/packages.yaml etc/spack/packages.yaml; fi
-
 #=============================================================================
 # Building
 #=============================================================================
-script:
-  - share/spack/qa/run-$TEST_SUITE-tests
-  - if [[ "$COVERAGE" == "true" ]]; then codecov --env PYTHON_VERSION --required --flags "${TEST_SUITE}${TRAVIS_OS_NAME}"; fi
+script: share/spack/qa/run-$TEST_SUITE-tests
+
+after_success:
+  - if [[ $TEST_SUITE == unit && $TRAVIS_PYTHON_VERSION == 2.7 && $TRAVIS_OS_NAME == "linux" ]]; then coveralls; fi
 
 #=============================================================================
 # Notifications

CODE_OF_CONDUCT.md

@@ -1,46 +0,0 @@
-# Contributor Covenant Code of Conduct
-
-## Our Pledge
-
-In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
-
-## Our Standards
-
-Examples of behavior that contributes to creating a positive environment include:
-
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
-
-Examples of unacceptable behavior by participants include:
-
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
-
-## Our Responsibilities
-
-Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
-
-Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
-
-## Scope
-
-This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
-
-## Enforcement
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at maintainers@spack.io. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
-
-Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
-
-## Attribution
-
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
-
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/

CONTRIBUTING.md

@@ -1,5 +0,0 @@
-# Contributing to Spack
-
-Before contributing to Spack you should read the
-[Contribution Guide](https://spack.readthedocs.io/en/latest/contribution_guide.html),
-which is maintained as part of Spack's documentation.

LICENSE

@@ -1,197 +1,135 @@
-		  GNU LESSER GENERAL PUBLIC LICENSE
-		       Version 2.1, February 1999
+########################################################################
+GNU LESSER GENERAL PUBLIC LICENSE (Lesser GPL)
+Version 2.1, February 1999
+########################################################################
+Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+Produced at the Lawrence Livermore National Laboratory.
 
- Copyright (C) 1991, 1999 Free Software Foundation, Inc.
- 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
+This file is part of Spack.
+Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+LLNL-CODE-647188
 
-[This is the first released version of the Lesser GPL.  It also counts
- as the successor of the GNU Library Public License, version 2, hence
- the version number 2.1.]
+For details, see https://github.com/llnl/spack
 
-			    Preamble
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License (as
+published by the Free Software Foundation) version 2.1, February 1999.
 
-  The licenses for most software are designed to take away your
-freedom to share and change it.  By contrast, the GNU General Public
-Licenses are intended to guarantee your freedom to share and change
-free software--to make sure the software is free for all its users.
+This program is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+conditions of the GNU Lesser General Public License for more details.
 
-  This license, the Lesser General Public License, applies to some
-specially designated software packages--typically libraries--of the
-Free Software Foundation and other authors who decide to use it.  You
-can use it too, but we suggest you first think carefully about whether
-this license or the ordinary General Public License is the better
-strategy to use in any particular case, based on the explanations below.
+You should have received a copy of the GNU Lesser General Public
+License along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 
-  When we speak of free software, we are referring to freedom of use,
-not price.  Our General Public Licenses are designed to make sure that
-you have the freedom to distribute copies of free software (and charge
-for this service if you wish); that you receive source code or can get
-it if you want it; that you can change the software and use pieces of
-it in new free programs; and that you are informed that you can do
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+########################################################################
+LLNL NOTICE AND TERMS AND CONDITIONS OF THE GNU LGPL
 
-  To protect your rights, we need to make restrictions that forbid
-distributors to deny you these rights or to ask you to surrender these
-rights.  These restrictions translate to certain responsibilities for
-you if you distribute copies of the library or if you modify it.
+LLNL Preamble Notice
 
-  For example, if you distribute copies of the library, whether gratis
-or for a fee, you must give the recipients all the rights that we gave
-you.  You must make sure that they, too, receive or can get the source
-code.  If you link other code with the library, you must provide
-complete object files to the recipients, so that they can relink them
-with the library after making changes to the library and recompiling
-it.  And you must show them these terms so they know their rights.
+A. This notice is required to be provided under LLNL's contract with
+   the U.S. Department of Energy (DOE). This work was produced at the
+   Lawrence Livermore National Laboratory under Contract
+   No. DE-AC52-07NA27344 with the DOE.
 
-  We protect your rights with a two-step method: (1) we copyright the
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+B. Neither the United States Government nor Lawrence Livermore
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+   warranty, express or implied, or assumes any liability or
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+   information, apparatus, product, or process disclosed, or
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-  To protect each distributor, we want to make it very clear that
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+   those of the United States Government or Lawrence Livermore
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+   product endorsement purposes.
 
-  Finally, software patents pose a constant threat to the existence of
-any free program.  We wish to make sure that a company cannot
-effectively restrict the users of a free program by obtaining a
-restrictive license from a patent holder.  Therefore, we insist that
-any patent license obtained for a version of the library must be
-consistent with the full freedom of use specified in this license.
+The precise terms and conditions for copying, distribution and
+modification follows.
 
-  Most GNU software, including some libraries, is covered by the
-ordinary GNU General Public License.  This license, the GNU Lesser
-General Public License, applies to certain designated libraries, and
-is quite different from the ordinary General Public License.  We use
-this license for certain libraries in order to permit linking those
-libraries into non-free programs.
+########################################################################
+GNU LESSER GENERAL PUBLIC LICENSE
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
 
-  When a program is linked with a library, whether statically or using
-a shared library, the combination of the two is legally speaking a
-combined work, a derivative of the original library.  The ordinary
-General Public License therefore permits such linking only if the
-entire combination fits its criteria of freedom.  The Lesser General
-Public License permits more lax criteria for linking other code with
-the library.
-
-  We call this license the "Lesser" General Public License because it
-does Less to protect the user's freedom than the ordinary General
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-system.
-
-  Although the Lesser General Public License is Less protective of the
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-   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
-
-  0. This License Agreement applies to any software library or other
+0. This License Agreement applies to any software library or other
 program which contains a notice placed by the copyright holder or
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-this Lesser General Public License (also called "this License").
-Each licensee is addressed as "you".
+this Lesser General Public License (also called "this License"). Each
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@@ -208,191 +146,189 @@ with the Library (or with a work based on the Library) on a volume of
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@@ -402,102 +338,56 @@ impose that choice.
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NOTICE

@@ -1,32 +0,0 @@
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README.md

@@ -1,30 +1,31 @@
-# <img src="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo.svg" width="64" valign="middle" alt="Spack"/> Spack
+![image](share/spack/logo/spack-logo-text-64.png "Spack")
+============
 
-[![Build Status](https://travis-ci.org/spack/spack.svg?branch=develop)](https://travis-ci.org/spack/spack)
-[![codecov](https://codecov.io/gh/spack/spack/branch/develop/graph/badge.svg)](https://codecov.io/gh/spack/spack)
-[![Read the Docs](https://readthedocs.org/projects/spack/badge/?version=latest)](https://spack.readthedocs.io)
-[![Slack](https://spackpm.herokuapp.com/badge.svg)](https://spackpm.herokuapp.com)
+[![Build Status](https://travis-ci.org/LLNL/spack.svg?branch=develop)](https://travis-ci.org/LLNL/spack)
+[![Coverage Status](https://coveralls.io/repos/github/LLNL/spack/badge.svg?branch=develop)](https://coveralls.io/github/LLNL/spack?branch=develop)
 
-Spack is a multi-platform package manager that builds and installs
-multiple versions and configurations of software. It works on Linux,
-macOS, and many supercomputers. Spack is non-destructive: installing a
-new version of a package does not break existing installations, so many
-configurations of the same package can coexist.
+Spack is a package management tool designed to support multiple
+versions and configurations of software on a wide variety of platforms
+and environments. It was designed for large supercomputing centers,
+where many users and application teams share common installations of
+software on clusters with exotic architectures, using libraries that
+do not have a standard ABI. Spack is non-destructive: installing a new
+version does not break existing installations, so many configurations
+can coexist on the same system.
 
-Spack offers a simple "spec" syntax that allows users to specify versions
-and configuration options. Package files are written in pure Python, and
-specs allow package authors to write a single script for many different
-builds of the same package.  With Spack, you can build your software
-*all* the ways you want to.
+Most importantly, Spack is simple. It offers a simple spec syntax so
+that users can specify versions and configuration options
+concisely. Spack is also simple for package authors: package files are
+written in pure Python, and specs allow package authors to write a
+single build script for many different builds of the same package.
 
 See the
 [Feature Overview](http://spack.readthedocs.io/en/latest/features.html)
 for examples and highlights.
 
-To install spack and your first package, make sure you have Python.
-Then:
+To install spack and install your first package:
 
-    $ git clone https://github.com/spack/spack.git
+    $ git clone https://github.com/llnl/spack.git
     $ cd spack/bin
     $ ./spack install libelf
 
@@ -34,16 +35,15 @@ Documentation
 [**Full documentation**](http://spack.readthedocs.io/) for Spack is
 the first place to look.
 
-Try the
-[**Spack Tutorial**](http://spack.readthedocs.io/en/latest/tutorial.html),
-to learn how to use spack, write packages, or deploy packages for users
-at your site.
+We've also got a [**Spack 101 Tutorial**](http://spack.readthedocs.io/en/latest/tutorial_sc16.html),
+so you can learn Spack yourself, or teach users at your own site.
 
 See also:
   * [Technical paper](http://www.computer.org/csdl/proceedings/sc/2015/3723/00/2807623.pdf) and
     [slides](https://tgamblin.github.io/files/Gamblin-Spack-SC15-Talk.pdf) on Spack's design and implementation.
   * [Short presentation](https://tgamblin.github.io/files/Gamblin-Spack-Lightning-Talk-BOF-SC15.pdf) from the *Getting Scientific Software Installed* BOF session at Supercomputing 2015.
 
+
 Get Involved!
 ------------------------
 
@@ -53,44 +53,37 @@ packages to bugfixes, or even new core features.
 
 ### Mailing list
 
-If you are interested in contributing to spack, join the mailing list.
-We're using Google Groups for this:
+If you are interested in contributing to spack, the first step is to
+join the mailing list.  We're using a Google Group for this, and you
+can join it here:
 
   * [Spack Google Group](https://groups.google.com/d/forum/spack)
 
-### Slack channel
-
-Spack has a Slack channel where you can chat about all things Spack:
-
-  * [Spack on Slack](https://spackpm.slack.com)
-
-[Sign up here](https://spackpm.herokuapp.com) to get an invitation mailed
-to you.
-
 ### Contributions
 
 Contributing to Spack is relatively easy.  Just send us a
 [pull request](https://help.github.com/articles/using-pull-requests/).
 When you send your request, make ``develop`` the destination branch on the
-[Spack repository](https://github.com/spack/spack).
+[Spack repository](https://github.com/LLNL/spack).
 
 Your PR must pass Spack's unit tests and documentation tests, and must be
-[PEP 8](https://www.python.org/dev/peps/pep-0008/) compliant.  We enforce
-these guidelines with [Travis CI](https://travis-ci.org/spack/spack).  To
-run these tests locally, and for helpful tips on git, see our
+[PEP 8](https://www.python.org/dev/peps/pep-0008/) compliant.
+We enforce these guidelines with [Travis CI](https://travis-ci.org/LLNL/spack).
+To run these tests locally, and for helpful tips on git, see our
 [Contribution Guide](http://spack.readthedocs.io/en/latest/contribution_guide.html).
 
-Spack uses a rough approximation of the
-[Git Flow](http://nvie.com/posts/a-successful-git-branching-model/)
+Spack uses a rough approximation of the [Git
+Flow](http://nvie.com/posts/a-successful-git-branching-model/)
 branching model.  The ``develop`` branch contains the latest
-contributions, and ``master`` is always tagged and points to the latest
-stable release.
+contributions, and ``master`` is always tagged and points to the
+latest stable release.
+
 
 Authors
 ----------------
-Many thanks go to Spack's [contributors](https://github.com/spack/spack/graphs/contributors).
+Many thanks go to Spack's [contributors](https://github.com/llnl/spack/graphs/contributors).
 
-Spack was created by Todd Gamblin, tgamblin@llnl.gov.
+Spack was originally written by Todd Gamblin, tgamblin@llnl.gov.
 
 ### Citing Spack
 
@@ -104,8 +97,6 @@ If you are referencing Spack in a publication, please cite the following paper:
 Release
 ----------------
 Spack is released under an LGPL license.  For more details see the
-NOTICE and LICENSE files.
+LICENSE file.
 
 ``LLNL-CODE-647188``
-
-![Analytics](https://ga-beacon.appspot.com/UA-101208306-3/welcome-page?pixel)

bin/sbang

@@ -1,14 +1,14 @@
 #!/bin/bash
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -104,27 +104,18 @@ lines=0
 while read line && ((lines < 2)) ; do
     if [[ "$line" = '#!'* ]]; then
         interpreter="${line#\#!}"
-    elif [[ "$line" = '//!'*node* ]]; then
-        interpreter="${line#//!}"
     elif [[ "$line" = '--!'*lua* ]]; then
         interpreter="${line#--!}"
     fi
     lines=$((lines+1))
 done < "$script"
-# this is ineeded for scripts with sbang parameter
-# like ones in intltool
-# #!/<spack-long-path>/perl -w
-# this is the interpreter line with all the parameters as a vector
-interpreter_v=(${interpreter})
-# this is the single interpreter path 
-interpreter_f="${interpreter_v[0]}"
 
 # Invoke any interpreter found, or raise an error if none was found.
-if [[ -n "$interpreter_f" ]]; then
-    if [[ "${interpreter_f##*/}" = "perl" ]]; then
-        exec $interpreter_v -x "$@"
+if [[ -n "$interpreter" ]]; then
+    if [[ "${interpreter##*/}" = "perl" ]]; then
+        exec $interpreter -x "$@"
     else
-        exec $interpreter_v "$@"
+        exec $interpreter "$@"
     fi
 else
     echo "error: sbang found no interpreter in $script"

bin/spack

@@ -1,14 +1,15 @@
 #!/usr/bin/env python
+# flake8: noqa
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -23,38 +24,27 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-from __future__ import print_function
-
-import os
 import sys
-
-if sys.version_info[:2] < (2, 6):
+if (sys.version_info[0] > 2) or (sys.version_info[:2] < (2, 6)):
     v_info = sys.version_info[:3]
-    sys.exit("Spack requires Python 2.6 or higher."
+    sys.exit("Spack requires Python 2.6 or 2.7. "
              "This is Python %d.%d.%d." % v_info)
 
+import os
+import inspect
+
 # Find spack's location and its prefix.
-spack_file = os.path.realpath(os.path.expanduser(__file__))
-spack_prefix = os.path.dirname(os.path.dirname(spack_file))
+SPACK_FILE = os.path.realpath(os.path.expanduser(__file__))
+os.environ["SPACK_FILE"] = SPACK_FILE
+SPACK_PREFIX = os.path.dirname(os.path.dirname(SPACK_FILE))
 
 # Allow spack libs to be imported in our scripts
-spack_lib_path = os.path.join(spack_prefix, "lib", "spack")
-sys.path.insert(0, spack_lib_path)
+SPACK_LIB_PATH = os.path.join(SPACK_PREFIX, "lib", "spack")
+sys.path.insert(0, SPACK_LIB_PATH)
 
 # Add external libs
-spack_external_libs = os.path.join(spack_lib_path, "external")
-
-if sys.version_info[:2] == (2, 6):
-    sys.path.insert(0, os.path.join(spack_external_libs, 'py26'))
-
-sys.path.insert(0, spack_external_libs)
-
-# Handle vendoring of YAML specially, as it has two versions.
-if sys.version_info[0] == 2:
-    spack_yaml_libs = os.path.join(spack_external_libs, "yaml/lib")
-else:
-    spack_yaml_libs = os.path.join(spack_external_libs, "yaml/lib3")
-sys.path.insert(0, spack_yaml_libs)
+SPACK_EXTERNAL_LIBS = os.path.join(SPACK_LIB_PATH, "external")
+sys.path.insert(0, SPACK_EXTERNAL_LIBS)
 
 # Quick and dirty check to clean orphaned .pyc files left over from
 # previous revisions.  These files were present in earlier versions of
@@ -62,13 +52,13 @@ sys.path.insert(0, spack_yaml_libs)
 # imports.  If we leave them, Spack will fail in mysterious ways.
 # TODO: more elegant solution for orphaned pyc files.
 orphaned_pyc_files = [
-    os.path.join(spack_external_libs, 'functools.pyc'),
-    os.path.join(spack_external_libs, 'ordereddict.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'platforms', 'cray_xc.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'cmd', 'package-list.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'cmd', 'test-install.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'cmd', 'url-parse.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'test', 'yaml.pyc')
+    os.path.join(SPACK_EXTERNAL_LIBS, 'functools.pyc'),
+    os.path.join(SPACK_EXTERNAL_LIBS, 'ordereddict.pyc'),
+    os.path.join(SPACK_LIB_PATH, 'spack', 'platforms', 'cray_xc.pyc'),
+    os.path.join(SPACK_LIB_PATH, 'spack', 'cmd', 'package-list.pyc'),
+    os.path.join(SPACK_LIB_PATH, 'spack', 'cmd', 'test-install.pyc'),
+    os.path.join(SPACK_LIB_PATH, 'spack', 'cmd', 'url-parse.pyc'),
+    os.path.join(SPACK_LIB_PATH, 'spack', 'test', 'yaml.pyc')
 ]
 
 for pyc_file in orphaned_pyc_files:
@@ -77,9 +67,146 @@ for pyc_file in orphaned_pyc_files:
     try:
         os.remove(pyc_file)
     except OSError as e:
-        print("WARNING: Spack may fail mysteriously. "
-              "Couldn't remove orphaned .pyc file: %s" % pyc_file)
+        print ("WARNING: Spack may fail mysteriously. "
+               "Couldn't remove orphaned .pyc file: %s" % pyc_file)
 
-# Once we've set up the system path, run the spack main method
-import spack.main  # noqa
-sys.exit(spack.main.main())
+# If there is no working directory, use the spack prefix.
+try:
+    working_dir = os.getcwd()
+except OSError:
+    os.chdir(SPACK_PREFIX)
+    working_dir = SPACK_PREFIX
+
+# clean up the scope and start using spack package instead.
+del SPACK_FILE, SPACK_PREFIX, SPACK_LIB_PATH
+import llnl.util.tty as tty
+from llnl.util.tty.color import *
+import spack
+from spack.error import SpackError
+import argparse
+
+# Command parsing
+parser = argparse.ArgumentParser(
+    formatter_class=argparse.RawTextHelpFormatter,
+    description="Spack: the Supercomputing PACKage Manager." + colorize("""
+
+spec expressions:
+  PACKAGE [CONSTRAINTS]
+
+    CONSTRAINTS:
+      @c{@version}
+      @g{%compiler  @compiler_version}
+      @B{+variant}
+      @r{-variant} or @r{~variant}
+      @m{=architecture}
+      [^DEPENDENCY [CONSTRAINTS] ...]"""))
+
+parser.add_argument('-d', '--debug', action='store_true',
+                    help="Write out debug logs during compile")
+parser.add_argument('-D', '--pdb', action='store_true',
+                    help="Run spack under the pdb debugger")
+parser.add_argument('-k', '--insecure', action='store_true',
+                    help="Do not check ssl certificates when downloading.")
+parser.add_argument('-m', '--mock', action='store_true',
+                    help="Use mock packages instead of real ones.")
+parser.add_argument('-p', '--profile', action='store_true',
+                    help="Profile execution using cProfile.")
+parser.add_argument('-v', '--verbose', action='store_true',
+                    help="Print additional output during builds")
+parser.add_argument('-s', '--stacktrace', action='store_true',
+                    help="Add stacktrace information to all printed statements")
+parser.add_argument('-V', '--version', action='version',
+                    version="%s" % spack.spack_version)
+
+# each command module implements a parser() function, to which we pass its
+# subparser for setup.
+subparsers = parser.add_subparsers(metavar='SUBCOMMAND', dest="command")
+
+
+import spack.cmd
+for cmd in spack.cmd.commands:
+    module = spack.cmd.get_module(cmd)
+    cmd_name = cmd.replace('_', '-')
+    subparser = subparsers.add_parser(cmd_name, help=module.description)
+    module.setup_parser(subparser)
+
+
+def _main(args, unknown_args):
+    # Set up environment based on args.
+    tty.set_verbose(args.verbose)
+    tty.set_debug(args.debug)
+    tty.set_stacktrace(args.stacktrace)
+    spack.debug = args.debug
+
+    if spack.debug:
+        import spack.util.debug as debug
+        debug.register_interrupt_handler()
+
+    # Run any available pre-run hooks
+    spack.hooks.pre_run()
+
+    spack.spack_working_dir = working_dir
+    if args.mock:
+        from spack.repository import RepoPath
+        spack.repo.swap(RepoPath(spack.mock_packages_path))
+
+    # If the user asked for it, don't check ssl certs.
+    if args.insecure:
+        tty.warn("You asked for --insecure. Will NOT check SSL certificates.")
+        spack.insecure = True
+
+    # Try to load the particular command asked for and run it
+    command = spack.cmd.get_command(args.command.replace('-', '_'))
+
+    # Allow commands to inject an optional argument and get unknown args
+    # if they want to handle them.
+    info = dict(inspect.getmembers(command))
+    varnames = info['__code__'].co_varnames
+    argcount = info['__code__'].co_argcount
+
+    # Actually execute the command
+    try:
+        if argcount == 3 and varnames[2] == 'unknown_args':
+            return_val = command(parser, args, unknown_args)
+        else:
+            if unknown_args:
+                tty.die('unrecognized arguments: %s' % ' '.join(unknown_args))
+            return_val = command(parser, args)
+    except SpackError as e:
+        e.die()
+    except KeyboardInterrupt:
+        sys.stderr.write('\n')
+        tty.die("Keyboard interrupt.")
+
+    # Allow commands to return values if they want to exit with some other code.
+    if return_val is None:
+        sys.exit(0)
+    elif isinstance(return_val, int):
+        sys.exit(return_val)
+    else:
+        tty.die("Bad return value from command %s: %s"
+                % (args.command, return_val))
+
+
+def main(args):
+    # Just print help and exit if run with no arguments at all
+    if len(args) == 1:
+        parser.print_help()
+        sys.exit(1)
+
+    # actually parse the args.
+    args, unknown = parser.parse_known_args()
+
+    if args.profile:
+        import cProfile
+        cProfile.runctx('_main(args, unknown)', globals(), locals(),
+                        sort='time')
+    elif args.pdb:
+        import pdb
+        pdb.runctx('_main(args, unknown)', globals(), locals())
+    else:
+        _main(args, unknown)
+
+
+if __name__ == '__main__':
+    main(sys.argv)

bin/spack-python

@@ -1,14 +1,14 @@
 #!/bin/sh
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as

conftest.py

@@ -1,52 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-import pytest
-
-
-# Hooks to add command line options or set other custom behaviors.
-# They must be placed here to be found by pytest. See:
-#
-# https://docs.pytest.org/en/latest/writing_plugins.html
-#
-def pytest_addoption(parser):
-    group = parser.getgroup("Spack specific command line options")
-    group.addoption(
-        '--fast', action='store_true', default=False,
-        help='runs only "fast" unit tests, instead of the whole suite')
-
-
-def pytest_collection_modifyitems(config, items):
-    if not config.getoption('--fast'):
-        # --fast not given, run all the tests
-        return
-
-    slow_tests = ['db', 'network', 'maybeslow']
-    skip_as_slow = pytest.mark.skip(
-        reason='skipped slow test [--fast command line option given]'
-    )
-    for item in items:
-        if any(x in item.keywords for x in slow_tests):
-            item.add_marker(skip_as_slow)

etc/spack/defaults/config.yaml

@@ -18,9 +18,6 @@ config:
   # You can use $spack here to refer to the root of the spack instance.
   install_tree: $spack/opt/spack
 
-  # Locations where templates should be found
-  template_dirs:
-    - $spack/templates
 
   # Locations where different types of modules should be installed.
   module_roots:
@@ -69,9 +66,3 @@ config:
   # If set to true, `spack install` and friends will NOT clean
   # potentially harmful variables from the build environment. Use wisely.
   dirty: false
-
-
-  # The default number of jobs to use when running `make` in parallel.
-  # If set to 4, for example, `spack install` will run `make -j4`.
-  # If not set, all available cores are used by default.
-  # build_jobs: 4

etc/spack/defaults/modules.yaml

@@ -40,7 +40,3 @@ modules:
       - PKG_CONFIG_PATH
     '':
       - CMAKE_PREFIX_PATH
-
-  lmod:
-    hierarchy:
-      - mpi

etc/spack/defaults/packages.yaml

@@ -17,23 +17,7 @@ packages:
   all:
     compiler: [gcc, intel, pgi, clang, xl, nag]
     providers:
-      awk: [gawk]
-      blas: [openblas]
-      daal: [intel-daal]
-      elf: [elfutils]
-      gl: [mesa, opengl]
-      golang: [gcc]
-      ipp: [intel-ipp]
-      java: [jdk]
-      lapack: [openblas]
-      mkl: [intel-mkl]
-      mpe: [mpe2]
       mpi: [openmpi, mpich]
-      opencl: [pocl]
-      openfoam: [openfoam-com, openfoam-org, foam-extend]
+      blas: [openblas]
+      lapack: [openblas]
       pil: [py-pillow]
-      pkgconfig: [pkgconf, pkg-config]
-      scalapack: [netlib-scalapack]
-      szip: [libszip, libaec]
-      tbb: [intel-tbb]
-      jpeg: [libjpeg-turbo, libjpeg]

issue_template.md

@@ -1,36 +0,0 @@
-If you want to report a build error for some package, or a bug in core please use the following template as a guideline:
-
------
-
-Summary
-
-### Expected Result
-
-What you expected
-
-### Actual Result
-
-What happened instead
-
-### Steps to reproduce the issue
-
-```console
-$ spack <command1> <spec>
-$ spack <command2> <spec>
-...
-```
-
-### Information on your system
-
-This includes:
-
- 1. which platform you are using
- 2. any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.)
-
------
-
-We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
-
-If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
-
-Other than that, thanks for taking the time to contribute to Spack!

lib/spack/docs/.gitignore

@@ -1,5 +1,5 @@
-package_list.html
+package_list.rst
 command_index.rst
 spack*.rst
-llnl*.rst
+modules.rst
 _build

lib/spack/docs/Makefile

@@ -3,12 +3,13 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    = -E
-SPHINXBUILD   = sphinx-build
+JOBS          ?= $(shell python -c 'import multiprocessing; print multiprocessing.cpu_count()')
+SPHINXBUILD   = sphinx-build -j $(JOBS)
 PAPER         =
 BUILDDIR      = _build
 
 export PYTHONPATH := ../../spack:$(PYTHONPATH)
-APIDOC_FILES  = spack*.rst llnl*.rst
+APIDOC_FILES  = spack*.rst
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
@@ -57,8 +58,7 @@ upload:
 	git push -f github gh-pages
 
 apidoc:
-	sphinx-apidoc -f -T -o . ../spack
-	sphinx-apidoc -f -T -o . ../llnl
+	sphinx-apidoc -T -o . $(PYTHONPATH)/spack
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
@@ -83,7 +83,7 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
 clean:
-	-rm -f command_index.rst
+	-rm -f package_list.rst command_index.rst modules.rst
 	-rm -rf $(BUILDDIR)/* $(APIDOC_FILES)
 
 html:

lib/spack/docs/_themes/sphinx_rtd_theme/footer.html

@@ -24,7 +24,7 @@
 
     <br/>
     Written by Todd Gamblin (<a href="mailto:tgamblin@llnl.gov">tgamblin@llnl.gov</a>) and
-    many <a href="https://github.com/spack/spack/graphs/contributors">contributors.</a> LLNL-CODE-647188.
+    many contributors. LLNL-CODE-647188.
 
     {%- if last_updated %}
       <br/>

lib/spack/docs/basic_usage.rst

@@ -808,46 +808,17 @@ Specifying Specs by Hash
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 Complicated specs can become cumbersome to enter on the command line,
-especially when many of the qualifications are necessary to distinguish
-between similar installs. To avoid this, when referencing an existing spec,
+especially when many of the qualifications are necessary to
+distinguish between similar installs, for example when using the
+``uninstall`` command. To avoid this, when referencing an existing spec,
 Spack allows you to reference specs by their hash. We previously
 discussed the spec hash that Spack computes. In place of a spec in any
 command, substitute ``/<hash>`` where ``<hash>`` is any amount from
-the beginning of a spec hash.
+the beginning of a spec hash. If the given spec hash is sufficient
+to be unique, Spack will replace the reference with the spec to which
+it refers. Otherwise, it will prompt for a more qualified hash.
 
-For example, lets say that you accidentally installed two different
-``mvapich2`` installations. If you want to uninstall one of them but don't
-know what the difference is, you can run:
-
-.. code-block:: console
-
-   $ spack find --long mvapich2
-   ==> 2 installed packages.
-   -- linux-centos7-x86_64 / gcc@6.3.0 ----------
-   qmt35td mvapich2@2.2%gcc
-   er3die3 mvapich2@2.2%gcc
-
-
-You can then uninstall the latter installation using:
-
-.. code-block:: console
-
-   $ spack uninstall /er3die3
-
-
-Or, if you want to build with a specific installation as a dependency,
-you can use:
-
-.. code-block:: console
-
-   $ spack install trilinos ^/er3die3
-
-
-If the given spec hash is sufficiently long as to be unique, Spack will
-replace the reference with the spec to which it refers. Otherwise, it will
-prompt for a more qualified hash.
-
-Note that this will not work to reinstall a dependency uninstalled by
+Note that this will not work to reinstall a depencency uninstalled by
 ``spack uninstall --force``.
 
 .. _cmd-spack-providers:

lib/spack/docs/binary_caches.rst

@@ -1,132 +0,0 @@
-.. _binary_caches:
-
-============
-Build caches
-============
-
-Some sites may encourage users to set up their own test environments
-before carrying out central installations, or some users may prefer to set
-up these environments on their own motivation. To reduce the load of
-recompiling otherwise identical package specs in different installations,
-installed packages can be put into build cache tarballs, uploaded to
-your Spack mirror and then downloaded and installed by others.
-
-
---------------------------
-Creating build cache files
---------------------------
-
-A compressed tarball of an installed package is created. Tarballs are created
-for all of its link and run dependency packages as well. Compressed tarballs are
-signed with gpg and signature and tarball and put in a ``.spack`` file. Optionally,
-the rpaths (and ids and deps on macOS) can be changed to paths relative to
-the Spack install tree before the tarball is created.
-
-Build caches are created via:
-
-.. code-block:: console
-
-   $ spack buildcache create spec
-
-
----------------------------------------
-Finding or installing build cache files
----------------------------------------
-
-To find build caches or install build caches, a Spack mirror must be configured
-with:
-
-.. code-block:: console
-
-   $ spack mirror add <name> <url>
-
-Build caches are found via:
-
-.. code-block:: console
-
-   $ spack buildcache list
-
-Build caches are installed via:
-
-.. code-block:: console
-
-   $ spack buildcache install
-
-
-----------
-Relocation
-----------
-
-Initial build and later installation do not necessarily happen at the same
-location. Spack provides a relocation capability and corrects for RPATHs and
-non-relocatable scripts. However, many packages compile paths into binary
-artifacts directly. In such cases, the build instructions of this package would
-need to be adjusted for better re-locatability.
-
-.. _cmd-spack-buildcache:
-
---------------------
-``spack buildcache``
---------------------
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-``spack buildcache create``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Create tarball of installed Spack package and all dependencies.
-Tarballs are checksummed and signed if gpg2 is available.
-Places them in a directory ``build_cache`` that can be copied to a mirror.
-Commands like ``spack buildcache install`` will search Spack mirrors for build_cache to get the list of build caches.
-
-==============  ========================================================================================================================
-Arguments       Description
-==============  ========================================================================================================================
-``<specs>``     list of partial specs or hashes with a leading ``/`` to match from installed packages and used for creating build caches
-``-d <path>``   directory in which ``build_cache`` directory is created, defaults to ``.``
-``-f``          overwrite ``.spack`` file in ``build_cache`` directory if it exists
-``-k <key>``    the key to sign package with. In the case where multiple keys exist, the package will be unsigned unless ``-k`` is used.
-``-r``          make paths in binaries relative before creating tarball
-``-y``          answer yes to all create unsigned ``build_cache`` questions
-==============  ========================================================================================================================
-
-^^^^^^^^^^^^^^^^^^^^^^^^^
-``spack buildcache list``
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Retrieves all specs for build caches available on a Spack mirror.
-
-==============  =====================================================================================
-Arguments       Description
-==============  =====================================================================================
-``<specs>``     list of partial package specs to be matched against specs downloaded for build caches
-==============  =====================================================================================
-
-E.g. ``spack buildcache list gcc`` with print only commands to install ``gcc`` package(s)
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-``spack buildcache install``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Retrieves all specs for build caches available on a Spack mirror and installs build caches
-with specs matching the specs input.
-
-==============  ==============================================================================================
-Arguments       Description
-==============  ==============================================================================================
-``<specs>``     list of partial package specs or hashes with a leading ``/`` to be installed from build caches
-``-f``          remove install directory if it exists before unpacking tarball
-``-y``          answer yes to all to don't verify package with gpg questions
-==============  ==============================================================================================
-
-^^^^^^^^^^^^^^^^^^^^^^^^^
-``spack buildcache keys``
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-List public keys available on Spack mirror.
-
-=========  ==============================================
-Arguments  Description
-=========  ==============================================
-``-i``     trust the keys downloaded with prompt for each
-``-y``     answer yes to all trust all keys downloaded
-=========  ==============================================

lib/spack/docs/build_settings.rst

@@ -71,9 +71,9 @@ package lacks a spec component, such as missing a compiler or
 package version, then Spack will guess the missing component based
 on its most-favored packages, and it may guess incorrectly.
 
-Each package version and compiler listed in an external should
+Each package version and compilers listed in an external should
 have entries in Spack's packages and compiler configuration, even
-though the package and compiler may not ever be built.
+though the package and compiler may not every be built.
 
 The packages configuration can tell Spack to use an external location
 for certain package versions, but it does not restrict Spack to using

lib/spack/docs/conf.py

@@ -1,14 +1,14 @@
 # flake8: noqa
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -49,11 +49,8 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath('exts'))
 sys.path.insert(0, os.path.abspath('../external'))
-if sys.version_info[0] < 3:
-    sys.path.insert(0, os.path.abspath('../external/yaml/lib'))
-else:
-    sys.path.insert(0, os.path.abspath('../external/yaml/lib3'))
 sys.path.append(os.path.abspath('..'))
 
 # Add the Spack bin directory to the path so that we can use its output in docs.
@@ -61,6 +58,11 @@
 os.environ['SPACK_ROOT'] = spack_root
 os.environ['PATH'] += '%s%s/bin' % (os.pathsep, spack_root)
 
+# Get the spack version for use in the docs
+spack_version =  subprocess.Popen(
+    [spack_root + '/bin/spack', '-V'],
+    stderr=subprocess.PIPE).communicate()[1].strip().split('.')
+
 # Set an environment variable so that colify will print output like it would to
 # a terminal.
 os.environ['COLIFY_SIZE'] = '25x120'
@@ -68,10 +70,9 @@
 #
 # Generate package list using spack command
 #
-with open('package_list.html', 'w') as plist_file:
+with open('package_list.rst', 'w') as plist_file:
     subprocess.Popen(
-        [spack_root + '/bin/spack', 'list', '--format=html'],
-        stdout=plist_file)
+        [spack_root + '/bin/spack', 'list', '--format=rst'], stdout=plist_file)
 
 #
 # Find all the `cmd-spack-*` references and add them to a command index
@@ -90,21 +91,10 @@
     for cmd in sorted(command_names):
         index.write('   * :ref:`%s`\n' % cmd)
 
-#
+
 # Run sphinx-apidoc
-#
-# Remove any previous API docs
-# Read the Docs doesn't clean up after previous builds
-# Without this, the API Docs will never actually update
-#
-apidoc_args = [
-    '--force',         # Older versions of Sphinx ignore the first argument
-    '--force',         # Overwrite existing files
-    '--no-toc',        # Don't create a table of contents file
-    '--output-dir=.',  # Directory to place all output
-]
-sphinx_apidoc(apidoc_args + ['../spack'])
-sphinx_apidoc(apidoc_args + ['../llnl'])
+sphinx_apidoc(['-T', '-o', '.', '../spack'])
+os.remove('modules.rst')
 
 #
 # Exclude everything in spack.__all__ from indexing.  All of these
@@ -120,31 +110,17 @@
 for line in fileinput.input('spack.rst', inplace=1):
     if handling_spack:
         if not line.startswith('    :noindex:'):
-            print('    :noindex: %s' % ' '.join(spack.__all__))
+            print '    :noindex: %s' % ' '.join(spack.__all__)
         handling_spack = False
 
     if line.startswith('.. automodule::'):
         handling_spack = (line == '.. automodule:: spack\n')
 
-    sys.stdout.write(line)
+    print line,
 
 # Enable todo items
 todo_include_todos = True
 
-#
-# Disable duplicate cross-reference warnings.
-#
-from sphinx.domains.python import PythonDomain
-class PatchedPythonDomain(PythonDomain):
-    def resolve_xref(self, env, fromdocname, builder, typ, target, node, contnode):
-        if 'refspecific' in node:
-            del node['refspecific']
-        return super(PatchedPythonDomain, self).resolve_xref(
-            env, fromdocname, builder, typ, target, node, contnode)
-
-def setup(sphinx):
-    sphinx.override_domain(PatchedPythonDomain)
-
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -154,7 +130,6 @@ def setup(sphinx):
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.graphviz',
-              'sphinx.ext.napoleon',
               'sphinx.ext.todo',
               'sphinxcontrib.programoutput']
 
@@ -181,16 +156,16 @@ def setup(sphinx):
 
 # General information about the project.
 project = u'Spack'
-copyright = u'2013-2017, Lawrence Livermore National Laboratory.'
+copyright = u'2013-2015, Lawrence Livermore National Laboratory.'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = str(spack.spack_version.up_to(2))
+version = '.'.join(spack_version[:2])
 # The full version, including alpha/beta/rc tags.
-release = str(spack.spack_version.up_to(2))
+release = '.'.join(spack_version[:2])
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -250,7 +225,7 @@ def setup(sphinx):
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = '../../../share/spack/logo/spack-logo-white-text.svg'
+html_logo = '../../../share/spack/logo/spack-logo-white-text-48.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

lib/spack/docs/config_yaml.rst

@@ -14,6 +14,27 @@ see the default settings by looking at
 These settings can be overridden in ``etc/spack/config.yaml`` or
 ``~/.spack/config.yaml``.  See :ref:`configuration-scopes` for details.
 
+.. _config-file-variables:
+
+------------------------------
+Config file variables
+------------------------------
+
+You may notice some variables prefixed with ``$`` in the settings above.
+Spack understands several variables that can be used in values of
+configuration parameters.  They are:
+
+  * ``$spack``: path to the prefix of this spack installation
+  * ``$tempdir``: default system temporary directory (as specified in
+    Python's `tempfile.tempdir
+    <https://docs.python.org/2/library/tempfile.html#tempfile.tempdir>`_
+    variable.
+  * ``$user``: name of the current user
+
+Note that, as with shell variables, you can write these as ``$varname``
+or with braces to distinguish the variable from surrounding characters:
+``${varname}``.
+
 --------------------
 ``install_tree``
 --------------------
@@ -21,43 +42,6 @@ These settings can be overridden in ``etc/spack/config.yaml`` or
 The location where Spack will install packages and their dependencies.
 Default is ``$spack/opt/spack``.
 
----------------------------------------------------
-``install_hash_length`` and ``install_path_scheme``
----------------------------------------------------
-
-The default Spack installation path can be very long and can create
-problems for scripts with hardcoded shebangs. There are two parameters
-to help with that. Firstly, the ``install_hash_length`` parameter can
-set the length of the hash in the installation path from 1 to 32. The
-default path uses the full 32 characters.
-
-Secondly, it is
-also possible to modify the entire installation scheme. By default
-Spack uses
-``${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}``
-where the tokens that are available for use in this directive are the
-same as those understood by the ``Spec.format`` method. Using this parameter it
-is possible to use a different package layout or reduce the depth of
-the installation paths. For example
-
-     .. code-block:: yaml
-
-       config:
-         install_path_scheme: '${PACKAGE}/${VERSION}/${HASH:7}'
-
-would install packages into sub-directories using only the package
-name, version and a hash length of 7 characters.
-
-When using either parameter to set the hash length it only affects the
-representation of the hash in the installation directory. You
-should be aware that the smaller the hash length the more likely
-naming conflicts will occur. These parameters are independent of those
-used to configure module names.
-
-.. warning:: Modifying the installation hash length or path scheme after
-   packages have been installed will prevent Spack from being
-   able to find the old installation directories.
-
 --------------------
 ``module_roots``
 --------------------
@@ -78,8 +62,8 @@ See :ref:`modules` for details.
 ``build_stage``
 --------------------
 
-Spack is designed to run out of a user home directory, and on many
-systems the home directory is a (slow) network filesystem.  On most systems,
+Spack is designed to run out of a user home directories, and on many
+systems the home directory a (slow) network filesystem.  On most systems,
 building in a temporary filesystem results in faster builds than building
 in the home directory.  Usually, there is also more space available in
 the temporary location than in the home directory. So, Spack tries to
@@ -101,12 +85,12 @@ See :ref:`config-file-variables` for more on ``$tempdir`` and ``$spack``.
 
 When Spack builds a package, it creates a temporary directory within the
 ``build_stage``, and it creates a symbolic link to that directory in
-``$spack/var/spack/stage``. This is used to track the stage.
+``$spack/var/spack/stage``. This is used totrack the stage.
 
 After a package is successfully installed, Spack deletes the temporary
 directory it used to build.  Unsuccessful builds are not deleted, but you
-can manually purge them with :ref:`spack clean --stage
-<cmd-spack-clean>`.
+can manually purge them with :ref:`spack purge --stage
+<cmd-spack-purge>`.
 
 .. note::
 
@@ -121,8 +105,8 @@ can manually purge them with :ref:`spack clean --stage
 
 Location to cache downloaded tarballs and repositories.  By default these
 are stored in ``$spack/var/spack/cache``.  These are stored indefinitely
-by default. Can be purged with :ref:`spack clean --downloads
-<cmd-spack-clean>`.
+by default. Can be purged with :ref:`spack purge --downloads
+<cmd-spack-purge>`.
 
 --------------------
 ``misc_cache``
@@ -130,7 +114,7 @@ by default. Can be purged with :ref:`spack clean --downloads
 
 Temporary directory to store long-lived cache files, such as indices of
 packages available in repositories.  Defaults to ``~/.spack/cache``.  Can
-be purged with :ref:`spack clean --misc-cache <cmd-spack-clean>`.
+be purged with :ref:`spack purge --misc-cache <cmd-spack-purge>`.
 
 --------------------
 ``verify_ssl``
@@ -159,24 +143,7 @@ the way packages build. This includes ``LD_LIBRARY_PATH``, ``CPATH``,
 ``LIBRARY_PATH``, ``DYLD_LIBRARY_PATH``, and others.
 
 By default, builds are ``clean``, but on some machines, compilers and
-other tools may need custom ``LD_LIBRARY_PATH`` settings to run.  You can
+other tools may need custom ``LD_LIBRARY_PATH`` setings to run.  You can
 set ``dirty`` to ``true`` to skip the cleaning step and make all builds
 "dirty" by default.  Be aware that this will reduce the reproducibility
 of builds.
-
---------------
-``build_jobs``
---------------
-
-Unless overridden in a package or on the command line, Spack builds all
-packages in parallel. For a build system that uses Makefiles, this means
-running ``make -j<build_jobs>``, where ``build_jobs`` is the number of
-threads to use.
-
-The default parallelism is equal to the number of cores on your machine.
-If you work on a shared login node or have a strict ulimit, it may be
-necessary to set the default to a lower value. By setting ``build_jobs``
-to 4, for example, commands like ``spack install`` will run ``make -j4``
-instead of hogging every core.
-
-To build all software in serial, set ``build_jobs`` to 1.

lib/spack/docs/configuration.rst

@@ -45,27 +45,20 @@ Configuration Scopes
 -------------------------
 
 Spack pulls configuration data from files in several directories. There
-are four configuration scopes.  From lowest to highest:
+are three configuration scopes.  From lowest to highest:
 
-#. **defaults**: Stored in ``$(prefix)/etc/spack/defaults/``. These are
+1. **defaults**: Stored in ``$(prefix)/etc/spack/defaults/``. These are
    the "factory" settings. Users should generally not modify the settings
    here, but should override them in other configuration scopes. The
    defaults here will change from version to version of Spack.
 
-#. **system**: Stored in ``/etc/spack``. These are settings for this
-   machine, or for all machines on which this file system is
-   mounted. The site scope can be used for settings idiosyncratic to a
-   particular machine, such as the locations of compilers or external
-   packages. These settings are presumably controlled by someone with
-   root access on the machine.
-
-#. **site**: Stored in ``$(prefix)/etc/spack/``.  Settings here affect
+2. **site**: Stored in ``$(prefix)/etc/spack/``.  Settings here affect
    only *this instance* of Spack, and they override defaults.  The site
    scope can can be used for per-project settings (one spack instance per
    project) or for site-wide settings on a multi-user machine (e.g., for
    a common spack instance).
 
-#. **user**: Stored in the home directory: ``~/.spack/``. These settings
+3. **user**: Stored in the home directory: ``~/.spack/``. These settings
    affect all instances of Spack and take the highest precedence.
 
 Each configuration directory may contain several configuration files,
@@ -85,25 +78,22 @@ Platform-specific scopes
 -------------------------
 
 For each scope above, there can *also* be platform-specific settings.
-For example, on Blue Gene/Q machines, Spack needs to know the location
-of cross-compilers for the compute nodes.  This configuration is in
-``etc/spack/defaults/bgq/compilers.yaml``.  It will take precedence
-over settings in the ``defaults`` scope, but can still be overridden
-by settings in ``system``, ``system/bgq``, ``site``, ``site/bgq``,
-``user``, or ``user/bgq``. So, the full scope precedence is:
+For example, on Blue Gene/Q machines, Spack needs to know the location of
+cross-compilers for the compute nodes.  This configuration is in
+``etc/spack/defaults/bgq/compilers.yaml``.  It will take precedence over
+settings in the ``defaults`` scope, but can still be overridden by
+settings in ``site``, ``site/bgq``, ``user``, or ``user/bgq``. So, the
+full scope precedence is:
 
 1. ``defaults``
 2. ``defaults/<platform>``
-3. ``system``
-4. ``system/<platform>``
-5. ``site``
-6. ``site/<platform>``
-7. ``user``
-8. ``user/<platform>``
+3. ``site``
+4. ``site/<platform>``
+5. ``user``
+6. ``user/<platform>``
 
 You can get the name to use for ``<platform>`` by running ``spack arch
---platform``. The system config scope has a ``<platform>`` section for
-sites at which ``/etc`` is mounted on multiple heterogeneous machines.
+--platform``.
 
 -------------------------
 Scope precedence
@@ -261,52 +251,3 @@ The merged configuration would look like this:
        - /lustre-scratch/$user
        - ~/mystage
    $ _
-
-.. _config-file-variables:
-
-------------------------------
-Config file variables
-------------------------------
-
-Spack understands several variables which can be used in config file paths
-where ever they appear. There are three sets of these variables, Spack specific 
-variables, environment variables, and user path variables. Spack specific
-variables and environment variables both are indicated by prefixing the variable
-name with ``$``. User path variables are indicated at the start of the path with
-``~`` or ``~user``. Let's discuss each in turn.
-
-^^^^^^^^^^^^^^^^^^^^^^^^
-Spack Specific Variables
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Spack understands several special variables. These are:
-
-  * ``$spack``: path to the prefix of this spack installation
-  * ``$tempdir``: default system temporary directory (as specified in
-    Python's `tempfile.tempdir
-    <https://docs.python.org/2/library/tempfile.html#tempfile.tempdir>`_
-    variable.
-  * ``$user``: name of the current user
-
-Note that, as with shell variables, you can write these as ``$varname``
-or with braces to distinguish the variable from surrounding characters:
-``${varname}``. Their names are also case insensitive meaning that ``$SPACK``
-works just as well as ``$spack``. These special variables are also
-substituted first, so any environment variables with the same name will not
-be used.
-
-^^^^^^^^^^^^^^^^^^^^^
-Environment Variables
-^^^^^^^^^^^^^^^^^^^^^
-
-Spack then uses ``os.path.expandvars`` to expand any remaining environment
-variables.
-
-^^^^^^^^^^^^^^
-User Variables
-^^^^^^^^^^^^^^
-
-Spack also uses the ``os.path.expanduser`` function on the path to expand
-any user tilde paths such as ``~`` or ``~user``. These tilde paths must appear
-at the beginning of the path or ``os.path.expanduser`` will not properly
-expand them.

lib/spack/docs/contribution_guide.rst

@@ -26,38 +26,21 @@ Spack uses a rough approximation of the `Git Flow <http://nvie.com/posts/a-succe
 branching model. The develop branch contains the latest contributions, and
 master is always tagged and points to the latest stable release. Therefore, when
 you send your request, make ``develop`` the destination branch on the
-`Spack repository <https://github.com/spack/spack>`_.
+`Spack repository <https://github.com/LLNL/spack>`_.
 
 ----------------------
 Continuous Integration
 ----------------------
 
-Spack uses `Travis CI <https://travis-ci.org/spack/spack>`_ for Continuous Integration
+Spack uses `Travis CI <https://travis-ci.org/LLNL/spack>`_ for Continuous Integration
 testing. This means that every time you submit a pull request, a series of tests will
-be run to make sure you didn't accidentally introduce any bugs into Spack. **Your PR
-will not be accepted until it passes all of these tests.** While you can certainly wait
+be run to make sure you didn't accidentally introduce any bugs into Spack. Your PR
+will not be accepted until it passes all of these tests. While you can certainly wait
 for the results of these tests after submitting a PR, we recommend that you run them
 locally to speed up the review process.
 
-.. note::
-
-   Oftentimes, Travis will fail for reasons other than a problem with your PR.
-   For example, apt-get, pip, or homebrew will fail to download one of the
-   dependencies for the test suite, or a transient bug will cause the unit tests
-   to timeout. If Travis fails, click the "Details" link and click on the test(s)
-   that is failing. If it doesn't look like it is failing for reasons related to
-   your PR, you have two options. If you have write permissions for the Spack
-   repository, you should see a "Restart job" button on the right-hand side. If
-   not, you can close and reopen your PR to rerun all of the tests. If the same
-   test keeps failing, there may be a problem with your PR. If you notice that
-   every recent PR is failing with the same error message, it may be that Travis
-   is down or one of Spack's dependencies put out a new release that is causing
-   problems. If this is the case, please file an issue.
-
-
 If you take a look in ``$SPACK_ROOT/.travis.yml``, you'll notice that we test
-against Python 2.6, 2.7, and 3.3-3.6 on both macOS and Linux. We currently
-perform 3 types of tests:
+against Python 2.6 and 2.7. We currently perform 3 types of tests:
 
 ^^^^^^^^^^
 Unit Tests
@@ -92,10 +75,7 @@ This allows you to develop iteratively: make a change, test that change, make
 another change, test that change, etc. To get a list of all available unit
 tests, run:
 
-.. command-output:: spack test --list
-
-A more detailed list of available unit tests can be found by running
-``spack test --long-list``.
+.. command-output:: spack test --collect-only
 
 Unit tests are crucial to making sure bugs aren't introduced into Spack. If you
 are modifying core Spack libraries or adding new functionality, please consider
@@ -104,7 +84,7 @@ adding new unit tests or strengthening existing tests.
 .. note::
 
    There is also a ``run-unit-tests`` script in ``share/spack/qa`` that
-   runs the unit tests. Afterwards, it reports back to Codecov with the
+   runs the unit tests. Afterwards, it reports back to Coverage with the
    percentage of Spack that is covered by unit tests. This script is
    designed for Travis CI. If you want to run the unit tests yourself, we
    suggest you use ``spack test``.
@@ -141,7 +121,7 @@ command:
    "extends" in ``package.py`` files.
 
 More approved flake8 exemptions can be found
-`here <https://github.com/spack/spack/blob/develop/.flake8>`_.
+`here <https://github.com/LLNL/spack/blob/develop/.flake8>`_.
 
 If all is well, you'll see something like this:
 
@@ -171,22 +151,20 @@ However, if you aren't compliant with PEP 8, flake8 will complain:
 
 Most of the error messages are straightforward, but if you don't understand what
 they mean, just ask questions about them when you submit your PR. The line numbers
-will change if you add or delete lines, so simply run ``spack flake8`` again
+will change if you add or delete lines, so simply run ``run-flake8-tests`` again
 to update them.
 
 .. tip::
 
    Try fixing flake8 errors in reverse order. This eliminates the need for
-   multiple runs of ``spack flake8`` just to re-compute line numbers and
-   makes it much easier to fix errors directly off of the Travis output.
+   multiple runs of ``flake8`` just to re-compute line numbers and makes it
+   much easier to fix errors directly off of the Travis output.
 
 .. warning::
 
    Flake8 requires setuptools in order to run. If you installed ``py-flake8``
    with Spack, make sure to add ``py-setuptools`` to your ``PYTHONPATH``.
-   The easiest way to do this is to run ``spack activate py-flake8`` so that
-   all of the dependencies are symlinked to a central location. If you see an
-   error message like:
+   Otherwise, you will get an error message like:
 
    .. code-block:: console
 
@@ -195,8 +173,6 @@ to update them.
           from pkg_resources import load_entry_point
       ImportError: No module named pkg_resources
 
-   that means Flake8 couldn't find setuptools in your ``PYTHONPATH``.
-
 ^^^^^^^^^^^^^^^^^^^
 Documentation Tests
 ^^^^^^^^^^^^^^^^^^^
@@ -210,7 +186,6 @@ Building the documentation requires several dependencies, all of which can be
 installed with Spack:
 
 * sphinx
-* sphinxcontrib-programoutput
 * graphviz
 * git
 * mercurial
@@ -218,26 +193,20 @@ installed with Spack:
 
 .. warning::
 
-   Sphinx has `several required dependencies <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-sphinx/package.py>`_.
+   Sphinx has `several required dependencies <https://github.com/LLNL/spack/blob/develop/var/spack/repos/builtin/packages/py-sphinx/package.py>`_.
    If you installed ``py-sphinx`` with Spack, make sure to add all of these
-   dependencies to your ``PYTHONPATH``. The easiest way to do this is to run:
+   dependencies to your ``PYTHONPATH``. The easiest way to do this is to run
+   ``spack activate py-sphinx`` so that all of the dependencies are symlinked
+   to a central location. If you see an error message like:
 
    .. code-block:: console
 
-      $ spack activate py-sphinx
-      $ spack activate py-sphinxcontrib-programoutput
+      Traceback (most recent call last):
+        File: "/usr/bin/flake8", line 5, in <module>
+          from pkg_resources import load_entry_point
+      ImportError: No module named pkg_resources
 
-   so that all of the dependencies are symlinked to a central location.
-   If you see an error message like:
-
-   .. code-block:: console
-
-      Extension error:
-      Could not import extension sphinxcontrib.programoutput (exception: No module named sphinxcontrib.programoutput)
-      make: *** [html] Error 1
-
-   that means Sphinx couldn't find ``py-sphinxcontrib-programoutput`` in your
-   ``PYTHONPATH``.
+   that means Sphinx couldn't find setuptools in your ``PYTHONPATH``.
 
 Once all of the dependencies are installed, you can try building the documentation:
 
@@ -252,11 +221,11 @@ your PR is accepted.
 
 .. note::
 
-   There is also a ``run-doc-tests`` script in ``share/spack/qa``. The only
-   difference between running this script and running ``make`` by hand is that
-   the script will exit immediately if it encounters an error or warning. This
-   is necessary for Travis CI. If you made a lot of documentation changes, it is
-   much quicker to run ``make`` by hand so that you can see all of the warnings
+   There is also a ``run-doc-tests`` script in the Quality Assurance directory.
+   The only difference between running this script and running ``make`` by hand
+   is that the script will exit immediately if it encounters an error or warning.
+   This is necessary for Travis CI. If you made a lot of documentation tests, it
+   is much quicker to run ``make`` by hand so that you can see all of the warnings
    at once.
 
 If you are editing the documentation, you should obviously be running the
@@ -304,37 +273,6 @@ Documentation changes can result in much more obfuscated warning messages.
 If you don't understand what they mean, feel free to ask when you submit
 your PR.
 
---------
-Coverage
---------
-
-Spack uses `Codecov <https://codecov.io/>`_ to generate and report unit test
-coverage. This helps us tell what percentage of lines of code in Spack are
-covered by unit tests. Although code covered by unit tests can still contain
-bugs, it is much less error prone than code that is not covered by unit tests.
-
-Codecov provides `browser extensions <https://github.com/codecov/browser-extension>`_
-for Google Chrome, Firefox, and Opera. These extensions integrate with GitHub
-and allow you to see coverage line-by-line when viewing the Spack repository.
-If you are new to Spack, a great way to get started is to write unit tests to
-increase coverage!
-
-Unlike with Travis, Codecov tests are not required to pass in order for your
-PR to be merged. If you modify core Spack libraries, we would greatly
-appreciate unit tests that cover these changed lines. Otherwise, we have no
-way of knowing whether or not your changes introduce a bug. If you make
-substantial changes to the core, we may request unit tests to increase coverage.
-
-.. note::
-
-   If the only files you modified are package files, we do not care about
-   coverage on your PR. You may notice that the Codecov tests fail even though
-   you didn't modify any core files. This means that Spack's overall coverage
-   has increased since you branched off of develop. This is a good thing!
-   If you really want to get the Codecov tests to pass, you can rebase off of
-   the latest develop, but again, this is not required.
-
-
 -------------
 Git Workflows
 -------------

lib/spack/docs/developer_guide.rst

@@ -300,46 +300,6 @@ Stage objects
 Writing commands
 ----------------
 
-Adding a new command to Spack is easy. Simply add a ``<name>.py`` file to
-``lib/spack/spack/cmd/``, where ``<name>`` is the name of the subcommand.
-At the bare minimum, two functions are required in this file:
-
-^^^^^^^^^^^^^^^^^^
-``setup_parser()``
-^^^^^^^^^^^^^^^^^^
-
-Unless your command doesn't accept any arguments, a ``setup_parser()``
-function is required to define what arguments and flags your command takes.
-See the `Argparse documentation <https://docs.python.org/2.7/library/argparse.html>`_
-for more details on how to add arguments.
-
-Some commands have a set of subcommands, like ``spack compiler find`` or
-``spack module refresh``. You can add subparsers to your parser to handle
-this. Check out ``spack edit --command compiler`` for an example of this.
-
-A lot of commands take the same arguments and flags. These arguments should
-be defined in ``lib/spack/spack/cmd/common/arguments.py`` so that they don't
-need to be redefined in multiple commands.
-
-^^^^^^^^^^^^
-``<name>()``
-^^^^^^^^^^^^
-
-In order to run your command, Spack searches for a function with the same
-name as your command in ``<name>.py``. This is the main method for your
-command, and can call other helper methods to handle common tasks.
-
-Remember, before adding a new command, think to yourself whether or not this
-new command is actually necessary. Sometimes, the functionality you desire
-can be added to an existing command. Also remember to add unit tests for
-your command. If it isn't used very frequently, changes to the rest of
-Spack can cause your command to break without sufficient unit tests to
-prevent this from happening.
-
-Whenever you add/remove/rename a command or flags for an existing command,
-make sure to update Spack's `Bash tab completion script
-<https://github.com/adamjstewart/spack/blob/develop/share/spack/spack-completion.bash>`_.
-
 ----------
 Unit tests
 ----------
@@ -352,121 +312,14 @@ Unit testing
 Developer commands
 ------------------
 
-.. _cmd-spack-doc:
-
 ^^^^^^^^^^^^^
 ``spack doc``
 ^^^^^^^^^^^^^
 
-.. _cmd-spack-test:
-
 ^^^^^^^^^^^^^^
 ``spack test``
 ^^^^^^^^^^^^^^
 
-.. _cmd-spack-python:
-
-^^^^^^^^^^^^^^^^
-``spack python``
-^^^^^^^^^^^^^^^^
-
-``spack python`` is a command that lets you import and debug things as if
-you were in a Spack interactive shell. Without any arguments, it is similar
-to a normal interactive Python shell, except you can import spack and any
-other Spack modules:
-
-.. code-block:: console
-
-   $ spack python
-   Spack version 0.10.0
-   Python 2.7.13, Linux x86_64
-   >>> from spack.version import Version
-   >>> a = Version('1.2.3')
-   >>> b = Version('1_2_3')
-   >>> a == b
-   True
-   >>> c = Version('1.2.3b')
-   >>> c > a
-   True
-   >>>
-
-You can also run a single command:
-
-.. code-block:: console
-
-   $ spack python -c 'import distro; distro.linux_distribution()'
-   ('Fedora', '25', 'Workstation Edition')
-
-or a file:
-
-.. code-block:: console
-
-   $ spack python ~/test_fetching.py
-
-just like you would with the normal ``python`` command.
-
-.. _cmd-spack-url:
-
-^^^^^^^^^^^^^
-``spack url``
-^^^^^^^^^^^^^
-
-A package containing a single URL can be used to download several different
-versions of the package. If you've ever wondered how this works, all of the
-magic is in :mod:`spack.url`. This module contains methods for extracting
-the name and version of a package from its URL. The name is used by
-``spack create`` to guess the name of the package. By determining the version
-from the URL, Spack can replace it with other versions to determine where to
-download them from.
-
-The regular expressions in ``parse_name_offset`` and ``parse_version_offset``
-are used to extract the name and version, but they aren't perfect. In order
-to debug Spack's URL parsing support, the ``spack url`` command can be used.
-
-"""""""""""""""""""
-``spack url parse``
-"""""""""""""""""""
-
-If you need to debug a single URL, you can use the following command:
-
-.. command-output:: spack url parse http://cache.ruby-lang.org/pub/ruby/2.2/ruby-2.2.0.tar.gz
-
-You'll notice that the name and version of this URL are correctly detected,
-and you can even see which regular expressions it was matched to. However,
-you'll notice that when it substitutes the version number in, it doesn't
-replace the ``2.2`` with ``9.9`` where we would expect ``9.9.9b`` to live.
-This particular package may require a ``list_url`` or ``url_for_version``
-function.
-
-This command also accepts a ``--spider`` flag. If provided, Spack searches
-for other versions of the package and prints the matching URLs.
-
-""""""""""""""""""
-``spack url list``
-""""""""""""""""""
-
-This command lists every URL in every package in Spack. If given the
-``--color`` and ``--extrapolation`` flags, it also colors the part of
-the string that it detected to be the name and version. The
-``--incorrect-name`` and ``--incorrect-version`` flags can be used to
-print URLs that were not being parsed correctly.
-
-"""""""""""""""""""""
-``spack url summary``
-"""""""""""""""""""""
-
-This command attempts to parse every URL for every package in Spack
-and prints a summary of how many of them are being correctly parsed.
-It also prints a histogram showing which regular expressions are being
-matched and how frequently:
-
-.. command-output:: spack url summary
-
-This command is essential for anyone adding or changing the regular
-expressions that parse names and versions. By running this command
-before and after the change, you can make sure that your regular
-expression fixes more packages than it breaks.
-
 ---------
 Profiling
 ---------

lib/spack/docs/exts/sphinxcontrib/LICENSE

@@ -0,0 +1,25 @@
+Copyright (c) 2010, 2011, 2012 Sebastian Wiesner <lunaryorn@googlemail.com>
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+* Redistributions of source code must retain the above copyright
+  notice, this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright
+  notice, this list of conditions and the following disclaimer in the
+  documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

lib/spack/docs/exts/sphinxcontrib/__init__.py

@@ -0,0 +1,9 @@
+# -*- coding: utf-8 -*-
+"""
+    sphinxcontrib
+    ~~~~~~~~~~~~~
+
+    Contains 3rd party Sphinx extensions.
+"""
+
+__import__('pkg_resources').declare_namespace(__name__)

lib/spack/docs/exts/sphinxcontrib/programoutput.py

@@ -0,0 +1,263 @@
+# -*- coding: utf-8 -*-
+# Copyright (c) 2010, 2011, 2012, Sebastian Wiesner <lunaryorn@gmail.com>
+# All rights reserved.
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+"""
+    sphinxcontrib.programoutput
+    ===========================
+
+    This extension provides a directive to include the output of commands as
+    literal block while building the docs.
+
+    .. moduleauthor::  Sebastian Wiesner  <lunaryorn@gmail.com>
+"""
+
+from __future__ import (print_function, division, unicode_literals,
+                        absolute_import)
+
+import sys
+import os
+import shlex
+from subprocess import Popen, PIPE, STDOUT
+from collections import defaultdict, namedtuple
+
+from docutils import nodes
+from docutils.parsers import rst
+from docutils.parsers.rst.directives import flag, unchanged, nonnegative_int
+
+
+__version__ = '0.9'
+
+
+class program_output(nodes.Element):
+    pass
+
+
+def _slice(value):
+    parts = [int(v.strip()) for v in value.split(',')]
+    if len(parts) > 2:
+        raise ValueError('too many slice parts')
+    return tuple((parts + [None] * 2)[:2])
+
+
+class ProgramOutputDirective(rst.Directive):
+    has_content = False
+    final_argument_whitespace = True
+    required_arguments = 1
+
+    option_spec = dict(shell=flag, prompt=flag, nostderr=flag,
+                       ellipsis=_slice, extraargs=unchanged,
+                       returncode=nonnegative_int, cwd=unchanged)
+
+    def run(self):
+        env = self.state.document.settings.env
+
+        node = program_output()
+        node.line = self.lineno
+        node['command'] = self.arguments[0]
+
+        if self.name == 'command-output':
+            node['show_prompt'] = True
+        else:
+            node['show_prompt'] = 'prompt' in self.options
+
+        node['hide_standard_error'] = 'nostderr' in self.options
+        node['extraargs'] = self.options.get('extraargs', '')
+        _, cwd = env.relfn2path(self.options.get('cwd', '/'))
+        node['working_directory'] = cwd
+        node['use_shell'] = 'shell' in self.options
+        node['returncode'] = self.options.get('returncode', 0)
+        if 'ellipsis' in self.options:
+            node['strip_lines'] = self.options['ellipsis']
+        return [node]
+
+
+_Command = namedtuple(
+    'Command', 'command shell hide_standard_error working_directory')
+
+
+class Command(_Command):
+    """
+    A command to be executed.
+    """
+
+    def __new__(cls, command, shell=False, hide_standard_error=False,
+                working_directory='/'):
+        if isinstance(command, list):
+            command = tuple(command)
+        # `chdir()` resolves symlinks, so we need to resolve them too for
+        # caching to make sure that different symlinks to the same directory
+        # don't result in different cache keys.  Also normalize paths to make
+        # sure that identical paths are also equal as strings.
+        working_directory = os.path.normpath(os.path.realpath(
+            working_directory))
+        return _Command.__new__(cls, command, shell, hide_standard_error,
+                                working_directory)
+
+    @classmethod
+    def from_program_output_node(cls, node):
+        """
+        Create a command from a :class:`program_output` node.
+        """
+        extraargs = node.get('extraargs', '')
+        command = (node['command'] + ' ' + extraargs).strip()
+        return cls(command, node['use_shell'],
+                   node['hide_standard_error'], node['working_directory'])
+
+    def execute(self):
+        """
+        Execute this command.
+
+        Return the :class:`~subprocess.Popen` object representing the running
+        command.
+        """
+        if self.shell:
+            if sys.version_info[0] < 3 and isinstance(self.command, unicode):
+                command = self.command.encode(sys.getfilesystemencoding())
+            else:
+                command = self.command
+        else:
+            if sys.version_info[0] < 3 and isinstance(self.command, unicode):
+                command = shlex.split(self.command.encode(
+                    sys.getfilesystemencoding()))
+            elif isinstance(self.command, str):
+                command = shlex.split(self.command)
+            else:
+                command = self.command
+        return Popen(command, shell=self.shell, stdout=PIPE,
+                     stderr=PIPE if self.hide_standard_error else STDOUT,
+                     cwd=self.working_directory)
+
+    def get_output(self):
+        """
+        Get the output of this command.
+
+        Return a tuple ``(returncode, output)``.  ``returncode`` is the
+        integral return code of the process, ``output`` is the output as
+        unicode string, with final trailing spaces and new lines stripped.
+        """
+        process = self.execute()
+        output = process.communicate()[0].decode(
+            sys.getfilesystemencoding(), 'replace').rstrip()
+        return process.returncode, output
+
+    def __str__(self):
+        if isinstance(self.command, tuple):
+            return repr(list(self.command))
+        return repr(self.command)
+
+
+class ProgramOutputCache(defaultdict):
+    """
+    Execute command and cache their output.
+
+    This class is a mapping.  Its keys are :class:`Command` objects represeting
+    command invocations.  Its values are tuples of the form ``(returncode,
+    output)``, where ``returncode`` is the integral return code of the command,
+    and ``output`` is the output as unicode string.
+
+    The first time, a key is retrieved from this object, the command is
+    invoked, and its result is cached.  Subsequent access to the same key
+    returns the cached value.
+    """
+
+    def __missing__(self, command):
+        """
+        Called, if a command was not found in the cache.
+
+        ``command`` is an instance of :class:`Command`.
+        """
+        result = command.get_output()
+        self[command] = result
+        return result
+
+
+def run_programs(app, doctree):
+    """
+    Execute all programs represented by ``program_output`` nodes in
+    ``doctree``.  Each ``program_output`` node in ``doctree`` is then
+    replaced with a node, that represents the output of this program.
+
+    The program output is retrieved from the cache in
+    ``app.env.programoutput_cache``.
+    """
+    if app.config.programoutput_use_ansi:
+        # enable ANSI support, if requested by config
+        from sphinxcontrib.ansi import ansi_literal_block
+        node_class = ansi_literal_block
+    else:
+        node_class = nodes.literal_block
+
+    cache = app.env.programoutput_cache
+
+    for node in doctree.traverse(program_output):
+        command = Command.from_program_output_node(node)
+        try:
+            returncode, output = cache[command]
+        except EnvironmentError as error:
+            error_message = 'Command {0} failed: {1}'.format(command, error)
+            error_node = doctree.reporter.error(error_message, base_node=node)
+            node.replace_self(error_node)
+        else:
+            if returncode != node['returncode']:
+                app.warn('Unexpected return code {0} from command {1}'.format(
+                    returncode, command))
+
+            # replace lines with ..., if ellipsis is specified
+            if 'strip_lines' in node:
+                lines = output.splitlines()
+                start, stop = node['strip_lines']
+                lines[start:stop] = ['...']
+                output = '\n'.join(lines)
+
+            if node['show_prompt']:
+                tmpl = app.config.programoutput_prompt_template
+                output = tmpl.format(command=node['command'], output=output,
+                                     returncode=returncode)
+
+            new_node = node_class(output, output)
+            new_node['language'] = 'text'
+            node.replace_self(new_node)
+
+
+def init_cache(app):
+    """
+    Initialize the cache for program output at
+    ``app.env.programoutput_cache``, if not already present (e.g. being
+    loaded from a pickled environment).
+
+    The cache is of type :class:`ProgramOutputCache`.
+    """
+    if not hasattr(app.env, 'programoutput_cache'):
+        app.env.programoutput_cache = ProgramOutputCache()
+
+
+def setup(app):
+    app.add_config_value('programoutput_use_ansi', False, 'env')
+    app.add_config_value('programoutput_prompt_template',
+                         '$ {command}\n{output}', 'env')
+    app.add_directive('program-output', ProgramOutputDirective)
+    app.add_directive('command-output', ProgramOutputDirective)
+    app.connect(str('builder-inited'), init_cache)
+    app.connect(str('doctree-read'), run_programs)

lib/spack/docs/getting_started.rst

@@ -11,10 +11,9 @@ Prerequisites
 Spack has the following minimum requirements, which must be installed
 before Spack is run:
 
-1. Python 2 (2.6 or 2.7) or 3 (3.3 - 3.6)
+1. Python 2.6 or 2.7
 2. A C/C++ compiler
 3. The ``git`` and ``curl`` commands.
-4. If using the ``gpg`` subcommand, ``gnupg2`` is required.
 
 These requirements can be easily installed on most modern Linux systems;
 on Macintosh, XCode is required.  Spack is designed to run on HPC
@@ -27,11 +26,11 @@ Installation
 ------------
 
 Getting Spack is easy.  You can clone it from the `github repository
-<https://github.com/spack/spack>`_ using this command:
+<https://github.com/llnl/spack>`_ using this command:
 
 .. code-block:: console
 
-   $ git clone https://github.com/spack/spack.git
+   $ git clone https://github.com/llnl/spack.git
 
 This will create a directory called ``spack``.
 
@@ -52,7 +51,7 @@ For a richer experience, use Spack's shell support:
 
 .. code-block:: console
 
-   # For bash/zsh users
+   # For bash users
    $ export SPACK_ROOT=/path/to/spack
    $ . $SPACK_ROOT/share/spack/setup-env.sh
 
@@ -60,15 +59,10 @@ For a richer experience, use Spack's shell support:
    $ setenv SPACK_ROOT /path/to/spack
    $ source $SPACK_ROOT/share/spack/setup-env.csh
 
-
 This automatically adds Spack to your ``PATH`` and allows the ``spack``
-command to be used to execute spack :ref:`commands <shell-support>` and
+command to :ref:`load environment modules <shell-support>` and execute
 :ref:`useful packaging commands <packaging-shell-support>`.
 
-If :ref:`environment-modules or dotkit <InstallEnvironmentModules>` is
-installed and available, the ``spack`` command can also load and unload
-:ref:`modules <modules>`.
-
 ^^^^^^^^^^^^^^^^^
 Clean Environment
 ^^^^^^^^^^^^^^^^^
@@ -91,20 +85,30 @@ Check Installation
 With Spack installed, you should be able to run some basic Spack
 commands.  For example:
 
-.. command-output:: spack spec netcdf
+.. code-block:: console
 
+    $ spack spec netcdf
+      ...
+      netcdf@4.4.1%gcc@5.3.0~hdf4+mpi arch=linux-SuSE11-x86_64
+          ^curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
+              ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
+              ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
+          ^hdf5@1.10.0-patch1%gcc@5.3.0+cxx~debug+fortran+mpi+shared~szip~threadsafe arch=linux-SuSE11-x86_64
+              ^openmpi@1.10.1%gcc@5.3.0~mxm~pmi~psm~psm2~slurm~sqlite3~thread_multiple~tm+verbs+vt arch=linux-SuSE11-x86_64
+          ^m4@1.4.17%gcc@5.3.0+sigsegv arch=linux-SuSE11-x86_64
+              ^libsigsegv@2.10%gcc@5.3.0 arch=linux-SuSE11-x86_64
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 Optional: Alternate Prefix
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 You may want to run Spack out of a prefix other than the git repository
-you cloned.  The ``spack clone`` command provides this
+you cloned.  The ``spack bootstrap`` command provides this
 functionality.  To install spack in a new directory, simply type:
 
 .. code-block:: console
 
-   $ spack clone /my/favorite/prefix
+   $ spack bootstrap /my/favorite/prefix
 
 This will install a new spack script in ``/my/favorite/prefix/bin``,
 which you can use just like you would the regular spack script.  Each
@@ -221,7 +225,7 @@ If you want to see specifics on a particular compiler, you can run
        f77 = /usr/local/bin/ifort-15.0.090
        fc  = /usr/local/bin/ifort-15.0.090
      modules = []
-     operating_system = centos6
+     operating system = centos6
    ...
 
 This shows which C, C++, and Fortran compilers were detected by Spack.
@@ -321,6 +325,19 @@ by adding the following to your ``packages.yaml`` file:
        compiler: [gcc@4.9.3]
 
 
+.. tip::
+
+    If you are building your own compiler, some users prefer to have a
+    Spack instance just for that.  For example, create a new Spack in
+    ``~/spack-tools`` and then run ``~/spack-tools/bin/spack install
+    gcc@4.9.3``.  Once the compiler is built, don't build anything
+    more in that Spack instance; instead, create a new "real" Spack
+    instance, configure Spack to use the compiler you've just built,
+    and then build your application software in the new Spack
+    instance.  Following this tip makes it easy to delete all your
+    Spack packages *except* the compiler.
+
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Compilers Requiring Modules
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -398,62 +415,14 @@ provides no Fortran compilers.  The user is therefore forced to use a
 mixed toolchain: XCode-provided Clang for C/C++ and GNU ``gfortran`` for
 Fortran.
 
-#. You need to make sure that Xcode is installed. Run the following command:
+#. You need to make sure that command-line tools are installed. To that
+   end run ``$ xcode-select --install``.
 
-   .. code-block:: console
-
-      $ xcode-select --install
-
-
-   If the Xcode command-line tools are already installed, you will see an
-   error message:
-
-   .. code-block:: none
-
-      xcode-select: error: command line tools are already installed, use "Software Update" to install updates
-
-
-#. For most packages, the Xcode command-line tools are sufficient. However,
-   some packages like ``qt`` require the full Xcode suite. You can check
-   to see which you have installed by running:
-
-   .. code-block:: console
-
-      $ xcode-select -p
-
-
-   If the output is:
-
-   .. code-block:: none
-
-      /Applications/Xcode.app/Contents/Developer
-
-
-   you already have the full Xcode suite installed. If the output is:
-
-   .. code-block:: none
-
-      /Library/Developer/CommandLineTools
-
-
-   you only have the command-line tools installed. The full Xcode suite can
-   be installed through the App Store. Make sure you launch the Xcode
-   application and accept the license agreement before using Spack.
-   It may ask you to install additional components. Alternatively, the license
-   can be accepted through the command line:
-
-   .. code-block:: console
-
-      $ sudo xcodebuild -license accept
-
-
-   Note: the flag is ``-license``, not ``--license``.
-
-#. Run ``spack compiler find`` to locate Clang.
+#. Run ``$ spack compiler find`` to locate Clang.
 
 #. There are different ways to get ``gfortran`` on macOS. For example, you can
-   install GCC with Spack (``spack install gcc``) or with Homebrew
-   (``brew install gcc``).
+   install GCC with Spack (``$ spack install gcc``) or with Homebrew
+   (``$ brew install gcc``).
 
 #. The only thing left to do is to edit ``~/.spack/compilers.yaml`` to provide
    the path to ``gfortran``:
@@ -469,7 +438,7 @@ Fortran.
             fc: /path/to/bin/gfortran
 
    If you used Spack to install GCC, you can get the installation prefix by
-   ``spack location -i gcc`` (this will only work if you have a single version
+   ``$ spack location -i gcc`` (this will only work if you have a single version
    of GCC installed). Whereas for Homebrew, GCC is installed in
    ``/usr/local/Cellar/gcc/x.y.z``.
 
@@ -681,7 +650,6 @@ Or it can be set permanently in your ``compilers.yaml``:
       fflags: -mismatch
     spec: nag@6.1
 
-
 ---------------
 System Packages
 ---------------
@@ -744,22 +712,19 @@ example:
 
     $ curl -O https://github.com/ImageMagick/ImageMagick/archive/7.0.2-7.tar.gz
 
-To tell Spack to use the system-supplied OpenSSL, first determine what
-version you have:
+The recommended way to tell Spack to use the system-supplied OpenSSL is
+to add the following to ``packages.yaml``.  Note that the ``@system``
+"version" means "I don't care what version it is, just use what is
+there."  This is reasonable for OpenSSL, which has a stable API.
 
-.. code-block:: console
-
-   $ openssl version
-   OpenSSL 1.0.2g  1 Mar 2016
-
-Then add the following to ``~/.spack/packages.yaml``:
 
 .. code-block:: yaml
 
     packages:
         openssl:
             paths:
-                openssl@1.0.2g: /usr
+                openssl@system: /usr
+            version: [system]
             buildable: False
 
 
@@ -775,7 +740,8 @@ to add the following to ``packages.yaml``:
     packages:
         netlib-lapack:
             paths:
-                netlib-lapack@3.6.1: /usr
+                netlib-lapack@system: /usr
+            version: [system]
             buildable: False
         all:
             providers:
@@ -784,9 +750,11 @@ to add the following to ``packages.yaml``:
 
 .. note::
 
-   Above we pretend that the system-provided BLAS / LAPACK is ``netlib-lapack``
-   only because it is the only BLAS / LAPACK provider which use standard names
-   for libraries (as opposed to, for example, ``libopenblas.so``).
+   The ``@system`` "version" means "I don't care what version it is,
+   just use what is there." Above we pretend that the system-provided
+   Blas/Lapack is ``netlib-lapack`` only because it is the only BLAS / LAPACK
+   provider which use standard names for libraries (as opposed to, for example,
+   `libopenblas.so`).
 
    Although we specify external package in ``/usr``, Spack is smart enough not
    to add ``/usr/lib`` to RPATHs, where it could cause unrelated system
@@ -816,7 +784,7 @@ This problem is related to OpenSSL, and in some cases might be solved
 by installing a new version of ``git`` and ``openssl``:
 
 #. Run ``spack install git``
-#. Add the output of ``spack module loads git`` to your ``.bashrc``.
+#. Add the output of ``spack module loads git`` to your ``.bahsrc``.
 
 If this doesn't work, it is also possible to disable checking of SSL
 certificates by using:
@@ -889,10 +857,6 @@ well.  They can generally be activated as in the ``curl`` example above;
 or some systems might already have an appropriate hand-built
 environment module that may be loaded.  Either way works.
 
-If you find that you are missing some of these programs, ``spack`` can
-build some of them for you with ``spack bootstrap``. Currently supported
-programs are ``environment-modules``.
-
 A few notes on specific programs in this list:
 
 """"""""""""""""""""""""""
@@ -926,37 +890,55 @@ Once ``curl`` has been installed, you can similarly install the others.
 Environment Modules
 """""""""""""""""""
 
-In order to use Spack's generated module files, you must have
-installed ``environment-modules`` or ``lmod``. The simplest way
-to get the latest version of either of these tools is installing
-it as part of Spack's bootstrap procedure:
+In order to use Spack's generated environment modules, you must have
+installed one of *Environment Modules* or *Lmod*.  On many Linux
+distributions, this can be installed from the vendor's repository.  For
+example: ``yum install environment-modules`` (Fedora/RHEL/CentOS).  If
+your Linux distribution does not have Environment Modules, you can get it
+with Spack:
+
+#. Consider using system tcl (as long as your system has Tcl version 8.0 or later):
+
+   #) Identify its location using ``which tclsh``
+   #) Identify its version using ``echo 'puts $tcl_version;exit 0' | tclsh``
+   #) Add to ``~/.spack/packages.yaml`` and modify as appropriate:
+
+      .. code-block:: yaml
+
+         packages:
+             tcl:
+                 paths:
+                     tcl@8.5: /usr
+                 version: [8.5]
+                 buildable: False
+
+#. Install with:
+
+   .. code-block:: console
+
+      $ spack install environment-modules
+
+#. Activate with the following script (or apply the updates to your
+   ``.bashrc`` file manually):
+
+   .. code-block:: sh
+
+      TMP=`tempfile`
+      echo >$TMP
+      MODULE_HOME=`spack location --install-dir environment-modules`
+      MODULE_VERSION=`ls -1 $MODULE_HOME/Modules | head -1`
+      ${MODULE_HOME}/Modules/${MODULE_VERSION}/bin/add.modules <$TMP
+      cp .bashrc $TMP
+      echo "MODULE_VERSION=${MODULE_VERSION}" > .bashrc
+      cat $TMP >>.bashrc
+
+This adds to your ``.bashrc`` (or similar) files, enabling Environment
+Modules when you log in.  Re-load your .bashrc (or log out and in
+again), and then test that the ``module`` command is found with:
 
 .. code-block:: console
 
-   $ spack bootstrap
-
-.. warning::
-   At the moment ``spack bootstrap`` is only able to install ``environment-modules``.
-   Extending its capabilities to prefer ``lmod`` where possible is in the roadmap,
-   and likely to happen before the next release.
-
-Alternatively, on many Linux distributions, you can install a pre-built binary
-from the vendor's repository. On Fedora/RHEL/CentOS, for example, this can be
-done with the command:
-
-.. code-block:: console
-
-   $ yum install environment-modules
-
-Once you have the tool installed and available in your path, you can source
-Spack's setup file:
-
-.. code-block:: console
-
-   $ source share/spack/setup-env.sh
-
-This activates :ref:`shell support <shell-support>` and makes commands like
-``spack load`` available for use.
+   $ module avail
 
 
 ^^^^^^^^^^^^^^^^^
@@ -1014,89 +996,6 @@ written in C/C++/Fortran would need it.  A potential workaround is to
 load a recent ``binutils`` into your environment and use the ``--dirty``
 flag.
 
------------
-GPG Signing
------------
-
-.. _cmd-spack-gpg:
-
-^^^^^^^^^^^^^
-``spack gpg``
-^^^^^^^^^^^^^
-
-Spack has support for signing and verifying packages using GPG keys. A
-separate keyring is used for Spack, so any keys available in the user's home
-directory are not used.
-
-^^^^^^^^^^^^^^^^^^
-``spack gpg init``
-^^^^^^^^^^^^^^^^^^
-
-When Spack is first installed, its keyring is empty. Keys stored in
-:file:`var/spack/gpg` are the default keys for a Spack installation. These
-keys may be imported by running ``spack gpg init``. This will import the
-default keys into the keyring as trusted keys.
-
-^^^^^^^^^^^^^
-Trusting keys
-^^^^^^^^^^^^^
-
-Additional keys may be added to the keyring using
-``spack gpg trust <keyfile>``. Once a key is trusted, packages signed by the
-owner of they key may be installed.
-
-^^^^^^^^^^^^^
-Creating keys
-^^^^^^^^^^^^^
-
-You may also create your own key so that you may sign your own packages using
-``spack gpg create <name> <email>``. By default, the key has no expiration,
-but it may be set with the ``--expires <date>`` flag (see the ``gnupg2``
-documentation for accepted date formats). It is also recommended to add a
-comment as to the use of the key using the ``--comment <comment>`` flag. The
-public half of the key can also be exported for sharing with others so that
-they may use packages you have signed using the ``--export <keyfile>`` flag.
-Secret keys may also be later exported using the
-``spack gpg export <location> [<key>...]`` command.
-
-.. note::
-
-   Key creation speed
-      The creation of a new GPG key requires generating a lot of random numbers.
-      Depending on the entropy produced on your system, the entire process may
-      take a long time (even a few minutes). To speed it up you may install
-      tools like ``rngd``, which is usually available as a package in the host OS.
-      On e.g. an Ubuntu machine you need to give the following commands:
-
-      .. code-block:: console
-
-         $ sudo apt-get install rng-tools
-         $ sudo rngd -r /dev/urandom
-
-      before generating the keys.
-
-^^^^^^^^^^^^
-Listing keys
-^^^^^^^^^^^^
-
-In order to list the keys available in the keyring, the
-``spack gpg list`` command will list trusted keys with the ``--trusted`` flag
-and keys available for signing using ``--signing``. If you would like to
-remove keys from your keyring, ``spack gpg untrust <keyid>``. Key IDs can be
-email addresses, names, or (best) fingerprints.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Signing and Verifying Packages
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-In order to sign a package, ``spack gpg sign <file>`` should be used. By
-default, the signature will be written to ``<file>.asc``, but that may be
-changed by using the ``--output <file>`` flag. If there is only one signing
-key available, it will be used, but if there is more than one, the key to use
-must be specified using the ``--key <keyid>`` flag. The ``--clearsign`` flag
-may also be used to create a signed file which contains the contents, but it
-is not recommended. Signed packages may be verified by using
-``spack gpg verify <file>``.
 
 .. _cray-support:
 
@@ -1192,13 +1091,10 @@ Here's an example of an external configuration for cray modules:
 .. code-block:: yaml
 
    packages:
-     mpich:
+     mpi:
        modules:
          mpich@7.3.1%gcc@5.2.0 arch=cray_xc-haswell-CNL10: cray-mpich
          mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-haswell-CNL10: cray-mpich
-     all:
-       providers:
-         mpi: [mpich]
 
 This tells Spack that for whatever package that depends on mpi, load the
 cray-mpich module into the environment. You can then be able to use whatever
@@ -1215,7 +1111,7 @@ Here is an example of a full packages.yaml used at NERSC
 .. code-block:: yaml
 
    packages:
-     mpich:
+     mpi:
        modules:
          mpich@7.3.1%gcc@5.2.0 arch=cray_xc-CNL10-ivybridge: cray-mpich
          mpich@7.3.1%intel@16.0.0.109 arch=cray_xc-SuSE11-ivybridge: cray-mpich
@@ -1232,8 +1128,6 @@ Here is an example of a full packages.yaml used at NERSC
        buildable: False
      all:
        compiler: [gcc@5.2.0, intel@16.0.0.109]
-       providers:
-         mpi: [mpich]
 
 Here we tell spack that whenever we want to build with gcc use version 5.2.0 or
 if we want to build with intel compilers, use version 16.0.0.109. We add a spec

lib/spack/docs/index.rst

@@ -4,13 +4,9 @@
    contain the root `toctree` directive.
 
 ===================
-Spack
+Spack Documentation
 ===================
 
-.. epigraph::
-
-   `These are docs for the Spack package manager. For sphere packing, see` `pyspack <https://pyspack.readthedocs.io>`_.
-
 Spack is a package management tool designed to support multiple
 versions and configurations of software on a wide variety of platforms
 and environments.  It was designed for large supercomputing centers,
@@ -29,12 +25,12 @@ maintain a single file for many different builds of the same package.
 See the :doc:`features` for examples and highlights.
 
 Get spack from the `github repository
-<https://github.com/spack/spack>`_ and install your first
+<https://github.com/llnl/spack>`_ and install your first
 package:
 
 .. code-block:: console
 
-   $ git clone https://github.com/spack/spack.git
+   $ git clone https://github.com/llnl/spack.git
    $ cd spack/bin
    $ ./spack install libelf
 
@@ -50,8 +46,7 @@ or refer to the full manual below.
    getting_started
    basic_usage
    workflows
-   tutorial
-   known_issues
+   tutorial_sc16
 
 .. toctree::
    :maxdepth: 2
@@ -63,7 +58,6 @@ or refer to the full manual below.
    mirrors
    module_file_support
    repositories
-   binary_caches
    command_index
    package_list
 
@@ -74,8 +68,7 @@ or refer to the full manual below.
    contribution_guide
    packaging_guide
    developer_guide
-   Spack API Docs <spack>
-   LLNL API Docs <llnl>
+   API Docs <spack>
 
 ==================
 Indices and tables

lib/spack/docs/known_issues.rst

@@ -1,90 +0,0 @@
-============
-Known Issues
-============
-
-This is a list of known bugs in Spack. It provides ways of getting around these
-problems if you encounter them.
-
------------------------------------------------------------------
-Default variants are not taken into account during concretization
------------------------------------------------------------------
-
-**Status:** Expected to be fixed in the next release
-
-Current concretization algorithm does not take into account default values
-of variants when adding extra constraints to the spec via CLI. For example
-you may encounter the following error when trying to specify which MPI provider
-to use:
-
-.. code-block:: console
-
-   $ spack install hdf5 ^openmpi
-   ==> Error: hdf5 does not depend on openmpi
-
-although the hdf5 package contains:
-
-.. code-block:: python
-
-   variant('mpi', default=True, description='Enable MPI support')
-   depends_on('mpi', when='+mpi')
-
-A workaround is to explicitly activate the variant related to the dependency:
-
-.. code-block:: console
-
-   $ spack install hdf5+mpi ^openmpi
-
-See https://github.com/spack/spack/issues/397 for further details.
-
-
----------------------------------------------------
-Variants are not properly forwarded to dependencies
----------------------------------------------------
-
-**Status:** Expected to be fixed in the next release
-
-Sometimes, a variant of a package can also affect how its dependencies are
-built. For example, in order to build MPI support for a package, it may
-require that its dependencies are also built with MPI support. In the
-``package.py``, this looks like:
-
-.. code-block:: python
-
-   depends_on('hdf5~mpi', when='~mpi')
-   depends_on('hdf5+mpi', when='+mpi')
-
-Spack handles this situation properly for *immediate* dependencies, and
-builds ``hdf5`` with the same variant you used for the package that
-depends on it. However, for *indirect* dependencies (dependencies of
-dependencies), Spack does not backtrack up the DAG far enough to handle
-this. Users commonly run into this situation when trying to build R with
-X11 support:
-
-.. code-block:: console
-
-   $ spack install r+X
-   ...
-   ==> Error: Invalid spec: 'cairo@1.14.8%gcc@6.2.1+X arch=linux-fedora25-x86_64 ^bzip2@1.0.6%gcc@6.2.1+shared arch=linux-fedora25-x86_64 ^font-util@1.3.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^fontconfig@2.12.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^freetype@2.7.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^gettext@0.19.8.1%gcc@6.2.1+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-fedora25-x86_64 ^glib@2.53.1%gcc@6.2.1~libmount arch=linux-fedora25-x86_64 ^inputproto@2.3.2%gcc@6.2.1 arch=linux-fedora25-x86_64 ^kbproto@1.0.7%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libffi@3.2.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libpng@1.6.29%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libpthread-stubs@0.4%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libx11@1.6.5%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxau@1.0.8%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxcb@1.12%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxdmcp@1.1.2%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxext@1.3.3%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxml2@2.9.4%gcc@6.2.1~python arch=linux-fedora25-x86_64 ^libxrender@0.9.10%gcc@6.2.1 arch=linux-fedora25-x86_64 ^ncurses@6.0%gcc@6.2.1~symlinks arch=linux-fedora25-x86_64 ^openssl@1.0.2k%gcc@6.2.1 arch=linux-fedora25-x86_64 ^pcre@8.40%gcc@6.2.1+utf arch=linux-fedora25-x86_64 ^pixman@0.34.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^pkg-config@0.29.2%gcc@6.2.1+internal_glib arch=linux-fedora25-x86_64 ^python@2.7.13%gcc@6.2.1+shared~tk~ucs4 arch=linux-fedora25-x86_64 ^readline@7.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^renderproto@0.11.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^sqlite@3.18.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^tar^util-macros@1.19.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xcb-proto@1.12%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xextproto@7.3.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xproto@7.0.31%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xtrans@1.3.5%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xz@5.2.3%gcc@6.2.1 arch=linux-fedora25-x86_64 ^zlib@1.2.11%gcc@6.2.1+pic+shared arch=linux-fedora25-x86_64'.
-   Package cairo requires variant ~X, but spec asked for +X
-
-A workaround is to explicitly activate the variants of dependencies as well:
-
-.. code-block:: console
-
-   $ spack install r+X ^cairo+X ^pango+X
-
-See https://github.com/spack/spack/issues/267 and
-https://github.com/spack/spack/issues/2546 for further details.
-
-
-----------------------------
-``spack setup`` doesn't work
-----------------------------
-
-**Status:** Work in progress
-
-Spack provides a ``setup`` command that is useful for the development of
-software outside of Spack. Unfortunately, this command no longer works.
-See https://github.com/spack/spack/issues/2597 and
-https://github.com/spack/spack/issues/2662 for details. This is expected
-to be fixed by https://github.com/spack/spack/pull/2664.

lib/spack/docs/mirrors.rst

@@ -162,7 +162,7 @@ your site.
 
 Once you have a mirror, you need to let spack know about it.  This is
 relatively simple.  First, figure out the URL for the mirror.  If it's
-a directory, you can use a file URL like this one:
+a file, you can use a file URL like this one:
 
 .. code-block:: none
 
@@ -237,7 +237,7 @@ as other Spack mirrors (so it can be copied anywhere and referenced with a URL
 like other mirrors). The mirror is maintained locally (within the Spack
 installation directory) at :file:`var/spack/cache/`. It is always enabled (and
 is always searched first when attempting to retrieve files for an installation)
-but can be cleared with :ref:`clean <cmd-spack-clean>`; the cache directory can also
+but can be cleared with :ref:`purge <cmd-spack-purge>`; the cache directory can also
 be deleted manually without issue.
 
 Caching includes retrieved tarball archives and source control repositories, but

lib/spack/docs/module_file_generation.svg

@@ -1,989 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<svg
-   xmlns:dc="http://purl.org/dc/elements/1.1/"
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lib/spack/docs/module_file_support.rst

@@ -7,10 +7,16 @@ Modules
 The use of module systems to manage user environment in a controlled way
 is a common practice at HPC centers that is often embraced also by individual
 programmers on their development machines. To support this common practice
-Spack integrates with `Environment Modules
+Spack provides integration with `Environment Modules
 <http://modules.sourceforge.net/>`_ ,  `LMod
-<http://lmod.readthedocs.io/en/latest/>`_ and `Dotkit <https://computing.llnl.gov/?set=jobs&page=dotkit>`_ by
-providing post-install hooks that generate module files and commands to manipulate them.
+<http://lmod.readthedocs.io/en/latest/>`_ and `Dotkit <https://computing.llnl.gov/?set=jobs&page=dotkit>`_ by:
+
+* generating module files after a successful installation
+* providing commands that can leverage the spec syntax to manipulate modules
+
+In the following you will see how to activate shell support for commands in Spack
+that requires it, and discover what benefits this may bring with respect to deal
+directly with automatically generated module files.
 
 .. note::
 
@@ -20,58 +26,13 @@ providing post-install hooks that generate module files and commands to manipula
 
 .. _shell-support:
 
-----------------------------
-Using module files via Spack
-----------------------------
-
-If you have installed a supported module system either manually or through
-``spack bootstrap``, you should be able to run either ``module avail`` or
-``use -l spack`` to see what module files have been installed.  Here is
-sample output of those programs, showing lots of installed packages:
-
-.. code-block:: console
-
-   $ module avail
-
-   --------------------------------------------------------------- ~/spack/share/spack/modules/linux-ubuntu14-x86_64 ---------------------------------------------------------------
-   autoconf-2.69-gcc-4.8-qextxkq       hwloc-1.11.6-gcc-6.3.0-akcisez             m4-1.4.18-gcc-4.8-ev2znoc                   openblas-0.2.19-gcc-6.3.0-dhkmed6        py-setuptools-34.2.0-gcc-6.3.0-fadur4s
-   automake-1.15-gcc-4.8-maqvukj       isl-0.18-gcc-4.8-afi6taq                   m4-1.4.18-gcc-6.3.0-uppywnz                 openmpi-2.1.0-gcc-6.3.0-go2s4z5          py-six-1.10.0-gcc-6.3.0-p4dhkaw
-   binutils-2.28-gcc-4.8-5s7c6rs       libiconv-1.15-gcc-4.8-at46wg3              mawk-1.3.4-gcc-4.8-acjez57                  openssl-1.0.2k-gcc-4.8-dkls5tk           python-2.7.13-gcc-6.3.0-tyehea7
-   bison-3.0.4-gcc-4.8-ek4luo5         libpciaccess-0.13.4-gcc-6.3.0-gmufnvh      mawk-1.3.4-gcc-6.3.0-ostdoms                openssl-1.0.2k-gcc-6.3.0-gxgr5or         readline-7.0-gcc-4.8-xhufqhn
-   bzip2-1.0.6-gcc-4.8-iffrxzn         libsigsegv-2.11-gcc-4.8-pp2cvte            mpc-1.0.3-gcc-4.8-g5mztc5                   pcre-8.40-gcc-4.8-r5pbrxb                readline-7.0-gcc-6.3.0-zzcyicg
-   bzip2-1.0.6-gcc-6.3.0-bequudr       libsigsegv-2.11-gcc-6.3.0-7enifnh          mpfr-3.1.5-gcc-4.8-o7xm7az                  perl-5.24.1-gcc-4.8-dg5j65u              sqlite-3.8.5-gcc-6.3.0-6zoruzj
-   cmake-3.7.2-gcc-6.3.0-fowuuby       libtool-2.4.6-gcc-4.8-7a523za              mpich-3.2-gcc-6.3.0-dmvd3aw                 perl-5.24.1-gcc-6.3.0-6uzkpt6            tar-1.29-gcc-4.8-wse2ass
-   curl-7.53.1-gcc-4.8-3fz46n6         libtool-2.4.6-gcc-6.3.0-n7zmbzt            ncurses-6.0-gcc-4.8-dcpe7ia                 pkg-config-0.29.2-gcc-4.8-ib33t75        tcl-8.6.6-gcc-4.8-tfxzqbr
-   expat-2.2.0-gcc-4.8-mrv6bd4         libxml2-2.9.4-gcc-4.8-ryzxnsu              ncurses-6.0-gcc-6.3.0-ucbhcdy               pkg-config-0.29.2-gcc-6.3.0-jpgubk3      util-macros-1.19.1-gcc-6.3.0-xorz2x2
-   flex-2.6.3-gcc-4.8-yf345oo          libxml2-2.9.4-gcc-6.3.0-rltzsdh            netlib-lapack-3.6.1-gcc-6.3.0-js33dog       py-appdirs-1.4.0-gcc-6.3.0-jxawmw7       xz-5.2.3-gcc-4.8-mew4log
-   gcc-6.3.0-gcc-4.8-24puqve           lmod-7.4.1-gcc-4.8-je4srhr                 netlib-scalapack-2.0.2-gcc-6.3.0-5aidk4l    py-numpy-1.12.0-gcc-6.3.0-oemmoeu        xz-5.2.3-gcc-6.3.0-3vqeuvb
-   gettext-0.19.8.1-gcc-4.8-yymghlh    lua-5.3.4-gcc-4.8-im75yaz                  netlib-scalapack-2.0.2-gcc-6.3.0-hjsemcn    py-packaging-16.8-gcc-6.3.0-i2n3dtl      zip-3.0-gcc-4.8-rwar22d
-   gmp-6.1.2-gcc-4.8-5ub2wu5           lua-luafilesystem-1_6_3-gcc-4.8-wkey3nl    netlib-scalapack-2.0.2-gcc-6.3.0-jva724b    py-pyparsing-2.1.10-gcc-6.3.0-tbo6gmw    zlib-1.2.11-gcc-4.8-pgxsxv7
-   help2man-1.47.4-gcc-4.8-kcnqmau     lua-luaposix-33.4.0-gcc-4.8-mdod2ry        netlib-scalapack-2.0.2-gcc-6.3.0-rgqfr6d    py-scipy-0.19.0-gcc-6.3.0-kr7nat4        zlib-1.2.11-gcc-6.3.0-7cqp6cj
-
-The names should look familiar, as they resemble the output from ``spack find``.
-You *can* use the modules here directly.  For example, you could type either of these commands
-to load the ``cmake`` module:
-
-.. code-block:: console
-
-   $ use cmake-3.7.2-gcc-6.3.0-fowuuby
-
-.. code-block:: console
-
-   $ module load cmake-3.7.2-gcc-6.3.0-fowuuby
-
-Neither of these is particularly pretty, easy to remember, or
-easy to type. Luckily, Spack has its own interface for using modules and dotkits.
-
-^^^^^^^^^^^^^
+-------------
 Shell support
-^^^^^^^^^^^^^
+-------------
 
-To enable additional Spack commands for loading and unloading module files,
-and to add the correct path to ``MODULEPATH``,  you need to source the appropriate
-setup file in the ``$SPACK_ROOT/share/spack`` directory. This will activate shell
-support for the commands that need it. For ``bash``, ``ksh`` or ``zsh`` users:
+You can enable shell support by sourcing the appropriate setup file
+in the ``$SPACK_ROOT/share/spack`` directory.
+For ``bash`` or ``ksh`` users:
 
 .. code-block:: console
 
@@ -81,20 +42,73 @@ For ``csh`` and ``tcsh`` instead:
 
 .. code-block:: console
 
-   $ set SPACK_ROOT ...
    $ source $SPACK_ROOT/share/spack/setup-env.csh
 
-Note that in the latter case it is necessary to explicitly set ``SPACK_ROOT``
-before sourcing the setup file (you will get a meaningful error message
-if you don't).
 
-When ``bash`` and ``ksh`` users update their environment with ``setup-env.sh``, it will check for spack-installed environment modules and add the ``module`` command to their environment; This only occurs if the module command is not already available. You can install ``environment-modules`` with ``spack bootstrap`` as described in :ref:`InstallEnvironmentModules`.
+.. note::
+  You can put the source line in your ``.bashrc`` or ``.cshrc`` to
+  have Spack's shell support available on the command line at any login.
 
-Finally, if you want to have Spack's shell support available on the command line at
-any login you can put this source line in one of the files that are sourced
-at startup (like ``.profile``, ``.bashrc`` or ``.cshrc``). Be aware though
-that the startup time may be slightly increased because of that.
 
+----------------------------
+Using module files via Spack
+----------------------------
+
+If you have shell support enabled you should be able to run either
+``module avail`` or ``use -l spack`` to see what module/dotkit files have
+been installed.  Here is sample output of those programs, showing lots
+of installed packages.
+
+.. code-block:: console
+
+   $ module avail
+
+   ------- ~/spack/share/spack/modules/linux-debian7-x86_64 --------
+   adept-utils@1.0%gcc@4.4.7-5adef8da   libelf@0.8.13%gcc@4.4.7
+   automaded@1.0%gcc@4.4.7-d9691bb0     libelf@0.8.13%intel@15.0.0
+   boost@1.55.0%gcc@4.4.7               mpc@1.0.2%gcc@4.4.7-559607f5
+   callpath@1.0.1%gcc@4.4.7-5dce4318    mpfr@3.1.2%gcc@4.4.7
+   dyninst@8.1.2%gcc@4.4.7-b040c20e     mpich@3.0.4%gcc@4.4.7
+   gcc@4.9.1%gcc@4.4.7-93ab98c5         mpich@3.0.4%gcc@4.9.0
+   gmp@6.0.0a%gcc@4.4.7                 mrnet@4.1.0%gcc@4.4.7-72b7881d
+   graphlib@2.0.0%gcc@4.4.7             netgauge@2.4.6%gcc@4.9.0-27912b7b
+   launchmon@1.0.1%gcc@4.4.7            stat@2.1.0%gcc@4.4.7-51101207
+   libNBC@1.1.1%gcc@4.9.0-27912b7b      sundials@2.5.0%gcc@4.9.0-27912b7b
+   libdwarf@20130729%gcc@4.4.7-b52fac98
+
+.. code-block:: console
+
+   $ use -l spack
+
+   spack ----------
+     adept-utils@1.0%gcc@4.4.7-5adef8da - adept-utils @1.0
+     automaded@1.0%gcc@4.4.7-d9691bb0 - automaded @1.0
+     boost@1.55.0%gcc@4.4.7 - boost @1.55.0
+     callpath@1.0.1%gcc@4.4.7-5dce4318 - callpath @1.0.1
+     dyninst@8.1.2%gcc@4.4.7-b040c20e - dyninst @8.1.2
+     gmp@6.0.0a%gcc@4.4.7 - gmp @6.0.0a
+     libNBC@1.1.1%gcc@4.9.0-27912b7b - libNBC @1.1.1
+     libdwarf@20130729%gcc@4.4.7-b52fac98 - libdwarf @20130729
+     libelf@0.8.13%gcc@4.4.7 - libelf @0.8.13
+     libelf@0.8.13%intel@15.0.0 - libelf @0.8.13
+     mpc@1.0.2%gcc@4.4.7-559607f5 - mpc @1.0.2
+     mpfr@3.1.2%gcc@4.4.7 - mpfr @3.1.2
+     mpich@3.0.4%gcc@4.4.7 - mpich @3.0.4
+     mpich@3.0.4%gcc@4.9.0 - mpich @3.0.4
+     netgauge@2.4.6%gcc@4.9.0-27912b7b - netgauge @2.4.6
+     sundials@2.5.0%gcc@4.9.0-27912b7b - sundials @2.5.0
+
+The names here should look familiar, they're the same ones from
+``spack find``.  You *can* use the names here directly.  For example,
+you could type either of these commands to load the callpath module:
+
+.. code-block:: console
+
+   $ use callpath@1.0.1%gcc@4.4.7-5dce4318
+
+.. code-block:: console
+
+   $ module load callpath@1.0.1%gcc@4.4.7-5dce4318
 
 .. _cmd-spack-load:
 
@@ -102,11 +116,12 @@ that the startup time may be slightly increased because of that.
 ``spack load / unload``
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-Once you have shell support enabled you can use the same spec syntax
-you're used to:
+Neither of these is particularly pretty, easy to remember, or
+easy to type.  Luckily, Spack has its own interface for using modules
+and dotkits.  You can use the same spec syntax you're used to:
 
 =========================  ==========================
-Modules                    Dotkit
+Environment Modules        Dotkit
 =========================  ==========================
 ``spack load <spec>``      ``spack use <spec>``
 ``spack unload <spec>``    ``spack unuse <spec>``
@@ -195,7 +210,7 @@ Scripts to load modules recursively may be made with the command:
 
     $ spack module loads --dependencies <spec>
 
-An equivalent alternative using `process substitution <http://tldp.org/LDP/abs/html/process-sub.html>`_ is:
+An equivalent alternative is:
 
 .. code-block :: console
 
@@ -281,46 +296,43 @@ For example, consider the following on one system:
     # antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
     module load linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
 
--------------------------
-Module file customization
--------------------------
+----------------------------
+Auto-generating Module Files
+----------------------------
 
 Module files are generated by post-install hooks after the successful
-installation of a package. The table below summarizes the essential
+installation of a package. The following table summarizes the essential
 information associated with the different file formats
 that can be generated by Spack:
 
-  +-----------------------------+--------------------+-------------------------------+----------------------------------+----------------------+
-  |                             | **Hook name**      |  **Default root directory**   | **Default template file**        | **Compatible tools** |
-  +=============================+====================+===============================+==================================+======================+
-  |  **Dotkit**                 | ``dotkit``         |  share/spack/dotkit           | templates/modules/modulefile.dk  | DotKit               |
-  +-----------------------------+--------------------+-------------------------------+----------------------------------+----------------------+
-  |  **TCL - Non-Hierarchical** | ``tcl``            |  share/spack/modules          | templates/modules/modulefile.tcl | Env. Modules/LMod    |
-  +-----------------------------+--------------------+-------------------------------+----------------------------------+----------------------+
-  |  **Lua - Hierarchical**     | ``lmod``           |  share/spack/lmod             | templates/modules/modulefile.lua | LMod                 |
-  +-----------------------------+--------------------+-------------------------------+----------------------------------+----------------------+
+  +-----------------------------+--------------------+-------------------------------+----------------------+
+  |                             | **Hook name**      |  **Default root directory**   | **Compatible tools** |
+  +=============================+====================+===============================+======================+
+  |  **Dotkit**                 | ``dotkit``         |   share/spack/dotkit          |  DotKit              |
+  +-----------------------------+--------------------+-------------------------------+----------------------+
+  |  **TCL - Non-Hierarchical** | ``tcl``            |  share/spack/modules          | Env. Modules/LMod    |
+  +-----------------------------+--------------------+-------------------------------+----------------------+
+  |  **Lua - Hierarchical**     | ``lmod``           |   share/spack/lmod            | LMod                 |
+  +-----------------------------+--------------------+-------------------------------+----------------------+
 
 
-Spack ships with sensible defaults for the generation of module files, but
-you can customize many aspects of it to accommodate package or site specific needs.
-In general you can override or extend the default behavior by:
+Though Spack ships with sensible defaults for the generation of module files,
+one can customize many aspects of it to accommodate package or site specific needs.
+These customizations are enabled by either:
 
  1. overriding certain callback APIs in the Python packages
  2. writing specific rules in the ``modules.yaml`` configuration file
- 3. writing your own templates to override or extend the defaults
 
-The former method let you express changes in the run-time environment
-that are needed to use the installed software properly, e.g. injecting variables
-from language interpreters into their extensions. The latter two instead permit to
-fine tune the filesystem layout, content and creation of module files to meet
-site specific conventions.
+The former method fits best cases that are site independent, e.g. injecting variables
+from language interpreters into their extensions. The latter instead permits to
+fine tune the content, naming and creation of module files to meet site specific conventions.
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Override API calls in ``package.py``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^
+``Package`` file API
+^^^^^^^^^^^^^^^^^^^^
 
-There are two methods that you can override in any ``package.py`` to affect the
-content of the module files generated by Spack. The first one:
+There are two methods that can be overridden in any ``package.py`` to affect the
+content of generated module files. The first one is:
 
 .. code-block:: python
 
@@ -328,8 +340,8 @@ content of the module files generated by Spack. The first one:
        """Set up the compile and runtime environments for a package."""
        pass
 
-can alter the content of the module file associated with the same package where it is overridden.
-The second method:
+and can alter the content of *the same package where it is overridden*
+by adding actions to ``run_env``. The second method is:
 
 .. code-block:: python
 
@@ -337,13 +349,12 @@ The second method:
        """Set up the environment of packages that depend on this one"""
        pass
 
-can instead inject run-time environment modifications in the module files of packages
-that depend on it. In both cases you need to fill ``run_env`` with the desired
-list of environment modifications.
+and has similar effects on module file of dependees. Even in this case
+``run_env`` must be filled with the desired list of environment modifications.
 
 .. note::
  The ``r`` package and callback APIs
-  An example in which it is crucial to override both methods
+  A typical example in which overriding both methods prove to be useful
   is given by the ``r`` package. This package installs libraries and headers
   in non-standard locations and it is possible to prepend the appropriate directory
   to the corresponding environment variables:
@@ -364,36 +375,37 @@ list of environment modifications.
   it appropriately in the override of the second method:
 
   .. literalinclude:: ../../../var/spack/repos/builtin/packages/r/package.py
-     :pyobject: R.setup_dependent_environment
+     :lines: 128-129,146-151
 
 .. _modules-yaml:
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-Write a configuration file
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+---------------------------------
+Configuration in ``modules.yaml``
+---------------------------------
 
-The configuration files that control module generation behavior
-are named ``modules.yaml``. The default configuration:
+The name of the configuration file that controls module generation behavior
+is ``modules.yaml``. The default configuration:
 
 .. literalinclude:: ../../../etc/spack/defaults/modules.yaml
    :language: yaml
 
-activates the hooks to generate ``tcl`` and ``dotkit`` module files and inspects
+activates generation for ``tcl`` and ``dotkit`` module files and inspects
 the installation folder of each package for the presence of a set of subdirectories
 (``bin``, ``man``, ``share/man``, etc.). If any is found its full path is prepended
 to the environment variables listed below the folder name.
 
-""""""""""""""""""""
-Activate other hooks
-""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Activation of other systems
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Any other module file generator shipped with Spack can be activated adding it to the
 list under the ``enable`` key in the module file. Currently the only generator that
-is not active by default is ``lmod``, which produces hierarchical lua module files.
+is not activated by default is ``lmod``, which produces hierarchical lua module files.
+For each module system that can be enabled a finer configuration is possible.
 
-Each module system can then be configured separately. In fact, you should list configuration
-options that affect a particular type of module files under a top level key corresponding
-to the generator being customized:
+Directives that are aimed at driving the generation of a particular type of module files
+should be listed under a top level key that corresponds to the generator being
+customized:
 
 .. code-block:: yaml
 
@@ -409,21 +421,24 @@ to the generator being customized:
      lmod:
        # contains lmod specific customizations
 
-In general, the configuration options that you can use in ``modules.yaml`` will
-either change the layout of the module files on the filesystem, or they will affect
-their content. For the latter point it is possible to use anonymous specs
-to fine tune the set of packages on which the modifications should be applied.
+All these module sections allow for both:
+
+1. global directives that usually affect the whole layout of modules or the naming scheme
+2. directives that affect only a set of packages and modify their content
+
+For the latter point in particular it is possible to use anonymous specs
+to select an appropriate set of packages on which the modifications should be applied.
 
 .. _anonymous_specs:
 
-""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Selection by anonymous specs
-""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-In the configuration file you can use *anonymous specs* (i.e. specs
-that **are not required to have a root package** and are thus used just
-to express constraints) to apply certain modifications on a selected set
-of the installed software. For instance, in the snippet below:
+The procedure to select packages using anonymous specs is a natural
+extension of using them to install packages, the only difference being
+that specs in this case **are not required to have a root package**.
+Consider for instance this snippet:
 
 .. code-block:: yaml
 
@@ -452,7 +467,8 @@ of the installed software. For instance, in the snippet below:
            unset:
            - FOOBAR
 
-you are instructing Spack to set the environment variable ``BAR=bar`` for every module,
+During module file generation, the configuration above will instruct
+Spack to set the environment variable ``BAR=bar`` for every module,
 unless the associated spec satisfies ``^openmpi`` in which case ``BAR=baz``.
 In addition in any spec that satisfies ``zlib`` the value ``foo`` will be
 prepended to ``LD_LIBRARY_PATH`` and in any spec that satisfies ``zlib%gcc@4.8``
@@ -464,15 +480,15 @@ the variable ``FOOBAR`` will be unset.
      first, no matter where they appear in the configuration file. All the other
      spec constraints are instead evaluated top to bottom.
 
-""""""""""""""""""""""""""""""""""""""""""""
-Blacklist or whitelist specific module files
-""""""""""""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Blacklist or whitelist the generation of specific module files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-You can use anonymous specs also to prevent module files from being written or
-to force them to be written. Consider the case where you want to hide from users
-all the boilerplate software that you had to build in order to bootstrap a new
-compiler. Suppose for instance that ``gcc@4.4.7`` is the compiler provided by
-your system. If you write a configuration file like:
+Anonymous specs are also used to prevent module files from being written or
+to force them to be written. A common case for that at HPC centers is to hide
+from users all of the software that needs to be built with system compilers.
+Suppose for instance to have ``gcc@4.4.7`` provided by your system. Then
+with a configuration file like this one:
 
 .. code-block:: yaml
 
@@ -481,13 +497,13 @@ your system. If you write a configuration file like:
        whitelist: ['gcc', 'llvm']  # Whitelist will have precedence over blacklist
        blacklist: ['%gcc@4.4.7']   # Assuming gcc@4.4.7 is the system compiler
 
-you will prevent the generation of module files for any package that
-is compiled with ``gcc@4.4.7``, with the only exception of any ``gcc``
+you will skip the generation of module files for any package that
+is compiled with ``gcc@4.4.7``, with the exception of any ``gcc``
 or any ``llvm`` installation.
 
-"""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Customize the naming scheme
-"""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The names of environment modules generated by spack are not always easy to
 fully comprehend due to the long hash in the name. There are two module
@@ -535,9 +551,7 @@ most likely via the ``+blas`` variant specification.
          tcl:
            naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
            all:
-             conflict:
-               - '${PACKAGE}'
-               - 'intel/14.0.1'
+             conflict: ['${PACKAGE}', 'intel/14.0.1']
 
      will create module files that will conflict with ``intel/14.0.1`` and with the
      base directory of the same module, effectively preventing the possibility to
@@ -549,9 +563,9 @@ most likely via the ``+blas`` variant specification.
 .. note::
    LMod hierarchical module files
      When ``lmod`` is activated Spack will generate a set of hierarchical lua module
-     files that are understood by LMod. The hierarchy will always contain the
-     two layers ``Core`` / ``Compiler`` but can be further extended to
-     any of the virtual dependencies present in Spack. A case that could be useful in
+     files that are understood by LMod. The generated hierarchy always contains the
+     three layers ``Core`` / ``Compiler`` / ``MPI`` but can be further extended to
+     any other virtual dependency present in Spack. A case that could be useful in
      practice is for instance:
 
      .. code-block:: yaml
@@ -560,14 +574,11 @@ most likely via the ``+blas`` variant specification.
          enable:
            - lmod
          lmod:
-           core_compilers:
-             - 'gcc@4.8'
-           hierarchy:
-             - 'mpi'
-             - 'lapack'
+           core_compilers: ['gcc@4.8']
+           hierarchical_scheme: ['lapack']
 
-     that will generate a hierarchy in which the ``lapack`` and ``mpi`` layer can be switched
-     independently. This allows a site to build the same libraries or applications against different
+     that will generate a hierarchy in which the ``lapack`` layer is treated as the ``mpi``
+     one. This allows a site to build the same libraries or applications against different
      implementations of ``mpi`` and ``lapack``, and let LMod switch safely from one to the
      other.
 
@@ -576,14 +587,15 @@ most likely via the ``+blas`` variant specification.
    For hierarchies that are deeper than three layers ``lmod spider`` may have some issues.
    See `this discussion on the LMod project <https://github.com/TACC/Lmod/issues/114>`_.
 
-""""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Filter out environment modifications
-""""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Modifications to certain environment variables in module files are there by
-default, for instance because they are generated by prefix inspections.
-If you want to prevent modifications to some environment variables, you can
-do so by using the environment blacklist:
+Modifications to certain environment variables in module files are generated by
+default, for instance by prefix inspections in the default configuration file.
+There are cases though where some of these modifications are unwanted.
+Suppose you need to avoid having ``CPATH`` and ``LIBRARY_PATH``
+modified by your ``dotkit`` modules:
 
 .. code-block:: yaml
 
@@ -598,11 +610,11 @@ The configuration above will generate dotkit module files that will not contain
 modifications to either ``CPATH`` or ``LIBRARY_PATH`` and environment module
 files that instead will contain these modifications.
 
-"""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^
 Autoload dependencies
-"""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^
 
-In some cases it can be useful to have module files that automatically load
+In some cases it can be useful to have module files directly autoload
 their dependencies.  This may be the case for Python extensions, if not
 activated using ``spack activate``:
 
@@ -614,9 +626,8 @@ activated using ``spack activate``:
          autoload: 'direct'
 
 The configuration file above will produce module files that will
-load their direct dependencies if the package installed depends on ``python``.
-The allowed values for the ``autoload`` statement are either ``none``,
-``direct`` or ``all``.
+automatically load their direct dependencies. The allowed values for the
+``autoload`` statement are either ``none``, ``direct`` or ``all``.
 
 .. note::
   TCL prerequisites

lib/spack/docs/package_list.rst

@@ -1,12 +0,0 @@
-.. _package-list:
-
-============
-Package List
-============
-
-This is a list of things you can install using Spack.  It is
-automatically generated based on the packages in the latest Spack
-release.
-
-.. raw:: html
-   :file: package_list.html

lib/spack/docs/requirements.txt

@@ -1,5 +0,0 @@
-# These dependencies should be installed using pip in order
-# to build the documentation.
-
-sphinx
-sphinxcontrib-programoutput

lib/spack/docs/tutorial/examples/0.package.py

@@ -1,13 +1,13 @@
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -40,7 +40,7 @@
 from spack import *
 
 
-class Mpileaks(Package):
+class Mpileaks(AutotoolsPackage):
     """FIXME: Put a proper description of your package here."""
 
     # FIXME: Add a proper url for your package's homepage here.
@@ -50,9 +50,14 @@ class Mpileaks(Package):
     version('1.0', '8838c574b39202a57d7c2d68692718aa')
 
     # FIXME: Add dependencies if required.
+    # depends_on('m4', type='build')
+    # depends_on('autoconf', type='build')
+    # depends_on('automake', type='build')
+    # depends_on('libtool', type='build')
     # depends_on('foo')
 
-    def install(self, spec, prefix):
-        # FIXME: Unknown build system
-        make()
-        make('install')
+    def configure_args(self):
+        # FIXME: Add arguments other than --prefix
+        # FIXME: If not needed delete the function
+        args = []
+        return args

lib/spack/docs/tutorial/examples/1.package.py

@@ -1,13 +1,13 @@
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -25,18 +25,24 @@
 from spack import *
 
 
-class Mpileaks(Package):
+class Mpileaks(AutotoolsPackage):
     """Tool to detect and report MPI objects like MPI_Requests and
     MPI_Datatypes."""
 
     homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"  # NOQA
+    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
+
     version('1.0', '8838c574b39202a57d7c2d68692718aa')
 
     # FIXME: Add dependencies if required.
+    # depends_on('m4', type='build')
+    # depends_on('autoconf', type='build')
+    # depends_on('automake', type='build')
+    # depends_on('libtool', type='build')
     # depends_on('foo')
 
-    def install(self, spec, prefix):
-        # FIXME: Unknown build system
-        make()
-        make('install')
+    def configure_args(self):
+        # FIXME: Add arguments other than --prefix
+        # FIXME: If not needed delete the function
+        args = []
+        return args

lib/spack/docs/tutorial/examples/2.package.py

@@ -1,13 +1,13 @@
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -25,7 +25,7 @@
 from spack import *
 
 
-class Mpileaks(Package):
+class Mpileaks(AutotoolsPackage):
     """Tool to detect and report MPI objects like MPI_Requests and
     MPI_Datatypes."""
 
@@ -38,7 +38,8 @@ class Mpileaks(Package):
     depends_on('adept-utils')
     depends_on('callpath')
 
-    def install(self, spec, prefix):
-        # FIXME: Unknown build system
-        make()
-        make('install')
+    def configure_args(self):
+        # FIXME: Add arguments other than --prefix
+        # FIXME: If not needed delete the function
+        args = []
+        return args

lib/spack/docs/tutorial/examples/3.package.py

@@ -1,13 +1,13 @@
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -25,10 +25,9 @@
 from spack import *
 
 
-class Mpileaks(Package):
+class Mpileaks(AutotoolsPackage):
     """Tool to detect and report MPI objects like MPI_Requests and
     MPI_Datatypes."""
-
     homepage = "https://github.com/hpc/mpileaks"
     url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
 
@@ -38,7 +37,7 @@ class Mpileaks(Package):
     depends_on('adept-utils')
     depends_on('callpath')
 
-    def install(self, spec, prefix):
-        configure()
-        make()
-        make('install')
+    def configure_args(self):
+        args = ['--with-adept-utils=%s' % self.spec['adept-utils'].prefix,
+                '--with-callpath=%s' % self.spec['callpath'].prefix]
+        return args

lib/spack/docs/tutorial/examples/4.package.py

@@ -1,13 +1,13 @@
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -25,7 +25,7 @@
 from spack import *
 
 
-class Mpileaks(Package):
+class Mpileaks(AutotoolsPackage):
     """Tool to detect and report MPI objects like MPI_Requests and
     MPI_Datatypes."""
 
@@ -34,13 +34,17 @@ class Mpileaks(Package):
 
     version('1.0', '8838c574b39202a57d7c2d68692718aa')
 
+    variant('stackstart', default=0, description='Specify the number of stack frames to truncate.')
+
     depends_on('mpi')
     depends_on('adept-utils')
     depends_on('callpath')
 
-    def install(self, spec, prefix):
-        configure('--with-adept-utils=%s' % self.spec['adept-utils'].prefix,
-                  '--with-callpath=%s' % self.spec['callpath'].prefix,
-                  '--prefix=%s' % self.spec.prefix)
-        make()
-        make('install')
+    def configure_args(self):
+        args = ['--with-adept-utils=%s' % self.spec['adept-utils'].prefix,
+                '--with-callpath=%s' % self.spec['callpath'].prefix]
+        stackstart = int(self.spec.variants['stackstart'].value)
+        if stackstart:
+            args.extend(['--with-stack-start-c=%s' % stackstart,
+                         '--with-stack-start-fortran=%s' % stackstart])
+        return args

lib/spack/docs/tutorial/examples/5.package.py

@@ -1,53 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Mpileaks(Package):
-    """Tool to detect and report MPI objects like MPI_Requests and
-    MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    variant('stackstart', values=int, default=0, description='Specify the number of stack frames to truncate.')
-
-    depends_on('mpi')
-    depends_on('adept-utils')
-    depends_on('callpath')
-
-    def install(self, spec, prefix):
-        stackstart = int(self.spec.variants['stackstart'].value)
-        confargs = ['--with-adept-utils=%s' % self.spec['adept-utils'].prefix,
-                    '--with-callpath=%s' % self.spec['callpath'].prefix,
-                    '--prefix=%s' % self.spec.prefix]
-        if stackstart:
-            confargs.extend(['--with-stack-start-c=%s' % stackstart,
-                             '--with-stack-start-fortran=%s' % stackstart])
-        configure(*confargs)
-        make()
-        make('install')

lib/spack/docs/tutorial/examples/Autotools/0.package.py

@@ -1,46 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Mpileaks(AutoToolsPackage):
-    """Tool to detect and report leaked MPI objects like MPI_Requests and
-       MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    depends_on("mpi")
-    depends_on("adept-utils")
-    depends_on("callpath")
-
-    def install(self, spec, prefix):
-        configure("--prefix=" + prefix,
-                  "--with-adept-utils=" + spec['adept-utils'].prefix,
-                  "--with-callpath=" + spec['callpath'].prefix)
-        make()
-        make("install")

lib/spack/docs/tutorial/examples/Autotools/1.package.py

@@ -1,51 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Mpileaks(AutoToolsPackage):
-    """Tool to detect and report leaked MPI objects like MPI_Requests and
-       MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    variant("stackstart", values=int, default=0,
-            description="Specify the number of stack frames to truncate")
-
-    depends_on("mpi")
-    depends_on("adept-utils")
-    depends_on("callpath")
-
-    def configure_args(self):
-        stackstart = int(self.spec.variants['stackstart'].value)
-        args = ["--with-adept-utils=" + spec['adept-utils'].prefix,
-                "--with-callpath=" + spec['callpath'].prefix]
-        if stackstart:
-            args.extend(['--with-stack-start-c=%s' % stackstart,
-                         '--with-stack-start-fortran=%s' % stackstart])
-        return args

lib/spack/docs/tutorial/examples/Cmake/0.package.py

@@ -1,60 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-#
-# This is a template package file for Spack.  We've put "FIXME"
-# next to all the things you'll want to change. Once you've handled
-# them, you can save this file and test your package like this:
-#
-#     spack install callpath
-#
-# You can edit this file again by typing:
-#
-#     spack edit callpath
-#
-# See the Spack documentation for more information on packaging.
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
-from spack import *
-
-
-class Callpath(CMakePackage):
-    """FIXME: Put a proper description of your package here."""
-
-    # FIXME: Add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
-    url      = "https://github.com/llnl/callpath/archive/v1.0.1.tar.gz"
-
-    version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a')
-
-    # FIXME: Add dependencies if required.
-    # depends_on('foo')
-
-    def cmake_args(self):
-        # FIXME: Add arguments other than
-        # FIXME: CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE
-        # FIXME: If not needed delete this function
-        args = []
-        return args

lib/spack/docs/tutorial/examples/Cmake/1.package.py

@@ -1,42 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Callpath(CMakePackage):
-    """Library for representing callpaths consistently in
-       distributed-memory performance tools."""
-
-    homepage = "https://github.com/llnl/callpath"
-    url      = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz"
-
-    version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a')
-
-    depends_on("elf", type="link")
-    depends_on("libdwarf")
-    depends_on("dyninst")
-    depends_on("adept-utils")
-    depends_on("mpi")
-    depends_on("cmake@2.8:", type="build")

lib/spack/docs/tutorial/examples/Cmake/2.package.py

@@ -1,52 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Callpath(CMakePackage):
-    """Library for representing callpaths consistently in
-       distributed-memory performance tools."""
-
-    homepage = "https://github.com/llnl/callpath"
-    url      = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz"
-
-    version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a')
-
-    depends_on("elf", type="link")
-    depends_on("libdwarf")
-    depends_on("dyninst")
-    depends_on("adept-utils")
-    depends_on("mpi")
-    depends_on("cmake@2.8:", type="build")
-
-    def cmake_args(self):
-        args = ["-DCALLPATH_WALKER=dyninst"]
-
-        if self.spec.satisfies("^dyninst@9.3.0:"):
-            std.flag = self.compiler.cxx_flag
-            args.append("-DCMAKE_CXX_FLAGS='{0}' -fpermissive'".format(
-                std_flag))
-
-        return args

lib/spack/docs/tutorial/examples/Makefile/0.package.py

@@ -1,45 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Bowtie(MakefilePackage):
-    """FIXME: Put a proper description of your package here."""
-
-    # FIXME: Add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
-    url      = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
-    version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
-    # FIXME: Add dependencies if required.
-    # depends_on('foo')
-
-    def edit(self, spec, prefix):
-        # FIXME: Edit the Makefile if necessary
-        # FIXME: If not needed delete this function
-        # makefile = FileFilter('Makefile')
-        # makefile.filter('CC = .*', 'CC = cc')
-        return

lib/spack/docs/tutorial/examples/Makefile/1.package.py

@@ -1,46 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Bowtie(MakefilePackage):
-    """Bowtie is an ultrafast, memory efficient short read aligner
-    for short DNA sequences (reads) from next-gen sequencers."""
-
-    homepage = "https://sourceforge.net/projects/bowtie-bio/"
-    url      = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
-    version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
-    variant("tbb", default=False, description="Use Intel thread building block")
-
-    depends_on("tbb", when="+tbb")
-
-    def edit(self, spec, prefix):
-        # FIXME: Edit the Makefile if necessary
-        # FIXME: If not needed delete this function
-        # makefile = FileFilter('Makefile')
-        # makefile.filter('CC = .*', 'CC = cc')
-        return

lib/spack/docs/tutorial/examples/Makefile/2.package.py

@@ -1,44 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Bowtie(MakefilePackage):
-    """Bowtie is an ultrafast, memory efficient short read aligner
-    for short DNA sequences (reads) from next-gen sequencers."""
-
-    homepage = "https://sourceforge.net/projects/bowtie-bio/"
-    url      = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
-    version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
-    variant("tbb", default=False, description="Use Intel thread building block")
-
-    depends_on("tbb", when="+tbb")
-
-    def edit(self, spec, prefix):
-        makefile = FileFilter("Makefile")
-        makefile.filter('CC= .*', 'CC = ' + env['CC'])
-        makefile.filter('CXX = .*', 'CXX = ' + env['CXX'])

lib/spack/docs/tutorial/examples/Makefile/3.package.py

@@ -1,53 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Bowtie(MakefilePackage):
-    """Bowtie is an ultrafast, memory efficient short read aligner
-    for short DNA sequences (reads) from next-gen sequencers."""
-
-    homepage = "https://sourceforge.net/projects/bowtie-bio/"
-    url      = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
-    version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
-    variant("tbb", default=False, description="Use Intel thread building block")
-
-    depends_on("tbb", when="+tbb")
-
-    def edit(self, spec, prefix):
-        makefile = FileFilter("Makefile")
-        makefile.filter('CC= .*', 'CC = ' + env['CC'])
-        makefile.filter('CXX = .*', 'CXX = ' + env['CXX'])
-
-    def build(self, spec, prefix):
-        if "+tbb" in spec:
-            make()
-        else:
-            make("NO_TBB=1")
-
-    def install(self, spec, prefix):
-        make('prefix={0}'.format(self.prefix), 'install')

lib/spack/docs/tutorial/examples/PyPackage/0.package.py

@@ -1,60 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-#
-# This is a template package file for Spack.  We've put "FIXME"
-# next to all the things you'll want to change. Once you've handled
-# them, you can save this file and test your package like this:
-#
-#     spack install py-pandas
-#
-# You can edit this file again by typing:
-#
-#     spack edit py-pandas
-#
-# See the Spack documentation for more information on packaging.
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
-from spack import *
-
-
-class PyPandas(PythonPackage):
-    """FIXME: Put a proper description of your package here."""
-
-    # FIXME: Add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
-    url      = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz"
-
-    version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3')
-
-    # FIXME: Add dependencies if required.
-    # depends_on('py-setuptools', type='build')
-    # depends_on('py-foo',        type=('build', 'run'))
-
-    def build_args(self, spec, prefix):
-        # FIXME: Add arguments other than --prefix
-        # FIXME: If not needed delete this function
-        args = []
-        return args

lib/spack/docs/tutorial/examples/PyPackage/1.package.py

@@ -1,51 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class PyPandas(PythonPackage):
-    """pandas is a Python package providing fast, flexible, and expressive
-       data structures designed to make working with relational or
-       labeled data both easy and intuitive. It aims to be the
-       fundamental high-level building block for doing practical, real
-       world data analysis in Python. Additionally, it has the broader
-       goal of becoming the most powerful and flexible open source data
-       analysis / manipulation tool available in any language.
-    """
-    homepage = "http://pandas.pydata.org/"
-    url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz"
-
-    version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3')
-    version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
-    version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
-    version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
-
-    depends_on('py-dateutil', type=('build', 'run'))
-    depends_on('py-numpy', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
-    depends_on('py-cython', type='build')
-    depends_on('py-pytz', type=('build', 'run'))
-    depends_on('py-numexpr', type=('build', 'run'))
-    depends_on('py-bottleneck', type=('build', 'run'))

lib/spack/docs/tutorial_advanced_packaging.rst

@@ -1,512 +0,0 @@
-.. _advanced-packaging-tutorial:
-
-============================
-Advanced Topics in Packaging
-============================
-
-Spack tries to automatically configure packages with information from
-dependencies such that all you need to do is to list the dependencies
-(i.e. with the ``depends_on`` directive) and the build system (for example
-by deriving from :code:`CmakePackage`).
-
-However, there are many special cases. Often you need to retrieve details
-about dependencies to set package-specific configuration options, or to
-define package-specific environment variables used by the package's build
-system. This tutorial covers how to retrieve build information from
-dependencies, and how you can automatically provide important information to
-dependents in your package.
-
-----------------------
-Setup for the tutorial
-----------------------
-
-The simplest way to follow along with this tutorial is to use our Docker image,
-which comes with Spack and various packages pre-installed:
-
-.. code-block:: console
-
-  $ docker pull alalazo/spack:advanced_packaging_tutorial
-  $ docker run --rm -h advanced-packaging-tutorial -it alalazo/spack:advanced_packaging_tutorial
-  root@advanced-packaging-tutorial:/#
-  root@advanced-packaging-tutorial:/# spack find
-  ==> 20 installed packages.
-  -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  arpack-ng@3.5.0  hdf5@1.10.1   libpciaccess@0.13.5  libtool@2.4.6  m4@1.4.18  ncurses@6.0          openblas@0.2.20  openssl@1.0.2k     superlu@5.2.1       xz@5.2.3
-  cmake@3.9.4      hwloc@1.11.8  libsigsegv@2.11      libxml2@2.9.4  mpich@3.2  netlib-lapack@3.6.1  openmpi@3.0.0    pkg-config@0.29.2  util-macros@1.19.1  zlib@1.2.11
-
-If you already started the image, you can set the ``EDITOR`` environment
-variable to your preferred editor (``vi``, ``emacs``, and ``nano`` are included in the image)
-and move directly to :ref:`adv_pkg_tutorial_start`.
-
-If you choose not to use the Docker image, you can clone the Spack repository
-and build the necessary bits yourself:
-
-.. code-block:: console
-
-  $ git clone https://github.com/spack/spack.git
-  Cloning into 'spack'...
-  remote: Counting objects: 92731, done.
-  remote: Compressing objects: 100% (1108/1108), done.
-  remote: Total 92731 (delta 1964), reused 4186 (delta 1637), pack-reused 87932
-  Receiving objects: 100% (92731/92731), 33.31 MiB | 64.00 KiB/s, done.
-  Resolving deltas: 100% (43557/43557), done.
-  Checking connectivity... done.
-
-  $ cd spack
-  $ git checkout tutorials/advanced_packaging
-  Branch tutorials/advanced_packaging set up to track remote branch tutorials/advanced_packaging from origin.
-  Switched to a new branch 'tutorials/advanced_packaging'
-
-At this point you can install the software that will be used
-during the rest of the tutorial (the output of the commands is omitted
-for the sake of brevity):
-
-.. code-block:: console
-
-  $ spack install openblas
-  $ spack install netlib-lapack
-  $ spack install mpich
-  $ spack install openmpi
-  $ spack install --only=dependencies armadillo ^openblas
-  $ spack install --only=dependencies netcdf
-  $ spack install --only=dependencies elpa
-
-Now, you are ready to set your preferred ``EDITOR`` and continue with
-the rest of the tutorial.
-
-
-.. _adv_pkg_tutorial_start:
-
-------------------------------
-Retrieving library information
-------------------------------
-
-Although Spack attempts to help packages locate their dependency libraries
-automatically (e.g. by setting PKG_CONFIG_PATH and CMAKE_PREFIX_PATH), a
-package may have unique configuration options that are required to locate
-libraries. When a package needs information about dependency libraries, the
-general approach in Spack is to query the dependencies for the locations of
-their libraries and set configuration options accordingly. By default most
-Spack packages know how to automatically locate their libraries. This section
-covers how to retrieve library information from dependencies and how to locate
-libraries when the default logic doesn't work.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Accessing dependency libraries
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-If you need to access the libraries of a dependency, you can do so
-via the ``libs`` property of the spec, for example in the ``arpack-ng``
-package:
-
-.. code-block:: python
-
-    def install(self, spec, prefix):
-        lapack_libs = spec['lapack'].libs.joined(';')
-        blas_libs = spec['blas'].libs.joined(';')
-
-        cmake(*[
-            '-DLAPACK_LIBRARIES={0}'.format(lapack_libs),
-            '-DBLAS_LIBRARIES={0}'.format(blas_libs)
-        ], '.')
-
-Note that ``arpack-ng`` is querying virtual dependencies, which Spack
-automatically resolves to the installed implementation (e.g. ``openblas``
-for ``blas``).
-
-We've started work on a package for ``armadillo``. You should open it,
-read through the comment that starts with ``# TUTORIAL:`` and complete
-the ``cmake_args`` section:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit armadillo
-
-If you followed the instructions in the package, when you are finished your
-``cmake_args`` method should look like:
-
-.. code-block:: python
-
-  def cmake_args(self):
-        spec = self.spec
-
-        return [
-            # ARPACK support
-            '-DARPACK_LIBRARY={0}'.format(spec['arpack-ng'].libs.joined(";")),
-            # BLAS support
-            '-DBLAS_LIBRARY={0}'.format(spec['blas'].libs.joined(";")),
-            # LAPACK support
-            '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].libs.joined(";")),
-            # SuperLU support
-            '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
-            '-DSuperLU_LIBRARY={0}'.format(spec['superlu'].libs.joined(";")),
-            # HDF5 support
-            '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
-        ]
-
-As you can see, getting the list of libraries that your dependencies provide
-is as easy as accessing the their ``libs`` attribute. Furthermore, the interface
-remains the same whether you are querying regular or virtual dependencies.
-
-At this point you can complete the installation of ``armadillo`` using ``openblas``
-as a LAPACK provider:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install armadillo ^openblas
-  ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
-  ...
-  ==> superlu is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-5.2.1-q2mbtw2wo4kpzis2e2n227ip2fquxrno
-  ==> Installing armadillo
-  ==> Using cached archive: /usr/local/var/spack/cache/armadillo/armadillo-8.100.1.tar.xz
-  ==> Staging archive: /usr/local/var/spack/stage/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4/armadillo-8.100.1.tar.xz
-  ==> Created stage in /usr/local/var/spack/stage/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4
-  ==> Applied patch undef_linux.patch
-  ==> Building armadillo [CMakePackage]
-  ==> Executing phase: 'cmake'
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed armadillo
-    Fetch: 0.01s.  Build: 3.96s.  Total: 3.98s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4
-
-Hopefully the installation went fine and the code we added expanded to the right list
-of semicolon separated libraries (you are encouraged to open ``armadillo``'s
-build logs to double check).
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Providing libraries to dependents
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Spack provides a default implementation for ``libs`` which often works
-out of the box. A user can write a package definition without having to
-implement a ``libs`` property and dependents can retrieve its libraries
-as shown in the above section. However, the default implementation assumes that
-libraries follow the naming scheme ``lib<package name>.so`` (or e.g.
-``lib<package name>.a`` for static libraries). Packages which don't
-follow this naming scheme must implement this function themselves, e.g.
-``opencv``:
-
-.. code-block:: python
-
-    @property
-    def libs(self):
-        shared = "+shared" in self.spec
-        return find_libraries(
-            "libopencv_*", root=self.prefix, shared=shared, recurse=True
-        )
-
-This issue is common for packages which implement an interface (i.e.
-virtual package providers in Spack). If we try to build another version of
-``armadillo`` tied to ``netlib-lapack`` we'll notice that this time the
-installation won't complete:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install  armadillo ^netlib-lapack
-  ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
-  ...
-  ==> openmpi is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f
-  ==> Installing arpack-ng
-  ==> Using cached archive: /usr/local/var/spack/cache/arpack-ng/arpack-ng-3.5.0.tar.gz
-  ==> Already staged arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un in /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un
-  ==> No patches needed for arpack-ng
-  ==> Building arpack-ng [Package]
-  ==> Executing phase: 'install'
-  ==> Error: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z
-  RuntimeError: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z
-
-  /usr/local/var/spack/repos/builtin/packages/arpack-ng/package.py:105, in install:
-       5             options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
-       6
-       7             # Make sure we use Spack's blas/lapack:
-    >> 8             lapack_libs = spec['lapack'].libs.joined(';')
-       9             blas_libs = spec['blas'].libs.joined(';')
-       10
-       11            options.extend([
-
-  See build log for details:
-    /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un/arpack-ng-3.5.0/spack-build.out
-
-Unlike ``openblas`` which provides a library named ``libopenblas.so``,
-``netlib-lapack`` provides ``liblapack.so``, so it needs to implement
-customized library search logic. Let's edit it:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit netlib-lapack
-
-and follow the instructions in the ``# TUTORIAL:`` comment as before.
-What we need to implement is:
-
-.. code-block:: python
-
-  @property
-  def lapack_libs(self):
-      shared = True if '+shared' in self.spec else False
-      return find_libraries(
-          'liblapack', root=self.prefix, shared=shared, recurse=True
-      )
-
-i.e. a property that returns the correct list of libraries for the LAPACK interface.
-
-We use the name ``lapack_libs`` rather than ``libs`` because
-``netlib-lapack`` can also provide ``blas``, and when it does it is provided
-as a separate library file. Using this name ensures that when
-dependents ask for ``lapack`` libraries, ``netlib-lapack`` will retrieve only
-the libraries associated with the ``lapack`` interface. Now we can finally
-install ``armadillo ^netlib-lapack``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install  armadillo ^netlib-lapack
-  ...
-
-  ==> Building armadillo [CMakePackage]
-  ==> Executing phase: 'cmake'
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed armadillo
-    Fetch: 0.01s.  Build: 3.75s.  Total: 3.76s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-sxmpu5an4dshnhickh6ykchyfda7jpyn
-
-Since each implementation of a virtual package is responsible for locating the
-libraries associated with the interfaces it provides, dependents do not need
-to include special-case logic for different implementations and for example
-need only ask for :code:`spec['blas'].libs`.
-
----------------------------------------
-Modifying a package's build environment
----------------------------------------
-
-Spack sets up several environment variables like PATH by default to aid in
-building a package, but many packages make use of environment variables which
-convey specific information about their dependencies, for example MPICC. This
-section covers how update your Spack packages so that package-specific
-environment variables are defined at build-time.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Set environment variables in dependent packages at build-time
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Dependencies can set environment variables that are required when their
-dependents build. For example, when a package depends on a python extension
-like py-numpy, Spack's ``python`` package will add it to ``PYTHONPATH``
-so it is available at build time; this is required because the default setup
-that spack does is not sufficient for python to import modules.
-
-To provide environment setup for a dependent, a package can implement the
-:py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
-function. This function takes as a parameter a :py:class:`EnvironmentModifications <spack.environment.EnvironmentModifications>`
-object which includes convenience methods to update the environment. For
-example an MPI implementation can set ``MPICC`` for packages that depend on it:
-
-.. code-block:: python
-
-  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-      spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
-
-In this case packages which depend on ``mpi`` will have ``MPICC`` defined in
-their environment when they build. This section is focused on modifying the
-build-time environment represented by ``spack_env``, but it's worth noting that
-modifications to ``run_env`` are included in Spack's automatically-generated
-module files.
-
-We can practice by editing the ``mpich`` package to set the ``MPICC``
-environment variable in the build-time environment of dependent packages.
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit mpich
-
-Once you're finished the method should look like this:
-
-.. code-block:: python
-
-  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-      spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
-      spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
-      spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
-      spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
-
-      spack_env.set('MPICH_CC', spack_cc)
-      spack_env.set('MPICH_CXX', spack_cxx)
-      spack_env.set('MPICH_F77', spack_f77)
-      spack_env.set('MPICH_F90', spack_fc)
-      spack_env.set('MPICH_FC', spack_fc)
-
-At this point we can, for instance, install ``netlib-scalapack``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich
-  ...
-  ==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
-  ==> No patches needed for netlib-scalapack
-  ==> Building netlib-scalapack [CMakePackage]
-  ==> Executing phase: 'cmake'
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed netlib-scalapack
-    Fetch: 0.01s.  Build: 3m 59.86s.  Total: 3m 59.87s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
-
-
-and double check the environment logs to verify that every variable was
-set to the correct value.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Set environment variables in your own package
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Packages can modify their own build-time environment by implementing the
-:py:func:`setup_environment <spack.package.PackageBase.setup_environment>` function.
-For ``qt`` this looks like:
-
-.. code-block:: python
-
-    def setup_environment(self, spack_env, run_env):
-        spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
-        run_env.set('QTDIR', self.prefix)
-
-When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment.
-
-To contrast with ``qt``'s :py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
-function:
-
-.. code-block:: python
-
-    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        spack_env.set('QTDIR', self.prefix)
-
-Let's see how it works by completing the ``elpa`` package:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit elpa
-
-In the end your method should look like:
-
-.. code-block:: python
-
-  def setup_environment(self, spack_env, run_env):
-      spec = self.spec
-
-      spack_env.set('CC', spec['mpi'].mpicc)
-      spack_env.set('FC', spec['mpi'].mpifc)
-      spack_env.set('CXX', spec['mpi'].mpicxx)
-      spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
-
-      spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags)
-      spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags)
-
-At this point it's possible to proceed with the installation of ``elpa``.
-
-----------------------
-Other Packaging Topics
-----------------------
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Attach attributes to other packages
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Build tools usually also provide a set of executables that can be used
-when another package is being installed. Spack gives the opportunity
-to monkey-patch dependent modules and attach attributes to them. This
-helps make the packager experience as similar as possible to what would
-have been the manual installation of the same package.
-
-An example here is the ``automake`` package, which overrides
-:py:func:`setup_dependent_package <spack.package.PackageBase.setup_dependent_package>`:
-
-.. code-block:: python
-
-  def setup_dependent_package(self, module, dependent_spec):
-      # Automake is very likely to be a build dependency,
-      # so we add the tools it provides to the dependent module
-      executables = ['aclocal', 'automake']
-      for name in executables:
-          setattr(module, name, self._make_executable(name))
-
-so that every other package that depends on it can use directly ``aclocal``
-and ``automake`` with the usual function call syntax of :py:class:`Executable <spack.util.executable.Executable>`:
-
-.. code-block:: python
-
-  aclocal('--force')
-
-^^^^^^^^^^^^^^^^^^^^^^^
-Extra query parameters
-^^^^^^^^^^^^^^^^^^^^^^^
-
-An advanced feature of the Spec's build-interface protocol is the support
-for extra parameters after the subscript key. In fact, any of the keys used in the query
-can be followed by a comma separated list of extra parameters which can be
-inspected by the package receiving the request to fine-tune a response.
-
-Let's look at an example and try to install ``netcdf``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install netcdf
-  ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
-  ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
-  ...
-  ==> Error: AttributeError: 'list' object has no attribute 'search_flags'
-  AttributeError: AttributeError: 'list' object has no attribute 'search_flags'
-
-  /usr/local/var/spack/repos/builtin/packages/netcdf/package.py:207, in configure_args:
-       50            # used instead.
-       51            hdf5_hl = self.spec['hdf5:hl']
-       52            CPPFLAGS.append(hdf5_hl.headers.cpp_flags)
-    >> 53            LDFLAGS.append(hdf5_hl.libs.search_flags)
-       54
-       55            if '+parallel-netcdf' in self.spec:
-       56                config_args.append('--enable-pnetcdf')
-
-  See build log for details:
-    /usr/local/var/spack/stage/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj/netcdf-4.4.1.1/spack-build.out
-
-We can see from the error that ``netcdf`` needs to know how to link the *high-level interface*
-of ``hdf5``, and thus passes the extra parameter ``hl`` after the request to retrieve it.
-Clearly the implementation in the ``hdf5`` package is not complete, and we need to fix it:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit hdf5
-
-If you followed the instructions correctly, the code added to the
-``lib`` property should be similar to:
-
-.. code-block:: python
-  :emphasize-lines: 1
-
-  query_parameters = self.spec.last_query.extra_parameters
-  key = tuple(sorted(query_parameters))
-  libraries = query2libraries[key]
-  shared = '+shared' in self.spec
-  return find_libraries(
-      libraries, root=self.prefix, shared=shared, recurse=True
-  )
-
-where we highlighted the line retrieving  the extra parameters. Now we can successfully
-complete the installation of ``netcdf``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install netcdf
-  ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
-  ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
-  ...
-  ==> Installing netcdf
-  ==> Using cached archive: /usr/local/var/spack/cache/netcdf/netcdf-4.4.1.1.tar.gz
-  ==> Already staged netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj in /usr/local/var/spack/stage/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj
-  ==> Already patched netcdf
-  ==> Building netcdf [AutotoolsPackage]
-  ==> Executing phase: 'autoreconf'
-  ==> Executing phase: 'configure'
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed netcdf
-    Fetch: 0.01s.  Build: 24.61s.  Total: 24.62s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj

lib/spack/docs/tutorial_buildsystems.rst

@@ -1,795 +0,0 @@
-.. _build-systems-tutorial:
-
-==============================
-Spack Package Build Systems
-==============================
-
-You may begin to notice after writing a couple of package template files a
-pattern emerge for some packages. For example, you may find yourself writing
-an :code:`install()` method that invokes: :code:`configure`, :code:`cmake`,
-:code:`make`, :code:`make install`. You may also find yourself writing
-:code:`"prefix=" + prefix` as an argument to :code:`configure` or :code:`cmake`.
-Rather than having you repeat these lines for all packages, Spack has
-classes that can take care of these patterns. In addition,
-these package files allow for finer grained control of these build systems.
-In this section, we will describe each build system and give examples on
-how these can be manipulated to install a package.
-
------------------------
-Package Class Hierarchy
------------------------
-
-.. graphviz::
-
-    digraph G {
-
-        node [
-            shape = "record"
-        ]
-        edge [
-            arrowhead = "empty"
-        ]
-
-        PackageBase -> Package [dir=back]
-        PackageBase -> MakefilePackage [dir=back]
-        PackageBase -> AutotoolsPackage [dir=back]
-        PackageBase -> CMakePackage [dir=back]
-        PackageBase -> PythonPackage [dir=back]
-    }
-
-The above diagram gives a high level view of the class hierarchy and how each
-package relates. Each subclass inherits from the :code:`PackageBaseClass`
-super class. The bulk of the work is done in this super class which includes
-fetching, extracting to a staging directory and installing. Each subclass
-then adds additional build-system-specific functionality. In the following
-sections, we will go over examples of how to utilize each subclass and to see
-how powerful these abstractions are when packaging.
-
------------------
-Package
------------------
-
-We've already seen examples of a :code:`Package` class in our walkthrough for writing
-package files, so we won't be spending much time with them here. Briefly,
-the Package class allows for abitrary control over the build process, whereas
-subclasses rely on certain patterns (e.g. :code:`configure` :code:`make`
-:code:`make install`) to be useful. :code:`Package` classes are particularly useful
-for packages that have a non-conventional way of being built since the packager
-can utilize some of Spack's helper functions to customize the building and
-installing of a package.
-
--------------------
-Autotools
--------------------
-
-As we have seen earlier, packages using :code:`Autotools` use :code:`configure`,
-:code:`make` and :code:`make install` commands to execute the build and
-install process. In our :code:`Package` class, your typical build incantation will
-consist of the following:
-
-.. code-block:: python
-
-    def install(self, spec, prefix):
-        configure("--prefix=" + prefix)
-        make()
-        make("install")
-
-You'll see that this looks similar to what we wrote in our packaging tutorial.
-
-The :code:`Autotools` subclass aims to simplify writing package files and provides
-convenience methods to manipulate each of the different phases for a :code:`Autotools`
-build system.
-
-:code:`Autotools` packages consist of four phases:
-
-1. :code:`autoreconf()`
-2. :code:`configure()`
-3. :code:`build()`
-4. :code:`install()`
-
-
-Each of these phases have sensible defaults. Let's take a quick look at some
-the internals of the :code:`Autotools` class:
-
-.. code-block:: console
-
-    $ spack edit --build-system autotools
-
-
-This will open the :code:`AutotoolsPackage` file in your text editor.
-
-.. note::
-    The examples showing code for these classes is abridged to avoid having
-    long examples. We only show what is relevant to the packager.
-
-
-.. literalinclude:: ../../../lib/spack/spack/build_systems/autotools.py
-    :language: python
-    :emphasize-lines: 42,45,62
-    :lines: 40-95,259-267
-    :linenos:
-
-
-Important to note are the highlighted lines. These properties allow the
-packager to set what build targets and install targets they want for their
-package. If, for example, we wanted to add as our build target :code:`foo`
-then we can append to our :code:`build_targets` property:
-
-.. code-block:: python
-
-    build_targets = ["foo"]
-
-Which is similiar to invoking make in our Package
-
-.. code-block:: python
-
-     make("foo")
-
-This is useful if we have packages that ignore environment variables and need
-a command-line argument.
-
-Another thing to take note of is in the :code:`configure()` method.
-Here we see that the :code:`prefix` argument is already included since it is a
-common pattern amongst packages using :code:`Autotools`. We then only have to
-override :code:`configure_args()`, which will then return it's output to
-to :code:`configure()`. Then, :code:`configure()` will append the common
-arguments
-
-Packagers also have the option to run :code:`autoreconf` in case a package
-needs to update the build system and generate a new :code:`configure`. Though,
-for the most part this will be unnecessary.
-
-Let's look at the :code:`mpileaks` package.py file that we worked on earlier:
-
-.. code-block:: console
-
-    $ spack edit mpileaks
-
-Notice that mpileaks is a :code:`Package` class but uses the :code:`Autotools`
-build system. Although this package is acceptable let's make this into an
-:code:`AutotoolsPackage` class and simplify it further.
-
-.. literalinclude:: tutorial/examples/Autotools/0.package.py
-   :language: python
-   :emphasize-lines: 28
-   :linenos:
-
-We first inherit from the :code:`AutotoolsPackage` class.
-
-
-Although we could keep the :code:`install()` method, most of it can be handled
-by the :code:`AutotoolsPackage` base class. In fact, the only thing that needs
-to be overridden is :code:`configure_args()`.
-
-.. literalinclude:: tutorial/examples/Autotools/1.package.py
-   :language: python
-   :emphasize-lines: 42,43
-   :linenos:
-
-Since Spack takes care of setting the prefix for us we can exclude that as
-an argument to :code:`configure`. Our packages look simpler, and the packager
-does not need to worry about whether they have properly included :code:`configure`
-and :code:`make`.
-
-This version of the :code:`mpileaks` package installs the same as the previous,
-but the :code:`AutotoolsPackage` class lets us do it with a cleaner looking
-package file.
-
------------------
-Makefile
------------------
-
-Packages that utilize :code:`Make` or a :code:`Makefile` usually require you
-to edit a :code:`Makefile` to set up platform and compiler specific variables.
-These packages are handled by the :code:`Makefile` subclass which provides
-convenience methods to help write these types of packages.
-
-A :code:`MakefilePackage` class has three phases that can be overridden. These include:
-
-    1. :code:`edit()`
-    2. :code:`build()`
-    3. :code:`install()`
-
-Packagers then have the ability to control how a :code:`Makefile` is edited, and
-what targets to include for the build phase or install phase.
-
-Let's also take a look inside the :code:`MakefilePackage` class:
-
-.. code-block:: console
-
-    $ spack edit --build-system makefile
-
-Take note of the following:
-
-
-.. literalinclude:: ../../../lib/spack/spack/build_systems/makefile.py
-   :language: python
-   :lines: 33-79,89-107
-   :emphasize-lines: 48,54,61
-   :linenos:
-
-Similar to :code:`Autotools`, :code:`MakefilePackage` class has properties
-that can be set by the packager. We can also override the different
-methods highlighted.
-
-
-Let's try to recreate the Bowtie_ package:
-
-.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
-
-
-.. code-block:: console
-
-    $ spack create -f https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip
-    ==> This looks like a URL for bowtie
-    ==> Found 1 version of bowtie:
-
-    1.2.1.1  https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip
-
-    ==> How many would you like to checksum? (default is 1, q to abort) 1
-    ==> Downloading...
-    ==> Fetching https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip
-    ######################################################################## 100.0%
-    ==> Checksummed 1 version of bowtie
-    ==> This package looks like it uses the makefile build system
-    ==> Created template for bowtie package
-    ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/bowtie/package.py
-
-Once the fetching is completed, Spack will open up your text editor in the
-usual fashion and create a template of a :code:`MakefilePackage` package.py.
-
-.. literalinclude:: tutorial/examples/Makefile/0.package.py
-   :language: python
-   :linenos:
-
-Spack was successfully able to detect that :code:`Bowtie` uses :code:`Make`.
-Let's add in the rest of our details for our package:
-
-.. literalinclude:: tutorial/examples/Makefile/1.package.py
-   :language: python
-   :emphasize-lines: 29,30,32,33,37,39
-   :linenos:
-
-As we mentioned earlier, most packages using a :code:`Makefile` have hard-coded
-variables that must be edited. These variables are fine if you happen to not
-care about setup or types of compilers used but Spack is designed to work with
-any compiler. The :code:`MakefilePackage` subclass makes it easy to edit
-these :code:`Makefiles` by having an :code:`edit()` method that
-can be overridden.
-
-Let's take a look at the default :code:`Makefile` that :code:`Bowtie` provides.
-If we look inside, we see that :code:`CC` and :code:`CXX` point to our GNU
-compiler:
-
-.. code-block:: console
-
-    $ spack stage bowtie
-
-.. note::
-    As usual make sure you have shell support activated with spack:
-        :code:`source /path/to/spack_root/spack/share/spack/setup-env.sh`
-
-.. code-block:: console
-
-    $ spack cd -s bowtie
-    $ cd bowtie-1.2
-    $ vim Makefile
-
-
-.. code-block:: make
-
-    CPP = g++ -w
-    CXX = $(CPP)
-    CC = gcc
-    LIBS = $(LDFLAGS) -lz
-    HEADERS = $(wildcard *.h)
-
-To fix this, we need to use the :code:`edit()` method to write our custom
-:code:`Makefile`.
-
-.. literalinclude:: tutorial/examples/Makefile/2.package.py
-   :language: python
-   :emphasize-lines: 42,43,44
-   :linenos:
-
-Here we use a :code:`FileFilter` object to edit our :code:`Makefile`. It takes
-in a regular expression and then replaces :code:`CC` and :code:`CXX` to whatever
-Spack sets :code:`CC` and :code:`CXX` environment variables to. This allows us to
-build :code:`Bowtie` with whatever compiler we specify through Spack's
-:code:`spec` syntax.
-
-Let's change the build and install phases of our package:
-
-.. literalinclude:: tutorial/examples/Makefile/3.package.py
-   :language: python
-   :emphasize-lines: 46, 52
-   :linenos:
-
-Here demonstrate another strategy that we can use to manipulate our package
-We can provide command-line arguments to :code:`make()`. Since :code:`Bowtie`
-can use :code:`tbb` we can either add :code:`NO_TBB=1` as a argument to prevent
-:code:`tbb` support or we can just invoke :code:`make` with no arguments.
-
-:code:`Bowtie` requires our :code:`install_target` to provide a path to
-the install directory. We can do this by providing :code:`prefix=` as a command
-line argument to :code:`make()`.
-
-Let's look at a couple of other examples and go through them:
-
-.. code-block:: console
-
-    $ spack edit cbench
-
-Some packages allow environment variables to be set and will honor them.
-Packages that use :code:`?=` for assignment in their :code:`Makefile`
-can be set using environment variables. In our :code:`cbench` example we
-set two environment variables in our :code:`edit()` method:
-
-.. code-block:: python
-
-    def edit(self, spec, prefix):
-        # The location of the Cbench source tree
-        env['CBENCHHOME'] = self.stage.source_path
-
-        # The location that will contain all your tests and your results
-        env['CBENCHTEST'] = prefix
-
-        # ... more code
-
-As you may have noticed, we didn't really write anything to the :code:`Makefile`
-but rather we set environment variables that will override variables set in
-the :code:`Makefile`.
-
-Some packages include a configuration file that sets certain compiler variables,
-platform specific variables, and the location of dependencies or libraries.
-If the file is simple and only requires a couple of changes, we can overwrite
-those entries with our :code:`FileFilter` object. If the configuration involves
-complex changes, we can write a new configuration file from scratch.
-
-Let's look at an example of this in the :code:`elk` package:
-
-.. code-block:: console
-
-    $ spack edit elk
-
-.. code-block:: python
-
-        def edit(self, spec, prefix):
-        # Dictionary of configuration options
-            config = {
-                'MAKE': 'make',
-                'AR':   'ar'
-            }
-
-            # Compiler-specific flags
-            flags = ''
-            if self.compiler.name == 'intel':
-                flags = '-O3 -ip -unroll -no-prec-div'
-            elif self.compiler.name == 'gcc':
-                flags = '-O3 -ffast-math -funroll-loops'
-            elif self.compiler.name == 'pgi':
-                flags = '-O3 -lpthread'
-            elif self.compiler.name == 'g95':
-                flags = '-O3 -fno-second-underscore'
-            elif self.compiler.name == 'nag':
-                flags = '-O4 -kind=byte -dusty -dcfuns'
-            elif self.compiler.name == 'xl':
-                flags = '-O3'
-            config['F90_OPTS'] = flags
-            config['F77_OPTS'] = flags
-
-            # BLAS/LAPACK support
-            # Note: BLAS/LAPACK must be compiled with OpenMP support
-            # if the +openmp variant is chosen
-            blas = 'blas.a'
-            lapack = 'lapack.a'
-            if '+blas' in spec:
-                blas = spec['blas'].libs.joined()
-            if '+lapack' in spec:
-                lapack = spec['lapack'].libs.joined()
-            # lapack must come before blas
-            config['LIB_LPK'] = ' '.join([lapack, blas])
-
-            # FFT support
-            if '+fft' in spec:
-                config['LIB_FFT'] = join_path(spec['fftw'].prefix.lib,
-                                            'libfftw3.so')
-                config['SRC_FFT'] = 'zfftifc_fftw.f90'
-            else:
-                config['LIB_FFT'] = 'fftlib.a'
-                config['SRC_FFT'] = 'zfftifc.f90'
-
-            # MPI support
-            if '+mpi' in spec:
-                config['F90'] = spec['mpi'].mpifc
-                config['F77'] = spec['mpi'].mpif77
-            else:
-                config['F90'] = spack_fc
-                config['F77'] = spack_f77
-                config['SRC_MPI'] = 'mpi_stub.f90'
-
-            # OpenMP support
-            if '+openmp' in spec:
-                config['F90_OPTS'] += ' ' + self.compiler.openmp_flag
-                config['F77_OPTS'] += ' ' + self.compiler.openmp_flag
-            else:
-                config['SRC_OMP'] = 'omp_stub.f90'
-
-            # Libxc support
-            if '+libxc' in spec:
-                config['LIB_libxc'] = ' '.join([
-                    join_path(spec['libxc'].prefix.lib, 'libxcf90.so'),
-                    join_path(spec['libxc'].prefix.lib, 'libxc.so')
-                ])
-                config['SRC_libxc'] = ' '.join([
-                    'libxc_funcs.f90',
-                    'libxc.f90',
-                    'libxcifc.f90'
-                ])
-            else:
-                config['SRC_libxc'] = 'libxcifc_stub.f90'
-
-            # Write configuration options to include file
-            with open('make.inc', 'w') as inc:
-                for key in config:
-                    inc.write('{0} = {1}\n'.format(key, config[key]))
-
-:code:`config` is just a dictionary that we can add key-value pairs to. By the
-end of the :code:`edit()` method we write the contents of our dictionary to
-:code:`make.inc`.
-
----------------
-CMake
----------------
-
-CMake_ is another common build system that has been gaining popularity. It works
-in a similar manner to :code:`Autotools` but with differences in variable names,
-the number of configuration options available, and the handling of shared libraries.
-Typical build incantations look like this:
-
-.. _CMake: https://cmake.org
-
-.. code-block:: python
-
-    def install(self, spec, prefix):
-        cmake("-DCMAKE_INSTALL_PREFIX:PATH=/path/to/install_dir ..")
-        make()
-        make("install")
-
-As you can see from the example above, it's very similar to invoking
-:code:`configure` and :code:`make` in an :code:`Autotools` build system. However,
-the variable names and options differ. Most options in CMake are prefixed
-with a :code:`'-D'` flag to indicate a configuration setting.
-
-In the :code:`CMakePackage` class we can override the following phases:
-
-1. :code:`cmake()`
-2. :code:`build()`
-3. :code:`install()`
-
-The :code:`CMakePackage` class also provides sensible defaults so we only need to
-override :code:`cmake_args()`.
-
-Let's look at these defaults in the :code:`CMakePackage` class:
-
-.. code-block:: console
-
-    $ spack edit --build-system cmake
-
-
-And go into a bit of detail on the highlighted sections:
-
-
-.. literalinclude:: ../../../lib/spack/spack/build_systems/cmake.py
-   :language: python
-   :lines: 37-92, 94-155, 174-211
-   :emphasize-lines: 57,68,86,94,96,99,100,101,102,111,117,135,136
-   :linenos:
-
-Some :code:`CMake` packages use different generators. Spack is able to support
-Unix-Makefile_ generators as well as Ninja_ generators.
-
-.. _Unix-Makefile: https://cmake.org/cmake/help/v3.4/generator/Unix%20Makefiles.html
-.. _Ninja: https://cmake.org/cmake/help/v3.4/generator/Ninja.html
-
-Default generator is :code:`Unix Makefile`.
-
-Next we setup the build type. In :code:`CMake` you can specify the build type
-that you want. Options include:
-
-1. empty
-2. Debug
-3. Release
-4. RelWithDebInfo
-5. MinSizeRel
-
-With these options you can specify whether you want your executable to have
-the debug version only, release version or the release with debug information.
-Release executables tend to be more optimized than Debug. In Spack, we set
-the default as RelWithDebInfo unless otherwise specified through a variant.
-
-Spack then automatically sets up the :code:`-DCMAKE_INSTALL_PREFIX` path,
-appends the build type (RelDebInfo default), and then specifies a verbose
-:code:`Makefile`.
-
-Next we add the :code:`rpaths` to :code:`-DCMAKE_INSTALL_RPATH:STRING`.
-
-
-Finally we add to :code:`-DCMAKE_PREFIX_PATH:STRING` the locations of all our
-dependencies so that :code:`CMake` can find them.
-
-In the end our :code:`cmake` line will look like this (example is :code:`xrootd`):
-
-.. code-block:: console
-
-    $ cmake $HOME/spack/var/spack/stage/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/xrootd-4.6.0 -G Unix Makefiles -DCMAKE_INSTALL_PREFIX:PATH=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_FIND_FRAMEWORK:STRING=LAST -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE -DCMAKE_INSTALL_RPATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib:$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib64 -DCMAKE_PREFIX_PATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/cmake-3.9.4-hally3vnbzydiwl3skxcxcbzsscaasx5
-
-
-Saves a lot of typing doesn't it?
-
-
-Let's try to recreate callpath_:
-
-.. _callpath: https://github.com/LLNL/callpath.git
-
-.. code-block:: console
-
-    $ spack create -f https://github.com/llnl/callpath/archive/v1.0.3.tar.gz
-    ==> This looks like a URL for callpath
-    ==> Found 4 versions of callpath:
-
-    1.0.3  https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz
-    1.0.2  https://github.com/LLNL/callpath/archive/v1.0.2.tar.gz
-    1.0.1  https://github.com/LLNL/callpath/archive/v1.0.1.tar.gz
-    1.0    https://github.com/LLNL/callpath/archive/v1.0.tar.gz
-
-    ==> How many would you like to checksum? (default is 1, q to abort) 1
-    ==> Downloading...
-    ==> Fetching https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz
-    ######################################################################## 100.0%
-    ==> Checksummed 1 version of callpath
-    ==> This package looks like it uses the cmake build system
-    ==> Created template for callpath package
-    ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/callpath/package.py
-
-
-which then produces the following template:
-
-.. literalinclude:: tutorial/examples/Cmake/0.package.py
-   :language: python
-   :linenos:
-
-Again we fill in the details:
-
-.. literalinclude:: tutorial/examples/Cmake/1.package.py
-   :language: python
-   :linenos:
-   :emphasize-lines: 28,32,33,37,38,39,40,41,42
-
-As mentioned earlier, Spack will use sensible defaults to prevent repeated code
-and to make writing :code:`CMake` package files simpler.
-
-In callpath, we want to add options to :code:`CALLPATH_WALKER` as well as add
-compiler flags. We add the following options like so:
-
-.. literalinclude:: tutorial/examples/Cmake/2.package.py
-   :language: python
-   :linenos:
-   :emphasize-lines: 45,49,50
-
-Now we can control our build options using :code:`cmake_args()`. If defaults are
-sufficient enough for the package, we can leave this method out.
-
-:code:`CMakePackage` classes allow for control of other features in the
-build system. For example, you can specify the path to the "out of source"
-build directory and also point to the root of the :code:`CMakeLists.txt` file if it
-is placed in a non-standard location.
-
-A good example of a package that has its :code:`CMakeLists.txt` file located at a
-different location is found in :code:`spades`.
-
-.. code-block:: console
-
-    $ spack edit spade
-
-.. code-block:: python
-
-    root_cmakelists_dir = "src"
-
-Here :code:`root_cmakelists_dir` will tell Spack where to find the location
-of :code:`CMakeLists.txt`. In this example, it is located a directory level below in
-the :code:`src` directory.
-
-Some :code:`CMake` packages also require the :code:`install` phase to be
-overridden. For example, let's take a look at :code:`sniffles`.
-
-.. code-block:: console
-
-    $ spack edit sniffles
-
-In the :code:`install()` method, we have to manually install our targets
-so we override the :code:`install()` method to do it for us:
-
-.. code-block:: python
-
-    # the build process doesn't actually install anything, do it by hand
-    def install(self, spec, prefix):
-        mkdir(prefix.bin)
-        src = "bin/sniffles-core-{0}".format(spec.version.dotted)
-        binaries = ['sniffles', 'sniffles-debug']
-        for b in binaries:
-            install(join_path(src, b), join_path(prefix.bin, b))
-
-
---------------
-PythonPackage
---------------
-
-Python extensions and modules are built differently from source than most
-applications. Python uses a :code:`setup.py` script to install Python modules.
-The script consists of a call to :code:`setup()` which provides the information
-required to build a module to Distutils. If you're familiar with pip or
-easy_install, setup.py does the same thing.
-
-These modules are usually installed using the following line:
-
-.. code-block:: console
-
-    $ python setup.py install
-
-There are also a list of commands and phases that you can call. To see the full
-list you can run:
-
-.. code-block:: console
-
-    $ python setup.py --help-commands
-    Standard commands:
-        build             build everything needed to install
-        build_py          "build" pure Python modules (copy to build directory)
-        build_ext         build C/C++ extensions (compile/link to build directory)
-        build_clib        build C/C++ libraries used by Python extensions
-        build_scripts     "build" scripts (copy and fixup #! line)
-        clean             (no description available)
-        install           install everything from build directory
-        install_lib       install all Python modules (extensions and pure Python)
-        install_headers   install C/C++ header files
-        install_scripts   install scripts (Python or otherwise)
-        install_data      install data files
-        sdist             create a source distribution (tarball, zip file, etc.)
-        register          register the distribution with the Python package index
-        bdist             create a built (binary) distribution
-        bdist_dumb        create a "dumb" built distribution
-        bdist_rpm         create an RPM distribution
-        bdist_wininst     create an executable installer for MS Windows
-        upload            upload binary package to PyPI
-        check             perform some checks on the package
-
-
-To see the defaults that Spack has for each a methods, we will take a look
-at the :code:`PythonPackage` class:
-
-.. code-block:: console
-
-    $ spack edit --build-system python
-
-We see the following:
-
-
-.. literalinclude:: ../../../lib/spack/spack/build_systems/python.py
-   :language: python
-   :lines: 35, 161-364
-   :linenos:
-
-Each of these methods have sensible defaults or they can be overridden.
-
-We can write package files for Python packages using the :code:`Package` class,
-but the class brings with it a lot of methods that are useless for Python packages.
-Instead, Spack has a :code: `PythonPackage` subclass that allows packagers
-of Python modules to be able to invoke :code:`setup.py` and use :code:`Distutils`,
-which is much more familiar to a typical python user.
-
-
-We will write a package file for Pandas_:
-
-.. _pandas: https://pandas.pydata.org
-
-.. code-block:: console
-
-    $ spack create -f https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz
-    ==> This looks like a URL for pandas
-    ==> Warning: Spack was unable to fetch url list due to a certificate verification problem. You can try running spack -k, which will not check SSL certificates. Use this at your own risk.
-    ==> Found 1 version of pandas:
-
-    0.19.0  https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz
-
-    ==> How many would you like to checksum? (default is 1, q to abort) 1
-    ==> Downloading...
-    ==> Fetching https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz
-    ######################################################################## 100.0%
-    ==> Checksummed 1 version of pandas
-    ==> This package looks like it uses the python build system
-    ==> Changing package name from pandas to py-pandas
-    ==> Created template for py-pandas package
-    ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/py-pandas/package.py
-
-And we are left with the following template:
-
-.. literalinclude:: tutorial/examples/PyPackage/0.package.py
-   :language: python
-   :linenos:
-
-As you can see this is not any different than any package template that we have
-written. We have the choice of providing build options or using the sensible
-defaults
-
-Luckily for us, there is no need to provide build args.
-
-Next we need to find the dependencies of a package. Dependencies are usually
-listed in :code:`setup.py`. You can find the dependencies by searching for
-:code:`install_requires` keyword in that file. Here it is for :code:`Pandas`:
-
-.. code-block:: python
-
-    # ... code
-    if sys.version_info[0] >= 3:
-
-    setuptools_kwargs = {
-                         'zip_safe': False,
-                         'install_requires': ['python-dateutil >= 2',
-                                              'pytz >= 2011k',
-                                              'numpy >= %s' % min_numpy_ver],
-                         'setup_requires': ['numpy >= %s' % min_numpy_ver],
-                         }
-    if not _have_setuptools:
-        sys.exit("need setuptools/distribute for Py3k"
-                 "\n$ pip install distribute")
-
-    # ... more code
-
-You can find a more comprehensive list at the Pandas documentation_.
-
-.. _documentation: https://pandas.pydata.org/pandas-docs/stable/install.html
-
-
-By reading the documentation and :code:`setup.py` we found that :code:`Pandas`
-depends on :code:`python-dateutil`, :code:`pytz`, and :code:`numpy`, :code:`numexpr`,
-and finally :code:`bottleneck`.
-
-Here is the completed :code:`Pandas` script:
-
-.. literalinclude:: tutorial/examples/PyPackage/1.package.py
-   :language: python
-   :linenos:
-
-It is quite important to declare all the dependencies of a Python package.
-Spack can "activate" Python packages to prevent the user from having to
-load each dependency module explictly. If a dependency is missed, Spack will
-be unable to properly activate the package and it will cause an issue. To
-learn more about extensions go to :ref:`cmd-spack-extensions`.
-
-From this example, you can see that building Python modules is made easy
-through the :code:`PythonPackage` class.
-
--------------------
-Other Build Systems
--------------------
-
-Although we won't get in depth with any of the other build systems that Spack
-supports, it is worth mentioning that Spack does provide subclasses
-for the following build systems:
-
-1. :code:`IntelPackage`
-2. :code:`SconsPackage`
-3. :code:`WafPackage`
-4. :code:`RPackage`
-5. :code:`PerlPackage`
-6. :code:`QMake`
-
-
-Each of these classes have their own abstractions to help assist in writing
-package files. For whatever doesn't fit nicely into the other build-systems,
-you can use the :code:`Package` class.
-
-Hopefully by now you can see how we aim to make packaging simple and
-robust through these classes. If you want to learn more about these build
-systems, check out :ref:`installation_procedure` in the Packaging Guide.

lib/spack/docs/tutorial_configuration.rst

@@ -1,843 +0,0 @@
-.. _configs-tutorial:
-
-======================
-Configuration Tutorial
-======================
-
-This tutorial will guide you through various configuration options
-that allow you to customize Spack's behavior with respect to
-software installation. We will first cover the configuration file
-hierarchy. Then, we will cover configuration options for compilers,
-focusing on how it can be used to extend Spack's compiler auto-detection.
-Next, we will cover the packages configuration file, focusing on
-how it can be used to override default build options as well as
-specify external package installations to use. Finally, we will
-briefly touch on the config configuration file, which manages more
-high-level Spack configuration options.
-
-For all of these features we will demonstrate how we build up a full
-configuration file. For some we will then demonstrate how the
-configuration affects the install command, and for others we will use
-the ``spack spec`` command to demonstrate how the configuration
-changes have affected Spack's concretization algorithm. The provided
-output is all from a server running Ubuntu version 16.04.
-
-.. _configs-tutorial-scopes:
-
---------------------
-Configuration Scopes
---------------------
-
-Depending on your use case, you may want to provide configuration
-settings common to everyone on your team, or you may want to set
-default behaviors specific to a single user account. Spack provides
-4 configuration *scopes* to handle this customization. These scopes,
-in order of decreasing priority, are:
-
-======================   ==================================
-Scope                    Directory
-======================   ==================================
-User configurations      ``~/.spack``
-Project configurations   ``$SPACK_ROOT/etc/spack``
-System configurations    ``/etc/spack``
-Default configurations   ``$SPACK_ROOT/etc/spack/defaults``
-======================   ==================================
-
-Spack's default configuration settings reside in
-``$SPACK_ROOT/etc/spack/defaults``. These are useful for reference,
-but should never be directly edited. To override these settings,
-create new configuration files in any of the higher-priority
-configuration scopes.
-
-A particular cluster may have multiple Spack installations associated
-with different projects. To provide settings common to all Spack
-installations, put your configuration files in ``/etc/spack``.
-To provide settings specific to a particular Spack installation,
-you can use the ``$SPACK_ROOT/etc/spack`` directory.
-
-For settings specific to a particular user, you will want to add
-configuration files to the ``~/.spack`` directory. When Spack first
-checked for compilers on your system, you may have noticed that it
-placed your compiler configuration in this directory.
-
-Some facilities manage multiple platforms from a single shared
-filesystem. In order to handle this, each of the configuration
-scopes listed above has two *sub-scopes*: platform-specific and
-platform-independent. For example, compiler settings can be stored
-in ``compilers.yaml`` configuration files in the following locations:
-
-- ``~/.spack/<platform>/compilers.yaml``
-- ``~/.spack/compilers.yaml``
-- ``$SPACK_ROOT/etc/spack/<platform>/compilers.yaml``
-- ``$SPACK_ROOT/etc/spack/compilers.yaml``
-- ``/etc/spack/<platform>/compilers.yaml``
-- ``/etc/spack/compilers.yaml``
-- ``$SPACK_ROOT/etc/defaults/<platform>/compilers.yaml``
-- ``$SPACK_ROOT/etc/defaults/compilers.yaml``
-
-These files are listed in decreasing order of precedence, so files in
-``~/.spack/<platform>`` will override settings in ``~/.spack``.
-
-Spack configurations are YAML dictionaries. Every configuration file
-begins with a top-level dictionary that tells Spack which
-configuration set it modifies. When Spack checks it's configuration,
-the configuration scopes are updated as dictionaries in increasing
-order of precedence, allowing higher precedence files to override
-lower. YAML dictionaries use a colon ":" to specify key-value
-pairs. Spack extends YAML syntax slightly to allow a double-colon
-"::" to specify a key-value pair. When a double-colon is used to
-specify a key-value pair, instead of adding that section Spack
-replaces what was in that section with the new value. For example, a
-user compilers configuration file as follows:
-
-.. code-block:: yaml
-
-   compilers::
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags: {}
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/gcc
-         cxx: /usr/bin/g++
-         f77: /usr/bin/gfortran
-         fc: /usr/bin/gfortran
-       spec: gcc@5.4.0
-       target: x86_64
-
-
-ensures that no other compilers are used, as the user configuration
-scope is the last scope searched and the ``compilers::`` line replaces
-all previous configuration files information. If the same
-configuration file had a single colon instead of the double colon, it
-would add the gcc version 5.4.0 compiler to whatever other compilers
-were listed in other configuration files.
-
-.. _configs-tutorial-compilers:
-
-----------------------
-Compiler Configuration
-----------------------
-
-For most tasks, we can use Spack with the compilers auto-detected the
-first time Spack runs on a system. As we discussed in the basic
-installation section, we can also tell Spack where compilers are
-located using the ``spack compiler add`` command. However, in some
-circumstances we want even more fine-grained control over the
-compilers available. This section will teach you how to exercise that
-control using the compilers configuration file.
-
-We will start by opening the compilers configuration file
-
-.. code-block:: console
-
-   $ spack config edit compilers
-
-
-.. code-block:: yaml
-
-   compilers:
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags: {}
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/clang
-         cxx: /usr/bin/clang++
-         f77: null
-         fc: null
-       spec: clang@3.8.0-2ubuntu4
-       target: x86_64
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags: {}
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/gcc
-         cxx: /usr/bin/g++
-         f77: /usr/bin/gfortran
-         fc: /usr/bin/gfortran
-       spec: gcc@5.4.0
-       target: x86_64
-
-
-This specifies one version of the gcc compiler and one version of the
-clang compiler with no flang compiler. Now suppose we have a code that
-we want to compile with the clang compiler for C/C++ code, but with
-gfortran for Fortran components. We can do this by adding another entry
-to the ``compilers.yaml`` file.
-
-.. code-block:: yaml
-
-   - compiler:
-     environment: {}
-     extra_rpaths: []
-     flags: {}
-     modules: []
-     operating_system: ubuntu16.04
-     paths:
-       cc: /usr/bin/clang
-       cxx: /usr/bin/clang++
-       f77: /usr/bin/gfortran
-       fc: /usr/bin/gfortran
-     spec: clang@3.8.0-gfortran
-     target: x86_64
-
-
-Let's talk about the sections of this compiler entry that we've changed.
-The biggest change we've made is to the ``paths`` section. This lists
-the paths to the compilers to use for each language/specification.
-In this case, we point to the clang compiler for C/C++ and the gfortran
-compiler for both specifications of Fortran. We've also changed the
-``spec`` entry for this compiler. The ``spec`` entry is effectively the
-name of the compiler for Spack. It consists of a name and a version
-number, separated by the ``@`` sigil. The name must be one of the supported
-compiler names in Spack (gcc, intel, pgi, xl, xl_r, clang, nag, cce).
-The version number can be an arbitrary string of alphanumeric characters,
-as well as ``-``, ``.``, and ``_``. The ``target`` and ``operating_system``
-sections we leave unchanged. These sections specify when Spack can use
-different compilers, and are primarily useful for configuration files that
-will be used across multiple systems.
-
-We can verify that our new compiler works by invoking it now:
-
-.. code-block:: console
-
-   $ spack install zlib %clang@3.8.0-gfortran
-   ...
-
-
-This new compiler also works on Fortran codes:
-
-.. code-block:: console
-
-   $ spack install cfitsio %clang@3.8.0-gfortran
-   ...
-
-
-^^^^^^^^^^^^^^
-Compiler Flags
-^^^^^^^^^^^^^^
-
-Some compilers may require specific compiler flags to work properly in
-a particular computing environment. Spack provides configuration
-options for setting compiler flags every time a specific compiler is
-invoked. These flags become part of the package spec and therefore of
-the build provenance. As on the command line, the flags are set
-through the implicit build variables ``cflags``, ``cxxflags``, ``cppflags``,
-``fflags``, ``ldflags``, and ``ldlibs``.
-
-Let's open our compilers configuration file again and add a compiler flag.
-
-.. code-block:: yaml
-
-   - compiler:
-     environment: {}
-     extra_rpaths: []
-     flags:
-       cppflags: -g
-     modules: []
-     operating_system: ubuntu16.04
-     paths:
-       cc: /usr/bin/clang
-       cxx: /usr/bin/clang++
-       f77: /usr/bin/gfortran
-       fc: /usr/bin/gfortran
-     spec: clang@3.8.0-gfortran
-     target: x86_64
-
-
-We can test this out using the ``spack spec`` command to show how the
-spec is concretized.
-
-.. code-block:: console
-
-   $ spack spec cfitsio %clang@3.8.0-gfortran
-   Input spec
-   --------------------------------
-   cfitsio%clang@3.8.0-gfortran
-
-   Normalized
-   --------------------------------
-   cfitsio%clang@3.8.0-gfortran
-
-   Concretized
-   --------------------------------
-   cfitsio@3.410%clang@3.8.0-gfortran cppflags="-g" +bzip2+shared arch=linux-ubuntu16.04-x86_64
-       ^bzip2@1.0.6%clang@3.8.0-gfortran cppflags="-g" +shared arch=linux-ubuntu16.04-x86_64
-
-
-We can see that "cppflags=-g" has been added to every node in the DAG.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Advanced Compiler Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-There are three fields of the compiler configuration entry that we
-have not talked about yet.
-
-The ``modules`` field of the compiler is used primarily on Cray systems,
-but can be useful on any system that has compilers that are only
-useful when a particular module is loaded. Any modules in the
-``modules`` field of the compiler configuration will be loaded as part
-of the build environment for packages using that compiler.
-
-The ``extra_rpaths`` field of the compiler configuration is used for
-compilers that do not rpath all of their dependencies by
-default. Since compilers are generally installed externally to Spack,
-Spack is unable to manage compiler dependencies and enforce
-rpath usage. This can lead to packages not finding link dependencies
-imposed by the compiler properly. For compilers that impose link
-dependencies on the resulting executables that are not rpath'ed into
-the executable automatically, the ``extra_rpath`` field of the compiler
-configuration tells Spack which dependencies to rpath into every
-executable created by that compiler. The executables will then be able
-to find the link dependencies imposed by the compiler.
-
-The ``environment`` field of the compiler configuration is used for
-compilers that require environment variables to be set during build
-time. For example, if your Intel compiler suite requires the
-``INTEL_LICENSE_FILE`` environment variable to point to the proper
-license server, you can set this in ``compilers.yaml``.
-
--------------------------------
-Configuring Package Preferences
--------------------------------
-
-Package preferences in Spack are managed through the ``packages.yaml``
-configuration file. First, we will look at the default
-``packages.yaml`` file.
-
-.. code-block:: console
-
-   $ spack config --scope defaults edit packages
-
-
-.. literalinclude:: ../../../etc/spack/defaults/packages.yaml
-   :language: yaml
-
-
-This sets the default preferences for compilers and for providers of
-virtual packages. To illustrate how this works, suppose we want to
-change the preferences to prefer the clang compiler and to prefer
-mpich over openmpi. Currently, we prefer gcc and openmpi
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.1%gcc@5.4.0+cxx~debug+fortran+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^openmpi@3.0.0%gcc@5.4.0~cuda fabrics= ~java schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
-           ^hwloc@1.11.7%gcc@5.4.0~cuda+libxml2~pci arch=linux-ubuntu16.04-x86_64
-               ^libxml2@2.9.4%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
-                   ^pkg-config@0.29.2%gcc@5.4.0+internal_glib arch=linux-ubuntu16.04-x86_64
-                   ^xz@5.2.3%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                   ^zlib@1.2.11%gcc@5.4.0+pic+shared arch=linux-ubuntu16.04-x86_64
-
-
-Now we will open the packages configuration file and update our
-preferences.
-
-.. code-block:: console
-
-  $ spack config edit packages
-
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-
-
-Because of the configuration scoping we discussed earlier, this
-overrides the default settings just for these two items.
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^mpich@3.2%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+pic+shared arch=linux-ubuntu16.04-x86_64
-
-
-^^^^^^^^^^^^^^^^^^^
-Variant Preferences
-^^^^^^^^^^^^^^^^^^^
-
-The packages configuration file can also set variant preferences for
-package variants. For example, let's change our preferences to build all
-packages without shared libraries. We will accomplish this by turning
-off the ``shared`` variant on all packages that have one.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-
-
-We can check the effect of this command with ``spack spec hdf5`` again.
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^mpich@3.2%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-So far we have only made global changes to the package preferences. As
-we've seen throughout this tutorial, hdf5 builds with MPI enabled by
-default in Spack. If we were working on a project that would routinely
-need serial hdf5, that might get annoying quickly, having to type
-``hdf5~mpi`` all the time. Instead, we'll update our preferences for
-hdf5.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     hdf5:
-       variants: ~mpi
-
-
-Now hdf5 will concretize without an MPI dependency by default.
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-In general, every attribute that we can set for all packages we can
-set separately for an individual package.
-
-^^^^^^^^^^^^^^^^^
-External Packages
-^^^^^^^^^^^^^^^^^
-
-The packages configuration file also controls when Spack will build
-against an externally installed package. On these systems we have a
-pre-installed zlib.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     hdf5:
-       variants: ~mpi
-     zlib:
-       paths:
-         zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
-
-
-Here, we've told Spack that zlib 1.2.8 is installed on our system.
-We've also told it the installation prefix where zlib can be found.
-We don't know exactly which variants it was built with, but that's
-okay.
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.1%gcc@5.4.0~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-You'll notice that Spack is now using the external zlib installation,
-but the compiler used to build zlib is now overriding our compiler
-preference of clang. If we explicitly specify clang:
-
-.. code-block:: console
-
-   $ spack spec hdf5 %clang
-   Input spec
-   --------------------------------
-   hdf5%clang
-
-   Normalized
-   --------------------------------
-   hdf5%clang
-       ^zlib@1.1.2:
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-Spack concretizes to both hdf5 and zlib being built with clang.
-This has a side-effect of rebuilding zlib. If we want to force
-Spack to use the system zlib, we have two choices. We can either
-specify it on the command line, or we can tell Spack that it's
-not allowed to build its own zlib. We'll go with the latter.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     hdf5:
-       variants: ~mpi
-     zlib:
-       paths:
-         zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-
-
-Now Spack will be forced to choose the external zlib.
-
-.. code-block:: console
-
-   $ spack spec hdf5 %clang
-   Input spec
-   --------------------------------
-   hdf5%clang
-
-   Normalized
-   --------------------------------
-   hdf5%clang
-       ^zlib@1.1.2:
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-This gets slightly more complicated with virtual dependencies. Suppose
-we don't want to build our own MPI, but we now want a parallel version
-of hdf5? Well, fortunately we have mpich installed on these systems.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     hdf5:
-       variants: ~mpi
-     zlib:
-       paths:
-         zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-     mpich:
-       paths:
-         mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-
-
-If we concretize ``hdf5+mpi`` with this configuration file, we will just
-build with an alternate MPI implementation.
-
-.. code-block:: console
-
-   $ spack spec hdf5 %clang +mpi
-   Input spec
-   --------------------------------
-   hdf5%clang+mpi
-
-   Normalized
-   --------------------------------
-   hdf5%clang+mpi
-       ^mpi
-       ^zlib@1.1.2:
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^openmpi@3.0.0%clang@3.8.0-2ubuntu4~cuda fabrics=verbs ~java schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
-           ^hwloc@1.11.8%clang@3.8.0-2ubuntu4~cuda+libxml2+pci arch=linux-ubuntu16.04-x86_64
-               ^libpciaccess@0.13.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                       ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00 +sigsegv arch=linux-ubuntu16.04-x86_64
-                           ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^pkg-config@0.29.2%clang@3.8.0-2ubuntu4+internal_glib arch=linux-ubuntu16.04-x86_64
-                   ^util-macros@1.19.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-               ^libxml2@2.9.4%clang@3.8.0-2ubuntu4~python arch=linux-ubuntu16.04-x86_64
-                   ^xz@5.2.3%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^zlib@1.2.8%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
-
-
-We have only expressed a preference for mpich over other MPI
-implementations, and Spack will happily build with one we haven't
-forbid it from using. We could resolve this by requesting
-``hdf5%clang+mpi^mpich`` explicitly, or we can configure Spack not to
-use any other MPI implementation. Since we're focused on
-configurations here and the former can get tedious, we'll need to
-modify our ``packages.yaml`` file again.
-
-While we're at it, we can configure hdf5 to build with MPI by default
-again.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     zlib:
-       paths:
-         zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-     mpich:
-       paths:
-         mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-     openmpi:
-       buildable: False
-     mvapich2:
-       buildable: False
-     intel-mpi:
-       buildable: False
-     spectrum-mpi:
-       buildable: False
-     intel-parallel-studio:
-       buildable: False
-
-Now that we have configured Spack not to build any of the possible
-providers for MPI we can try again.
-
-.. code-block:: console
-
-   $ spack spec hdf5 %clang
-   Input spec
-   --------------------------------
-   hdf5%clang
-
-   Normalized
-   --------------------------------
-   hdf5%clang
-       ^mpi
-       ^zlib@1.1.2:
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.8%gcc@5.4.0+pic+shared arch=linux-ubuntu16.04-x86_64
-
-
-By configuring most of our package preferences in ``packages.yaml``,
-we can cut down on the amount of work we need to do when specifying
-a spec on the command line. In addition to compiler and variant
-preferences, we can specify version preferences as well. Anything
-that you can specify on the command line can be specified in
-``packages.yaml`` with the exact same spec syntax.
-
-.. warning::
-
-   Make sure to delete or move the ``packages.yaml`` you have been
-   editing up to this point. Otherwise, it will change the hashes
-   of your packages, leading to differences in the output of later
-   tutorial sections.
-
-
------------------
-High-level Config
------------------
-
-In addition to compiler and package settings, Spack allows customization
-of several high-level settings. These settings are stored in the generic
-``config.yaml`` configuration file. You can see the default settings by
-running:
-
-.. code-block:: console
-
-   $ spack config --scope defaults edit config
-
-
-.. literalinclude:: ../../../etc/spack/defaults/config.yaml
-   :language: yaml
-
-
-As you can see, many of the directories Spack uses can be customized.
-For example, you can tell Spack to install packages to a prefix
-outside of the ``$SPACK_ROOT`` hierarchy. Module files can be
-written to a central location if you are using multiple Spack
-instances. If you have a fast scratch filesystem, you can run builds
-from this filesystem with the following ``config.yaml``:
-
-.. code-block:: yaml
-
-   config:
-     build_stage:
-       - /scratch/$user
-
-
-On systems with compilers that absolutely *require* environment variables
-like ``LD_LIBRARY_PATH``, it is possible to prevent Spack from cleaning
-the build environment with the ``dirty`` setting:
-
-.. code-block:: yaml
-
-   config:
-     dirty: true
-
-
-However, this is strongly discouraged, as it can pull unwanted libraries
-into the build.
-
-One last setting that may be of interest to many users is the ability
-to customize the parallelism of Spack builds. By default, Spack
-installs all packages in parallel with the number of jobs equal to the
-number of cores on the node. For example, on a node with 36 cores,
-this will look like:
-
-.. code-block:: console
-
-   $ spack install --verbose zlib
-   ==> Installing zlib
-   ==> Using cached archive: ~/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
-   ==> Staging archive: ~/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
-   ==> Created stage in ~/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-   ==> No patches needed for zlib
-   ==> Building zlib [Package]
-   ==> Executing phase: 'install'
-   ==> './configure' '--prefix=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
-   Checking for shared library support...
-   Building shared library libz.so.1.2.11 with ~/spack/lib/spack/env/gcc/gcc.
-   Checking for size_t... Yes.
-   Checking for off64_t... Yes.
-   Checking for fseeko... Yes.
-   Checking for strerror... Yes.
-   Checking for unistd.h... Yes.
-   Checking for stdarg.h... Yes.
-   Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
-   Checking for vsnprintf() in stdio.h... Yes.
-   Checking for return value of vsnprintf()... Yes.
-   Checking for attribute(visibility) support... Yes.
-   ==> 'make' '-j36'
-   ...
-   ==> 'make' '-j36' 'install'
-   ...
-
-
-As you can see, we are building with all 36 cores on the node. If you are
-on a shared login node, this can slow down the system for other users. If
-you have a strict ulimit or restriction on the number of available licenses,
-you may not be able to build at all with this many cores. On nodes with 64+
-cores, you may not see a significant speedup of the build anyway. To limit
-the number of cores our build uses, set ``build_jobs`` like so:
-
-.. code-block:: yaml
-
-   config:
-     build_jobs: 4
-
-
-If we uninstall and reinstall zlib, we see that it now uses only 4 cores:
-
-.. code-block:: console
-
-   $ spack install -v zlib
-   ==> Installing zlib
-   ==> Using cached archive: ~/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
-   ==> Staging archive: ~/spack/var/spack/stage/zlib-1.2.11-ezuwp4pa52e75v6iweawzwymmf4ahxxn/zlib-1.2.11.tar.gz
-   ==> Created stage in ~/spack/var/spack/stage/zlib-1.2.11-ezuwp4pa52e75v6iweawzwymmf4ahxxn
-   ==> No patches needed for zlib
-   ==> Building zlib [Package]
-   ==> Executing phase: 'install'
-   ==> './configure' '--prefix=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/zlib-1.2.11-ezuwp4pa52e75v6iweawzwymmf4ahxxn'
-   Checking for shared library support...
-   Building shared library libz.so.1.2.11 with ~/spack/lib/spack/env/gcc/gcc.
-   Checking for size_t... Yes.
-   Checking for off64_t... Yes.
-   Checking for fseeko... Yes.
-   Checking for strerror... Yes.
-   Checking for unistd.h... Yes.
-   Checking for stdarg.h... Yes.
-   Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
-   Checking for vsnprintf() in stdio.h... Yes.
-   Checking for return value of vsnprintf()... Yes.
-   Checking for attribute(visibility) support... Yes.
-   ==> 'make' '-j4'
-   ...
-   ==> 'make' '-j4' 'install'
-   ...
-
-
-Obviously, if you want to build everything in serial for whatever reason,
-you would set ``build_jobs`` to 1.
-

lib/spack/docs/tutorial_sc16.rst

@@ -4,9 +4,9 @@
 Tutorial: Spack 101
 =============================
 
-This is a full day introduction to Spack with lectures and live demos.  It
-was presented as a tutorial at `Supercomputing 2017
-<http://sc17.supercomputing.org>`_.  You can use these materials to teach
+This is a 3-hour introduction to Spack with lectures and live demos.  It
+was presented as a tutorial at `Supercomputing 2016
+<http://sc16.supercomputing.org>`_.  You can use these materials to teach
 a course on Spack at your own site, or you can just skip ahead and read
 the live demo scripts to see how Spack is used in practice.
 
@@ -15,18 +15,19 @@ the live demo scripts to see how Spack is used in practice.
 .. rubric:: Slides
 
 .. figure:: tutorial/sc16-tutorial-slide-preview.png
-   :target: http://spack.io/slides/Spack-SC17-Tutorial.pdf
+   :target: http://llnl.github.io/spack/files/Spack-SC16-Tutorial.pdf
    :height: 72px
    :align: left
    :alt: Slide Preview
 
-`Download Slides <http://spack.io/slides/Spack-SC17-Tutorial.pdf>`_.
+`Download Slides <http://llnl.github.io/spack/files/Spack-SC16-Tutorial.pdf>`_.
 
 **Full citation:** Todd Gamblin, Massimiliano Culpo, Gregory Becker, Matt
 Legendre, Greg Lee, Elizabeth Fischer, and Benedikt Hegner.
 `Managing HPC Software Complexity with Spack
-<http://sc17.supercomputing.org/presentation/?id=tut151&sess=sess233>`_.
-Tutorial presented at Supercomputing 2017. November 13, 2017, Denver, CO, USA.
+<http://sc16.supercomputing.org/presentation/?id=tut166&sess=sess209>`_.
+Tutorial presented at Supercomputing 2016. November 13, 2016, Salt Lake
+City, UT, USA.
 
 .. _sc16-live-demos:
 
@@ -36,18 +37,12 @@ These scripts will take you step-by-step through basic Spack tasks.  They
 correspond to sections in the slides above.
 
   1. :ref:`basics-tutorial`
-  2. :ref:`configs-tutorial`
-  3. :ref:`packaging-tutorial`
-  4. :ref:`build-systems-tutorial`
-  5. :ref:`advanced-packaging-tutorial`
-  6. :ref:`modules-tutorial`
+  2. :ref:`packaging-tutorial`
+  3. :ref:`modules-tutorial`
 
 Full contents:
 
 .. toctree::
-   tutorial_basics
-   tutorial_configuration
-   tutorial_packaging
-   tutorial_buildsystems
-   tutorial_advanced_packaging
-   tutorial_modules
+   tutorial_sc16_spack_basics
+   tutorial_sc16_packaging
+   tutorial_sc16_modules

lib/spack/docs/tutorial_sc16_modules.rst

@@ -0,0 +1,982 @@
+.. _modules-tutorial:
+
+=============================
+Module Configuration Tutorial
+=============================
+
+This tutorial will guide you through the customization of both
+content and naming of module files generated by Spack.
+
+Starting from the default Spack settings you will add an increasing
+number of directives to the ``modules.yaml`` configuration file to
+satisfy a number of constraints that mimic those that you may encounter
+in a typical production environment at HPC sites.
+
+Even though the focus will be for the most part on customizing
+TCL non-hierarchical module files, everything
+you'll see applies also to other kinds of module files generated by Spack.
+
+The generation of Lua hierarchical
+module files will be addressed at the end of the tutorial,
+and you'll see that with minor modifications
+to an existing ``modules.yaml`` written for TCL
+non-hierarchical  modules you'll get almost
+for free the possibility to try a hierarchical layout.
+
+Let's start!
+
+.. _module_file_tutorial_prerequisites:
+
+-------------
+Prerequisites
+-------------
+
+Before proceeding further ensure:
+
+- you have LMod or Environment Modules available
+- have :ref:`shell support <shell-support>` activated in Spack
+
+If you need to install Lmod or Environment module you can refer
+to the documentation :ref:`here <InstallEnvironmentModules>`.
+
+
+^^^^^^^^^^^^^^^^^^
+Add a new compiler
+^^^^^^^^^^^^^^^^^^
+
+Spack automatically scans the environment to search for available
+compilers on first use. On a Ubuntu 14.04 a fresh clone will show
+something like this:
+
+.. code-block:: console
+
+  $ uname -a
+  Linux nuvolari 4.4.0-45-generic #66~14.04.1-Ubuntu SMP Wed Oct 19 15:05:38 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
+
+  $ spack compilers
+  ==> Available compilers
+  -- gcc ----------------------------------------------------------
+  gcc@4.8
+
+For the purpose of building a limited set of packages with some features
+that will help showcasing the capabilities of
+module customization the first thing we need is to build a new compiler:
+
+.. code-block:: console
+
+  $ spack install gcc@6.2.0
+  # ...
+  # Wait a long time
+  # ...
+
+Then we can use shell support for modules to add it to the list of known compilers:
+
+.. code-block:: console
+
+  # The name of the generated module may vary
+  $ module load gcc-6.2.0-gcc-4.8-twd5nqg
+
+  $ spack compiler add
+  ==> Added 1 new compiler to ~/.spack/linux/compilers.yaml
+      gcc@6.2.0
+
+  $ spack compilers
+  ==> Available compilers
+  -- gcc ----------------------------------------------------------
+  gcc@6.2.0  gcc@4.8
+
+Note that the final 7 digits hash at the end of the generated module may vary depending
+on architecture or package version.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Build software that will be used in the tutorial
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Next you should install a few modules that will be used in the tutorial:
+
+.. code-block:: console
+
+  $ spack install netlib-scalapack ^openmpi ^openblas
+  # ...
+
+The packages you need to install are:
+
+- ``netlib-scalapack ^openmpi ^openblas``
+- ``netlib-scalapack ^mpich ^openblas``
+- ``netlib-scalapack ^openmpi ^netlib-lapack``
+- ``netlib-scalapack ^mpich ^netlib-lapack``
+- ``py-scipy ^openblas``
+
+In the end your environment should look something like:
+
+.. code-block:: console
+
+  $ module avail
+
+  ------------------------------------------------------------------------ ~/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
+     binutils-2.27-gcc-4.8-dz3xevw         libpciaccess-0.13.4-gcc-6.2.0-eo2siet      lzo-2.09-gcc-6.2.0-jcngz72                  netlib-scalapack-2.0.2-gcc-6.2.0-wnimqhw    python-2.7.12-gcc-6.2.0-qu7rc5p
+     bzip2-1.0.6-gcc-6.2.0-csoc2mq         libsigsegv-2.10-gcc-4.8-avb6azw            m4-1.4.17-gcc-4.8-iggewke                   netlib-scalapack-2.0.2-gcc-6.2.0-wojunhq    sqlite-3.8.5-gcc-6.2.0-td3zfe7
+     cmake-3.5.2-gcc-6.2.0-6poypqg         libsigsegv-2.10-gcc-6.2.0-g3qpmbi          m4-1.4.17-gcc-6.2.0-lhgqa6s                 nettle-3.2-gcc-6.2.0-djdthlh                tcl-8.6.5-gcc-4.8-atddxu7
+     curl-7.50.3-gcc-6.2.0-2ffacqm         libtool-2.4.6-gcc-6.2.0-kiepac6            mpc-1.0.3-gcc-4.8-lylv7lk                   openblas-0.2.19-gcc-6.2.0-js33umc           util-macros-1.19.0-gcc-6.2.0-uoukuqk
+     expat-2.2.0-gcc-6.2.0-bxqnjar         libxml2-2.9.4-gcc-6.2.0-3k4ykbe            mpfr-3.1.4-gcc-4.8-bldfx3w                  openmpi-2.0.1-gcc-6.2.0-s3qbtby             xz-5.2.2-gcc-6.2.0-t5lk6in
+     gcc-6.2.0-gcc-4.8-twd5nqg             lmod-6.4.5-gcc-4.8-7v7bh7b                 mpich-3.2-gcc-6.2.0-5n5xoep                 openssl-1.0.2j-gcc-6.2.0-hibnfda            zlib-1.2.8-gcc-4.8-bds4ies
+     gmp-6.1.1-gcc-4.8-uq52e2n             lua-5.3.2-gcc-4.8-xozf2hx                  ncurses-6.0-gcc-4.8-u62fit4                 pkg-config-0.29.1-gcc-6.2.0-rslsgcs         zlib-1.2.8-gcc-6.2.0-asydrba
+     gmp-6.1.1-gcc-6.2.0-3cfh3hi           lua-luafilesystem-1_6_3-gcc-4.8-sbzejlz    ncurses-6.0-gcc-6.2.0-7tb426s               py-nose-1.3.7-gcc-6.2.0-4gl5c42
+     hwloc-1.11.4-gcc-6.2.0-3ostwel        lua-luaposix-33.4.0-gcc-4.8-xf7y2p5        netlib-lapack-3.6.1-gcc-6.2.0-mirer2l       py-numpy-1.11.1-gcc-6.2.0-i3rpk4e
+     isl-0.14-gcc-4.8-cq73t5m              lz4-131-gcc-6.2.0-cagoem4                  netlib-scalapack-2.0.2-gcc-6.2.0-6bqlxqy    py-scipy-0.18.1-gcc-6.2.0-e6uljfi
+     libarchive-3.2.1-gcc-6.2.0-2b54aos    lzma-4.32.7-gcc-6.2.0-sfmeynw              netlib-scalapack-2.0.2-gcc-6.2.0-hpqb3dp    py-setuptools-25.2.0-gcc-6.2.0-hkqauaa
+
+------------------------------------------------
+Filter unwanted modifications to the environment
+------------------------------------------------
+
+The non-hierarchical TCL module files that have been generated so far
+follow the default rules for module generation, which are given
+:ref:`here <modules-yaml>` in the reference part of the manual. Taking a
+look at the ``gcc`` module you'll see something like:
+
+.. code-block:: console
+
+  $ module show gcc-6.2.0-gcc-4.8-twd5nqg
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+     ~/spack/share/spack/modules/linux-Ubuntu14-x86_64/gcc-6.2.0-gcc-4.8-twd5nqg:
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  whatis("gcc @6.2.0 ")
+  prepend_path("PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/bin")
+  prepend_path("CMAKE_PREFIX_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/")
+  prepend_path("MANPATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/share/man")
+  prepend_path("PKG_CONFIG_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64/pkgconfig")
+  prepend_path("LIBRARY_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
+  prepend_path("LD_LIBRARY_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
+  prepend_path("CPATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/include")
+  help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
+  Fortran, and Java.
+  ]])
+
+As expected, a few environment variables representing paths will be modified
+by the modules according to the default prefix inspection rules.
+
+Consider now the case that your site has decided that e.g. ``CPATH`` and
+``LIBRARY_PATH`` modifications should not be present in module files. What you can
+do to abide by the rules is to create a configuration file ``~/.spack/modules.yaml``
+with the following content:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      all:
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+
+Next you should regenerate all the module files:
+
+.. code-block:: console
+
+  $ spack module refresh --module-type tcl
+  ==> You are about to regenerate tcl module files for:
+
+  -- linux-Ubuntu14-x86_64 / gcc@4.8 ------------------------------
+  dz3xevw binutils@2.27  uq52e2n gmp@6.1.1  avb6azw libsigsegv@2.10  xozf2hx lua@5.3.2                xf7y2p5 lua-luaposix@33.4.0  lylv7lk mpc@1.0.3   u62fit4 ncurses@6.0  bds4ies zlib@1.2.8
+  twd5nqg gcc@6.2.0      cq73t5m isl@0.14   7v7bh7b lmod@6.4.5       sbzejlz lua-luafilesystem@1_6_3  iggewke m4@1.4.17            bldfx3w mpfr@3.1.4  atddxu7 tcl@8.6.5
+
+  ...
+
+  ==> Do you want to proceed ? [y/n]
+  y
+  ==> Regenerating tcl module files
+
+If you take a look now at the module for ``gcc`` you'll see that the unwanted
+paths have disappeared:
+
+.. code-block:: console
+
+  $ module show gcc-6.2.0-gcc-4.8-twd5nqg
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+     ~/spack/share/spack/modules/linux-Ubuntu14-x86_64/gcc-6.2.0-gcc-4.8-twd5nqg:
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  whatis("gcc @6.2.0 ")
+  prepend_path("PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/bin")
+  prepend_path("CMAKE_PREFIX_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/")
+  prepend_path("MANPATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/share/man")
+  prepend_path("PKG_CONFIG_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64/pkgconfig")
+  prepend_path("LD_LIBRARY_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
+  help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
+  Fortran, and Java.
+  ]])
+
+----------------------------------------------
+Prevent some module files from being generated
+----------------------------------------------
+
+Another common request at many sites is to avoid exposing software that
+is only needed as an intermediate step when building a newer stack.
+Let's try to prevent the generation of
+module files for anything that is compiled with ``gcc@4.8`` (the OS provided compiler).
+
+To do this you should add a ``blacklist`` keyword to the configuration file:
+
+.. code-block:: yaml
+  :emphasize-lines: 3,4
+
+  modules:
+    tcl:
+      blacklist:
+        -  '%gcc@4.8'
+      all:
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+
+and regenerate the module files:
+
+.. code-block:: console
+
+  $ spack module refresh --module-type tcl --delete-tree
+  ==> You are about to regenerate tcl module files for:
+
+  -- linux-Ubuntu14-x86_64 / gcc@4.8 ------------------------------
+  dz3xevw binutils@2.27  uq52e2n gmp@6.1.1  avb6azw libsigsegv@2.10  xozf2hx lua@5.3.2                xf7y2p5 lua-luaposix@33.4.0  lylv7lk mpc@1.0.3   u62fit4 ncurses@6.0  bds4ies zlib@1.2.8
+  twd5nqg gcc@6.2.0      cq73t5m isl@0.14   7v7bh7b lmod@6.4.5       sbzejlz lua-luafilesystem@1_6_3  iggewke m4@1.4.17            bldfx3w mpfr@3.1.4  atddxu7 tcl@8.6.5
+
+  -- linux-Ubuntu14-x86_64 / gcc@6.2.0 ----------------------------
+  csoc2mq bzip2@1.0.6   2b54aos libarchive@3.2.1     sfmeynw lzma@4.32.7          wnimqhw netlib-scalapack@2.0.2  s3qbtby openmpi@2.0.1      hkqauaa py-setuptools@25.2.0
+  6poypqg cmake@3.5.2   eo2siet libpciaccess@0.13.4  jcngz72 lzo@2.09             6bqlxqy netlib-scalapack@2.0.2  hibnfda openssl@1.0.2j     qu7rc5p python@2.7.12
+  2ffacqm curl@7.50.3   g3qpmbi libsigsegv@2.10      lhgqa6s m4@1.4.17            wojunhq netlib-scalapack@2.0.2  rslsgcs pkg-config@0.29.1  td3zfe7 sqlite@3.8.5
+  bxqnjar expat@2.2.0   kiepac6 libtool@2.4.6        5n5xoep mpich@3.2            hpqb3dp netlib-scalapack@2.0.2  4gl5c42 py-nose@1.3.7      uoukuqk util-macros@1.19.0
+  3cfh3hi gmp@6.1.1     3k4ykbe libxml2@2.9.4        7tb426s ncurses@6.0          djdthlh nettle@3.2              i3rpk4e py-numpy@1.11.1    t5lk6in xz@5.2.2
+  3ostwel hwloc@1.11.4  cagoem4 lz4@131              mirer2l netlib-lapack@3.6.1  js33umc openblas@0.2.19         e6uljfi py-scipy@0.18.1    asydrba zlib@1.2.8
+
+  ==> Do you want to proceed ? [y/n]
+  y
+
+  $ module avail
+
+  ------------------------------------------------------------------------ ~/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
+     bzip2-1.0.6-gcc-6.2.0-csoc2mq            libsigsegv-2.10-gcc-6.2.0-g3qpmbi    ncurses-6.0-gcc-6.2.0-7tb426s               openmpi-2.0.1-gcc-6.2.0-s3qbtby           sqlite-3.8.5-gcc-6.2.0-td3zfe7
+     cmake-3.5.2-gcc-6.2.0-6poypqg            libtool-2.4.6-gcc-6.2.0-kiepac6      netlib-lapack-3.6.1-gcc-6.2.0-mirer2l       openssl-1.0.2j-gcc-6.2.0-hibnfda          util-macros-1.19.0-gcc-6.2.0-uoukuqk
+     curl-7.50.3-gcc-6.2.0-2ffacqm            libxml2-2.9.4-gcc-6.2.0-3k4ykbe      netlib-scalapack-2.0.2-gcc-6.2.0-6bqlxqy    pkg-config-0.29.1-gcc-6.2.0-rslsgcs       xz-5.2.2-gcc-6.2.0-t5lk6in
+     expat-2.2.0-gcc-6.2.0-bxqnjar            lz4-131-gcc-6.2.0-cagoem4            netlib-scalapack-2.0.2-gcc-6.2.0-hpqb3dp    py-nose-1.3.7-gcc-6.2.0-4gl5c42           zlib-1.2.8-gcc-6.2.0-asydrba
+     gmp-6.1.1-gcc-6.2.0-3cfh3hi              lzma-4.32.7-gcc-6.2.0-sfmeynw        netlib-scalapack-2.0.2-gcc-6.2.0-wnimqhw    py-numpy-1.11.1-gcc-6.2.0-i3rpk4e
+     hwloc-1.11.4-gcc-6.2.0-3ostwel           lzo-2.09-gcc-6.2.0-jcngz72           netlib-scalapack-2.0.2-gcc-6.2.0-wojunhq    py-scipy-0.18.1-gcc-6.2.0-e6uljfi
+     libarchive-3.2.1-gcc-6.2.0-2b54aos       m4-1.4.17-gcc-6.2.0-lhgqa6s          nettle-3.2-gcc-6.2.0-djdthlh                py-setuptools-25.2.0-gcc-6.2.0-hkqauaa
+     libpciaccess-0.13.4-gcc-6.2.0-eo2siet    mpich-3.2-gcc-6.2.0-5n5xoep          openblas-0.2.19-gcc-6.2.0-js33umc           python-2.7.12-gcc-6.2.0-qu7rc5p
+
+This time it is convenient to pass the option ``--delete-tree`` to the command that
+regenerates the module files to instruct it to delete the existing tree and regenerate
+a new one instead of overwriting the files in the existing directory.
+
+If you pay careful attention you'll see though that we went too far in blacklisting modules:
+the module for ``gcc@6.2.0`` disappeared as it was bootstrapped with ``gcc@4.8``. To specify
+exceptions to the blacklist rules you can use ``whitelist``:
+
+.. code-block:: yaml
+  :emphasize-lines: 3,4
+
+  modules:
+    tcl:
+      whitelist:
+        -  gcc
+      blacklist:
+        -  '%gcc@4.8'
+      all:
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+
+``whitelist`` rules always have precedence over ``blacklist`` rules. If you regenerate the modules again:
+
+.. code-block:: console
+
+  $ spack module refresh --module-type tcl -y
+
+you'll see that now the module for ``gcc@6.2.0`` has reappeared:
+
+.. code-block:: console
+
+  $ module avail gcc-6.2.0-gcc-4.8-twd5nqg
+
+  ------------------------------------------------------------------------ ~/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
+     gcc-6.2.0-gcc-4.8-twd5nqg
+
+-------------------------
+Change module file naming
+-------------------------
+
+The next step in making  module files more user-friendly is to
+improve their naming scheme.
+To reduce the length of the hash or remove it altogether you can
+use the ``hash_length`` keyword in the configuration file:
+
+.. TODO: give reasons to remove hashes if they are not evident enough?
+
+.. code-block:: yaml
+  :emphasize-lines: 3
+
+  modules:
+    tcl:
+      hash_length: 0
+      whitelist:
+        -  gcc
+      blacklist:
+        -  '%gcc@4.8'
+      all:
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+
+If you try to regenerate the module files now you will get an error:
+
+.. code-block:: console
+
+  $ spack module refresh --module-type tcl --delete-tree -y
+  ==> Error: Name clashes detected in module files:
+
+  file : ~/spack/share/spack/modules/linux-Ubuntu14-x86_64/netlib-scalapack-2.0.2-gcc-6.2.0
+  spec : netlib-scalapack@2.0.2%gcc@6.2.0~fpic+shared arch=linux-Ubuntu14-x86_64
+  spec : netlib-scalapack@2.0.2%gcc@6.2.0~fpic+shared arch=linux-Ubuntu14-x86_64
+  spec : netlib-scalapack@2.0.2%gcc@6.2.0~fpic+shared arch=linux-Ubuntu14-x86_64
+  spec : netlib-scalapack@2.0.2%gcc@6.2.0~fpic+shared arch=linux-Ubuntu14-x86_64
+
+  ==> Error: Operation aborted
+
+.. note::
+  We try to check for errors upfront!
+   In Spack we check for errors upfront whenever possible, so don't worry about your module files:
+   as a name clash was detected nothing has been changed on disk.
+
+The problem here is that without
+the hashes the four different flavors of ``netlib-scalapack`` map to the same module file
+name. We have the possibility to add suffixes to differentiate them:
+
+.. code-block:: yaml
+ :emphasize-lines: 9-11,14-17
+
+  modules:
+    tcl:
+      hash_length: 0
+      whitelist:
+        -  gcc
+      blacklist:
+        -  '%gcc@4.8'
+      all:
+        suffixes:
+          '^openblas': openblas
+          '^netlib-lapack': netlib
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+      netlib-scalapack:
+        suffixes:
+          '^openmpi': openmpi
+          '^mpich': mpich
+
+As you can see it is possible to specify rules that applies only to a
+restricted set of packages using :ref:`anonymous specs <anonymous_specs>`.
+Regenerating module files now we obtain:
+
+.. code-block:: console
+
+  $ spack module refresh --module-type tcl --delete-tree -y
+  ==> Regenerating tcl module files
+  $ module avail
+
+  ------------------------------------------------------------------------ ~/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
+     bzip2-1.0.6-gcc-6.2.0         libpciaccess-0.13.4-gcc-6.2.0    mpich-3.2-gcc-6.2.0                                  openblas-0.2.19-gcc-6.2.0             python-2.7.12-gcc-6.2.0
+     cmake-3.5.2-gcc-6.2.0         libsigsegv-2.10-gcc-6.2.0        ncurses-6.0-gcc-6.2.0                                openmpi-2.0.1-gcc-6.2.0               sqlite-3.8.5-gcc-6.2.0
+     curl-7.50.3-gcc-6.2.0         libtool-2.4.6-gcc-6.2.0          netlib-lapack-3.6.1-gcc-6.2.0                        openssl-1.0.2j-gcc-6.2.0              util-macros-1.19.0-gcc-6.2.0
+     expat-2.2.0-gcc-6.2.0         libxml2-2.9.4-gcc-6.2.0          netlib-scalapack-2.0.2-gcc-6.2.0-netlib-mpich        pkg-config-0.29.1-gcc-6.2.0           xz-5.2.2-gcc-6.2.0
+     gcc-6.2.0-gcc-4.8             lz4-131-gcc-6.2.0                netlib-scalapack-2.0.2-gcc-6.2.0-netlib-openmpi      py-nose-1.3.7-gcc-6.2.0               zlib-1.2.8-gcc-6.2.0
+     gmp-6.1.1-gcc-6.2.0           lzma-4.32.7-gcc-6.2.0            netlib-scalapack-2.0.2-gcc-6.2.0-openblas-mpich      py-numpy-1.11.1-gcc-6.2.0-openblas
+     hwloc-1.11.4-gcc-6.2.0        lzo-2.09-gcc-6.2.0               netlib-scalapack-2.0.2-gcc-6.2.0-openblas-openmpi    py-scipy-0.18.1-gcc-6.2.0-openblas
+     libarchive-3.2.1-gcc-6.2.0    m4-1.4.17-gcc-6.2.0              nettle-3.2-gcc-6.2.0                                 py-setuptools-25.2.0-gcc-6.2.0
+
+Finally we can set a ``naming_scheme`` to prevent users from loading
+modules that refer to different flavors of the same library/application:
+
+.. code-block:: yaml
+  :emphasize-lines: 4,10,11
+
+  modules:
+    tcl:
+      hash_length: 0
+      naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
+      whitelist:
+        -  gcc
+      blacklist:
+        -  '%gcc@4.8'
+      all:
+        conflict:
+          - '${PACKAGE}'
+        suffixes:
+          '^openblas': openblas
+          '^netlib-lapack': netlib
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+      netlib-scalapack:
+        suffixes:
+          '^openmpi': openmpi
+          '^mpich': mpich
+
+The final result should look like:
+
+.. code-block:: console
+
+  $ module avail
+
+  ------------------------------------------------------------------------ ~/spack/share/spack/modules/linux-Ubuntu14-x86_64 ------------------------------------------------------------------------
+     bzip2/1.0.6-gcc-6.2.0         libpciaccess/0.13.4-gcc-6.2.0    mpich/3.2-gcc-6.2.0                                      openblas/0.2.19-gcc-6.2.0             python/2.7.12-gcc-6.2.0
+     cmake/3.5.2-gcc-6.2.0         libsigsegv/2.10-gcc-6.2.0        ncurses/6.0-gcc-6.2.0                                    openmpi/2.0.1-gcc-6.2.0               sqlite/3.8.5-gcc-6.2.0
+     curl/7.50.3-gcc-6.2.0         libtool/2.4.6-gcc-6.2.0          netlib-lapack/3.6.1-gcc-6.2.0                            openssl/1.0.2j-gcc-6.2.0              util-macros/1.19.0-gcc-6.2.0
+     expat/2.2.0-gcc-6.2.0         libxml2/2.9.4-gcc-6.2.0          netlib-scalapack/2.0.2-gcc-6.2.0-netlib-mpich            pkg-config/0.29.1-gcc-6.2.0           xz/5.2.2-gcc-6.2.0
+     gcc/6.2.0-gcc-4.8             lz4/131-gcc-6.2.0                netlib-scalapack/2.0.2-gcc-6.2.0-netlib-openmpi          py-nose/1.3.7-gcc-6.2.0               zlib/1.2.8-gcc-6.2.0
+     gmp/6.1.1-gcc-6.2.0           lzma/4.32.7-gcc-6.2.0            netlib-scalapack/2.0.2-gcc-6.2.0-openblas-mpich          py-numpy/1.11.1-gcc-6.2.0-openblas
+     hwloc/1.11.4-gcc-6.2.0        lzo/2.09-gcc-6.2.0               netlib-scalapack/2.0.2-gcc-6.2.0-openblas-openmpi (D)    py-scipy/0.18.1-gcc-6.2.0-openblas
+     libarchive/3.2.1-gcc-6.2.0    m4/1.4.17-gcc-6.2.0              nettle/3.2-gcc-6.2.0                                     py-setuptools/25.2.0-gcc-6.2.0
+
+.. note::
+  TCL specific directive
+    The directives ``naming_scheme`` and ``conflict`` are TCL specific and do not apply
+    to the ``dotkit`` or ``lmod`` sections in the configuration file.
+
+------------------------------------
+Add custom environment modifications
+------------------------------------
+
+At many sites it is customary to set an environment variable in a
+package's module file that points to the folder in which the package
+is installed. You can achieve this with Spack by adding an
+``environment`` directive to the configuration file:
+
+.. code-block:: yaml
+  :emphasize-lines: 17-19
+
+  modules:
+    tcl:
+      hash_length: 0
+      naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
+      whitelist:
+        -  gcc
+      blacklist:
+        -  '%gcc@4.8'
+      all:
+        conflict:
+          - '${PACKAGE}'
+        suffixes:
+          '^openblas': openblas
+          '^netlib-lapack': netlib
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+        environment:
+          set:
+            '${PACKAGE}_ROOT': '${PREFIX}'
+      netlib-scalapack:
+        suffixes:
+          '^openmpi': openmpi
+          '^mpich': mpich
+
+There are many variable tokens available to use in the ``environment``
+and ``naming_scheme`` directives, such as ``${PACKAGE}``,
+``${VERSION}``, etc. (see the :meth:`~spack.spec.Spec.format` API
+documentation for the complete list).
+
+Regenerating the module files should result in something like:
+
+.. code-block:: console
+  :emphasize-lines: 14
+
+  $ spack module refresh -y --module-type tcl
+  ==> Regenerating tcl module files
+
+  $ module show gcc
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+     ~/spack/share/spack/modules/linux-Ubuntu14-x86_64/gcc/6.2.0-gcc-4.8:
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  whatis("gcc @6.2.0 ")
+  prepend_path("PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/bin")
+  prepend_path("CMAKE_PREFIX_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/")
+  prepend_path("MANPATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/share/man")
+  prepend_path("PKG_CONFIG_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64/pkgconfig")
+  prepend_path("LD_LIBRARY_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
+  setenv("GCC_ROOT","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u")
+  conflict("gcc")
+  help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
+  Fortran, and Java.
+  ]])
+
+As you see the ``gcc`` module has the environment variable ``GCC_ROOT`` set.
+
+Sometimes it's also useful to apply environment modifications selectively and target
+only certain packages. You can, for instance set the common variables ``CC``, ``CXX``,
+etc. in the ``gcc`` module file and apply other custom modifications to the
+``openmpi`` modules as follows:
+
+.. code-block:: yaml
+  :emphasize-lines: 20-32
+
+  modules:
+    tcl:
+      hash_length: 0
+      naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
+      whitelist:
+        - gcc
+      blacklist:
+        - '%gcc@4.8'
+      all:
+        conflict:
+          - '${PACKAGE}'
+        suffixes:
+          '^openblas': openblas
+          '^netlib-lapack': netlib
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+        environment:
+          set:
+            '${PACKAGE}_ROOT': '${PREFIX}'
+      gcc:
+        environment:
+          set:
+            CC: gcc
+            CXX: g++
+            FC: gfortran
+            F90: gfortran
+            F77: gfortran
+      openmpi:
+        environment:
+          set:
+            SLURM_MPI_TYPE: pmi2
+            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
+      netlib-scalapack:
+        suffixes:
+          '^openmpi': openmpi
+          '^mpich': mpich
+
+This time we will be more selective and regenerate only the ``gcc`` and
+``openmpi`` module files:
+
+.. code-block:: console
+
+  $ spack module refresh -y --module-type tcl gcc
+  ==> Regenerating tcl module files
+
+  $ spack module refresh -y --module-type tcl openmpi
+  ==> Regenerating tcl module files
+
+  $ module show gcc
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+     ~/spack/share/spack/modules/linux-Ubuntu14-x86_64/gcc/6.2.0-gcc-4.8:
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  whatis("gcc @6.2.0 ")
+  prepend_path("PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/bin")
+  prepend_path("CMAKE_PREFIX_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/")
+  prepend_path("MANPATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/share/man")
+  prepend_path("PKG_CONFIG_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64/pkgconfig")
+  prepend_path("LD_LIBRARY_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u/lib64")
+  setenv("GCC_ROOT","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-4.8/gcc-6.2.0-twd5nqg33hrrssqclcfi5k42eccwxz5u")
+  setenv("CC","gcc")
+  setenv("CXX","g++")
+  setenv("F90","gfortran")
+  setenv("FC","gfortran")
+  setenv("F77","gfortran")
+  conflict("gcc")
+  help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
+  Fortran, and Java.
+  ]])
+
+  $ module show openmpi
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+     ~/spack/share/spack/modules/linux-Ubuntu14-x86_64/openmpi/2.0.1-gcc-6.2.0:
+  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  whatis("openmpi @2.0.1 ")
+  prepend_path("PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/bin")
+  prepend_path("CMAKE_PREFIX_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/")
+  prepend_path("LD_LIBRARY_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/lib")
+  prepend_path("PKG_CONFIG_PATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/lib/pkgconfig")
+  prepend_path("MANPATH","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w/share/man")
+  setenv("SLURM_MPI_TYPE","pmi2")
+  setenv("OMPI_MCA_BTL_OPENIB_WARN_DEFAULT_GID_PREFIX","0")
+  setenv("OPENMPI_ROOT","~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/openmpi-2.0.1-s3qbtbyh3y5y4gkchmhcuak7th44l53w")
+  conflict("openmpi")
+  help([[The Open MPI Project is an open source Message Passing Interface
+  implementation that is developed and maintained by a consortium of
+  academic, research, and industry partners. Open MPI is therefore able to
+  combine the expertise, technologies, and resources from all across the
+  High Performance Computing community in order to build the best MPI
+  library available. Open MPI offers advantages for system and software
+  vendors, application developers and computer science researchers.
+  ]])
+
+
+---------------------
+Autoload dependencies
+---------------------
+
+Spack can also generate module files that contain code to load the
+dependencies automatically. You can, for instance generate python
+modules that load their dependencies by adding the ``autoload``
+directive and assigning it the value ``direct``:
+
+.. code-block:: yaml
+  :emphasize-lines: 37,38
+
+  modules:
+    tcl:
+      hash_length: 0
+      naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
+      whitelist:
+        - gcc
+      blacklist:
+        - '%gcc@4.8'
+      all:
+        conflict:
+          - '${PACKAGE}'
+        suffixes:
+          '^openblas': openblas
+          '^netlib-lapack': netlib
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+        environment:
+          set:
+            '${PACKAGE}_ROOT': '${PREFIX}'
+      gcc:
+        environment:
+          set:
+            CC: gcc
+            CXX: g++
+            FC: gfortran
+            F90: gfortran
+            F77: gfortran
+      openmpi:
+        environment:
+          set:
+            SLURM_MPI_TYPE: pmi2
+            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
+      netlib-scalapack:
+        suffixes:
+          '^openmpi': openmpi
+          '^mpich': mpich
+      ^python:
+        autoload:  'direct'
+
+and regenerating the module files for every package that depends on ``python``:
+
+.. code-block:: console
+
+  $ spack module refresh -y --module-type tcl ^python
+  ==> Regenerating tcl module files
+
+Now the ``py-scipy`` module will be:
+
+.. code-block:: tcl
+
+  #%Module1.0
+  ## Module file created by spack (https://github.com/LLNL/spack) on 2016-11-02 20:53:21.283547
+  ##
+  ## py-scipy@0.18.1%gcc@6.2.0 arch=linux-Ubuntu14-x86_64-e6uljfi
+  ##
+  module-whatis "py-scipy @0.18.1"
+
+  proc ModulesHelp { } {
+  puts stderr "SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It"
+  puts stderr "provides many user-friendly and efficient numerical routines such as"
+  puts stderr "routines for numerical integration and optimization."
+  }
+
+  if ![ is-loaded python/2.7.12-gcc-6.2.0 ] {
+      puts stderr "Autoloading python/2.7.12-gcc-6.2.0"
+      module load python/2.7.12-gcc-6.2.0
+  }
+
+  if ![ is-loaded openblas/0.2.19-gcc-6.2.0 ] {
+      puts stderr "Autoloading openblas/0.2.19-gcc-6.2.0"
+      module load openblas/0.2.19-gcc-6.2.0
+  }
+
+  if ![ is-loaded py-numpy/1.11.1-gcc-6.2.0-openblas ] {
+      puts stderr "Autoloading py-numpy/1.11.1-gcc-6.2.0-openblas"
+      module load py-numpy/1.11.1-gcc-6.2.0-openblas
+  }
+
+  prepend-path CMAKE_PREFIX_PATH "~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/py-scipy-0.18.1-e6uljfiffgym4xvj6wveevqxfqnfb3gh/"
+  prepend-path LD_LIBRARY_PATH "~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/py-scipy-0.18.1-e6uljfiffgym4xvj6wveevqxfqnfb3gh/lib"
+  prepend-path PYTHONPATH "~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/py-scipy-0.18.1-e6uljfiffgym4xvj6wveevqxfqnfb3gh/lib/python2.7/site-packages"
+  setenv PY_SCIPY_ROOT "~/spack/opt/spack/linux-Ubuntu14-x86_64/gcc-6.2.0/py-scipy-0.18.1-e6uljfiffgym4xvj6wveevqxfqnfb3gh"
+  conflict py-scipy
+
+and will contain code to autoload all the dependencies:
+
+.. code-block:: console
+
+  $ module load py-scipy
+  Autoloading python/2.7.12-gcc-6.2.0
+  Autoloading openblas/0.2.19-gcc-6.2.0
+  Autoloading py-numpy/1.11.1-gcc-6.2.0-openblas
+
+-----------------------------
+Lua hierarchical module files
+-----------------------------
+
+In the final part of this tutorial you will modify ``modules.yaml`` to generate
+Lua hierarchical module files. You will see that most of the directives used before
+are also valid in the ``lmod`` context.
+
+^^^^^^^^^^^^^^^^^
+Core/Compiler/MPI
+^^^^^^^^^^^^^^^^^
+
+.. warning::
+  Only LMod supports Lua hierarchical module files
+    For this part of the tutorial you need to be using LMod to
+    manage your environment.
+
+The most common hierarchy is the so called ``Core/Compiler/MPI``. To have an idea
+how a hierarchy is organized you may refer to the
+`Lmod guide <https://www.tacc.utexas.edu/research-development/tacc-projects/lmod/user-guide/module-hierarchy>`_.
+Since ``lmod`` is not enabled by default, you need to add it to the list of
+enabled module file generators. The other things you need to do are:
+
+- change the ``tcl`` tag to ``lmod``
+- remove ``tcl`` specific directives (``naming_scheme`` and ``conflict``)
+- set which compilers are considered ``core``
+- remove the ``mpi`` related suffixes (as they will be substituted by hierarchies)
+
+After modifications the configuration file will be:
+
+.. code-block:: yaml
+  :emphasize-lines: 2-6
+
+  modules:
+    enable::
+      - lmod
+    lmod:
+      core_compilers:
+        - 'gcc@4.8'
+      hash_length: 0
+      whitelist:
+        - gcc
+      blacklist:
+        - '%gcc@4.8'
+      all:
+        suffixes:
+          '^openblas': openblas
+          '^netlib-lapack': netlib
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+        environment:
+          set:
+            '${PACKAGE}_ROOT': '${PREFIX}'
+      gcc:
+        environment:
+          set:
+            CC: gcc
+            CXX: g++
+            FC: gfortran
+            F90: gfortran
+            F77: gfortran
+      openmpi:
+        environment:
+          set:
+            SLURM_MPI_TYPE: pmi2
+            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
+
+
+.. note::
+  The double colon
+    The double colon after ``enable`` is intentional and it serves the
+    purpose of overriding the default list of enabled generators so
+    that only ``lmod`` will be active (see :ref:`the reference
+    manual <config-overrides>` for a more detailed explanation of
+    config scopes).
+
+The directive ``core_compilers`` accepts a list of compilers : everything built
+using these compilers will create a module in the ``Core`` part of the hierarchy. It is
+common practice to put the OS provided compilers in the list and only build common utilities
+and other compilers in ``Core``.
+
+If you regenerate the module files
+
+.. code-block:: console
+
+  $ spack module refresh --module-type lmod --delete-tree -y
+
+and update ``MODULEPATH`` to point to the ``Core`` folder, and
+list the available modules, you'll see:
+
+.. code-block:: console
+
+  $ module unuse ~/spack/share/spack/modules/linux-Ubuntu14-x86_64
+  $ module use ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core
+  $ module avail
+
+  ----------------------------------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core -----------------------------------------------------------------------
+     gcc/6.2.0
+
+The only module visible now is ``gcc``. Loading that you will make
+visible the ``Compiler`` part of the software stack that was built with ``gcc/6.2.0``:
+
+.. code-block:: console
+
+  $ module load gcc
+  $ module avail
+
+  -------------------------------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/gcc/6.2.0 ---------------------------------------------------------------------
+     binutils/2.27    curl/7.50.3    hwloc/1.11.4           libtool/2.4.6    lzo/2.09       netlib-lapack/3.6.1    openssl/1.0.2j              py-scipy/0.18.1-openblas    util-macros/1.19.0
+     bison/3.0.4      expat/2.2.0    libarchive/3.2.1       libxml2/2.9.4    m4/1.4.17      nettle/3.2             pkg-config/0.29.1           py-setuptools/25.2.0        xz/5.2.2
+     bzip2/1.0.6      flex/2.6.0     libpciaccess/0.13.4    lz4/131          mpich/3.2      openblas/0.2.19        py-nose/1.3.7               python/2.7.12               zlib/1.2.8
+     cmake/3.6.1      gmp/6.1.1      libsigsegv/2.10        lzma/4.32.7      ncurses/6.0    openmpi/2.0.1          py-numpy/1.11.1-openblas    sqlite/3.8.5
+
+  ----------------------------------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core -----------------------------------------------------------------------
+     gcc/6.2.0 (L)
+
+The same holds true for the ``MPI`` part of the stack, that you can enable by loading
+either ``mpich`` or ``openmpi``. The nice features of LMod will become evident
+once you'll try switching among different stacks:
+
+.. code-block:: console
+
+  $ module load mpich
+  $ module avail
+
+  ----------------------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/mpich/3.2-5n5xoep/gcc/6.2.0 ------------------------------------------------------------
+     netlib-scalapack/2.0.2-netlib    netlib-scalapack/2.0.2-openblas (D)
+
+  -------------------------------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/gcc/6.2.0 ---------------------------------------------------------------------
+     binutils/2.27    curl/7.50.3    hwloc/1.11.4           libtool/2.4.6    lzo/2.09           netlib-lapack/3.6.1    openssl/1.0.2j              py-scipy/0.18.1-openblas    util-macros/1.19.0
+     bison/3.0.4      expat/2.2.0    libarchive/3.2.1       libxml2/2.9.4    m4/1.4.17          nettle/3.2             pkg-config/0.29.1           py-setuptools/25.2.0        xz/5.2.2
+     bzip2/1.0.6      flex/2.6.0     libpciaccess/0.13.4    lz4/131          mpich/3.2   (L)    openblas/0.2.19        py-nose/1.3.7               python/2.7.12               zlib/1.2.8
+     cmake/3.6.1      gmp/6.1.1      libsigsegv/2.10        lzma/4.32.7      ncurses/6.0        openmpi/2.0.1          py-numpy/1.11.1-openblas    sqlite/3.8.5
+
+  ----------------------------------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core -----------------------------------------------------------------------
+     gcc/6.2.0 (L)
+
+  $ module load openblas netlib-scalapack/2.0.2-openblas
+  $ module list
+
+  Currently Loaded Modules:
+    1) gcc/6.2.0   2) mpich/3.2   3) openblas/0.2.19   4) netlib-scalapack/2.0.2-openblas
+
+  $ module load openmpi
+
+  Lmod is automatically replacing "mpich/3.2" with "openmpi/2.0.1"
+
+
+  Due to MODULEPATH changes the following have been reloaded:
+    1) netlib-scalapack/2.0.2-openblas
+
+This layout is already a great improvement over the usual non-hierarchical layout,
+but it still has an asymmetry: ``LAPACK`` providers are semantically the same as ``MPI``
+providers, but they are still not part of the hierarchy.  We'll see a possible solution
+next.
+
+.. Activate lmod and turn the previous modifications into lmod:
+   Add core compilers
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Extend the hierarchy to other virtual providers
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. warning::
+  This is an experimental feature
+    Having a hierarchy deeper than ``Core``/``Compiler``/``MPI`` is an experimental
+    feature, still not fully supported by ``module spider``,
+    see `here <https://github.com/TACC/Lmod/issues/114>`_. Furthermore its use
+    with hierarchies more complex than ``Core``/``Compiler``/``MPI``/``LAPACK``
+    has not been thoroughly tested in production environments.
+
+Spack permits you to generate Lua hierarchical module files where users
+can add an arbitrary list of virtual providers to the triplet
+``Core``/``Compiler``/``MPI``. A configuration file like:
+
+.. code-block:: yaml
+  :emphasize-lines: 7,8
+
+  modules:
+    enable::
+      - lmod
+    lmod:
+      core_compilers:
+        - 'gcc@4.8'
+      hierarchical_scheme:
+        - lapack
+      hash_length: 0
+      whitelist:
+        - gcc
+      blacklist:
+        - '%gcc@4.8'
+        - readline
+      all:
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+        environment:
+          set:
+            '${PACKAGE}_ROOT': '${PREFIX}'
+      gcc:
+        environment:
+          set:
+            CC: gcc
+            CXX: g++
+            FC: gfortran
+            F90: gfortran
+            F77: gfortran
+      openmpi:
+        environment:
+          set:
+            SLURM_MPI_TYPE: pmi2
+            OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
+
+will add ``lapack`` providers to the mix. After the usual regeneration of module files:
+
+.. code-block:: console
+
+  $ module purge
+  $ spack module refresh --module-type lmod --delete-tree -y
+  ==> Regenerating lmod module files
+
+you will have something like:
+
+.. code-block:: console
+
+  $ module load gcc
+  $ module load openblas
+  $ module load openmpi
+  $ module avail
+
+  --------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/openblas/0.2.19-js33umc/openmpi/2.0.1-s3qbtby/gcc/6.2.0 ----------------------------------------------
+     netlib-scalapack/2.0.2
+
+  -------------------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/openblas/0.2.19-js33umc/gcc/6.2.0 ---------------------------------------------------------
+     py-numpy/1.11.1    py-scipy/0.18.1
+
+  -------------------------------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/gcc/6.2.0 ---------------------------------------------------------------------
+     binutils/2.27    curl/7.50.3    hwloc/1.11.4           libtool/2.4.6    lzo/2.09       netlib-lapack/3.6.1        openssl/1.0.2j          python/2.7.12         zlib/1.2.8
+     bison/3.0.4      expat/2.2.0    libarchive/3.2.1       libxml2/2.9.4    m4/1.4.17      nettle/3.2                 pkg-config/0.29.1       sqlite/3.8.5
+     bzip2/1.0.6      flex/2.6.0     libpciaccess/0.13.4    lz4/131          mpich/3.2      openblas/0.2.19     (L)    py-nose/1.3.7           util-macros/1.19.0
+     cmake/3.6.1      gmp/6.1.1      libsigsegv/2.10        lzma/4.32.7      ncurses/6.0    openmpi/2.0.1       (L)    py-setuptools/25.2.0    xz/5.2.2
+
+  ----------------------------------------------------------------------- ~/spack/share/spack/lmod/linux-Ubuntu14-x86_64/Core -----------------------------------------------------------------------
+     gcc/6.2.0 (L)
+
+Now both the ``MPI`` and the ``LAPACK`` providers are handled by LMod as hierarchies:
+
+.. code-block:: console
+
+  $ module load py-numpy netlib-scalapack
+  $ module load mpich
+
+  Lmod is automatically replacing "openmpi/2.0.1" with "mpich/3.2"
+
+
+  Due to MODULEPATH changes the following have been reloaded:
+    1) netlib-scalapack/2.0.2
+
+  $ module load netlib-lapack
+
+  Lmod is automatically replacing "openblas/0.2.19" with "netlib-lapack/3.6.1"
+
+
+  Inactive Modules:
+    1) py-numpy
+
+  Due to MODULEPATH changes the following have been reloaded:
+    1) netlib-scalapack/2.0.2
+
+making the use of tags to differentiate them unnecessary.
+Note that because we only compiled ``py-numpy`` with ``openblas`` the module
+is made inactive when we switch the ``LAPACK`` provider. The user
+environment will now be consistent by design!

lib/spack/docs/tutorial_sc16_packaging.rst

@@ -43,7 +43,7 @@ A few things before we get started:
 Creating the Package File
 -------------------------
 
-Spack comes with a handy command to create a new package: ``spack create``.
+Spack comes with a handy command to create a new package: ``spack create``
 
 This command is given the location of a package's source code, downloads
 the code, and sets up some basic packaging infrastructure for you.  The
@@ -52,20 +52,12 @@ we run ``spack create`` on it:
 
 .. code-block:: console
 
-  $ spack create -t generic -f https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
-  ==> This looks like a URL for mpileaks
-  ==> Found 1 version of mpileaks:
-    
-    1.0  https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
-  
-  ==> How many would you like to checksum? (default is 1, q to abort) 1
+  $ spack create -f https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
+  ==> This looks like a URL for mpileaks version 1.0
+  ==> Creating template for package mpileaks
   ==> Downloading...
-  ==> Fetching https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
-  ############################################################################# 100.0%
-  ==> Checksummed 1 version of mpileaks
-  ==> Using specified package template: 'generic'
-  ==> Created template for mpileaks package
-  ==> Created package file: $SPACK_ROOT/var/spack/repos/builtin/packages/mpileaks/package.py
+  ==> Fetching https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
+  ###################################################################################### 100.0%
 
 And Spack should spawn a text editor with this file:
 
@@ -200,27 +192,29 @@ Now when we try to install this package a lot more happens:
 .. code-block:: console
 
   $ spack install mpileaks
-  ...
-  ==> libdwarf is already installed in SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libdwarf-20160507-er4jrjynul6uba7wiu5tasuj35roxw6m
-  ==> dyninst is already installed in SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/dyninst-9.3.2-t7mau34jv3e76mpspdzhf2p2a6k7qubg
-  ==> callpath is already installed in SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-ikbbkvfmsfmqzo624nvvrbooovf7egoc
   ==> Installing mpileaks
-  ==> Using cached archive: SPACK_ROOT/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
-  ==> Already staged mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7 in SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7
-  ==> No patches needed for mpileaks
-  ==> Building mpileaks [Package]
-  ==> Executing phase: 'install'
-  ==> Error: ProcessError: Command exited with status 2:
-      'make' '-j36'
-  
-  1 error found in build log:
-       1     ==> Executing phase: 'install'
-       2     ==> 'make' '-j36'
-    >> 3     make: *** No targets specified and no makefile found.  Stop.
-  
+  ==> openmpi is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz
+  ==> callpath is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/callpath-1.0.2-zm4pf3gasgxeibyu2y262suktvaazube
+  ==> adept-utils is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/adept-utils-1.0.1-7p7ezxwtajdglj6cmojy2vybjct4j4jz
+  ==> Using cached archive: /usr/workspace/wsa/legendre/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
+  ==> Already staged mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk in /usr/workspace/wsa/legendre/spack/var/spack/stage/mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk
+  ==> Already patched mpileaks
+  ==> Building mpileaks [AutotoolsPackage]
+  ==> Executing phase : 'autoreconf'
+  ==> Executing phase : 'configure'
+  ==> Error: ProcessError: Command exited with status 1:
+      './configure' '--prefix=/usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk'
+  /usr/workspace/wsa/legendre/spack/lib/spack/spack/build_systems/autotools.py:150, in configure:
+       145      def configure(self, spec, prefix):
+       146          """Runs configure with the arguments specified in `configure_args`
+       147          and an appropriately set prefix
+       148          """
+       149          options = ['--prefix={0}'.format(prefix)] + self.configure_args()
+    >> 150          inspect.getmodule(self).configure(*options)
+
   See build log for details:
-    SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7/mpileaks-1.0/spack-build.out
-  
+    /tmp/legendre/spack-stage/spack-stage-7V5yyk/mpileaks-1.0/spack-build.out
+
 Note that this command may take a while to run and produce more output if
 you don't have an MPI already installed or configured in Spack.
 
@@ -234,79 +228,44 @@ Debugging Package Builds
 ------------------------
 
 Our ``mpileaks`` package is still not building.  It may be obvious to
-many of you that we never ran the configure script.  Let's add a
-call to ``configure()`` to the top of the install routine. The resulting
-package.py is in ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/3.package.py``:
-
-.. literalinclude:: tutorial/examples/3.package.py
-  :lines: 25-
-  :language: python
-
-If we re-run we still get errors:
-
-.. code-block:: console
-
-  ==> Installing mpileaks
-  ==> Using cached archive: SPACK_ROOT/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
-  ==> Already staged mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7 in SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7
-  ==> No patches needed for mpileaks
-  ==> Building mpileaks [Package]
-  ==> Executing phase: 'install'
-  ==> Error: ProcessError: Command exited with status 1:
-      './configure'
-  
-  1 error found in build log:
-       [ ... ]
-       21    checking whether SPACK_ROOT/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
-       22    checking whether we are using the GNU C++ compiler... yes
-       23    checking whether SPACK_ROOT/lib/spack/env/gcc/g++ accepts -g... yes
-       24    checking dependency style of SPACK_ROOT/lib/spack/env/gcc/g++... gcc3
-       25    checking for SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
-       26    Checking whether SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
-    >> 27    configure: error: unable to locate adept-utils installation
-  
-  See build log for details:
-    SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7/mpileaks-1.0/spack-build.out
-  
-Again, the problem may be obvious.  But let's pretend we're not
-all intelligent developers and use this opportunity spend some
-time debugging.  We have a few options that can tell us about
+many of you that we're still missing the configure options.  But let's
+pretend we're not all intelligent developers and use this opportunity
+spend some time debugging.  We a few options that can tell us about
 what's going wrong:
 
 As per the error message, Spack has given us a ``spack-build.out`` debug log:
 
 .. code-block:: console
-  
-  ==> Executing phase: 'install'
-  ==> './configure'
+
+  ==> './configure' '--prefix=/usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk'
   checking metadata... no
   checking installation directory variables... yes
   checking for a BSD-compatible install... /usr/bin/install -c
   checking whether build environment is sane... yes
-  checking for a thread-safe mkdir -p... /bin/mkdir -p
+  checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
   checking for gawk... gawk
   checking whether make sets $(MAKE)... yes
-  checking for gcc... SPACK_ROOT/lib/spack/env/gcc/gcc
+  checking for gcc... /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc
   checking for C compiler default output file name... a.out
   checking whether the C compiler works... yes
   checking whether we are cross compiling... no
-  checking for suffix of executables... 
+  checking for suffix of executables...
   checking for suffix of object files... o
   checking whether we are using the GNU C compiler... yes
-  checking whether SPACK_ROOT/lib/spack/env/gcc/gcc accepts -g... yes
-  checking for SPACK_ROOT/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
+  checking whether /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc accepts -g... yes
+  checking for /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
   checking for style of include used by make... GNU
-  checking dependency style of SPACK_ROOT/lib/spack/env/gcc/gcc... gcc3
-  checking whether SPACK_ROOT/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
+  checking dependency style of /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc... gcc3
+  checking whether /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
   checking whether we are using the GNU C++ compiler... yes
-  checking whether SPACK_ROOT/lib/spack/env/gcc/g++ accepts -g... yes
-  checking dependency style of SPACK_ROOT/lib/spack/env/gcc/g++... gcc3
-  checking for SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
-  Checking whether SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
-  configure: error: unable to locate adept-utils installation
+  checking whether /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/g++ accepts -g... yes
+  checking dependency style of /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/g++... gcc3
+  checking for /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc... /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc
+  Checking whether /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc responds to '-showme:compile'... yes
+  configure: error: unable to locate ``adept-utils`` installation
 
-This gives us the output from the build, and mpileaks isn't
-finding its ``adept-utils`` package.  Spack has
+This gives us the output from the build, and it's fairly obvious that
+mpileaks isn't finding its ``adept-utils`` package.  Spack has
 automatically added the include and library directories of
 ``adept-utils`` to the compiler's search path, but some packages like
 mpileaks can sometimes be picky and still want things spelled out on
@@ -333,26 +292,26 @@ From here we can manually re-run the build:
   checking installation directory variables... yes
   checking for a BSD-compatible install... /usr/bin/install -c
   checking whether build environment is sane... yes
-  checking for a thread-safe mkdir -p... /bin/mkdir -p
+  checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
   checking for gawk... gawk
   checking whether make sets $(MAKE)... yes
-  checking for gcc... SPACK_ROOT/lib/spack/env/gcc/gcc
+  checking for gcc... /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc
   checking for C compiler default output file name... a.out
   checking whether the C compiler works... yes
   checking whether we are cross compiling... no
-  checking for suffix of executables... 
+  checking for suffix of executables...
   checking for suffix of object files... o
   checking whether we are using the GNU C compiler... yes
-  checking whether SPACK_ROOT/lib/spack/env/gcc/gcc accepts -g... yes
-  checking for SPACK_ROOT/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
+  checking whether /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc accepts -g... yes
+  checking for /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
   checking for style of include used by make... GNU
-  checking dependency style of SPACK_ROOT/lib/spack/env/gcc/gcc... gcc3
-  checking whether SPACK_ROOT/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
+  checking dependency style of /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc... gcc3
+  checking whether /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
   checking whether we are using the GNU C++ compiler... yes
-  checking whether SPACK_ROOT/lib/spack/env/gcc/g++ accepts -g... yes
-  checking dependency style of SPACK_ROOT/lib/spack/env/gcc/g++... gcc3
-  checking for SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
-  Checking whether SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
+  checking whether /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/g++ accepts -g... yes
+  checking dependency style of /usr/workspace/wsa/legendre/spack/lib/spack/env/gcc/g++... gcc3
+  checking for /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc... /usr/workspace/wsa  /legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc
+  Checking whether /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz/bin/mpicc responds to '-showme:compile'... yes
   configure: error: unable to locate adept-utils installation
 
 We're seeing the same error, but now we're in a shell where we can run
@@ -369,9 +328,9 @@ Specifying Configure Arguments
 
 Let's add the configure arguments to the mpileaks' ``package.py``.  This
 version can be found in
-``$SPACK_ROOT/lib/spack/docs/tutorial/examples/4.package.py``:
+``$SPACK_ROOT/lib/spack/docs/tutorial/examples/3.package.py``:
 
-.. literalinclude:: tutorial/examples/4.package.py
+.. literalinclude:: tutorial/examples/3.package.py
    :lines: 25-
    :language: python
 
@@ -380,35 +339,37 @@ This is all we need for working mpileaks!  If we install now we'll see:
 .. code-block:: console
 
   $ spack install mpileaks
-  ...
+  spack install mpileaks
   ==> Installing mpileaks
-  ==> Using cached archive: SPACK_ROOT/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
-  ==> Staging archive: SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7/mpileaks-1.0.tar.gz
-  ==> Created stage in SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7
-  ==> No patches needed for mpileaks
-  ==> Building mpileaks [Package]
-  ==> Executing phase: 'install'
+  ==> openmpi is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz
+  ==> callpath is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/callpath-1.0.2-zm4pf3gasgxeibyu2y262suktvaazube
+  ==> adept-utils is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/adept-utils-1.0.1-7p7ezxwtajdglj6cmojy2vybjct4j4jz
+  ==> Using cached archive: /usr/workspace/wsa/legendre/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
+  ==> Already staged mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk in /usr/workspace/wsa/legendre/spack/var/spack/stage/mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk
+  ==> Already patched mpileaks
+  ==> Building mpileaks [AutotoolsPackage]
+  ==> Executing phase : 'autoreconf'
+  ==> Executing phase : 'configure'
+  ==> Executing phase : 'build'
+  ==> Executing phase : 'install'
   ==> Successfully installed mpileaks
-  Fetch: 0.00s.  Build: 9.01s.  Total: 9.01s.
-  [+] SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7
+    Fetch: 0.00s.  Build: 14.08s.  Total: 14.08s.
+  [+] /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/mpileaks-1.0-eum4hmnlt6ovalwjnciaygfb3beja4gk
 
-
-There are some special circumstances in package that are worth highlighting.
-Normally spack would have automatically detected that mpileaks was an
-Autotools-based package when we ran ``spack create`` and made it an ``AutoToolsPackage`` class (except we added the ``-t generic`` option to skip this).  Instead of
-a full install routine we would have just written:
+We took a few shortcuts for this package that are worth highlighting.
+Spack automatically detected that mpileaks was an Autotools-based package
+when we ran ``spack create``.  If this had been a CMake-based package we
+would have been filling in a ``cmake_args`` function instead of
+``configure_args``.  If Spack hadn't been able to detect the build
+system, we'd be filling in a generic install method that would manually
+be calling build commands, such as is found in the ``zlib`` package:
 
 .. code-block:: python
 
-    def configure_args(self):
-        args = ['--with-adept-utils=%s' % self.spec['adept-utils'].prefix,
-                '--with-callpath=%s' % self.spec['callpath'].prefix]
-        return args
-
-Similarly, if this had been a CMake-based package we
-would have been filling in a ``cmake_args`` function instead of
-``configure_args``.  There are similar default package types for
-many build environments.
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')
 
 --------
 Variants
@@ -420,9 +381,9 @@ that it walks.  Let's add a variant to allow users to set this when they
 build in Spack.
 
 To do this, we'll add a variant to our package, as per the following (see
-``$SPACK_ROOT/lib/spack/docs/tutorial/examples/5.package.py``):
+``$SPACK_ROOT/lib/spack/docs/tutorial/examples/4.package.py``):
 
-.. literalinclude:: tutorial/examples/5.package.py
+.. literalinclude:: tutorial/examples/4.package.py
    :lines: 25-
    :language: python
 
@@ -433,15 +394,18 @@ configure line (output truncated for length):
 .. code-block:: console
 
   $ spack install --verbose mpileaks stackstart=4
-  ...
   ==> Installing mpileaks
-  ==> Using cached archive: SPACK_ROOT/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
-  ==> Staging archive: SPACK_ROOT/var/spack/stage/mpileaks-1.0-gxxi4fp57b4j6xalra5t65hyx5rj25t7/mpileaks-1.0.tar.gz
-  ==> Created stage in SPACK_ROOT/var/spack/stage/mpileaks-1.0-gxxi4fp57b4j6xalra5t65hyx5rj25t7
-  ==> No patches needed for mpileaks
-  ==> Building mpileaks [Package]
-  ==> Executing phase: 'install'
-  ==> './configure' '--with-adept-utils=SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/adept-utils-1.0.1-pm3gffhrnwsdtqthtvsfvs2tny4r65wb' '--with-callpath=SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-ikbbkvfmsfmqzo624nvvrbooovf7egoc' '--prefix=SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-gxxi4fp57b4j6xalra5t65hyx5rj25t7' '--with-stack-start-c=4' '--with-stack-start-fortran=4'
+  ==> openmpi is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/openmpi-2.0.1-5ee5j34c2y4kb5c3joygrgahidqnwhnz
+  ==> callpath is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/callpath-1.0.2-zm4pf3gasgxeibyu2y262suktvaazube
+  ==> adept-utils is already installed in /usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/adept-utils-1.0.1-7p7ezxwtajdglj6cmojy2vybjct4j4jz
+  ==> Using cached archive: /usr/workspace/wsa/legendre/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
+  ==> Staging archive: /usr/workspace/wsa/legendre/spack/var/spack/stage/mpileaks-1.0-otqo2opkhan5ksujt6tpmdftydrieig7/mpileaks-1.0.tar.gz
+  ==> Created stage in /usr/workspace/wsa/legendre/spack/var/spack/stage/mpileaks-1.0-otqo2opkhan5ksujt6tpmdftydrieig7
+  ==> Ran patch() for mpileaks
+  ==> Building mpileaks [AutotoolsPackage]
+  ==> Executing phase : 'autoreconf'
+  ==> Executing phase : 'configure'
+  ==> './configure' '--prefix=/usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/mpileaks-1.0-otqo2opkhan5ksujt6tpmdftydrieig7' '--with-adept-utils=/usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/adept-utils-1.0.1-7p7ezxwtajdglj6cmojy2vybjct4j4jz' '--with-callpath=/usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/callpath-1.0.2-zm4pf3gasgxeibyu2y262suktvaazube' '--with-stack-start-c=4' '--with-stack-start-fortran=4'
 
 ---------------
 The Spec Object

lib/spack/docs/workflows.rst

@@ -33,12 +33,24 @@ possible realization of a particular package, out of combinatorially
 many other realizations.  For example, here is a concrete spec
 instantiated from ``curl``:
 
-.. command-output:: spack spec curl
+.. code-block:: console
+
+   curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
+       ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
+       ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
 
 Spack's core concretization algorithm generates concrete specs by
 instantiating packages from its repo, based on a set of "hints",
 including user input and the ``packages.yaml`` file.  This algorithm
-may be accessed at any time with the ``spack spec`` command.
+may be accessed at any time with the ``spack spec`` command.  For
+example:
+
+.. code-block:: console
+
+   $ spack spec curl
+     curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
+         ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
+         ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
 
 Every time Spack installs a package, that installation corresponds to
 a concrete spec.  Only a vanishingly small fraction of possible
@@ -56,7 +68,7 @@ variant, compiler, etc.  For example, the following set is consistent:
 .. code-block:: console
 
    curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
-       ^openssl@1.0.2k%gcc@5.3.0 arch=linux-SuSE11-x86_64
+       ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
        ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
    zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
 
@@ -65,7 +77,7 @@ The following set is not consistent:
 .. code-block:: console
 
    curl@7.50.1%gcc@5.3.0 arch=linux-SuSE11-x86_64
-       ^openssl@1.0.2k%gcc@5.3.0 arch=linux-SuSE11-x86_64
+       ^openssl@system%gcc@5.3.0 arch=linux-SuSE11-x86_64
        ^zlib@1.2.8%gcc@5.3.0 arch=linux-SuSE11-x86_64
    zlib@1.2.7%gcc@5.3.0 arch=linux-SuSE11-x86_64
 
@@ -170,7 +182,7 @@ of usage:
 
 .. code-block:: sh
 
-   #!/bin/bash
+   #!/bin/sh
 
    compilers=(
        %gcc
@@ -355,7 +367,7 @@ Transitive Dependencies
 
 In the script above, each ``spack module loads`` command generates a
 *single* ``module load`` line.  Transitive dependencies do not usually
-need to be loaded, only modules the user needs in ``$PATH``.  This is
+need to be loaded, only modules the user needs in in ``$PATH``.  This is
 because Spack builds binaries with RPATH.  Spack's RPATH policy has
 some nice features:
 
@@ -476,11 +488,10 @@ if the view is built with hardlinks.
 
 .. FIXME: reference the relocation work of Hegner and Gartung (PR #1013)
 
-.. _cmd-spack-view:
 
-""""""""""""""
-``spack view``
-""""""""""""""
+""""""""""""""""""""""
+Using Filesystem Views
+""""""""""""""""""""""
 
 A filesystem view is created, and packages are linked in, by the ``spack
 view`` command's ``symlink`` and ``hardlink`` sub-commands.  The
@@ -1028,232 +1039,6 @@ or filesystem views.  However, it has some drawbacks:
    integrate Spack explicitly in their workflow.  Not all users are
    willing to do this.
 
-------------------------
-Using Spack on Travis-CI
-------------------------
-
-Spack can be deployed as a provider for userland software in
-`Travis-CI <https://http://travis-ci.org>`_.
-
-A starting-point for a ``.travis.yml`` file can look as follows.
-It uses `caching <https://docs.travis-ci.com/user/caching/>`_ for
-already built environments, so make sure to clean the Travis cache if
-you run into problems.
-
-The main points that are implemented below:
-
-#. Travis is detected as having up to 34 cores available, but only 2
-   are actually allocated for the user. We limit the parallelism of
-   the spack builds in the config.
-   (The Travis yaml parser is a bit buggy on the echo command.)
-
-#. Builds over 10 minutes need to be prefixed with ``travis_wait``.
-   Alternatively, generate output once with ``spack install -v``.
-
-#. Travis builds are non-interactive. This prevents using bash
-   aliases and functions for modules. We fix that by sourcing
-   ``/etc/profile`` first (or running everything in a subshell with
-   ``bash -l -c '...'``).
-
-.. code-block:: yaml
-
-   language: cpp
-   sudo: false
-   dist: trusty
-
-   cache:
-     apt: true
-     directories:
-       - $HOME/.cache
-
-   addons:
-     apt:
-       sources:
-         - ubuntu-toolchain-r-test
-       packages:
-         - g++-4.9
-         - environment-modules
-
-   env:
-     global:
-       - SPACK_ROOT: $HOME/.cache/spack
-       - PATH: $PATH:$HOME/.cache/spack/bin
-
-   before_install:
-     - export CXX=g++-4.9
-     - export CC=gcc-4.9
-     - export FC=gfortran-4.9
-     - export CXXFLAGS="-std=c++11"
-
-   install:
-     - if ! which spack >/dev/null; then
-         mkdir -p $SPACK_ROOT &&
-         git clone --depth 50 https://github.com/spack/spack.git $SPACK_ROOT &&
-         echo -e "config:""\n  build_jobs:"" 2" > $SPACK_ROOT/etc/spack/config.yaml;
-       fi
-     - travis_wait spack install cmake@3.7.2~openssl~ncurses
-     - travis_wait spack install boost@1.62.0~graph~iostream~locale~log~wave
-     - spack clean -a
-     - source /etc/profile &&
-       source $SPACK_ROOT/share/spack/setup-env.sh
-     - spack load cmake
-     - spack load boost
-
-   script:
-     - mkdir -p $HOME/build
-     - cd $HOME/build
-     - cmake $TRAVIS_BUILD_DIR
-     - make -j 2
-     - make test
-
-.. _workflow_create_docker_image:
-
------------------------------------
-Using Spack to Create Docker Images
------------------------------------
-
-Spack can be the ideal tool to set up images for Docker (and Singularity).
-
-An example ``Dockerfile`` is given below, downloading the latest spack
-version.
-
-The following functionality is prepared:
-
-#. Base image: the example starts from a minimal ubuntu.
-
-#. Installing as root: docker images are usually set up as root.
-   Since some autotools scripts might complain about this being unsafe, we set
-   ``FORCE_UNSAFE_CONFIGURE=1`` to avoid configure errors.
-
-#. Pre-install the spack dependencies, including modules from the packages.
-   This avoids needing to build those from scratch via ``spack bootstrap``.
-   Package installs are followed by a clean-up of the system package index,
-   to avoid outdated information and it saves space.
-
-#. Install spack in ``/usr/local``.
-   Add ``setup-env.sh`` to profile scripts, so commands in *login* shells
-   can use the whole spack functionality, including modules.
-
-#. Install an example package (``tar``).
-   As with system package managers above, ``spack install`` commands should be
-   concatenated with a ``&& spack clean -a`` in order to keep image sizes small.
-
-#. Add a startup hook to an *interactive login shell* so spack modules will be
-   usable.
-
-In order to build and run the image, execute:
-
-.. code-block:: bash
-
-   docker build -t spack .
-   docker run -it spack
-
-.. code-block:: docker
-
-   FROM       ubuntu:16.04
-   MAINTAINER Your Name <someone@example.com>
-
-   # general environment for docker
-   ENV        DEBIAN_FRONTEND=noninteractive \
-              SPACK_ROOT=/usr/local \
-              FORCE_UNSAFE_CONFIGURE=1
-
-   # install minimal spack depedencies
-   RUN        apt-get update \
-              && apt-get install -y --no-install-recommends \
-                 autoconf \
-                 build-essential \
-                 ca-certificates \
-                 coreutils \
-                 curl \
-                 environment-modules \
-                 git \
-                 python \
-                 unzip \
-                 vim \
-              && rm -rf /var/lib/apt/lists/*
-
-   # load spack environment on login
-   RUN        echo "source $SPACK_ROOT/share/spack/setup-env.sh" \
-              > /etc/profile.d/spack.sh
-
-   # spack settings
-   # note: if you wish to change default settings, add files alongside
-   #       the Dockerfile with your desired settings. Then uncomment this line
-   #COPY       packages.yaml modules.yaml $SPACK_ROOT/etc/spack/
-
-   # install spack
-   RUN        curl -s -L https://api.github.com/repos/spack/spack/tarball \
-              | tar xzC $SPACK_ROOT --strip 1
-   # note: at this point one could also run ``spack bootstrap`` to avoid
-   #       parts of the long apt-get install list above
-
-   # install software
-   RUN        spack install tar \
-              && spack clean -a
-
-   # need the modules already during image build?
-   #RUN        /bin/bash -l -c ' \
-   #                spack load tar \
-   #                && which tar'
-
-   # image run hook: the -l will make sure /etc/profile environments are loaded
-   CMD        /bin/bash -l
-
-^^^^^^^^^^^^^^
-Best Practices
-^^^^^^^^^^^^^^
-
-"""
-MPI
-"""
-Due to the dependency on Fortran for OpenMPI, which is the spack default
-implementation, consider adding ``gfortran`` to the ``apt-get install`` list.
-
-Recent versions of OpenMPI will require you to pass ``--allow-run-as-root``
-to your ``mpirun`` calls if started as root user inside Docker.
-
-For execution on HPC clusters, it can be helpful to import the docker
-image into Singularity in order to start a program with an *external*
-MPI. Otherwise, also add ``openssh-server`` to the ``apt-get install`` list.
-
-""""
-CUDA
-""""
-Starting from CUDA 9.0, Nvidia provides minimal CUDA images based on
-Ubuntu.
-Please see `their instructions <https://hub.docker.com/r/nvidia/cuda/>`_.
-Avoid double-installing CUDA by adding, e.g.
-
-.. code-block:: yaml
-
-   packages:
-     cuda:
-       paths:
-         cuda@9.0.176%gcc@5.4.0 arch=linux-ubuntu16-x86_64: /usr/local/cuda
-       buildable: False
-
-to your ``packages.yaml``.
-Then ``COPY`` in that file into the image as in the example above.
-
-Users will either need ``nvidia-docker`` or e.g. Singularity to *execute*
-device kernels.
-
-"""""""""""
-Singularity
-"""""""""""
-Importing and running the image created above into
-`Singularity <http://singularity.lbl.gov/>`_ works like a charm.
-Just use the `docker bootstraping mechanism <http://singularity.lbl.gov/quickstart#bootstrap-recipes>`_:
-
-.. code-block:: none
-
-   Bootstrap: docker
-   From: registry/user/image:tag
-
-   %runscript
-   exec /bin/bash -l
-
 ------------------
 Upstream Bug Fixes
 ------------------
@@ -1270,7 +1055,7 @@ Buggy New Version
 
 Sometimes, the old version of a package works fine, but a new version
 is buggy.  For example, it was once found that `Adios did not build
-with hdf5@1.10 <https://github.com/spack/spack/issues/1683>`_.  If the
+with hdf5@1.10 <https://github.com/LLNL/spack/issues/1683>`_.  If the
 old version of ``hdf5`` will work with ``adios``, the suggested
 procedure is:
 
@@ -1280,7 +1065,7 @@ procedure is:
    .. code-block:: python
 
       # Adios does not build with HDF5 1.10
-      # See: https://github.com/spack/spack/issues/1683
+      # See: https://github.com/LLNL/spack/issues/1683
       depends_on('hdf5@:1.9')
 
 #. Determine whether the problem is with ``hdf5`` or ``adios``, and
@@ -1293,7 +1078,7 @@ procedure is:
    .. code-block:: python
 
       # Adios up to v1.10.0 does not build with HDF5 1.10
-      # See: https://github.com/spack/spack/issues/1683
+      # See: https://github.com/LLNL/spack/issues/1683
       depends_on('hdf5@:1.9', when='@:1.10.0')
       depends_on('hdf5', when='@1.10.1:')
 

lib/spack/env/cc

@@ -1,14 +1,14 @@
 #!/bin/bash
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -45,7 +45,6 @@ parameters=(
     SPACK_PREFIX
     SPACK_ENV_PATH
     SPACK_DEBUG_LOG_DIR
-    SPACK_DEBUG_LOG_ID
     SPACK_COMPILER_SPEC
     SPACK_CC_RPATH_ARG
     SPACK_CXX_RPATH_ARG
@@ -59,7 +58,7 @@ parameters=(
 # The default compiler flags are passed from these variables:
 #   SPACK_CFLAGS, SPACK_CXXFLAGS, SPACK_FCFLAGS, SPACK_FFLAGS,
 #   SPACK_LDFLAGS, SPACK_LDLIBS
-# Debug env var is optional; set to "TRUE" for debug logging:
+# Debug env var is optional; set to true for debug logging:
 #   SPACK_DEBUG
 # Test command is used to unit test the compiler script.
 #   SPACK_TEST_COMMAND
@@ -99,25 +98,25 @@ case "$command" in
     cpp)
         mode=cpp
         ;;
-    cc|c89|c99|gcc|clang|icc|pgcc|xlc|xlc_r)
+    cc|c89|c99|gcc|clang|icc|pgcc|xlc)
         command="$SPACK_CC"
         language="C"
         comp="CC"
         lang_flags=C
         ;;
-    c++|CC|g++|clang++|icpc|pgc++|xlc++|xlc++_r)
+    c++|CC|g++|clang++|icpc|pgc++|xlc++)
         command="$SPACK_CXX"
         language="C++"
         comp="CXX"
         lang_flags=CXX
         ;;
-    ftn|f90|fc|f95|gfortran|flang|ifort|pgfortran|xlf90|xlf90_r|nagfor)
+    ftn|f90|fc|f95|gfortran|ifort|pgfortran|xlf90|nagfor)
         command="$SPACK_FC"
         language="Fortran 90"
         comp="FC"
         lang_flags=F
         ;;
-    f77|gfortran|flang|ifort|pgfortran|xlf|xlf_r|nagfor|ftn)
+    f77|gfortran|ifort|pgfortran|xlf|nagfor|ftn)
         command="$SPACK_F77"
         language="Fortran 77"
         comp="F77"
@@ -134,7 +133,7 @@ esac
 # If any of the arguments below are present, then the mode is vcheck.
 # In vcheck mode, nothing is added in terms of extra search paths or
 # libraries.
-if [[ -z $mode ]] || [[ $mode == ld ]]; then
+if [[ -z $mode ]]; then
     for arg in "$@"; do
         if [[ $arg == -v || $arg == -V || $arg == --version || $arg == -dumpversion ]]; then
             mode=vcheck
@@ -219,7 +218,7 @@ fi
 add_rpaths=true
 if [[ ($mode == ld || $mode == ccld) && "$SPACK_SHORT_SPEC" =~ "darwin" ]]; then
     for arg in "$@"; do
-        if [[ ($arg == -r && $mode == ld) || ($arg == -r && $mode == ccld) || ($arg == -Wl,-r && $mode == ccld) ]]; then
+        if [[ ($arg == -r && $mode == ld) || ($arg == -Wl,-r && $mode == ccld) ]]; then
             add_rpaths=false
             break
         fi
@@ -329,10 +328,8 @@ IFS=':' read -ra extra_rpaths <<< "$SPACK_COMPILER_EXTRA_RPATHS"
 for extra_rpath in "${extra_rpaths[@]}"; do
     if [[ $mode == ccld ]]; then
         $add_rpaths && args=("$rpath$extra_rpath" "${args[@]}")
-        args=("-L$extra_rpath" "${args[@]}")
     elif [[ $mode == ld ]]; then
         $add_rpaths && args=("-rpath" "$extra_rpath" "${args[@]}")
-        args=("-L$extra_rpath" "${args[@]}")
     fi
 done
 
@@ -356,8 +353,8 @@ fi
 # Write the input and output commands to debug logs if it's asked for.
 #
 if [[ $SPACK_DEBUG == TRUE ]]; then
-    input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_DEBUG_LOG_ID.in.log"
-    output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_DEBUG_LOG_ID.out.log"
+    input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
+    output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
     echo "[$mode] $command $input_command" >> "$input_log"
     echo "[$mode] ${full_command[@]}" >> "$output_log"
 fi

lib/spack/env/clang/flang

@@ -1 +0,0 @@
-../cc

lib/spack/env/xl_r/xlc++_r

@@ -1 +0,0 @@
-../cc

lib/spack/env/xl_r/xlc_r

@@ -1 +0,0 @@
-../cc

lib/spack/env/xl_r/xlf90_r

@@ -1 +0,0 @@
-../cc

lib/spack/env/xl_r/xlf_r

@@ -1 +0,0 @@
-../cc

lib/spack/external/__init__.py

@@ -1,13 +1,13 @@
 ##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
 # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License (as
@@ -22,113 +22,28 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-"""This module contains the following external, potentially separately
-licensed, packages that are included in Spack:
-
-argparse
---------
-
-* Homepage: https://pypi.python.org/pypi/argparse
-* Usage: We include our own version to be Python 2.6 compatible.
-* Version: 1.4.0
-* Note: This package has been slightly modified to improve
-  error message formatting. See the following commit if the
-  vendored copy ever needs to be updated again:
-  https://github.com/spack/spack/pull/6786/commits/dfcef577b77249106ea4e4c69a6cd9e64fa6c418
-
-ctest_log_parser
-----------------
-
-* Homepage: https://github.com/Kitware/CMake/blob/master/Source/CTest/cmCTestBuildHandler.cxx
-* Usage: Functions to parse build logs and extract error messages.
-* Version: Unversioned
-* Note: This is a homemade port of Kitware's CTest build handler.
-
-distro
-------
-
-* Homepage: https://pypi.python.org/pypi/distro
-* Usage: Provides a more stable linux distribution detection.
-* Version: 1.0.4 (last version supporting Python 2.6)
-
-functools
----------
-
-* Homepage: https://github.com/python/cpython/blob/2.7/Lib/functools.py
-* Usage: Used for implementation of total_ordering.
-* Version: Unversioned
-* Note: This is the functools.total_ordering implementation
-  from Python 2.7 backported so we can run on Python 2.6.
-
-jinja2
-------
-
-* Homepage: https://pypi.python.org/pypi/Jinja2
-* Usage: A modern and designer-friendly templating language for Python.
-* Version: 2.10
-
-jsonschema
-----------
-
-* Homepage: https://pypi.python.org/pypi/jsonschema
-* Usage: An implementation of JSON Schema for Python.
-* Version: 2.4.0 (last version before functools32 dependency was added)
-* Note: functools32 doesn't support Python 2.6 or 3.0, so jsonschema
-  cannot be upgraded any further
-
-markupsafe
-----------
-
-* Homepage: https://pypi.python.org/pypi/MarkupSafe
-* Usage: Implements a XML/HTML/XHTML Markup safe string for Python.
-* Version: 1.0
-
-orderddict
-----------
-
-* Homepage: https://pypi.org/project/ordereddict/
-* Usage: A drop-in substitute for Py2.7's new collections.OrderedDict
-  that works in Python 2.4-2.6.
-* Version: 1.1
-
-py
---
-
-* Homepage: https://pypi.python.org/pypi/py
-* Usage: Needed by pytest. Library with cross-python path,
-  ini-parsing, io, code, and log facilities.
-* Version: 1.4.34 (last version supporting Python 2.6)
-
-pyqver
-------
-
-* Homepage: https://github.com/ghewgill/pyqver
-* Usage: External script to query required python version of
-  python source code. Used for ensuring 2.6 compatibility.
-* Version: Unversioned
-
-pytest
-------
-
-* Homepage: https://pypi.python.org/pypi/pytest
-* Usage: Testing framework used by Spack.
-* Version: 3.2.5 (last version supporting Python 2.6)
-* Note: This package has been slightly modified to improve
-  Python 2.6 compatibility. See the following commit if the
-  vendored copy ever needs to be updated again:
-  https://github.com/spack/spack/pull/6801/commits/ff513c39f2c67ff615de5cbc581dd69a8ec96526
-
-pyyaml
-------
-
-* Homepage: https://pypi.python.org/pypi/PyYAML
-* Usage: Used for config files.
-* Version: 3.12
-
-six
----
-
-* Homepage: https://pypi.python.org/pypi/six
-* Usage: Python 2 and 3 compatibility utilities.
-* Version: 1.11.0
+"""
+This module contains external, potentially separately licensed,
+packages that are included in spack.
+
+So far:
+    argparse:    We include our own version to be Python 2.6 compatible.
+
+    distro:      Provides a more stable linux distribution detection.
+
+    functools:   Used for implementation of total_ordering.
+
+    jsonschema:  An implementation of JSON Schema for Python.
+
+    ordereddict: We include our own version to be Python 2.6 compatible.
+
+    py:          Needed by pytest.  Library with cross-python path,
+                 ini-parsing, io, code, and log facilities.
+
+    pyqver2:     External script to query required python version of
+                 python source code. Used for ensuring 2.6 compatibility.
+
+    pytest:      Testing framework used by Spack.
+
+    yaml:        Used for config files.
 """

lib/spack/external/_pytest/AUTHORS

@@ -0,0 +1,141 @@
+Holger Krekel, holger at merlinux eu
+merlinux GmbH, Germany, office at merlinux eu
+
+Contributors include::
+
+Abdeali JK
+Abhijeet Kasurde
+Ahn Ki-Wook
+Alexei Kozlenok
+Anatoly Bubenkoff
+Andreas Zeidler
+Andrzej Ostrowski
+Andy Freeland
+Anthon van der Neut
+Antony Lee
+Armin Rigo
+Aron Curzon
+Aviv Palivoda
+Ben Webb
+Benjamin Peterson
+Bernard Pratz
+Bob Ippolito
+Brian Dorsey
+Brian Okken
+Brianna Laugher
+Bruno Oliveira
+Cal Leeming
+Carl Friedrich Bolz
+Charles Cloud
+Charnjit SiNGH (CCSJ)
+Chris Lamb
+Christian Boelsen
+Christian Theunert
+Christian Tismer
+Christopher Gilling
+Daniel Grana
+Daniel Hahler
+Daniel Nuri
+Daniel Wandschneider
+Danielle Jenkins
+Dave Hunt
+David Díaz-Barquero
+David Mohr
+David Vierra
+Diego Russo
+Dmitry Dygalo
+Duncan Betts
+Edison Gustavo Muenz
+Edoardo Batini
+Eduardo Schettino
+Elizaveta Shashkova
+Endre Galaczi
+Eric Hunsberger
+Eric Siegerman
+Erik M. Bray
+Feng Ma
+Florian Bruhin
+Floris Bruynooghe
+Gabriel Reis
+Georgy Dyuldin
+Graham Horler
+Greg Price
+Grig Gheorghiu
+Grigorii Eremeev (budulianin)
+Guido Wesdorp
+Harald Armin Massa
+Ian Bicking
+Jaap Broekhuizen
+Jan Balster
+Janne Vanhala
+Jason R. Coombs
+Javier Domingo Cansino
+Javier Romero
+John Towler
+Jon Sonesen
+Jordan Guymon
+Joshua Bronson
+Jurko Gospodnetić
+Justyna Janczyszyn
+Kale Kundert
+Katarzyna Jachim
+Kevin Cox
+Lee Kamentsky
+Lev Maximov
+Lukas Bednar
+Luke Murphy
+Maciek Fijalkowski
+Maho
+Marc Schlaich
+Marcin Bachry
+Mark Abramowitz
+Markus Unterwaditzer
+Martijn Faassen
+Martin K. Scherer
+Martin Prusse
+Mathieu Clabaut
+Matt Bachmann
+Matt Williams
+Matthias Hafner
+mbyt
+Michael Aquilina
+Michael Birtwell
+Michael Droettboom
+Michael Seifert
+Mike Lundy
+Ned Batchelder
+Neven Mundar
+Nicolas Delaby
+Oleg Pidsadnyi
+Oliver Bestwalter
+Omar Kohl
+Pieter Mulder
+Piotr Banaszkiewicz
+Punyashloka Biswal
+Quentin Pradet
+Ralf Schmitt
+Raphael Pierzina
+Raquel Alegre
+Roberto Polli
+Romain Dorgueil
+Roman Bolshakov
+Ronny Pfannschmidt
+Ross Lawley
+Russel Winder
+Ryan Wooden
+Samuele Pedroni
+Simon Gomizelj
+Stefan Farmbauer
+Stefan Zimmermann
+Stefano Taschini
+Steffen Allner
+Stephan Obermann
+Tareq Alayan
+Ted Xiao
+Thomas Grainger
+Tom Viner
+Trevor Bekolay
+Tyler Goodlet
+Vasily Kuznetsov
+Wouter van Ackooy
+Xuecong Liao

lib/spack/external/_pytest/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2004-2016 Holger Krekel and others
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lib/spack/external/_pytest/README.rst

@@ -0,0 +1,102 @@
+.. image:: http://docs.pytest.org/en/latest/_static/pytest1.png
+   :target: http://docs.pytest.org
+   :align: center
+   :alt: pytest
+
+------
+
+.. image:: https://img.shields.io/pypi/v/pytest.svg
+   :target: https://pypi.python.org/pypi/pytest
+.. image:: https://img.shields.io/pypi/pyversions/pytest.svg
+  :target: https://pypi.python.org/pypi/pytest
+.. image:: https://img.shields.io/coveralls/pytest-dev/pytest/master.svg
+   :target: https://coveralls.io/r/pytest-dev/pytest
+.. image:: https://travis-ci.org/pytest-dev/pytest.svg?branch=master
+    :target: https://travis-ci.org/pytest-dev/pytest
+.. image:: https://ci.appveyor.com/api/projects/status/mrgbjaua7t33pg6b?svg=true
+    :target: https://ci.appveyor.com/project/pytestbot/pytest
+
+The ``pytest`` framework makes it easy to write small tests, yet
+scales to support complex functional testing for applications and libraries.
+
+An example of a simple test:
+
+.. code-block:: python
+
+    # content of test_sample.py
+    def inc(x):
+        return x + 1
+
+    def test_answer():
+        assert inc(3) == 5
+
+
+To execute it::
+
+    $ pytest
+    ============================= test session starts =============================    
+    collected 1 items
+
+    test_sample.py F
+
+    ================================== FAILURES ===================================
+    _________________________________ test_answer _________________________________
+
+        def test_answer():
+    >       assert inc(3) == 5
+    E       assert 4 == 5
+    E        +  where 4 = inc(3)
+
+    test_sample.py:5: AssertionError
+    ========================== 1 failed in 0.04 seconds ===========================
+
+
+Due to ``pytest``'s detailed assertion introspection, only plain ``assert`` statements are used. See `getting-started <http://docs.pytest.org/en/latest/getting-started.html#our-first-test-run>`_ for more examples.
+
+
+Features
+--------
+
+- Detailed info on failing `assert statements <http://docs.pytest.org/en/latest/assert.html>`_ (no need to remember ``self.assert*`` names);
+
+- `Auto-discovery
+  <http://docs.pytest.org/en/latest/goodpractices.html#python-test-discovery>`_
+  of test modules and functions;
+
+- `Modular fixtures <http://docs.pytest.org/en/latest/fixture.html>`_ for
+  managing small or parametrized long-lived test resources;
+
+- Can run `unittest <http://docs.pytest.org/en/latest/unittest.html>`_ (or trial),
+  `nose <http://docs.pytest.org/en/latest/nose.html>`_ test suites out of the box;
+
+- Python2.6+, Python3.3+, PyPy-2.3, Jython-2.5 (untested);
+
+- Rich plugin architecture, with over 150+ `external plugins <http://docs.pytest.org/en/latest/plugins.html#installing-external-plugins-searching>`_ and thriving community;
+
+
+Documentation
+-------------
+
+For full documentation, including installation, tutorials and PDF documents, please see http://docs.pytest.org.
+
+
+Bugs/Requests
+-------------
+
+Please use the `GitHub issue tracker <https://github.com/pytest-dev/pytest/issues>`_ to submit bugs or request features.
+
+
+Changelog
+---------
+
+Consult the `Changelog <http://docs.pytest.org/en/latest/changelog.html>`__ page for fixes and enhancements of each version.
+
+
+License
+-------
+
+Copyright Holger Krekel and others, 2004-2016.
+
+Distributed under the terms of the `MIT`_ license, pytest is free and open source software.
+
+.. _`MIT`: https://github.com/pytest-dev/pytest/blob/master/LICENSE

lib/spack/external/_pytest/__init__.py

@@ -1,8 +1,2 @@
-__all__ = ['__version__']
-
-try:
-    from ._version import version as __version__
-except ImportError:
-    # broken installation, we don't even try
-    # unknown only works because we do poor mans version compare
-    __version__ = 'unknown'
+#
+__version__ = '3.0.5'

lib/spack/external/_pytest/_argcomplete.py

@@ -57,29 +57,26 @@
   which should throw a KeyError: 'COMPLINE' (which is properly set by the
   global argcomplete script).
 """
-from __future__ import absolute_import, division, print_function
+
 import sys
 import os
 from glob import glob
 
-
 class FastFilesCompleter:
     'Fast file completer class'
-
     def __init__(self, directories=True):
         self.directories = directories
 
     def __call__(self, prefix, **kwargs):
         """only called on non option completions"""
-        if os.path.sep in prefix[1:]:
+        if os.path.sep in prefix[1:]: #
             prefix_dir = len(os.path.dirname(prefix) + os.path.sep)
         else:
             prefix_dir = 0
         completion = []
         globbed = []
         if '*' not in prefix and '?' not in prefix:
-            # we are on unix, otherwise no bash
-            if not prefix or prefix[-1] == os.path.sep:
+            if prefix[-1] == os.path.sep:  # we are on unix, otherwise no bash
                 globbed.extend(glob(prefix + '.*'))
             prefix += '*'
         globbed.extend(glob(prefix))
@@ -99,8 +96,7 @@ def __call__(self, prefix, **kwargs):
     filescompleter = FastFilesCompleter()
 
     def try_argcomplete(parser):
-        argcomplete.autocomplete(parser, always_complete_options=False)
+        argcomplete.autocomplete(parser)
 else:
-    def try_argcomplete(parser):
-        pass
+    def try_argcomplete(parser): pass
     filescompleter = None

lib/spack/external/_pytest/_code/__init__.py

@@ -1,5 +1,4 @@
 """ python inspection/code generation API """
-from __future__ import absolute_import, division, print_function
 from .code import Code  # noqa
 from .code import ExceptionInfo  # noqa
 from .code import Frame  # noqa

lib/spack/external/_pytest/_code/_py2traceback.py

@@ -2,10 +2,8 @@
 # CHANGES:
 # - some_str is replaced, trying to create unicode strings
 #
-from __future__ import absolute_import, division, print_function
 import types
 
-
 def format_exception_only(etype, value):
     """Format the exception part of a traceback.
 
@@ -31,7 +29,7 @@ def format_exception_only(etype, value):
     # would throw another exception and mask the original problem.
     if (isinstance(etype, BaseException) or
         isinstance(etype, types.InstanceType) or
-            etype is None or type(etype) is str):
+        etype is None or type(etype) is str):
         return [_format_final_exc_line(etype, value)]
 
     stype = etype.__name__
@@ -63,7 +61,6 @@ def format_exception_only(etype, value):
     lines.append(_format_final_exc_line(stype, value))
     return lines
 
-
 def _format_final_exc_line(etype, value):
     """Return a list of a single line -- normal case for format_exception_only"""
     valuestr = _some_str(value)
@@ -73,7 +70,6 @@ def _format_final_exc_line(etype, value):
         line = "%s: %s\n" % (etype, valuestr)
     return line
 
-
 def _some_str(value):
     try:
         return unicode(value)

lib/spack/external/_pytest/_code/code.py

@@ -1,16 +1,14 @@
-from __future__ import absolute_import, division, print_function
 import sys
 from inspect import CO_VARARGS, CO_VARKEYWORDS
 import re
 from weakref import ref
-from _pytest.compat import _PY2, _PY3, PY35, safe_str
 
 import py
 builtin_repr = repr
 
 reprlib = py.builtin._tryimport('repr', 'reprlib')
 
-if _PY3:
+if sys.version_info[0] >= 3:
     from traceback import format_exception_only
 else:
     from ._py2traceback import format_exception_only
@@ -18,7 +16,6 @@
 
 class Code(object):
     """ wrapper around Python code objects """
-
     def __init__(self, rawcode):
         if not hasattr(rawcode, "co_filename"):
             rawcode = getrawcode(rawcode)
@@ -27,7 +24,7 @@ def __init__(self, rawcode):
             self.firstlineno = rawcode.co_firstlineno - 1
             self.name = rawcode.co_name
         except AttributeError:
-            raise TypeError("not a code object: %r" % (rawcode,))
+            raise TypeError("not a code object: %r" %(rawcode,))
         self.raw = rawcode
 
     def __eq__(self, other):
@@ -83,7 +80,6 @@ def getargs(self, var=False):
             argcount += raw.co_flags & CO_VARKEYWORDS
         return raw.co_varnames[:argcount]
 
-
 class Frame(object):
     """Wrapper around a Python frame holding f_locals and f_globals
     in which expressions can be evaluated."""
@@ -121,7 +117,7 @@ def exec_(self, code, **vars):
         """
         f_locals = self.f_locals.copy()
         f_locals.update(vars)
-        py.builtin.exec_(code, self.f_globals, f_locals)
+        py.builtin.exec_(code, self.f_globals, f_locals )
 
     def repr(self, object):
         """ return a 'safe' (non-recursive, one-line) string repr for 'object'
@@ -145,7 +141,6 @@ def getargs(self, var=False):
                 pass     # this can occur when using Psyco
         return retval
 
-
 class TracebackEntry(object):
     """ a single entry in a traceback """
 
@@ -171,7 +166,7 @@ def relline(self):
         return self.lineno - self.frame.code.firstlineno
 
     def __repr__(self):
-        return "<TracebackEntry %s:%d>" % (self.frame.code.path, self.lineno + 1)
+        return "<TracebackEntry %s:%d>" %(self.frame.code.path, self.lineno+1)
 
     @property
     def statement(self):
@@ -250,21 +245,19 @@ def __str__(self):
             line = str(self.statement).lstrip()
         except KeyboardInterrupt:
             raise
-        except:  # noqa
+        except:
             line = "???"
-        return "  File %r:%d in %s\n  %s\n" % (fn, self.lineno + 1, name, line)
+        return "  File %r:%d in %s\n  %s\n" %(fn, self.lineno+1, name, line)
 
     def name(self):
         return self.frame.code.raw.co_name
     name = property(name, None, None, "co_name of underlaying code")
 
-
 class Traceback(list):
     """ Traceback objects encapsulate and offer higher level
         access to Traceback entries.
     """
     Entry = TracebackEntry
-
     def __init__(self, tb, excinfo=None):
         """ initialize from given python traceback object and ExceptionInfo """
         self._excinfo = excinfo
@@ -294,7 +287,7 @@ def cut(self, path=None, lineno=None, firstlineno=None, excludepath=None):
                 (excludepath is None or not hasattr(codepath, 'relto') or
                  not codepath.relto(excludepath)) and
                 (lineno is None or x.lineno == lineno) and
-                    (firstlineno is None or x.frame.code.firstlineno == firstlineno)):
+                (firstlineno is None or x.frame.code.firstlineno == firstlineno)):
                 return Traceback(x._rawentry, self._excinfo)
         return self
 
@@ -320,7 +313,7 @@ def getcrashentry(self):
         """ return last non-hidden traceback entry that lead
         to the exception of a traceback.
         """
-        for i in range(-1, -len(self) - 1, -1):
+        for i in range(-1, -len(self)-1, -1):
             entry = self[i]
             if not entry.ishidden():
                 return entry
@@ -335,33 +328,30 @@ def recursionindex(self):
             # id for the code.raw is needed to work around
             # the strange metaprogramming in the decorator lib from pypi
             # which generates code objects that have hash/value equality
-            # XXX needs a test
+            #XXX needs a test
             key = entry.frame.code.path, id(entry.frame.code.raw), entry.lineno
-            # print "checking for recursion at", key
-            values = cache.setdefault(key, [])
-            if values:
+            #print "checking for recursion at", key
+            l = cache.setdefault(key, [])
+            if l:
                 f = entry.frame
                 loc = f.f_locals
-                for otherloc in values:
+                for otherloc in l:
                     if f.is_true(f.eval(co_equal,
-                                        __recursioncache_locals_1=loc,
-                                        __recursioncache_locals_2=otherloc)):
+                        __recursioncache_locals_1=loc,
+                        __recursioncache_locals_2=otherloc)):
                         return i
-            values.append(entry.frame.f_locals)
+            l.append(entry.frame.f_locals)
         return None
 
 
 co_equal = compile('__recursioncache_locals_1 == __recursioncache_locals_2',
                    '?', 'eval')
 
-
 class ExceptionInfo(object):
     """ wraps sys.exc_info() objects and offers
         help for navigating the traceback.
     """
     _striptext = ''
-    _assert_start_repr = "AssertionError(u\'assert " if _PY2 else "AssertionError(\'assert "
-
     def __init__(self, tup=None, exprinfo=None):
         import _pytest._code
         if tup is None:
@@ -369,8 +359,8 @@ def __init__(self, tup=None, exprinfo=None):
             if exprinfo is None and isinstance(tup[1], AssertionError):
                 exprinfo = getattr(tup[1], 'msg', None)
                 if exprinfo is None:
-                    exprinfo = py.io.saferepr(tup[1])
-                if exprinfo and exprinfo.startswith(self._assert_start_repr):
+                    exprinfo = py._builtin._totext(tup[1])
+                if exprinfo and exprinfo.startswith('assert '):
                     self._striptext = 'AssertionError: '
         self._excinfo = tup
         #: the exception class
@@ -411,10 +401,10 @@ def _getreprcrash(self):
         exconly = self.exconly(tryshort=True)
         entry = self.traceback.getcrashentry()
         path, lineno = entry.frame.code.raw.co_filename, entry.lineno
-        return ReprFileLocation(path, lineno + 1, exconly)
+        return ReprFileLocation(path, lineno+1, exconly)
 
     def getrepr(self, showlocals=False, style="long",
-                abspath=False, tbfilter=True, funcargs=False):
+            abspath=False, tbfilter=True, funcargs=False):
         """ return str()able representation of this exception info.
             showlocals: show locals per traceback entry
             style: long|short|no|native traceback style
@@ -431,7 +421,7 @@ def getrepr(self, showlocals=False, style="long",
                 )), self._getreprcrash())
 
         fmt = FormattedExcinfo(showlocals=showlocals, style=style,
-                               abspath=abspath, tbfilter=tbfilter, funcargs=funcargs)
+            abspath=abspath, tbfilter=tbfilter, funcargs=funcargs)
         return fmt.repr_excinfo(self)
 
     def __str__(self):
@@ -475,15 +465,15 @@ def __init__(self, showlocals=False, style="long", abspath=True, tbfilter=True,
     def _getindent(self, source):
         # figure out indent for given source
         try:
-            s = str(source.getstatement(len(source) - 1))
+            s = str(source.getstatement(len(source)-1))
         except KeyboardInterrupt:
             raise
-        except:  # noqa
+        except:
             try:
                 s = str(source[-1])
             except KeyboardInterrupt:
                 raise
-            except:  # noqa
+            except:
                 return 0
         return 4 + (len(s) - len(s.lstrip()))
 
@@ -519,7 +509,7 @@ def get_source(self, source, line_index=-1, excinfo=None, short=False):
             for line in source.lines[:line_index]:
                 lines.append(space_prefix + line)
             lines.append(self.flow_marker + "   " + source.lines[line_index])
-            for line in source.lines[line_index + 1:]:
+            for line in source.lines[line_index+1:]:
                 lines.append(space_prefix + line)
         if excinfo is not None:
             indent = 4 if short else self._getindent(source)
@@ -552,10 +542,10 @@ def repr_locals(self, locals):
                     # _repr() function, which is only reprlib.Repr in
                     # disguise, so is very configurable.
                     str_repr = self._saferepr(value)
-                    # if len(str_repr) < 70 or not isinstance(value,
+                    #if len(str_repr) < 70 or not isinstance(value,
                     #                            (list, tuple, dict)):
-                    lines.append("%-10s = %s" % (name, str_repr))
-                    # else:
+                    lines.append("%-10s = %s" %(name, str_repr))
+                    #else:
                     #    self._line("%-10s =\\" % (name,))
                     #    # XXX
                     #    py.std.pprint.pprint(value, stream=self.excinfowriter)
@@ -581,14 +571,14 @@ def repr_traceback_entry(self, entry, excinfo=None):
             s = self.get_source(source, line_index, excinfo, short=short)
             lines.extend(s)
             if short:
-                message = "in %s" % (entry.name)
+                message = "in %s" %(entry.name)
             else:
                 message = excinfo and excinfo.typename or ""
             path = self._makepath(entry.path)
-            filelocrepr = ReprFileLocation(path, entry.lineno + 1, message)
+            filelocrepr = ReprFileLocation(path, entry.lineno+1, message)
             localsrepr = None
             if not short:
-                localsrepr = self.repr_locals(entry.locals)
+                localsrepr =  self.repr_locals(entry.locals)
             return ReprEntry(lines, reprargs, localsrepr, filelocrepr, style)
         if excinfo:
             lines.extend(self.get_exconly(excinfo, indent=4))
@@ -608,54 +598,24 @@ def repr_traceback(self, excinfo):
         traceback = excinfo.traceback
         if self.tbfilter:
             traceback = traceback.filter()
-
+        recursionindex = None
         if is_recursion_error(excinfo):
-            traceback, extraline = self._truncate_recursive_traceback(traceback)
-        else:
-            extraline = None
-
+            recursionindex = traceback.recursionindex()
         last = traceback[-1]
         entries = []
+        extraline = None
         for index, entry in enumerate(traceback):
             einfo = (last == entry) and excinfo or None
             reprentry = self.repr_traceback_entry(entry, einfo)
             entries.append(reprentry)
+            if index == recursionindex:
+                extraline = "!!! Recursion detected (same locals & position)"
+                break
         return ReprTraceback(entries, extraline, style=self.style)
 
-    def _truncate_recursive_traceback(self, traceback):
-        """
-        Truncate the given recursive traceback trying to find the starting point
-        of the recursion.
-
-        The detection is done by going through each traceback entry and finding the
-        point in which the locals of the frame are equal to the locals of a previous frame (see ``recursionindex()``.
-
-        Handle the situation where the recursion process might raise an exception (for example
-        comparing numpy arrays using equality raises a TypeError), in which case we do our best to
-        warn the user of the error and show a limited traceback.
-        """
-        try:
-            recursionindex = traceback.recursionindex()
-        except Exception as e:
-            max_frames = 10
-            extraline = (
-                '!!! Recursion error detected, but an error occurred locating the origin of recursion.\n'
-                '  The following exception happened when comparing locals in the stack frame:\n'
-                '    {exc_type}: {exc_msg}\n'
-                '  Displaying first and last {max_frames} stack frames out of {total}.'
-            ).format(exc_type=type(e).__name__, exc_msg=safe_str(e), max_frames=max_frames, total=len(traceback))
-            traceback = traceback[:max_frames] + traceback[-max_frames:]
-        else:
-            if recursionindex is not None:
-                extraline = "!!! Recursion detected (same locals & position)"
-                traceback = traceback[:recursionindex + 1]
-            else:
-                extraline = None
-
-        return traceback, extraline
 
     def repr_excinfo(self, excinfo):
-        if _PY2:
+        if sys.version_info[0] < 3:
             reprtraceback = self.repr_traceback(excinfo)
             reprcrash = excinfo._getreprcrash()
 
@@ -679,7 +639,7 @@ def repr_excinfo(self, excinfo):
                     e = e.__cause__
                     excinfo = ExceptionInfo((type(e), e, e.__traceback__)) if e.__traceback__ else None
                     descr = 'The above exception was the direct cause of the following exception:'
-                elif (e.__context__ is not None and not e.__suppress_context__):
+                elif e.__context__ is not None:
                     e = e.__context__
                     excinfo = ExceptionInfo((type(e), e, e.__traceback__)) if e.__traceback__ else None
                     descr = 'During handling of the above exception, another exception occurred:'
@@ -692,7 +652,7 @@ def repr_excinfo(self, excinfo):
 class TerminalRepr(object):
     def __str__(self):
         s = self.__unicode__()
-        if _PY2:
+        if sys.version_info[0] < 3:
             s = s.encode('utf-8')
         return s
 
@@ -705,7 +665,7 @@ def __unicode__(self):
         return io.getvalue().strip()
 
     def __repr__(self):
-        return "<%s instance at %0x>" % (self.__class__, id(self))
+        return "<%s instance at %0x>" %(self.__class__, id(self))
 
 
 class ExceptionRepr(TerminalRepr):
@@ -749,7 +709,6 @@ def toterminal(self, tw):
         self.reprtraceback.toterminal(tw)
         super(ReprExceptionInfo, self).toterminal(tw)
 
-
 class ReprTraceback(TerminalRepr):
     entrysep = "_ "
 
@@ -765,7 +724,7 @@ def toterminal(self, tw):
                 tw.line("")
             entry.toterminal(tw)
             if i < len(self.reprentries) - 1:
-                next_entry = self.reprentries[i + 1]
+                next_entry = self.reprentries[i+1]
                 if entry.style == "long" or \
                    entry.style == "short" and next_entry.style == "long":
                     tw.sep(self.entrysep)
@@ -773,14 +732,12 @@ def toterminal(self, tw):
         if self.extraline:
             tw.line(self.extraline)
 
-
 class ReprTracebackNative(ReprTraceback):
     def __init__(self, tblines):
         self.style = "native"
         self.reprentries = [ReprEntryNative(tblines)]
         self.extraline = None
 
-
 class ReprEntryNative(TerminalRepr):
     style = "native"
 
@@ -790,7 +747,6 @@ def __init__(self, tblines):
     def toterminal(self, tw):
         tw.write("".join(self.lines))
 
-
 class ReprEntry(TerminalRepr):
     localssep = "_ "
 
@@ -807,7 +763,7 @@ def toterminal(self, tw):
             for line in self.lines:
                 red = line.startswith("E   ")
                 tw.line(line, bold=True, red=red)
-            # tw.line("")
+            #tw.line("")
             return
         if self.reprfuncargs:
             self.reprfuncargs.toterminal(tw)
@@ -815,7 +771,7 @@ def toterminal(self, tw):
             red = line.startswith("E   ")
             tw.line(line, bold=True, red=red)
         if self.reprlocals:
-            # tw.sep(self.localssep, "Locals")
+            #tw.sep(self.localssep, "Locals")
             tw.line("")
             self.reprlocals.toterminal(tw)
         if self.reprfileloc:
@@ -828,7 +784,6 @@ def __str__(self):
                                self.reprlocals,
                                self.reprfileloc)
 
-
 class ReprFileLocation(TerminalRepr):
     def __init__(self, path, lineno, message):
         self.path = str(path)
@@ -845,7 +800,6 @@ def toterminal(self, tw):
         tw.write(self.path, bold=True, red=True)
         tw.line(":%s: %s" % (self.lineno, msg))
 
-
 class ReprLocals(TerminalRepr):
     def __init__(self, lines):
         self.lines = lines
@@ -854,7 +808,6 @@ def toterminal(self, tw):
         for line in self.lines:
             tw.line(line)
 
-
 class ReprFuncArgs(TerminalRepr):
     def __init__(self, args):
         self.args = args
@@ -863,11 +816,11 @@ def toterminal(self, tw):
         if self.args:
             linesofar = ""
             for name, value in self.args:
-                ns = "%s = %s" % (safe_str(name), safe_str(value))
+                ns = "%s = %s" %(name, value)
                 if len(ns) + len(linesofar) + 2 > tw.fullwidth:
                     if linesofar:
                         tw.line(linesofar)
-                    linesofar = ns
+                    linesofar =  ns
                 else:
                     if linesofar:
                         linesofar += ", " + ns
@@ -895,7 +848,7 @@ def getrawcode(obj, trycall=True):
         return obj
 
 
-if PY35:  # RecursionError introduced in 3.5
+if sys.version_info[:2] >= (3, 5):  # RecursionError introduced in 3.5
     def is_recursion_error(excinfo):
         return excinfo.errisinstance(RecursionError)  # noqa
 else:

lib/spack/external/_pytest/_code/source.py

@@ -1,9 +1,8 @@
-from __future__ import absolute_import, division, generators, print_function
+from __future__ import generators
 
 from bisect import bisect_right
 import sys
-import inspect
-import tokenize
+import inspect, tokenize
 import py
 cpy_compile = compile
 
@@ -20,7 +19,6 @@ class Source(object):
         possibly deindenting it.
     """
     _compilecounter = 0
-
     def __init__(self, *parts, **kwargs):
         self.lines = lines = []
         de = kwargs.get('deindent', True)
@@ -75,7 +73,7 @@ def strip(self):
         start, end = 0, len(self)
         while start < end and not self.lines[start].strip():
             start += 1
-        while end > start and not self.lines[end - 1].strip():
+        while end > start and not self.lines[end-1].strip():
             end -= 1
         source = Source()
         source.lines[:] = self.lines[start:end]
@@ -88,8 +86,8 @@ def putaround(self, before='', after='', indent=' ' * 4):
         before = Source(before)
         after = Source(after)
         newsource = Source()
-        lines = [(indent + line) for line in self.lines]
-        newsource.lines = before.lines + lines + after.lines
+        lines = [ (indent + line) for line in self.lines]
+        newsource.lines = before.lines + lines +  after.lines
         return newsource
 
     def indent(self, indent=' ' * 4):
@@ -97,7 +95,7 @@ def indent(self, indent=' ' * 4):
             all lines indented by the given indent-string.
         """
         newsource = Source()
-        newsource.lines = [(indent + line) for line in self.lines]
+        newsource.lines = [(indent+line) for line in self.lines]
         return newsource
 
     def getstatement(self, lineno, assertion=False):
@@ -136,8 +134,7 @@ def isparseable(self, deindent=True):
         try:
             import parser
         except ImportError:
-            def syntax_checker(x):
-                return compile(x, 'asd', 'exec')
+            syntax_checker = lambda x: compile(x, 'asd', 'exec')
         else:
             syntax_checker = parser.suite
 
@@ -146,8 +143,8 @@ def syntax_checker(x):
         else:
             source = str(self)
         try:
-            # compile(source+'\n', "x", "exec")
-            syntax_checker(source + '\n')
+            #compile(source+'\n', "x", "exec")
+            syntax_checker(source+'\n')
         except KeyboardInterrupt:
             raise
         except Exception:
@@ -167,8 +164,8 @@ def compile(self, filename=None, mode='exec',
         """
         if not filename or py.path.local(filename).check(file=0):
             if _genframe is None:
-                _genframe = sys._getframe(1)  # the caller
-            fn, lineno = _genframe.f_code.co_filename, _genframe.f_lineno
+                _genframe = sys._getframe(1) # the caller
+            fn,lineno = _genframe.f_code.co_filename, _genframe.f_lineno
             base = "<%d-codegen " % self._compilecounter
             self.__class__._compilecounter += 1
             if not filename:
@@ -183,7 +180,7 @@ def compile(self, filename=None, mode='exec',
             # re-represent syntax errors from parsing python strings
             msglines = self.lines[:ex.lineno]
             if ex.offset:
-                msglines.append(" " * ex.offset + '^')
+                msglines.append(" "*ex.offset + '^')
             msglines.append("(code was compiled probably from here: %s)" % filename)
             newex = SyntaxError('\n'.join(msglines))
             newex.offset = ex.offset
@@ -201,8 +198,8 @@ def compile(self, filename=None, mode='exec',
 # public API shortcut functions
 #
 
-
-def compile_(source, filename=None, mode='exec', flags=generators.compiler_flag, dont_inherit=0):
+def compile_(source, filename=None, mode='exec', flags=
+            generators.compiler_flag, dont_inherit=0):
     """ compile the given source to a raw code object,
         and maintain an internal cache which allows later
         retrieval of the source code for the code object
@@ -211,7 +208,7 @@ def compile_(source, filename=None, mode='exec', flags=generators.compiler_flag,
     if _ast is not None and isinstance(source, _ast.AST):
         # XXX should Source support having AST?
         return cpy_compile(source, filename, mode, flags, dont_inherit)
-    _genframe = sys._getframe(1)  # the caller
+    _genframe = sys._getframe(1) # the caller
     s = Source(source)
     co = s.compile(filename, mode, flags, _genframe=_genframe)
     return co
@@ -248,13 +245,12 @@ def getfslineno(obj):
 # helper functions
 #
 
-
 def findsource(obj):
     try:
         sourcelines, lineno = py.std.inspect.findsource(obj)
     except py.builtin._sysex:
         raise
-    except:  # noqa
+    except:
         return None, -1
     source = Source()
     source.lines = [line.rstrip() for line in sourcelines]
@@ -278,7 +274,7 @@ def deindent(lines, offset=None):
             line = line.expandtabs()
             s = line.lstrip()
             if s:
-                offset = len(line) - len(s)
+                offset = len(line)-len(s)
                 break
         else:
             offset = 0
@@ -297,11 +293,11 @@ def readline_generator(lines):
     try:
         for _, _, (sline, _), (eline, _), _ in tokenize.generate_tokens(lambda: next(it)):
             if sline > len(lines):
-                break  # End of input reached
+                break # End of input reached
             if sline > len(newlines):
                 line = lines[sline - 1].expandtabs()
                 if line.lstrip() and line[:offset].isspace():
-                    line = line[offset:]  # Deindent
+                    line = line[offset:] # Deindent
                 newlines.append(line)
 
             for i in range(sline, eline):
@@ -319,29 +315,29 @@ def get_statement_startend2(lineno, node):
     import ast
     # flatten all statements and except handlers into one lineno-list
     # AST's line numbers start indexing at 1
-    values = []
+    l = []
     for x in ast.walk(node):
         if isinstance(x, _ast.stmt) or isinstance(x, _ast.ExceptHandler):
-            values.append(x.lineno - 1)
+            l.append(x.lineno - 1)
             for name in "finalbody", "orelse":
                 val = getattr(x, name, None)
                 if val:
                     # treat the finally/orelse part as its own statement
-                    values.append(val[0].lineno - 1 - 1)
-    values.sort()
-    insert_index = bisect_right(values, lineno)
-    start = values[insert_index - 1]
-    if insert_index >= len(values):
+                    l.append(val[0].lineno - 1 - 1)
+    l.sort()
+    insert_index = bisect_right(l, lineno)
+    start = l[insert_index - 1]
+    if insert_index >= len(l):
         end = None
     else:
-        end = values[insert_index]
+        end = l[insert_index]
     return start, end
 
 
 def getstatementrange_ast(lineno, source, assertion=False, astnode=None):
     if astnode is None:
         content = str(source)
-        if sys.version_info < (2, 7):
+        if sys.version_info < (2,7):
             content += "\n"
         try:
             astnode = compile(content, "source", "exec", 1024)  # 1024 for AST
@@ -397,7 +393,7 @@ def getstatementrange_old(lineno, source, assertion=False):
                 raise IndexError("likely a subclass")
             if "assert" not in line and "raise" not in line:
                 continue
-        trylines = source.lines[start:lineno + 1]
+        trylines = source.lines[start:lineno+1]
         # quick hack to prepare parsing an indented line with
         # compile_command() (which errors on "return" outside defs)
         trylines.insert(0, 'def xxx():')
@@ -409,8 +405,10 @@ def getstatementrange_old(lineno, source, assertion=False):
             continue
 
         # 2. find the end of the statement
-        for end in range(lineno + 1, len(source) + 1):
+        for end in range(lineno+1, len(source)+1):
             trysource = source[start:end]
             if trysource.isparseable():
                 return start, end
     raise SyntaxError("no valid source range around line %d " % (lineno,))
+
+

lib/spack/external/_pytest/_pluggy.py

@@ -2,7 +2,7 @@
 imports symbols from vendored "pluggy" if available, otherwise
 falls back to importing "pluggy" from the default namespace.
 """
-from __future__ import absolute_import, division, print_function
+
 try:
     from _pytest.vendored_packages.pluggy import *  # noqa
     from _pytest.vendored_packages.pluggy import __version__  # noqa

lib/spack/external/_pytest/assertion/__init__.py

@@ -1,13 +1,12 @@
 """
 support for presenting detailed information in failing assertions.
 """
-from __future__ import absolute_import, division, print_function
 import py
+import os
 import sys
 
 from _pytest.assertion import util
 from _pytest.assertion import rewrite
-from _pytest.assertion import truncate
 
 
 def pytest_addoption(parser):
@@ -25,6 +24,10 @@ def pytest_addoption(parser):
                             expression information.""")
 
 
+def pytest_namespace():
+    return {'register_assert_rewrite': register_assert_rewrite}
+
+
 def register_assert_rewrite(*names):
     """Register one or more module names to be rewritten on import.
 
@@ -97,6 +100,12 @@ def pytest_collection(session):
             assertstate.hook.set_session(session)
 
 
+def _running_on_ci():
+    """Check if we're currently running on a CI system."""
+    env_vars = ['CI', 'BUILD_NUMBER']
+    return any(var in os.environ for var in env_vars)
+
+
 def pytest_runtest_setup(item):
     """Setup the pytest_assertrepr_compare hook
 
@@ -110,8 +119,8 @@ def callbinrepr(op, left, right):
 
         This uses the first result from the hook and then ensures the
         following:
-        * Overly verbose explanations are truncated unless configured otherwise
-          (eg. if running in verbose mode).
+        * Overly verbose explanations are dropped unless -vv was used or
+          running on a CI.
         * Embedded newlines are escaped to help util.format_explanation()
           later.
         * If the rewrite mode is used embedded %-characters are replaced
@@ -124,7 +133,14 @@ def callbinrepr(op, left, right):
             config=item.config, op=op, left=left, right=right)
         for new_expl in hook_result:
             if new_expl:
-                new_expl = truncate.truncate_if_required(new_expl, item)
+                if (sum(len(p) for p in new_expl[1:]) > 80*8 and
+                        item.config.option.verbose < 2 and
+                        not _running_on_ci()):
+                    show_max = 10
+                    truncated_lines = len(new_expl) - show_max
+                    new_expl[show_max:] = [py.builtin._totext(
+                        'Detailed information truncated (%d more lines)'
+                        ', use "-vv" to show' % truncated_lines)]
                 new_expl = [line.replace("\n", "\\n") for line in new_expl]
                 res = py.builtin._totext("\n~").join(new_expl)
                 if item.config.getvalue("assertmode") == "rewrite":

lib/spack/external/_pytest/assertion/rewrite.py

@@ -1,5 +1,5 @@
 """Rewrite assertion AST to produce nice error messages"""
-from __future__ import absolute_import, division, print_function
+
 import ast
 import _ast
 import errno
@@ -11,6 +11,7 @@
 import struct
 import sys
 import types
+from fnmatch import fnmatch
 
 import py
 from _pytest.assertion import util
@@ -36,11 +37,10 @@
 REWRITE_NEWLINES = sys.version_info[:2] != (2, 7) and sys.version_info < (3, 2)
 ASCII_IS_DEFAULT_ENCODING = sys.version_info[0] < 3
 
-if sys.version_info >= (3, 5):
+if sys.version_info >= (3,5):
     ast_Call = ast.Call
 else:
-    def ast_Call(a, b, c):
-        return ast.Call(a, b, c, None, None)
+    ast_Call = lambda a,b,c: ast.Call(a, b, c, None, None)
 
 
 class AssertionRewritingHook(object):
@@ -163,7 +163,11 @@ def _should_rewrite(self, name, fn_pypath, state):
         # modules not passed explicitly on the command line are only
         # rewritten if they match the naming convention for test files
         for pat in self.fnpats:
-            if fn_pypath.fnmatch(pat):
+            # use fnmatch instead of fn_pypath.fnmatch because the
+            # latter might trigger an import to fnmatch.fnmatch
+            # internally, which would cause this method to be
+            # called recursively
+            if fnmatch(fn_pypath.basename, pat):
                 state.trace("matched test file %r" % (fn,))
                 return True
 
@@ -210,12 +214,13 @@ def load_module(self, name):
             mod.__cached__ = pyc
             mod.__loader__ = self
             py.builtin.exec_(co, mod.__dict__)
-        except:  # noqa
-            if name in sys.modules:
-                del sys.modules[name]
+        except:
+            del sys.modules[name]
             raise
         return sys.modules[name]
 
+
+
     def is_package(self, name):
         try:
             fd, fn, desc = imp.find_module(name)
@@ -260,7 +265,7 @@ def _write_pyc(state, co, source_stat, pyc):
         fp = open(pyc, "wb")
     except IOError:
         err = sys.exc_info()[1].errno
-        state.trace("error writing pyc file at %s: errno=%s" % (pyc, err))
+        state.trace("error writing pyc file at %s: errno=%s" %(pyc, err))
         # we ignore any failure to write the cache file
         # there are many reasons, permission-denied, __pycache__ being a
         # file etc.
@@ -282,7 +287,6 @@ def _write_pyc(state, co, source_stat, pyc):
 cookie_re = re.compile(r"^[ \t\f]*#.*coding[:=][ \t]*[-\w.]+")
 BOM_UTF8 = '\xef\xbb\xbf'
 
-
 def _rewrite_test(config, fn):
     """Try to read and rewrite *fn* and return the code object."""
     state = config._assertstate
@@ -307,7 +311,7 @@ def _rewrite_test(config, fn):
         end2 = source.find("\n", end1 + 1)
         if (not source.startswith(BOM_UTF8) and
             cookie_re.match(source[0:end1]) is None and
-                cookie_re.match(source[end1 + 1:end2]) is None):
+            cookie_re.match(source[end1 + 1:end2]) is None):
             if hasattr(state, "_indecode"):
                 # encodings imported us again, so don't rewrite.
                 return None, None
@@ -332,7 +336,7 @@ def _rewrite_test(config, fn):
         return None, None
     rewrite_asserts(tree, fn, config)
     try:
-        co = compile(tree, fn.strpath, "exec", dont_inherit=True)
+        co = compile(tree, fn.strpath, "exec")
     except SyntaxError:
         # It's possible that this error is from some bug in the
         # assertion rewriting, but I don't know of a fast way to tell.
@@ -340,7 +344,6 @@ def _rewrite_test(config, fn):
         return None, None
     return stat, co
 
-
 def _make_rewritten_pyc(state, source_stat, pyc, co):
     """Try to dump rewritten code to *pyc*."""
     if sys.platform.startswith("win"):
@@ -354,7 +357,6 @@ def _make_rewritten_pyc(state, source_stat, pyc, co):
         if _write_pyc(state, co, source_stat, proc_pyc):
             os.rename(proc_pyc, pyc)
 
-
 def _read_pyc(source, pyc, trace=lambda x: None):
     """Possibly read a pytest pyc containing rewritten code.
 
@@ -412,8 +414,7 @@ def _saferepr(obj):
     return repr.replace(t("\n"), t("\\n"))
 
 
-from _pytest.assertion.util import format_explanation as _format_explanation  # noqa
-
+from _pytest.assertion.util import format_explanation as _format_explanation # noqa
 
 def _format_assertmsg(obj):
     """Format the custom assertion message given.
@@ -442,11 +443,9 @@ def _format_assertmsg(obj):
         s = s.replace(t("\\n"), t("\n~"))
     return s
 
-
 def _should_repr_global_name(obj):
     return not hasattr(obj, "__name__") and not py.builtin.callable(obj)
 
-
 def _format_boolop(explanations, is_or):
     explanation = "(" + (is_or and " or " or " and ").join(explanations) + ")"
     if py.builtin._istext(explanation):
@@ -455,7 +454,6 @@ def _format_boolop(explanations, is_or):
         t = py.builtin.bytes
     return explanation.replace(t('%'), t('%%'))
 
-
 def _call_reprcompare(ops, results, expls, each_obj):
     for i, res, expl in zip(range(len(ops)), results, expls):
         try:
@@ -489,7 +487,7 @@ def _call_reprcompare(ops, results, expls, each_obj):
     ast.Mult: "*",
     ast.Div: "/",
     ast.FloorDiv: "//",
-    ast.Mod: "%%",  # escaped for string formatting
+    ast.Mod: "%%", # escaped for string formatting
     ast.Eq: "==",
     ast.NotEq: "!=",
     ast.Lt: "<",
@@ -595,26 +593,23 @@ def run(self, mod):
         # docstrings and __future__ imports.
         aliases = [ast.alias(py.builtin.builtins.__name__, "@py_builtins"),
                    ast.alias("_pytest.assertion.rewrite", "@pytest_ar")]
-        doc = getattr(mod, "docstring", None)
-        expect_docstring = doc is None
-        if doc is not None and self.is_rewrite_disabled(doc):
-            return
+        expect_docstring = True
         pos = 0
-        lineno = 1
+        lineno = 0
         for item in mod.body:
             if (expect_docstring and isinstance(item, ast.Expr) and
                     isinstance(item.value, ast.Str)):
                 doc = item.value.s
-                if self.is_rewrite_disabled(doc):
+                if "PYTEST_DONT_REWRITE" in doc:
+                    # The module has disabled assertion rewriting.
                     return
+                lineno += len(doc) - 1
                 expect_docstring = False
             elif (not isinstance(item, ast.ImportFrom) or item.level > 0 or
                   item.module != "__future__"):
                 lineno = item.lineno
                 break
             pos += 1
-        else:
-            lineno = item.lineno
         imports = [ast.Import([alias], lineno=lineno, col_offset=0)
                    for alias in aliases]
         mod.body[pos:pos] = imports
@@ -640,9 +635,6 @@ def run(self, mod):
                       not isinstance(field, ast.expr)):
                     nodes.append(field)
 
-    def is_rewrite_disabled(self, docstring):
-        return "PYTEST_DONT_REWRITE" in docstring
-
     def variable(self):
         """Get a new variable."""
         # Use a character invalid in python identifiers to avoid clashing.
@@ -735,7 +727,7 @@ def visit_Assert(self, assert_):
         if isinstance(assert_.test, ast.Tuple) and self.config is not None:
             fslocation = (self.module_path, assert_.lineno)
             self.config.warn('R1', 'assertion is always true, perhaps '
-                             'remove parentheses?', fslocation=fslocation)
+                              'remove parentheses?', fslocation=fslocation)
         self.statements = []
         self.variables = []
         self.variable_counter = itertools.count()
@@ -799,7 +791,7 @@ def visit_BoolOp(self, boolop):
             if i:
                 fail_inner = []
                 # cond is set in a prior loop iteration below
-                self.on_failure.append(ast.If(cond, fail_inner, []))  # noqa
+                self.on_failure.append(ast.If(cond, fail_inner, [])) # noqa
                 self.on_failure = fail_inner
             self.push_format_context()
             res, expl = self.visit(v)
@@ -851,7 +843,7 @@ def visit_Call_35(self, call):
             new_kwargs.append(ast.keyword(keyword.arg, res))
             if keyword.arg:
                 arg_expls.append(keyword.arg + "=" + expl)
-            else:  # **args have `arg` keywords with an .arg of None
+            else: ## **args have `arg` keywords with an .arg of None
                 arg_expls.append("**" + expl)
 
         expl = "%s(%s)" % (func_expl, ', '.join(arg_expls))
@@ -905,6 +897,7 @@ def visit_Call_legacy(self, call):
     else:
         visit_Call = visit_Call_legacy
 
+
     def visit_Attribute(self, attr):
         if not isinstance(attr.ctx, ast.Load):
             return self.generic_visit(attr)

lib/spack/external/_pytest/assertion/truncate.py

@@ -1,102 +0,0 @@
-"""
-Utilities for truncating assertion output.
-
-Current default behaviour is to truncate assertion explanations at
-~8 terminal lines, unless running in "-vv" mode or running on CI.
-"""
-from __future__ import absolute_import, division, print_function
-import os
-
-import py
-
-
-DEFAULT_MAX_LINES = 8
-DEFAULT_MAX_CHARS = 8 * 80
-USAGE_MSG = "use '-vv' to show"
-
-
-def truncate_if_required(explanation, item, max_length=None):
-    """
-    Truncate this assertion explanation if the given test item is eligible.
-    """
-    if _should_truncate_item(item):
-        return _truncate_explanation(explanation)
-    return explanation
-
-
-def _should_truncate_item(item):
-    """
-    Whether or not this test item is eligible for truncation.
-    """
-    verbose = item.config.option.verbose
-    return verbose < 2 and not _running_on_ci()
-
-
-def _running_on_ci():
-    """Check if we're currently running on a CI system."""
-    env_vars = ['CI', 'BUILD_NUMBER']
-    return any(var in os.environ for var in env_vars)
-
-
-def _truncate_explanation(input_lines, max_lines=None, max_chars=None):
-    """
-    Truncate given list of strings that makes up the assertion explanation.
-
-    Truncates to either 8 lines, or 640 characters - whichever the input reaches
-    first. The remaining lines will be replaced by a usage message.
-    """
-
-    if max_lines is None:
-        max_lines = DEFAULT_MAX_LINES
-    if max_chars is None:
-        max_chars = DEFAULT_MAX_CHARS
-
-    # Check if truncation required
-    input_char_count = len("".join(input_lines))
-    if len(input_lines) <= max_lines and input_char_count <= max_chars:
-        return input_lines
-
-    # Truncate first to max_lines, and then truncate to max_chars if max_chars
-    # is exceeded.
-    truncated_explanation = input_lines[:max_lines]
-    truncated_explanation = _truncate_by_char_count(truncated_explanation, max_chars)
-
-    # Add ellipsis to final line
-    truncated_explanation[-1] = truncated_explanation[-1] + "..."
-
-    # Append useful message to explanation
-    truncated_line_count = len(input_lines) - len(truncated_explanation)
-    truncated_line_count += 1  # Account for the part-truncated final line
-    msg = '...Full output truncated'
-    if truncated_line_count == 1:
-        msg += ' ({0} line hidden)'.format(truncated_line_count)
-    else:
-        msg += ' ({0} lines hidden)'.format(truncated_line_count)
-    msg += ", {0}" .format(USAGE_MSG)
-    truncated_explanation.extend([
-        py.builtin._totext(""),
-        py.builtin._totext(msg),
-    ])
-    return truncated_explanation
-
-
-def _truncate_by_char_count(input_lines, max_chars):
-    # Check if truncation required
-    if len("".join(input_lines)) <= max_chars:
-        return input_lines
-
-    # Find point at which input length exceeds total allowed length
-    iterated_char_count = 0
-    for iterated_index, input_line in enumerate(input_lines):
-        if iterated_char_count + len(input_line) > max_chars:
-            break
-        iterated_char_count += len(input_line)
-
-    # Create truncated explanation with modified final line
-    truncated_result = input_lines[:iterated_index]
-    final_line = input_lines[iterated_index]
-    if final_line:
-        final_line_truncate_point = max_chars - iterated_char_count
-        final_line = final_line[:final_line_truncate_point]
-    truncated_result.append(final_line)
-    return truncated_result

lib/spack/external/_pytest/assertion/util.py

@@ -1,5 +1,4 @@
 """Utilities for assertion debugging"""
-from __future__ import absolute_import, division, print_function
 import pprint
 
 import _pytest._code
@@ -9,7 +8,7 @@
 except ImportError:
     Sequence = list
 
-
+BuiltinAssertionError = py.builtin.builtins.AssertionError
 u = py.builtin._totext
 
 # The _reprcompare attribute on the util module is used by the new assertion
@@ -53,11 +52,11 @@ def _split_explanation(explanation):
     """
     raw_lines = (explanation or u('')).split('\n')
     lines = [raw_lines[0]]
-    for values in raw_lines[1:]:
-        if values and values[0] in ['{', '}', '~', '>']:
-            lines.append(values)
+    for l in raw_lines[1:]:
+        if l and l[0] in ['{', '}', '~', '>']:
+            lines.append(l)
         else:
-            lines[-1] += '\\n' + values
+            lines[-1] += '\\n' + l
     return lines
 
 
@@ -82,7 +81,7 @@ def _format_lines(lines):
             stack.append(len(result))
             stackcnt[-1] += 1
             stackcnt.append(0)
-            result.append(u(' +') + u('  ') * (len(stack) - 1) + s + line[1:])
+            result.append(u(' +') + u('  ')*(len(stack)-1) + s + line[1:])
         elif line.startswith('}'):
             stack.pop()
             stackcnt.pop()
@@ -91,7 +90,7 @@ def _format_lines(lines):
             assert line[0] in ['~', '>']
             stack[-1] += 1
             indent = len(stack) if line.startswith('~') else len(stack) - 1
-            result.append(u('  ') * indent + line[1:])
+            result.append(u('  ')*indent + line[1:])
     assert len(stack) == 1
     return result
 
@@ -106,22 +105,16 @@ def _format_lines(lines):
 def assertrepr_compare(config, op, left, right):
     """Return specialised explanations for some operators/operands"""
     width = 80 - 15 - len(op) - 2  # 15 chars indentation, 1 space around op
-    left_repr = py.io.saferepr(left, maxsize=int(width // 2))
-    right_repr = py.io.saferepr(right, maxsize=width - len(left_repr))
+    left_repr = py.io.saferepr(left, maxsize=int(width//2))
+    right_repr = py.io.saferepr(right, maxsize=width-len(left_repr))
 
     summary = u('%s %s %s') % (ecu(left_repr), op, ecu(right_repr))
 
-    def issequence(x):
-        return (isinstance(x, (list, tuple, Sequence)) and not isinstance(x, basestring))
-
-    def istext(x):
-        return isinstance(x, basestring)
-
-    def isdict(x):
-        return isinstance(x, dict)
-
-    def isset(x):
-        return isinstance(x, (set, frozenset))
+    issequence = lambda x: (isinstance(x, (list, tuple, Sequence)) and
+                            not isinstance(x, basestring))
+    istext = lambda x: isinstance(x, basestring)
+    isdict = lambda x: isinstance(x, dict)
+    isset = lambda x: isinstance(x, (set, frozenset))
 
     def isiterable(obj):
         try:
@@ -263,8 +256,8 @@ def _compare_eq_dict(left, right, verbose=False):
     explanation = []
     common = set(left).intersection(set(right))
     same = dict((k, left[k]) for k in common if left[k] == right[k])
-    if same and verbose < 2:
-        explanation += [u('Omitting %s identical items, use -vv to show') %
+    if same and not verbose:
+        explanation += [u('Omitting %s identical items, use -v to show') %
                         len(same)]
     elif same:
         explanation += [u('Common items:')]
@@ -291,7 +284,7 @@ def _compare_eq_dict(left, right, verbose=False):
 def _notin_text(term, text, verbose=False):
     index = text.find(term)
     head = text[:index]
-    tail = text[index + len(term):]
+    tail = text[index+len(term):]
     correct_text = head + tail
     diff = _diff_text(correct_text, text, verbose)
     newdiff = [u('%s is contained here:') % py.io.saferepr(term, maxsize=42)]

lib/spack/external/_pytest/cacheprovider.py

@@ -1,21 +1,20 @@
 """
 merged implementation of the cache provider
 
-the name cache was not chosen to ensure pluggy automatically
+the name cache was not choosen to ensure pluggy automatically
 ignores the external pytest-cache
 """
-from __future__ import absolute_import, division, print_function
+
 import py
 import pytest
 import json
-import os
 from os.path import sep as _sep, altsep as _altsep
 
 
 class Cache(object):
     def __init__(self, config):
         self.config = config
-        self._cachedir = Cache.cache_dir_from_config(config)
+        self._cachedir = config.rootdir.join(".cache")
         self.trace = config.trace.root.get("cache")
         if config.getvalue("cacheclear"):
             self.trace("clearing cachedir")
@@ -23,16 +22,6 @@ def __init__(self, config):
                 self._cachedir.remove()
             self._cachedir.mkdir()
 
-    @staticmethod
-    def cache_dir_from_config(config):
-        cache_dir = config.getini("cache_dir")
-        cache_dir = os.path.expanduser(cache_dir)
-        cache_dir = os.path.expandvars(cache_dir)
-        if os.path.isabs(cache_dir):
-            return py.path.local(cache_dir)
-        else:
-            return config.rootdir.join(cache_dir)
-
     def makedir(self, name):
         """ return a directory path object with the given name.  If the
         directory does not yet exist, it will be created.  You can use it
@@ -100,31 +89,31 @@ def set(self, key, value):
 
 class LFPlugin:
     """ Plugin which implements the --lf (run last-failing) option """
-
     def __init__(self, config):
         self.config = config
         active_keys = 'lf', 'failedfirst'
         self.active = any(config.getvalue(key) for key in active_keys)
-        self.lastfailed = config.cache.get("cache/lastfailed", {})
-        self._previously_failed_count = None
-
-    def pytest_report_collectionfinish(self):
         if self.active:
-            if not self._previously_failed_count:
+            self.lastfailed = config.cache.get("cache/lastfailed", {})
+        else:
+            self.lastfailed = {}
+
+    def pytest_report_header(self):
+        if self.active:
+            if not self.lastfailed:
                 mode = "run all (no recorded failures)"
             else:
-                noun = 'failure' if self._previously_failed_count == 1 else 'failures'
-                suffix = " first" if self.config.getvalue("failedfirst") else ""
-                mode = "rerun previous {count} {noun}{suffix}".format(
-                    count=self._previously_failed_count, suffix=suffix, noun=noun
-                )
+                mode = "rerun last %d failures%s" % (
+                    len(self.lastfailed),
+                    " first" if self.config.getvalue("failedfirst") else "")
             return "run-last-failure: %s" % mode
 
     def pytest_runtest_logreport(self, report):
-        if (report.when == 'call' and report.passed) or report.skipped:
-            self.lastfailed.pop(report.nodeid, None)
-        elif report.failed:
+        if report.failed and "xfail" not in report.keywords:
             self.lastfailed[report.nodeid] = True
+        elif not report.failed:
+            if report.when == "call":
+                self.lastfailed.pop(report.nodeid, None)
 
     def pytest_collectreport(self, report):
         passed = report.outcome in ('passed', 'skipped')
@@ -146,24 +135,22 @@ def pytest_collection_modifyitems(self, session, config, items):
                     previously_failed.append(item)
                 else:
                     previously_passed.append(item)
-            self._previously_failed_count = len(previously_failed)
-            if not previously_failed:
+            if not previously_failed and previously_passed:
                 # running a subset of all tests with recorded failures outside
                 # of the set of tests currently executing
-                return
-            if self.config.getvalue("lf"):
+                pass
+            elif self.config.getvalue("failedfirst"):
+                items[:] = previously_failed + previously_passed
+            else:
                 items[:] = previously_failed
                 config.hook.pytest_deselected(items=previously_passed)
-            else:
-                items[:] = previously_failed + previously_passed
 
     def pytest_sessionfinish(self, session):
         config = self.config
         if config.getvalue("cacheshow") or hasattr(config, "slaveinput"):
             return
-
-        saved_lastfailed = config.cache.get("cache/lastfailed", {})
-        if saved_lastfailed != self.lastfailed:
+        prev_failed = config.cache.get("cache/lastfailed", None) is not None
+        if (session.testscollected and prev_failed) or self.lastfailed:
             config.cache.set("cache/lastfailed", self.lastfailed)
 
 
@@ -184,9 +171,6 @@ def pytest_addoption(parser):
     group.addoption(
         '--cache-clear', action='store_true', dest="cacheclear",
         help="remove all cache contents at start of test run.")
-    parser.addini(
-        "cache_dir", default='.cache',
-        help="cache directory path.")
 
 
 def pytest_cmdline_main(config):
@@ -195,6 +179,7 @@ def pytest_cmdline_main(config):
         return wrap_session(config, cacheshow)
 
 
+
 @pytest.hookimpl(tryfirst=True)
 def pytest_configure(config):
     config.cache = Cache(config)
@@ -234,12 +219,12 @@ def cacheshow(config, session):
     basedir = config.cache._cachedir
     vdir = basedir.join("v")
     tw.sep("-", "cache values")
-    for valpath in sorted(vdir.visit(lambda x: x.isfile())):
+    for valpath in vdir.visit(lambda x: x.isfile()):
         key = valpath.relto(vdir).replace(valpath.sep, "/")
         val = config.cache.get(key, dummy)
         if val is dummy:
             tw.line("%s contains unreadable content, "
-                    "will be ignored" % key)
+                  "will be ignored" % key)
         else:
             tw.line("%s contains:" % key)
             stream = py.io.TextIO()
@@ -250,8 +235,8 @@ def cacheshow(config, session):
     ddir = basedir.join("d")
     if ddir.isdir() and ddir.listdir():
         tw.sep("-", "cache directories")
-        for p in sorted(basedir.join("d").visit()):
-            # if p.check(dir=1):
+        for p in basedir.join("d").visit():
+            #if p.check(dir=1):
             #    print("%s/" % p.relto(basedir))
             if p.isfile():
                 key = p.relto(basedir)

lib/spack/external/_pytest/capture.py

@@ -2,19 +2,17 @@
 per-test stdout/stderr capturing mechanism.
 
 """
-from __future__ import absolute_import, division, print_function
+from __future__ import with_statement
 
 import contextlib
 import sys
 import os
-import io
-from io import UnsupportedOperation
 from tempfile import TemporaryFile
 
 import py
 import pytest
-from _pytest.compat import CaptureIO
 
+from py.io import TextIO
 unicode = py.builtin.text
 
 patchsysdict = {0: 'stdin', 1: 'stdout', 2: 'stderr'}
@@ -34,11 +32,8 @@ def pytest_addoption(parser):
 
 @pytest.hookimpl(hookwrapper=True)
 def pytest_load_initial_conftests(early_config, parser, args):
-    ns = early_config.known_args_namespace
-    if ns.capture == "fd":
-        _py36_windowsconsoleio_workaround(sys.stdout)
-    _colorama_workaround()
     _readline_workaround()
+    ns = early_config.known_args_namespace
     pluginmanager = early_config.pluginmanager
     capman = CaptureManager(ns.capture)
     pluginmanager.register(capman, "capturemanager")
@@ -135,7 +130,7 @@ def pytest_runtest_call(self, item):
         self.resumecapture()
         self.activate_funcargs(item)
         yield
-        # self.deactivate_funcargs() called from suspendcapture()
+        #self.deactivate_funcargs() called from suspendcapture()
         self.suspendcapture_item(item, "call")
 
     @pytest.hookimpl(hookwrapper=True)
@@ -172,7 +167,6 @@ def capsys(request):
     request.node._capfuncarg = c = CaptureFixture(SysCapture, request)
     return c
 
-
 @pytest.fixture
 def capfd(request):
     """Enable capturing of writes to file descriptors 1 and 2 and make
@@ -240,7 +234,6 @@ def safe_text_dupfile(f, mode, default_encoding="UTF8"):
 
 class EncodedFile(object):
     errors = "strict"  # possibly needed by py3 code (issue555)
-
     def __init__(self, buffer, encoding):
         self.buffer = buffer
         self.encoding = encoding
@@ -254,11 +247,6 @@ def writelines(self, linelist):
         data = ''.join(linelist)
         self.write(data)
 
-    @property
-    def name(self):
-        """Ensure that file.name is a string."""
-        return repr(self.buffer)
-
     def __getattr__(self, name):
         return getattr(object.__getattribute__(self, "buffer"), name)
 
@@ -326,11 +314,9 @@ def readouterr(self):
         return (self.out.snap() if self.out is not None else "",
                 self.err.snap() if self.err is not None else "")
 
-
 class NoCapture:
     __init__ = start = done = suspend = resume = lambda *args: None
 
-
 class FDCapture:
     """ Capture IO to/from a given os-level filedescriptor. """
 
@@ -403,7 +389,7 @@ def resume(self):
     def writeorg(self, data):
         """ write to original file descriptor. """
         if py.builtin._istext(data):
-            data = data.encode("utf8")  # XXX use encoding of original stream
+            data = data.encode("utf8") # XXX use encoding of original stream
         os.write(self.targetfd_save, data)
 
 
@@ -416,7 +402,7 @@ def __init__(self, fd, tmpfile=None):
             if name == "stdin":
                 tmpfile = DontReadFromInput()
             else:
-                tmpfile = CaptureIO()
+                tmpfile = TextIO()
         self.tmpfile = tmpfile
 
     def start(self):
@@ -462,8 +448,7 @@ def read(self, *args):
     __iter__ = read
 
     def fileno(self):
-        raise UnsupportedOperation("redirected stdin is pseudofile, "
-                                   "has no fileno()")
+        raise ValueError("redirected Stdin is pseudofile, has no fileno()")
 
     def isatty(self):
         return False
@@ -473,30 +458,12 @@ def close(self):
 
     @property
     def buffer(self):
-        if sys.version_info >= (3, 0):
+        if sys.version_info >= (3,0):
             return self
         else:
             raise AttributeError('redirected stdin has no attribute buffer')
 
 
-def _colorama_workaround():
-    """
-    Ensure colorama is imported so that it attaches to the correct stdio
-    handles on Windows.
-
-    colorama uses the terminal on import time. So if something does the
-    first import of colorama while I/O capture is active, colorama will
-    fail in various ways.
-    """
-
-    if not sys.platform.startswith('win32'):
-        return
-    try:
-        import colorama  # noqa
-    except ImportError:
-        pass
-
-
 def _readline_workaround():
     """
     Ensure readline is imported so that it attaches to the correct stdio
@@ -522,56 +489,3 @@ def _readline_workaround():
         import readline  # noqa
     except ImportError:
         pass
-
-
-def _py36_windowsconsoleio_workaround(stream):
-    """
-    Python 3.6 implemented unicode console handling for Windows. This works
-    by reading/writing to the raw console handle using
-    ``{Read,Write}ConsoleW``.
-
-    The problem is that we are going to ``dup2`` over the stdio file
-    descriptors when doing ``FDCapture`` and this will ``CloseHandle`` the
-    handles used by Python to write to the console. Though there is still some
-    weirdness and the console handle seems to only be closed randomly and not
-    on the first call to ``CloseHandle``, or maybe it gets reopened with the
-    same handle value when we suspend capturing.
-
-    The workaround in this case will reopen stdio with a different fd which
-    also means a different handle by replicating the logic in
-    "Py_lifecycle.c:initstdio/create_stdio".
-
-    :param stream: in practice ``sys.stdout`` or ``sys.stderr``, but given
-        here as parameter for unittesting purposes.
-
-    See https://github.com/pytest-dev/py/issues/103
-    """
-    if not sys.platform.startswith('win32') or sys.version_info[:2] < (3, 6):
-        return
-
-    # bail out if ``stream`` doesn't seem like a proper ``io`` stream (#2666)
-    if not hasattr(stream, 'buffer'):
-        return
-
-    buffered = hasattr(stream.buffer, 'raw')
-    raw_stdout = stream.buffer.raw if buffered else stream.buffer
-
-    if not isinstance(raw_stdout, io._WindowsConsoleIO):
-        return
-
-    def _reopen_stdio(f, mode):
-        if not buffered and mode[0] == 'w':
-            buffering = 0
-        else:
-            buffering = -1
-
-        return io.TextIOWrapper(
-            open(os.dup(f.fileno()), mode, buffering),
-            f.encoding,
-            f.errors,
-            f.newlines,
-            f.line_buffering)
-
-    sys.__stdin__ = sys.stdin = _reopen_stdio(sys.stdin, 'rb')
-    sys.__stdout__ = sys.stdout = _reopen_stdio(sys.stdout, 'wb')
-    sys.__stderr__ = sys.stderr = _reopen_stdio(sys.stderr, 'wb')

lib/spack/external/_pytest/compat.py

@@ -1,7 +1,6 @@
 """
 python version compatibility code
 """
-from __future__ import absolute_import, division, print_function
 import sys
 import inspect
 import types
@@ -10,8 +9,8 @@
 
 import py
 
-import _pytest
-from _pytest.outcomes import TEST_OUTCOME
+import  _pytest
+
 
 
 try:
@@ -20,7 +19,6 @@
     # Only available in Python 3.4+ or as a backport
     enum = None
 
-
 _PY3 = sys.version_info > (3, 0)
 _PY2 = not _PY3
 
@@ -28,10 +26,6 @@
 NoneType = type(None)
 NOTSET = object()
 
-PY35 = sys.version_info[:2] >= (3, 5)
-PY36 = sys.version_info[:2] >= (3, 6)
-MODULE_NOT_FOUND_ERROR = 'ModuleNotFoundError' if PY36 else 'ImportError'
-
 if hasattr(inspect, 'signature'):
     def _format_args(func):
         return str(inspect.signature(func))
@@ -48,18 +42,11 @@ def _format_args(func):
 
 
 def is_generator(func):
-    genfunc = inspect.isgeneratorfunction(func)
-    return genfunc and not iscoroutinefunction(func)
-
-
-def iscoroutinefunction(func):
-    """Return True if func is a decorated coroutine function.
-
-    Note: copied and modified from Python 3.5's builtin couroutines.py to avoid import asyncio directly,
-    which in turns also initializes the "logging" module as side-effect (see issue #8).
-    """
-    return (getattr(func, '_is_coroutine', False) or
-            (hasattr(inspect, 'iscoroutinefunction') and inspect.iscoroutinefunction(func)))
+    try:
+        return _pytest._code.getrawcode(func).co_flags & 32 # generator function
+    except AttributeError: # builtin functions have no bytecode
+        # assume them to not be generators
+        return False
 
 
 def getlocation(function, curdir):
@@ -68,7 +55,7 @@ def getlocation(function, curdir):
     lineno = py.builtin._getcode(function).co_firstlineno
     if fn.relto(curdir):
         fn = fn.relto(curdir)
-    return "%s:%d" % (fn, lineno + 1)
+    return "%s:%d" %(fn, lineno+1)
 
 
 def num_mock_patch_args(function):
@@ -79,21 +66,13 @@ def num_mock_patch_args(function):
     mock = sys.modules.get("mock", sys.modules.get("unittest.mock", None))
     if mock is not None:
         return len([p for p in patchings
-                    if not p.attribute_name and p.new is mock.DEFAULT])
+                        if not p.attribute_name and p.new is mock.DEFAULT])
     return len(patchings)
 
 
-def getfuncargnames(function, startindex=None, cls=None):
-    """
-    @RonnyPfannschmidt: This function should be refactored when we revisit fixtures. The
-    fixture mechanism should ask the node for the fixture names, and not try to obtain
-    directly from the function object well after collection has occurred.
-    """
-    if startindex is None and cls is not None:
-        is_staticmethod = isinstance(cls.__dict__.get(function.__name__, None), staticmethod)
-        startindex = 0 if is_staticmethod else 1
+def getfuncargnames(function, startindex=None):
     # XXX merge with main.py's varnames
-    # assert not isclass(function)
+    #assert not isclass(function)
     realfunction = function
     while hasattr(realfunction, "__wrapped__"):
         realfunction = realfunction.__wrapped__
@@ -119,7 +98,8 @@ def getfuncargnames(function, startindex=None, cls=None):
     return tuple(argnames[startindex:])
 
 
-if sys.version_info[:2] == (2, 6):
+
+if  sys.version_info[:2] == (2, 6):
     def isclass(object):
         """ Return true if the object is a class. Overrides inspect.isclass for
         python 2.6 because it will return True for objects which always return
@@ -131,12 +111,10 @@ def isclass(object):
 
 if _PY3:
     import codecs
-    imap = map
-    izip = zip
-    STRING_TYPES = bytes, str
-    UNICODE_TYPES = str,
 
-    def _ascii_escaped(val):
+    STRING_TYPES = bytes, str
+
+    def _escape_strings(val):
         """If val is pure ascii, returns it as a str().  Otherwise, escapes
         bytes objects into a sequence of escaped bytes:
 
@@ -166,11 +144,8 @@ def _ascii_escaped(val):
             return val.encode('unicode_escape').decode('ascii')
 else:
     STRING_TYPES = bytes, str, unicode
-    UNICODE_TYPES = unicode,
 
-    from itertools import imap, izip  # NOQA
-
-    def _ascii_escaped(val):
+    def _escape_strings(val):
         """In py2 bytes and str are the same type, so return if it's a bytes
         object, return it unchanged if it is a full ascii string,
         otherwise escape it into its binary form.
@@ -192,18 +167,8 @@ def get_real_func(obj):
     """ gets the real function object of the (possibly) wrapped object by
     functools.wraps or functools.partial.
     """
-    start_obj = obj
-    for i in range(100):
-        new_obj = getattr(obj, '__wrapped__', None)
-        if new_obj is None:
-            break
-        obj = new_obj
-    else:
-        raise ValueError(
-            ("could not find real function of {start}"
-             "\nstopped at {current}").format(
-                start=py.io.saferepr(start_obj),
-                current=py.io.saferepr(obj)))
+    while hasattr(obj, "__wrapped__"):
+        obj = obj.__wrapped__
     if isinstance(obj, functools.partial):
         obj = obj.func
     return obj
@@ -230,16 +195,14 @@ def getimfunc(func):
 
 
 def safe_getattr(object, name, default):
-    """ Like getattr but return default upon any Exception or any OutcomeException.
+    """ Like getattr but return default upon any Exception.
 
     Attribute access can potentially fail for 'evil' Python objects.
-    See issue #214.
-    It catches OutcomeException because of #2490 (issue #580), new outcomes are derived from BaseException
-    instead of Exception (for more details check #2707)
+    See issue214
     """
     try:
         return getattr(object, name, default)
-    except TEST_OUTCOME:
+    except Exception:
         return default
 
 
@@ -263,64 +226,5 @@ def safe_str(v):
         try:
             return str(v)
         except UnicodeError:
-            if not isinstance(v, unicode):
-                v = unicode(v)
             errors = 'replace'
-            return v.encode('utf-8', errors)
-
-
-COLLECT_FAKEMODULE_ATTRIBUTES = (
-    'Collector',
-    'Module',
-    'Generator',
-    'Function',
-    'Instance',
-    'Session',
-    'Item',
-    'Class',
-    'File',
-    '_fillfuncargs',
-)
-
-
-def _setup_collect_fakemodule():
-    from types import ModuleType
-    import pytest
-    pytest.collect = ModuleType('pytest.collect')
-    pytest.collect.__all__ = []  # used for setns
-    for attr in COLLECT_FAKEMODULE_ATTRIBUTES:
-        setattr(pytest.collect, attr, getattr(pytest, attr))
-
-
-if _PY2:
-    # Without this the test_dupfile_on_textio will fail, otherwise CaptureIO could directly inherit from StringIO.
-    from py.io import TextIO
-
-    class CaptureIO(TextIO):
-
-        @property
-        def encoding(self):
-            return getattr(self, '_encoding', 'UTF-8')
-
-else:
-    import io
-
-    class CaptureIO(io.TextIOWrapper):
-        def __init__(self):
-            super(CaptureIO, self).__init__(
-                io.BytesIO(),
-                encoding='UTF-8', newline='', write_through=True,
-            )
-
-        def getvalue(self):
-            return self.buffer.getvalue().decode('UTF-8')
-
-
-class FuncargnamesCompatAttr(object):
-    """ helper class so that Metafunc, Function and FixtureRequest
-    don't need to each define the "funcargnames" compatibility attribute.
-    """
-    @property
-    def funcargnames(self):
-        """ alias attribute for ``fixturenames`` for pre-2.3 compatibility"""
-        return self.fixturenames
+            return v.encode('ascii', errors)

lib/spack/external/_pytest/config.py

@@ -1,5 +1,4 @@
 """ command line options, ini-file and conftest.py processing. """
-from __future__ import absolute_import, division, print_function
 import argparse
 import shlex
 import traceback
@@ -8,8 +7,7 @@
 
 import py
 # DON't import pytest here because it causes import cycle troubles
-import sys
-import os
+import sys, os
 import _pytest._code
 import _pytest.hookspec  # the extension point definitions
 import _pytest.assertion
@@ -55,15 +53,15 @@ def main(args=None, plugins=None):
             return 4
         else:
             try:
+                config.pluginmanager.check_pending()
                 return config.hook.pytest_cmdline_main(config=config)
             finally:
                 config._ensure_unconfigure()
     except UsageError as e:
         for msg in e.args:
-            sys.stderr.write("ERROR: %s\n" % (msg,))
+            sys.stderr.write("ERROR: %s\n" %(msg,))
         return 4
 
-
 class cmdline:  # compatibility namespace
     main = staticmethod(main)
 
@@ -72,12 +70,6 @@ class UsageError(Exception):
     """ error in pytest usage or invocation"""
 
 
-class PrintHelp(Exception):
-    """Raised when pytest should print it's help to skip the rest of the
-    argument parsing and validation."""
-    pass
-
-
 def filename_arg(path, optname):
     """ Argparse type validator for filename arguments.
 
@@ -103,11 +95,10 @@ def directory_arg(path, optname):
 _preinit = []
 
 default_plugins = (
-    "mark main terminal runner python fixtures debugging unittest capture skipping "
-    "tmpdir monkeypatch recwarn pastebin helpconfig nose assertion "
-    "junitxml resultlog doctest cacheprovider freeze_support "
-    "setuponly setupplan warnings").split()
-
+     "mark main terminal runner python fixtures debugging unittest capture skipping "
+     "tmpdir monkeypatch recwarn pastebin helpconfig nose assertion "
+     "junitxml resultlog doctest cacheprovider freeze_support "
+     "setuponly setupplan").split()
 
 builtin_plugins = set(default_plugins)
 builtin_plugins.add("pytester")
@@ -117,7 +108,6 @@ def _preloadplugins():
     assert not _preinit
     _preinit.append(get_config())
 
-
 def get_config():
     if _preinit:
         return _preinit.pop(0)
@@ -128,7 +118,6 @@ def get_config():
         pluginmanager.import_plugin(spec)
     return config
 
-
 def get_plugin_manager():
     """
     Obtain a new instance of the
@@ -140,7 +129,6 @@ def get_plugin_manager():
     """
     return get_config().pluginmanager
 
-
 def _prepareconfig(args=None, plugins=None):
     warning = None
     if args is None:
@@ -165,7 +153,7 @@ def _prepareconfig(args=None, plugins=None):
         if warning:
             config.warn('C1', warning)
         return pluginmanager.hook.pytest_cmdline_parse(
-            pluginmanager=pluginmanager, args=args)
+                pluginmanager=pluginmanager, args=args)
     except BaseException:
         config._ensure_unconfigure()
         raise
@@ -173,14 +161,13 @@ def _prepareconfig(args=None, plugins=None):
 
 class PytestPluginManager(PluginManager):
     """
-    Overwrites :py:class:`pluggy.PluginManager <_pytest.vendored_packages.pluggy.PluginManager>` to add pytest-specific
+    Overwrites :py:class:`pluggy.PluginManager` to add pytest-specific
     functionality:
 
     * loading plugins from the command line, ``PYTEST_PLUGIN`` env variable and
       ``pytest_plugins`` global variables found in plugins being loaded;
     * ``conftest.py`` loading during start-up;
     """
-
     def __init__(self):
         super(PytestPluginManager, self).__init__("pytest", implprefix="pytest_")
         self._conftest_plugins = set()
@@ -211,8 +198,7 @@ def addhooks(self, module_or_class):
         """
         .. deprecated:: 2.8
 
-        Use :py:meth:`pluggy.PluginManager.add_hookspecs <_pytest.vendored_packages.pluggy.PluginManager.add_hookspecs>`
-        instead.
+        Use :py:meth:`pluggy.PluginManager.add_hookspecs` instead.
         """
         warning = dict(code="I2",
                        fslocation=_pytest._code.getfslineno(sys._getframe(1)),
@@ -241,7 +227,7 @@ def parse_hookimpl_opts(self, plugin, name):
 
     def parse_hookspec_opts(self, module_or_class, name):
         opts = super(PytestPluginManager, self).parse_hookspec_opts(
-            module_or_class, name)
+                                                module_or_class, name)
         if opts is None:
             method = getattr(module_or_class, name)
             if name.startswith("pytest_"):
@@ -264,10 +250,7 @@ def register(self, plugin, name=None):
         ret = super(PytestPluginManager, self).register(plugin, name)
         if ret:
             self.hook.pytest_plugin_registered.call_historic(
-                kwargs=dict(plugin=plugin, manager=self))
-
-            if isinstance(plugin, types.ModuleType):
-                self.consider_module(plugin)
+                      kwargs=dict(plugin=plugin, manager=self))
         return ret
 
     def getplugin(self, name):
@@ -282,11 +265,11 @@ def pytest_configure(self, config):
         # XXX now that the pluginmanager exposes hookimpl(tryfirst...)
         # we should remove tryfirst/trylast as markers
         config.addinivalue_line("markers",
-                                "tryfirst: mark a hook implementation function such that the "
-                                "plugin machinery will try to call it first/as early as possible.")
+            "tryfirst: mark a hook implementation function such that the "
+            "plugin machinery will try to call it first/as early as possible.")
         config.addinivalue_line("markers",
-                                "trylast: mark a hook implementation function such that the "
-                                "plugin machinery will try to call it last/as late as possible.")
+            "trylast: mark a hook implementation function such that the "
+            "plugin machinery will try to call it last/as late as possible.")
 
     def _warn(self, message):
         kwargs = message if isinstance(message, dict) else {
@@ -310,7 +293,7 @@ def _set_initial_conftests(self, namespace):
         """
         current = py.path.local()
         self._confcutdir = current.join(namespace.confcutdir, abs=True) \
-            if namespace.confcutdir else None
+                                if namespace.confcutdir else None
         self._noconftest = namespace.noconftest
         testpaths = namespace.file_or_dir
         foundanchor = False
@@ -321,7 +304,7 @@ def _set_initial_conftests(self, namespace):
             if i != -1:
                 path = path[:i]
             anchor = current.join(path, abs=1)
-            if exists(anchor):  # we found some file object
+            if exists(anchor): # we found some file object
                 self._try_load_conftest(anchor)
                 foundanchor = True
         if not foundanchor:
@@ -388,7 +371,7 @@ def _importconftest(self, conftestpath):
                     if path and path.relto(dirpath) or path == dirpath:
                         assert mod not in mods
                         mods.append(mod)
-            self.trace("loaded conftestmodule %r" % (mod))
+            self.trace("loaded conftestmodule %r" %(mod))
             self.consider_conftest(mod)
             return mod
 
@@ -398,7 +381,7 @@ def _importconftest(self, conftestpath):
     #
 
     def consider_preparse(self, args):
-        for opt1, opt2 in zip(args, args[1:]):
+        for opt1,opt2 in zip(args, args[1:]):
             if opt1 == "-p":
                 self.consider_pluginarg(opt2)
 
@@ -412,33 +395,38 @@ def consider_pluginarg(self, arg):
             self.import_plugin(arg)
 
     def consider_conftest(self, conftestmodule):
-        self.register(conftestmodule, name=conftestmodule.__file__)
+        if self.register(conftestmodule, name=conftestmodule.__file__):
+            self.consider_module(conftestmodule)
 
     def consider_env(self):
         self._import_plugin_specs(os.environ.get("PYTEST_PLUGINS"))
 
     def consider_module(self, mod):
-        self._import_plugin_specs(getattr(mod, 'pytest_plugins', []))
+        plugins = getattr(mod, 'pytest_plugins', [])
+        if isinstance(plugins, str):
+            plugins = [plugins]
+        self.rewrite_hook.mark_rewrite(*plugins)
+        self._import_plugin_specs(plugins)
 
     def _import_plugin_specs(self, spec):
-        plugins = _get_plugin_specs_as_list(spec)
-        for import_spec in plugins:
-            self.import_plugin(import_spec)
+        if spec:
+            if isinstance(spec, str):
+                spec = spec.split(",")
+            for import_spec in spec:
+                self.import_plugin(import_spec)
 
     def import_plugin(self, modname):
         # most often modname refers to builtin modules, e.g. "pytester",
         # "terminal" or "capture".  Those plugins are registered under their
         # basename for historic purposes but must be imported with the
         # _pytest prefix.
-        assert isinstance(modname, (py.builtin.text, str)), "module name as text required, got %r" % modname
-        modname = str(modname)
+        assert isinstance(modname, str)
         if self.get_plugin(modname) is not None:
             return
         if modname in builtin_plugins:
             importspec = "_pytest." + modname
         else:
             importspec = modname
-        self.rewrite_hook.mark_rewrite(importspec)
         try:
             __import__(importspec)
         except ImportError as e:
@@ -452,28 +440,11 @@ def import_plugin(self, modname):
             import pytest
             if not hasattr(pytest, 'skip') or not isinstance(e, pytest.skip.Exception):
                 raise
-            self._warn("skipped plugin %r: %s" % ((modname, e.msg)))
+            self._warn("skipped plugin %r: %s" %((modname, e.msg)))
         else:
             mod = sys.modules[importspec]
             self.register(mod, modname)
-
-
-def _get_plugin_specs_as_list(specs):
-    """
-    Parses a list of "plugin specs" and returns a list of plugin names.
-
-    Plugin specs can be given as a list of strings separated by "," or already as a list/tuple in
-    which case it is returned as a list. Specs can also be `None` in which case an
-    empty list is returned.
-    """
-    if specs is not None:
-        if isinstance(specs, str):
-            specs = specs.split(',') if specs else []
-        if not isinstance(specs, (list, tuple)):
-            raise UsageError("Plugin specs must be a ','-separated string or a "
-                             "list/tuple of strings for plugin names. Given: %r" % specs)
-        return list(specs)
-    return []
+            self.consider_module(mod)
 
 
 class Parser:
@@ -517,7 +488,7 @@ def getgroup(self, name, description="", after=None):
         for i, grp in enumerate(self._groups):
             if grp.name == after:
                 break
-        self._groups.insert(i + 1, group)
+        self._groups.insert(i+1, group)
         return group
 
     def addoption(self, *opts, **attrs):
@@ -555,7 +526,7 @@ def _getparser(self):
                     a = option.attrs()
                     arggroup.add_argument(*n, **a)
         # bash like autocompletion for dirs (appending '/')
-        optparser.add_argument(FILE_OR_DIR, nargs='*').completer = filescompleter
+        optparser.add_argument(FILE_OR_DIR, nargs='*').completer=filescompleter
         return optparser
 
     def parse_setoption(self, args, option, namespace=None):
@@ -699,7 +670,7 @@ def attrs(self):
         if self._attrs.get('help'):
             a = self._attrs['help']
             a = a.replace('%default', '%(default)s')
-            # a = a.replace('%prog', '%(prog)s')
+            #a = a.replace('%prog', '%(prog)s')
             self._attrs['help'] = a
         return self._attrs
 
@@ -783,7 +754,7 @@ def __init__(self, parser, extra_info=None):
             extra_info = {}
         self._parser = parser
         argparse.ArgumentParser.__init__(self, usage=parser._usage,
-                                         add_help=False, formatter_class=DropShorterLongHelpFormatter)
+            add_help=False, formatter_class=DropShorterLongHelpFormatter)
         # extra_info is a dict of (param -> value) to display if there's
         # an usage error to provide more contextual information to the user
         self.extra_info = extra_info
@@ -811,10 +782,9 @@ class DropShorterLongHelpFormatter(argparse.HelpFormatter):
     - shortcut if there are only two options and one of them is a short one
     - cache result on action object as this is called at least 2 times
     """
-
     def _format_action_invocation(self, action):
         orgstr = argparse.HelpFormatter._format_action_invocation(self, action)
-        if orgstr and orgstr[0] != '-':  # only optional arguments
+        if orgstr and orgstr[0] != '-': # only optional arguments
             return orgstr
         res = getattr(action, '_formatted_action_invocation', None)
         if res:
@@ -825,7 +795,7 @@ def _format_action_invocation(self, action):
             action._formatted_action_invocation = orgstr
             return orgstr
         return_list = []
-        option_map = getattr(action, 'map_long_option', {})
+        option_map =  getattr(action, 'map_long_option', {})
         if option_map is None:
             option_map = {}
         short_long = {}
@@ -843,7 +813,7 @@ def _format_action_invocation(self, action):
                     short_long[shortened] = xxoption
         # now short_long has been filled out to the longest with dashes
         # **and** we keep the right option ordering from add_argument
-        for option in options:
+        for option in options: #
             if len(option) == 2 or option[2] == ' ':
                 return_list.append(option)
             if option[2:] == short_long.get(option.replace('-', '')):
@@ -852,26 +822,22 @@ def _format_action_invocation(self, action):
         return action._formatted_action_invocation
 
 
+
 def _ensure_removed_sysmodule(modname):
     try:
         del sys.modules[modname]
     except KeyError:
         pass
 
-
 class CmdOptions(object):
     """ holds cmdline options as attributes."""
-
     def __init__(self, values=()):
         self.__dict__.update(values)
-
     def __repr__(self):
-        return "<CmdOptions %r>" % (self.__dict__,)
-
+        return "<CmdOptions %r>" %(self.__dict__,)
     def copy(self):
         return CmdOptions(self.__dict__)
 
-
 class Notset:
     def __repr__(self):
         return "<NOTSET>"
@@ -881,18 +847,6 @@ def __repr__(self):
 FILE_OR_DIR = 'file_or_dir'
 
 
-def _iter_rewritable_modules(package_files):
-    for fn in package_files:
-        is_simple_module = '/' not in fn and fn.endswith('.py')
-        is_package = fn.count('/') == 1 and fn.endswith('__init__.py')
-        if is_simple_module:
-            module_name, _ = os.path.splitext(fn)
-            yield module_name
-        elif is_package:
-            package_name = os.path.dirname(fn)
-            yield package_name
-
-
 class Config(object):
     """ access to configuration values, pluginmanager and plugin hooks.  """
 
@@ -910,7 +864,6 @@ def __init__(self, pluginmanager):
         self.trace = self.pluginmanager.trace.root.get("config")
         self.hook = self.pluginmanager.hook
         self._inicache = {}
-        self._override_ini = ()
         self._opt2dest = {}
         self._cleanup = []
         self._warn = self.pluginmanager._warn
@@ -943,11 +896,11 @@ def _ensure_unconfigure(self):
             fin = self._cleanup.pop()
             fin()
 
-    def warn(self, code, message, fslocation=None, nodeid=None):
+    def warn(self, code, message, fslocation=None):
         """ generate a warning for this test session. """
         self.hook.pytest_logwarning.call_historic(kwargs=dict(
             code=code, message=message,
-            fslocation=fslocation, nodeid=nodeid))
+            fslocation=fslocation, nodeid=None))
 
     def get_terminal_writer(self):
         return self.pluginmanager.get_plugin("terminalreporter")._tw
@@ -963,14 +916,14 @@ def notify_exception(self, excinfo, option=None):
         else:
             style = "native"
         excrepr = excinfo.getrepr(funcargs=True,
-                                  showlocals=getattr(option, 'showlocals', False),
-                                  style=style,
-                                  )
+            showlocals=getattr(option, 'showlocals', False),
+            style=style,
+        )
         res = self.hook.pytest_internalerror(excrepr=excrepr,
                                              excinfo=excinfo)
         if not py.builtin.any(res):
             for line in str(excrepr).split("\n"):
-                sys.stderr.write("INTERNALERROR> %s\n" % line)
+                sys.stderr.write("INTERNALERROR> %s\n" %line)
                 sys.stderr.flush()
 
     def cwd_relative_nodeid(self, nodeid):
@@ -1011,9 +964,8 @@ def _initini(self, args):
         self.invocation_dir = py.path.local()
         self._parser.addini('addopts', 'extra command line options', 'args')
         self._parser.addini('minversion', 'minimally required pytest version')
-        self._override_ini = ns.override_ini or ()
 
-    def _consider_importhook(self, args):
+    def _consider_importhook(self, args, entrypoint_name):
         """Install the PEP 302 import hook if using assertion re-writing.
 
         Needs to parse the --assert=<mode> option from the commandline
@@ -1028,34 +980,26 @@ def _consider_importhook(self, args):
             except SystemError:
                 mode = 'plain'
             else:
-                self._mark_plugins_for_rewrite(hook)
+                import pkg_resources
+                self.pluginmanager.rewrite_hook = hook
+                for entrypoint in pkg_resources.iter_entry_points('pytest11'):
+                    # 'RECORD' available for plugins installed normally (pip install)
+                    # 'SOURCES.txt' available for plugins installed in dev mode (pip install -e)
+                    # for installed plugins 'SOURCES.txt' returns an empty list, and vice-versa
+                    # so it shouldn't be an issue
+                    for metadata in ('RECORD', 'SOURCES.txt'):
+                        for entry in entrypoint.dist._get_metadata(metadata):
+                            fn = entry.split(',')[0]
+                            is_simple_module = os.sep not in fn and fn.endswith('.py')
+                            is_package = fn.count(os.sep) == 1 and fn.endswith('__init__.py')
+                            if is_simple_module:
+                                module_name, ext = os.path.splitext(fn)
+                                hook.mark_rewrite(module_name)
+                            elif is_package:
+                                package_name = os.path.dirname(fn)
+                                hook.mark_rewrite(package_name)
         self._warn_about_missing_assertion(mode)
 
-    def _mark_plugins_for_rewrite(self, hook):
-        """
-        Given an importhook, mark for rewrite any top-level
-        modules or packages in the distribution package for
-        all pytest plugins.
-        """
-        import pkg_resources
-        self.pluginmanager.rewrite_hook = hook
-
-        # 'RECORD' available for plugins installed normally (pip install)
-        # 'SOURCES.txt' available for plugins installed in dev mode (pip install -e)
-        # for installed plugins 'SOURCES.txt' returns an empty list, and vice-versa
-        # so it shouldn't be an issue
-        metadata_files = 'RECORD', 'SOURCES.txt'
-
-        package_files = (
-            entry.split(',')[0]
-            for entrypoint in pkg_resources.iter_entry_points('pytest11')
-            for metadata in metadata_files
-            for entry in entrypoint.dist._get_metadata(metadata)
-        )
-
-        for name in _iter_rewritable_modules(package_files):
-            hook.mark_rewrite(name)
-
     def _warn_about_missing_assertion(self, mode):
         try:
             assert False
@@ -1079,17 +1023,19 @@ def _preparse(self, args, addopts=True):
             args[:] = shlex.split(os.environ.get('PYTEST_ADDOPTS', '')) + args
             args[:] = self.getini("addopts") + args
         self._checkversion()
-        self._consider_importhook(args)
+        entrypoint_name = 'pytest11'
+        self._consider_importhook(args, entrypoint_name)
         self.pluginmanager.consider_preparse(args)
-        self.pluginmanager.load_setuptools_entrypoints('pytest11')
+        self.pluginmanager.load_setuptools_entrypoints(entrypoint_name)
         self.pluginmanager.consider_env()
         self.known_args_namespace = ns = self._parser.parse_known_args(args, namespace=self.option.copy())
+        confcutdir = self.known_args_namespace.confcutdir
         if self.known_args_namespace.confcutdir is None and self.inifile:
             confcutdir = py.path.local(self.inifile).dirname
             self.known_args_namespace.confcutdir = confcutdir
         try:
             self.hook.pytest_load_initial_conftests(early_config=self,
-                                                    args=args, parser=self._parser)
+                    args=args, parser=self._parser)
         except ConftestImportFailure:
             e = sys.exc_info()[1]
             if ns.help or ns.version:
@@ -1107,32 +1053,28 @@ def _checkversion(self):
             myver = pytest.__version__.split(".")
             if myver < ver:
                 raise pytest.UsageError(
-                    "%s:%d: requires pytest-%s, actual pytest-%s'" % (
-                        self.inicfg.config.path, self.inicfg.lineof('minversion'),
-                        minver, pytest.__version__))
+                    "%s:%d: requires pytest-%s, actual pytest-%s'" %(
+                    self.inicfg.config.path, self.inicfg.lineof('minversion'),
+                    minver, pytest.__version__))
 
     def parse(self, args, addopts=True):
         # parse given cmdline arguments into this config object.
         assert not hasattr(self, 'args'), (
-            "can only parse cmdline args at most once per Config object")
+                "can only parse cmdline args at most once per Config object")
         self._origargs = args
         self.hook.pytest_addhooks.call_historic(
-            kwargs=dict(pluginmanager=self.pluginmanager))
+                                  kwargs=dict(pluginmanager=self.pluginmanager))
         self._preparse(args, addopts=addopts)
         # XXX deprecated hook:
         self.hook.pytest_cmdline_preparse(config=self, args=args)
-        self._parser.after_preparse = True
-        try:
-            args = self._parser.parse_setoption(args, self.option, namespace=self.option)
+        args = self._parser.parse_setoption(args, self.option, namespace=self.option)
+        if not args:
+            cwd = os.getcwd()
+            if cwd == self.rootdir:
+                args = self.getini('testpaths')
             if not args:
-                cwd = os.getcwd()
-                if cwd == self.rootdir:
-                    args = self.getini('testpaths')
-                if not args:
-                    args = [cwd]
-            self.args = args
-        except PrintHelp:
-            pass
+                args = [cwd]
+        self.args = args
 
     def addinivalue_line(self, name, line):
         """ add a line to an ini-file option. The option must have been
@@ -1140,12 +1082,12 @@ def addinivalue_line(self, name, line):
         the first line in its value. """
         x = self.getini(name)
         assert isinstance(x, list)
-        x.append(line)  # modifies the cached list inline
+        x.append(line) # modifies the cached list inline
 
     def getini(self, name):
         """ return configuration value from an :ref:`ini file <inifiles>`. If the
         specified name hasn't been registered through a prior
-        :py:func:`parser.addini <_pytest.config.Parser.addini>`
+        :py:func:`parser.addini <pytest.config.Parser.addini>`
         call (usually from a plugin), a ValueError is raised. """
         try:
             return self._inicache[name]
@@ -1157,7 +1099,7 @@ def _getini(self, name):
         try:
             description, type, default = self._parser._inidict[name]
         except KeyError:
-            raise ValueError("unknown configuration value: %r" % (name,))
+            raise ValueError("unknown configuration value: %r" %(name,))
         value = self._get_override_ini_value(name)
         if value is None:
             try:
@@ -1170,10 +1112,10 @@ def _getini(self, name):
                 return []
         if type == "pathlist":
             dp = py.path.local(self.inicfg.config.path).dirpath()
-            values = []
+            l = []
             for relpath in shlex.split(value):
-                values.append(dp.join(relpath, abs=True))
-            return values
+                l.append(dp.join(relpath, abs=True))
+            return l
         elif type == "args":
             return shlex.split(value)
         elif type == "linelist":
@@ -1190,13 +1132,13 @@ def _getconftest_pathlist(self, name, path):
         except KeyError:
             return None
         modpath = py.path.local(mod.__file__).dirpath()
-        values = []
+        l = []
         for relroot in relroots:
             if not isinstance(relroot, py.path.local):
                 relroot = relroot.replace("/", py.path.local.sep)
                 relroot = modpath.join(relroot, abs=True)
-            values.append(relroot)
-        return values
+            l.append(relroot)
+        return l
 
     def _get_override_ini_value(self, name):
         value = None
@@ -1204,14 +1146,15 @@ def _get_override_ini_value(self, name):
         # and -o foo1=bar1 -o foo2=bar2 options
         # always use the last item if multiple value set for same ini-name,
         # e.g. -o foo=bar1 -o foo=bar2 will set foo to bar2
-        for ini_config_list in self._override_ini:
-            for ini_config in ini_config_list:
-                try:
-                    (key, user_ini_value) = ini_config.split("=", 1)
-                except ValueError:
-                    raise UsageError("-o/--override-ini expects option=value style.")
-                if key == name:
-                    value = user_ini_value
+        if self.getoption("override_ini", None):
+            for ini_config_list in self.option.override_ini:
+                for ini_config in ini_config_list:
+                    try:
+                        (key, user_ini_value) = ini_config.split("=", 1)
+                    except ValueError:
+                        raise UsageError("-o/--override-ini expects option=value style.")
+                    if key == name:
+                        value = user_ini_value
         return value
 
     def getoption(self, name, default=notset, skip=False):
@@ -1234,7 +1177,7 @@ def getoption(self, name, default=notset, skip=False):
                 return default
             if skip:
                 import pytest
-                pytest.skip("no %r option found" % (name,))
+                pytest.skip("no %r option found" %(name,))
             raise ValueError("no option named %r" % (name,))
 
     def getvalue(self, name, path=None):
@@ -1245,14 +1188,12 @@ def getvalueorskip(self, name, path=None):
         """ (deprecated, use getoption(skip=True)) """
         return self.getoption(name, skip=True)
 
-
 def exists(path, ignore=EnvironmentError):
     try:
         return path.check()
     except ignore:
         return False
 
-
 def getcfg(args, warnfunc=None):
     """
     Search the list of arguments for a valid ini-file for pytest,
@@ -1287,20 +1228,25 @@ def getcfg(args, warnfunc=None):
     return None, None, None
 
 
-def get_common_ancestor(paths):
+def get_common_ancestor(args):
+    # args are what we get after early command line parsing (usually
+    # strings, but can be py.path.local objects as well)
     common_ancestor = None
-    for path in paths:
-        if not path.exists():
+    for arg in args:
+        if str(arg)[0] == "-":
+            continue
+        p = py.path.local(arg)
+        if not p.exists():
             continue
         if common_ancestor is None:
-            common_ancestor = path
+            common_ancestor = p
         else:
-            if path.relto(common_ancestor) or path == common_ancestor:
+            if p.relto(common_ancestor) or p == common_ancestor:
                 continue
-            elif common_ancestor.relto(path):
-                common_ancestor = path
+            elif common_ancestor.relto(p):
+                common_ancestor = p
             else:
-                shared = path.common(common_ancestor)
+                shared = p.common(common_ancestor)
                 if shared is not None:
                     common_ancestor = shared
     if common_ancestor is None:
@@ -1311,29 +1257,9 @@ def get_common_ancestor(paths):
 
 
 def get_dirs_from_args(args):
-    def is_option(x):
-        return str(x).startswith('-')
-
-    def get_file_part_from_node_id(x):
-        return str(x).split('::')[0]
-
-    def get_dir_from_path(path):
-        if path.isdir():
-            return path
-        return py.path.local(path.dirname)
-
-    # These look like paths but may not exist
-    possible_paths = (
-        py.path.local(get_file_part_from_node_id(arg))
-        for arg in args
-        if not is_option(arg)
-    )
-
-    return [
-        get_dir_from_path(path)
-        for path in possible_paths
-        if path.exists()
-    ]
+    return [d for d in (py.path.local(x) for x in args
+                        if not str(x).startswith("-"))
+            if d.exists()]
 
 
 def determine_setup(inifile, args, warnfunc=None):
@@ -1356,7 +1282,7 @@ def determine_setup(inifile, args, warnfunc=None):
                 rootdir, inifile, inicfg = getcfg(dirs, warnfunc=warnfunc)
                 if rootdir is None:
                     rootdir = get_common_ancestor([py.path.local(), ancestor])
-                    is_fs_root = os.path.splitdrive(str(rootdir))[1] == '/'
+                    is_fs_root = os.path.splitdrive(str(rootdir))[1] == os.sep
                     if is_fs_root:
                         rootdir = ancestor
     return rootdir, inifile, inicfg or {}
@@ -1378,7 +1304,7 @@ def setns(obj, dic):
         else:
             setattr(obj, name, value)
             obj.__all__.append(name)
-            # if obj != pytest:
+            #if obj != pytest:
             #    pytest.__all__.append(name)
             setattr(pytest, name, value)
 

lib/spack/external/_pytest/debugging.py

@@ -1,8 +1,10 @@
 """ interactive debugging with PDB, the Python Debugger. """
-from __future__ import absolute_import, division, print_function
+from __future__ import absolute_import
 import pdb
 import sys
 
+import pytest
+
 
 def pytest_addoption(parser):
     group = parser.getgroup("general")
@@ -14,17 +16,19 @@ def pytest_addoption(parser):
         help="start a custom interactive Python debugger on errors. "
              "For example: --pdbcls=IPython.terminal.debugger:TerminalPdb")
 
+def pytest_namespace():
+    return {'set_trace': pytestPDB().set_trace}
 
 def pytest_configure(config):
-    if config.getvalue("usepdb_cls"):
-        modname, classname = config.getvalue("usepdb_cls").split(":")
-        __import__(modname)
-        pdb_cls = getattr(sys.modules[modname], classname)
-    else:
-        pdb_cls = pdb.Pdb
-
-    if config.getvalue("usepdb"):
+    if config.getvalue("usepdb") or config.getvalue("usepdb_cls"):
         config.pluginmanager.register(PdbInvoke(), 'pdbinvoke')
+        if config.getvalue("usepdb_cls"):
+            modname, classname = config.getvalue("usepdb_cls").split(":")
+            __import__(modname)
+            pdb_cls = getattr(sys.modules[modname], classname)
+        else:
+            pdb_cls = pdb.Pdb
+        pytestPDB._pdb_cls = pdb_cls
 
     old = (pdb.set_trace, pytestPDB._pluginmanager)
 
@@ -33,33 +37,30 @@ def fin():
         pytestPDB._config = None
         pytestPDB._pdb_cls = pdb.Pdb
 
-    pdb.set_trace = pytestPDB.set_trace
+    pdb.set_trace = pytest.set_trace
     pytestPDB._pluginmanager = config.pluginmanager
     pytestPDB._config = config
-    pytestPDB._pdb_cls = pdb_cls
     config._cleanup.append(fin)
 
-
 class pytestPDB:
     """ Pseudo PDB that defers to the real pdb. """
     _pluginmanager = None
     _config = None
     _pdb_cls = pdb.Pdb
 
-    @classmethod
-    def set_trace(cls):
+    def set_trace(self):
         """ invoke PDB set_trace debugging, dropping any IO capturing. """
         import _pytest.config
         frame = sys._getframe().f_back
-        if cls._pluginmanager is not None:
-            capman = cls._pluginmanager.getplugin("capturemanager")
+        if self._pluginmanager is not None:
+            capman = self._pluginmanager.getplugin("capturemanager")
             if capman:
                 capman.suspendcapture(in_=True)
-            tw = _pytest.config.create_terminal_writer(cls._config)
+            tw = _pytest.config.create_terminal_writer(self._config)
             tw.line()
             tw.sep(">", "PDB set_trace (IO-capturing turned off)")
-            cls._pluginmanager.hook.pytest_enter_pdb(config=cls._config)
-        cls._pdb_cls().set_trace(frame)
+            self._pluginmanager.hook.pytest_enter_pdb(config=self._config)
+        self._pdb_cls().set_trace(frame)
 
 
 class PdbInvoke:
@@ -73,7 +74,7 @@ def pytest_exception_interact(self, node, call, report):
 
     def pytest_internalerror(self, excrepr, excinfo):
         for line in str(excrepr).split("\n"):
-            sys.stderr.write("INTERNALERROR> %s\n" % line)
+            sys.stderr.write("INTERNALERROR> %s\n" %line)
             sys.stderr.flush()
         tb = _postmortem_traceback(excinfo)
         post_mortem(tb)

lib/spack/external/_pytest/deprecated.py

@@ -5,15 +5,10 @@
 Keeping it in a central location makes it easy to track what is deprecated and should
 be removed when the time comes.
 """
-from __future__ import absolute_import, division, print_function
-
-
-class RemovedInPytest4Warning(DeprecationWarning):
-    """warning class for features removed in pytest 4.0"""
 
 
 MAIN_STR_ARGS = 'passing a string to pytest.main() is deprecated, ' \
-    'pass a list of arguments instead.'
+                      'pass a list of arguments instead.'
 
 YIELD_TESTS = 'yield tests are deprecated, and scheduled to be removed in pytest 4.0'
 
@@ -26,17 +21,4 @@ class RemovedInPytest4Warning(DeprecationWarning):
 
 GETFUNCARGVALUE = "use of getfuncargvalue is deprecated, use getfixturevalue"
 
-RESULT_LOG = (
-    '--result-log is deprecated and scheduled for removal in pytest 4.0.\n'
-    'See https://docs.pytest.org/en/latest/usage.html#creating-resultlog-format-files for more information.'
-)
-
-MARK_INFO_ATTRIBUTE = RemovedInPytest4Warning(
-    "MarkInfo objects are deprecated as they contain the merged marks"
-)
-
-MARK_PARAMETERSET_UNPACKING = RemovedInPytest4Warning(
-    "Applying marks directly to parameters is deprecated,"
-    " please use pytest.param(..., marks=...) instead.\n"
-    "For more details, see: https://docs.pytest.org/en/latest/parametrize.html"
-)
+RESULT_LOG = '--result-log is deprecated and scheduled for removal in pytest 4.0'

lib/spack/external/_pytest/doctest.py

@@ -1,5 +1,5 @@
 """ discover and run doctests in modules and test files."""
-from __future__ import absolute_import, division, print_function
+from __future__ import absolute_import
 
 import traceback
 
@@ -22,29 +22,27 @@
     DOCTEST_REPORT_CHOICE_ONLY_FIRST_FAILURE,
 )
 
-
 def pytest_addoption(parser):
     parser.addini('doctest_optionflags', 'option flags for doctests',
-                  type="args", default=["ELLIPSIS"])
-    parser.addini("doctest_encoding", 'encoding used for doctest files', default="utf-8")
+        type="args", default=["ELLIPSIS"])
     group = parser.getgroup("collect")
     group.addoption("--doctest-modules",
-                    action="store_true", default=False,
-                    help="run doctests in all .py modules",
-                    dest="doctestmodules")
+        action="store_true", default=False,
+        help="run doctests in all .py modules",
+        dest="doctestmodules")
     group.addoption("--doctest-report",
-                    type=str.lower, default="udiff",
-                    help="choose another output format for diffs on doctest failure",
-                    choices=DOCTEST_REPORT_CHOICES,
-                    dest="doctestreport")
+        type=str.lower, default="udiff",
+        help="choose another output format for diffs on doctest failure",
+        choices=DOCTEST_REPORT_CHOICES,
+        dest="doctestreport")
     group.addoption("--doctest-glob",
-                    action="append", default=[], metavar="pat",
-                    help="doctests file matching pattern, default: test*.txt",
-                    dest="doctestglob")
+        action="append", default=[], metavar="pat",
+        help="doctests file matching pattern, default: test*.txt",
+        dest="doctestglob")
     group.addoption("--doctest-ignore-import-errors",
-                    action="store_true", default=False,
-                    help="ignore doctest ImportErrors",
-                    dest="doctest_ignore_import_errors")
+        action="store_true", default=False,
+        help="ignore doctest ImportErrors",
+        dest="doctest_ignore_import_errors")
 
 
 def pytest_collect_file(path, parent):
@@ -120,7 +118,7 @@ def repr_failure(self, excinfo):
                 lines = ["%03d %s" % (i + test.lineno + 1, x)
                          for (i, x) in enumerate(lines)]
                 # trim docstring error lines to 10
-                lines = lines[max(example.lineno - 9, 0):example.lineno + 1]
+                lines = lines[example.lineno - 9:example.lineno + 1]
             else:
                 lines = ['EXAMPLE LOCATION UNKNOWN, not showing all tests of that example']
                 indent = '>>>'
@@ -129,18 +127,18 @@ def repr_failure(self, excinfo):
                     indent = '...'
             if excinfo.errisinstance(doctest.DocTestFailure):
                 lines += checker.output_difference(example,
-                                                   doctestfailure.got, report_choice).split("\n")
+                        doctestfailure.got, report_choice).split("\n")
             else:
                 inner_excinfo = ExceptionInfo(excinfo.value.exc_info)
                 lines += ["UNEXPECTED EXCEPTION: %s" %
-                          repr(inner_excinfo.value)]
+                            repr(inner_excinfo.value)]
                 lines += traceback.format_exception(*excinfo.value.exc_info)
             return ReprFailDoctest(reprlocation, lines)
         else:
             return super(DoctestItem, self).repr_failure(excinfo)
 
     def reportinfo(self):
-        return self.fspath, self.dtest.lineno, "[doctest] %s" % self.name
+        return self.fspath, None, "[doctest] %s" % self.name
 
 
 def _get_flag_lookup():
@@ -173,16 +171,15 @@ def collect(self):
 
         # inspired by doctest.testfile; ideally we would use it directly,
         # but it doesn't support passing a custom checker
-        encoding = self.config.getini("doctest_encoding")
-        text = self.fspath.read_text(encoding)
+        text = self.fspath.read()
         filename = str(self.fspath)
         name = self.fspath.basename
         globs = {'__name__': '__main__'}
 
+
         optionflags = get_optionflags(self)
         runner = doctest.DebugRunner(verbose=0, optionflags=optionflags,
                                      checker=_get_checker())
-        _fix_spoof_python2(runner, encoding)
 
         parser = doctest.DocTestParser()
         test = parser.get_doctest(text, globs, name, filename, 0)
@@ -218,7 +215,6 @@ def collect(self):
         optionflags = get_optionflags(self)
         runner = doctest.DebugRunner(verbose=0, optionflags=optionflags,
                                      checker=_get_checker())
-
         for test in finder.find(module, module.__name__):
             if test.examples:  # skip empty doctests
                 yield DoctestItem(test.name, self, runner, test)
@@ -327,33 +323,6 @@ def _get_report_choice(key):
         DOCTEST_REPORT_CHOICE_NONE: 0,
     }[key]
 
-
-def _fix_spoof_python2(runner, encoding):
-    """
-    Installs a "SpoofOut" into the given DebugRunner so it properly deals with unicode output. This
-    should patch only doctests for text files because they don't have a way to declare their
-    encoding. Doctests in docstrings from Python modules don't have the same problem given that
-    Python already decoded the strings.
-
-    This fixes the problem related in issue #2434.
-    """
-    from _pytest.compat import _PY2
-    if not _PY2:
-        return
-
-    from doctest import _SpoofOut
-
-    class UnicodeSpoof(_SpoofOut):
-
-        def getvalue(self):
-            result = _SpoofOut.getvalue(self)
-            if encoding:
-                result = result.decode(encoding)
-            return result
-
-    runner._fakeout = UnicodeSpoof()
-
-
 @pytest.fixture(scope='session')
 def doctest_namespace():
     """

lib/spack/external/_pytest/fixtures.py

@@ -1,39 +1,22 @@
-from __future__ import absolute_import, division, print_function
-
-import inspect
 import sys
-import warnings
 
-import py
 from py._code.code import FormattedExcinfo
 
+import py
+import pytest
+import warnings
+
+import inspect
 import _pytest
-from _pytest import nodes
 from _pytest._code.code import TerminalRepr
 from _pytest.compat import (
     NOTSET, exc_clear, _format_args,
     getfslineno, get_real_func,
     is_generator, isclass, getimfunc,
     getlocation, getfuncargnames,
-    safe_getattr,
-    FuncargnamesCompatAttr,
 )
-from _pytest.outcomes import fail, TEST_OUTCOME
-
-
-if sys.version_info[:2] == (2, 6):
-    from ordereddict import OrderedDict
-else:
-    from collections import OrderedDict  # nopyqver
-
 
 def pytest_sessionstart(session):
-    import _pytest.python
-    scopename2class.update({
-        'class': _pytest.python.Class,
-        'module': _pytest.python.Module,
-        'function': _pytest.main.Item,
-    })
     session._fixturemanager = FixtureManager(session)
 
 
@@ -46,7 +29,6 @@ def pytest_sessionstart(session):
 scope2props["instance"] = scope2props["class"] + ("instance", )
 scope2props["function"] = scope2props["instance"] + ("function", "keywords")
 
-
 def scopeproperty(name=None, doc=None):
     def decoratescope(func):
         scopename = name or func.__name__
@@ -61,6 +43,19 @@ def provide(self):
     return decoratescope
 
 
+def pytest_namespace():
+    scopename2class.update({
+        'class': pytest.Class,
+        'module': pytest.Module,
+        'function': pytest.Item,
+    })
+    return {
+        'fixture': fixture,
+        'yield_fixture': yield_fixture,
+        'collect': {'_fillfuncargs': fillfixtures}
+    }
+
+
 def get_scope_node(node, scope):
     cls = scopename2class.get(scope)
     if cls is None:
@@ -78,7 +73,7 @@ def add_funcarg_pseudo_fixture_def(collector, metafunc, fixturemanager):
     # XXX we can probably avoid this algorithm  if we modify CallSpec2
     # to directly care for creating the fixturedefs within its methods.
     if not metafunc._calls[0].funcargs:
-        return  # this function call does not have direct parametrization
+        return # this function call does not have direct parametrization
     # collect funcargs of all callspecs into a list of values
     arg2params = {}
     arg2scope = {}
@@ -108,32 +103,36 @@ def add_funcarg_pseudo_fixture_def(collector, metafunc, fixturemanager):
         if scope != "function":
             node = get_scope_node(collector, scope)
             if node is None:
-                assert scope == "class" and isinstance(collector, _pytest.python.Module)
+                assert scope == "class" and isinstance(collector, pytest.Module)
                 # use module-level collector for class-scope (for now)
                 node = collector
         if node and argname in node._name2pseudofixturedef:
             arg2fixturedefs[argname] = [node._name2pseudofixturedef[argname]]
         else:
-            fixturedef = FixtureDef(fixturemanager, '', argname,
-                                    get_direct_param_fixture_func,
-                                    arg2scope[argname],
-                                    valuelist, False, False)
+            fixturedef =  FixtureDef(fixturemanager, '', argname,
+                           get_direct_param_fixture_func,
+                           arg2scope[argname],
+                           valuelist, False, False)
             arg2fixturedefs[argname] = [fixturedef]
             if node is not None:
                 node._name2pseudofixturedef[argname] = fixturedef
 
 
+
 def getfixturemarker(obj):
     """ return fixturemarker or None if it doesn't exist or raised
     exceptions."""
     try:
         return getattr(obj, "_pytestfixturefunction", None)
-    except TEST_OUTCOME:
+    except KeyboardInterrupt:
+        raise
+    except Exception:
         # some objects raise errors like request (from flask import request)
         # we don't expect them to be fixture functions
         return None
 
 
+
 def get_parametrized_fixture_keys(item, scopenum):
     """ return list of keys for all parametrized arguments which match
     the specified scope. """
@@ -143,10 +142,10 @@ def get_parametrized_fixture_keys(item, scopenum):
     except AttributeError:
         pass
     else:
-        # cs.indices.items() is random order of argnames.  Need to
-        # sort this so that different calls to
-        # get_parametrized_fixture_keys will be deterministic.
-        for argname, param_index in sorted(cs.indices.items()):
+        # cs.indictes.items() is random order of argnames but
+        # then again different functions (items) can change order of
+        # arguments so it doesn't matter much probably
+        for argname, param_index in cs.indices.items():
             if cs._arg2scopenum[argname] != scopenum:
                 continue
             if scopenum == 0:    # session
@@ -168,21 +167,20 @@ def reorder_items(items):
     for scopenum in range(0, scopenum_function):
         argkeys_cache[scopenum] = d = {}
         for item in items:
-            keys = OrderedDict.fromkeys(get_parametrized_fixture_keys(item, scopenum))
+            keys = set(get_parametrized_fixture_keys(item, scopenum))
             if keys:
                 d[item] = keys
     return reorder_items_atscope(items, set(), argkeys_cache, 0)
 
-
 def reorder_items_atscope(items, ignore, argkeys_cache, scopenum):
     if scopenum >= scopenum_function or len(items) < 3:
         return items
     items_done = []
     while 1:
         items_before, items_same, items_other, newignore = \
-            slice_items(items, ignore, argkeys_cache[scopenum])
+                slice_items(items, ignore, argkeys_cache[scopenum])
         items_before = reorder_items_atscope(
-            items_before, ignore, argkeys_cache, scopenum + 1)
+                            items_before, ignore, argkeys_cache,scopenum+1)
         if items_same is None:
             # nothing to reorder in this scope
             assert items_other is None
@@ -203,9 +201,9 @@ def slice_items(items, ignore, scoped_argkeys_cache):
         for i, item in enumerate(it):
             argkeys = scoped_argkeys_cache.get(item)
             if argkeys is not None:
-                newargkeys = OrderedDict.fromkeys(k for k in argkeys if k not in ignore)
-                if newargkeys:  # found a slicing key
-                    slicing_argkey, _ = newargkeys.popitem()
+                argkeys = argkeys.difference(ignore)
+                if argkeys:  # found a slicing key
+                    slicing_argkey = argkeys.pop()
                     items_before = items[:i]
                     items_same = [item]
                     items_other = []
@@ -213,7 +211,7 @@ def slice_items(items, ignore, scoped_argkeys_cache):
                     for item in it:
                         argkeys = scoped_argkeys_cache.get(item)
                         if argkeys and slicing_argkey in argkeys and \
-                                slicing_argkey not in ignore:
+                            slicing_argkey not in ignore:
                             items_same.append(item)
                         else:
                             items_other.append(item)
@@ -223,6 +221,17 @@ def slice_items(items, ignore, scoped_argkeys_cache):
     return items, None, None, None
 
 
+
+class FuncargnamesCompatAttr:
+    """ helper class so that Metafunc, Function and FixtureRequest
+    don't need to each define the "funcargnames" compatibility attribute.
+    """
+    @property
+    def funcargnames(self):
+        """ alias attribute for ``fixturenames`` for pre-2.3 compatibility"""
+        return self.fixturenames
+
+
 def fillfixtures(function):
     """ fill missing funcargs for a test function. """
     try:
@@ -245,10 +254,10 @@ def fillfixtures(function):
         request._fillfixtures()
 
 
+
 def get_direct_param_fixture_func(request):
     return request.param
 
-
 class FuncFixtureInfo:
     def __init__(self, argnames, names_closure, name2fixturedefs):
         self.argnames = argnames
@@ -287,6 +296,7 @@ def node(self):
         """ underlying collection node (depends on current request scope)"""
         return self._getscopeitem(self.scope)
 
+
     def _getnextfixturedef(self, argname):
         fixturedefs = self._arg2fixturedefs.get(argname, None)
         if fixturedefs is None:
@@ -308,6 +318,7 @@ def config(self):
         """ the pytest config object associated with this request. """
         return self._pyfuncitem.config
 
+
     @scopeproperty()
     def function(self):
         """ test function object if the request has a per-function scope. """
@@ -316,7 +327,7 @@ def function(self):
     @scopeproperty("class")
     def cls(self):
         """ class (can be None) where the test function was collected. """
-        clscol = self._pyfuncitem.getparent(_pytest.python.Class)
+        clscol = self._pyfuncitem.getparent(pytest.Class)
         if clscol:
             return clscol.obj
 
@@ -334,7 +345,7 @@ def instance(self):
     @scopeproperty()
     def module(self):
         """ python module object where the test function was collected. """
-        return self._pyfuncitem.getparent(_pytest.python.Module).obj
+        return self._pyfuncitem.getparent(pytest.Module).obj
 
     @scopeproperty()
     def fspath(self):
@@ -403,7 +414,7 @@ def cached_setup(self, setup, teardown=None, scope="module", extrakey=None):
         :arg extrakey: added to internal caching key of (funcargname, scope).
         """
         if not hasattr(self.config, '_setupcache'):
-            self.config._setupcache = {}  # XXX weakref?
+            self.config._setupcache = {} # XXX weakref?
         cachekey = (self.fixturename, self._getscopeitem(scope), extrakey)
         cache = self.config._setupcache
         try:
@@ -434,8 +445,7 @@ def getfuncargvalue(self, argname):
         from _pytest import deprecated
         warnings.warn(
             deprecated.GETFUNCARGVALUE,
-            DeprecationWarning,
-            stacklevel=2)
+            DeprecationWarning)
         return self.getfixturevalue(argname)
 
     def _get_active_fixturedef(self, argname):
@@ -460,13 +470,13 @@ class PseudoFixtureDef:
 
     def _get_fixturestack(self):
         current = self
-        values = []
+        l = []
         while 1:
             fixturedef = getattr(current, "_fixturedef", None)
             if fixturedef is None:
-                values.reverse()
-                return values
-            values.append(fixturedef)
+                l.reverse()
+                return l
+            l.append(fixturedef)
             current = current._parent_request
 
     def _getfixturevalue(self, fixturedef):
@@ -498,7 +508,7 @@ def _getfixturevalue(self, fixturedef):
                         source_lineno,
                     )
                 )
-                fail(msg)
+                pytest.fail(msg)
         else:
             # indices might not be set if old-style metafunc.addcall() was used
             param_index = funcitem.callspec.indices.get(argname, 0)
@@ -531,11 +541,11 @@ def _check_scope(self, argname, invoking_scope, requested_scope):
         if scopemismatch(invoking_scope, requested_scope):
             # try to report something helpful
             lines = self._factorytraceback()
-            fail("ScopeMismatch: You tried to access the %r scoped "
-                 "fixture %r with a %r scoped request object, "
-                 "involved factories\n%s" % (
-                     (requested_scope, argname, invoking_scope, "\n".join(lines))),
-                 pytrace=False)
+            pytest.fail("ScopeMismatch: You tried to access the %r scoped "
+                "fixture %r with a %r scoped request object, "
+                "involved factories\n%s" %(
+                (requested_scope, argname, invoking_scope, "\n".join(lines))),
+                pytrace=False)
 
     def _factorytraceback(self):
         lines = []
@@ -544,7 +554,7 @@ def _factorytraceback(self):
             fs, lineno = getfslineno(factory)
             p = self._pyfuncitem.session.fspath.bestrelpath(fs)
             args = _format_args(factory)
-            lines.append("%s:%d:  def %s%s" % (
+            lines.append("%s:%d:  def %s%s" %(
                 p, lineno, factory.__name__, args))
         return lines
 
@@ -560,13 +570,12 @@ def _getscopeitem(self, scope):
         return node
 
     def __repr__(self):
-        return "<FixtureRequest for %r>" % (self.node)
+        return "<FixtureRequest for %r>" %(self.node)
 
 
 class SubRequest(FixtureRequest):
     """ a sub request for handling getting a fixture from a
     test function/fixture. """
-
     def __init__(self, request, scope, param, param_index, fixturedef):
         self._parent_request = request
         self.fixturename = fixturedef.argname
@@ -575,8 +584,9 @@ def __init__(self, request, scope, param, param_index, fixturedef):
         self.param_index = param_index
         self.scope = scope
         self._fixturedef = fixturedef
+        self.addfinalizer = fixturedef.addfinalizer
         self._pyfuncitem = request._pyfuncitem
-        self._fixture_values = request._fixture_values
+        self._fixture_values  = request._fixture_values
         self._fixture_defs = request._fixture_defs
         self._arg2fixturedefs = request._arg2fixturedefs
         self._arg2index = request._arg2index
@@ -585,9 +595,6 @@ def __init__(self, request, scope, param, param_index, fixturedef):
     def __repr__(self):
         return "<SubRequest %r for %r>" % (self.fixturename, self._pyfuncitem)
 
-    def addfinalizer(self, finalizer):
-        self._fixturedef.addfinalizer(finalizer)
-
 
 class ScopeMismatchError(Exception):
     """ A fixture function tries to use a different fixture function which
@@ -619,7 +626,6 @@ def scope2index(scope, descr, where=None):
 
 class FixtureLookupError(LookupError):
     """ could not return a requested Fixture (missing or invalid). """
-
     def __init__(self, argname, request, msg=None):
         self.argname = argname
         self.request = request
@@ -642,9 +648,9 @@ def formatrepr(self):
                 lines, _ = inspect.getsourcelines(get_real_func(function))
             except (IOError, IndexError, TypeError):
                 error_msg = "file %s, line %s: source code not available"
-                addline(error_msg % (fspath, lineno + 1))
+                addline(error_msg % (fspath, lineno+1))
             else:
-                addline("file %s, line %s" % (fspath, lineno + 1))
+                addline("file %s, line %s" % (fspath, lineno+1))
                 for i, line in enumerate(lines):
                     line = line.rstrip()
                     addline("  " + line)
@@ -660,7 +666,7 @@ def formatrepr(self):
                 if faclist and name not in available:
                     available.append(name)
             msg = "fixture %r not found" % (self.argname,)
-            msg += "\n available fixtures: %s" % (", ".join(sorted(available)),)
+            msg += "\n available fixtures: %s" %(", ".join(sorted(available)),)
             msg += "\n use 'pytest --fixtures [testpath]' for help on them."
 
         return FixtureLookupErrorRepr(fspath, lineno, tblines, msg, self.argname)
@@ -686,16 +692,15 @@ def toterminal(self, tw):
                 tw.line('{0}       {1}'.format(FormattedExcinfo.flow_marker,
                                                line.strip()), red=True)
         tw.line()
-        tw.line("%s:%d" % (self.filename, self.firstlineno + 1))
+        tw.line("%s:%d" % (self.filename, self.firstlineno+1))
 
 
 def fail_fixturefunc(fixturefunc, msg):
     fs, lineno = getfslineno(fixturefunc)
-    location = "%s:%s" % (fs, lineno + 1)
+    location = "%s:%s" % (fs, lineno+1)
     source = _pytest._code.Source(fixturefunc)
-    fail(msg + ":\n\n" + str(source.indent()) + "\n" + location,
-         pytrace=False)
-
+    pytest.fail(msg + ":\n\n" + str(source.indent()) + "\n" + location,
+                pytrace=False)
 
 def call_fixture_func(fixturefunc, request, kwargs):
     yieldctx = is_generator(fixturefunc)
@@ -710,7 +715,7 @@ def teardown():
                 pass
             else:
                 fail_fixturefunc(fixturefunc,
-                                 "yield_fixture function has more than one 'yield'")
+                    "yield_fixture function has more than one 'yield'")
 
         request.addfinalizer(teardown)
     else:
@@ -720,7 +725,6 @@ def teardown():
 
 class FixtureDef:
     """ A container for a factory definition. """
-
     def __init__(self, fixturemanager, baseid, argname, func, scope, params,
                  unittest=False, ids=None):
         self._fixturemanager = fixturemanager
@@ -745,19 +749,10 @@ def addfinalizer(self, finalizer):
         self._finalizer.append(finalizer)
 
     def finish(self):
-        exceptions = []
         try:
             while self._finalizer:
-                try:
-                    func = self._finalizer.pop()
-                    func()
-                except:  # noqa
-                    exceptions.append(sys.exc_info())
-            if exceptions:
-                e = exceptions[0]
-                del exceptions  # ensure we don't keep all frames alive because of the traceback
-                py.builtin._reraise(*e)
-
+                func = self._finalizer.pop()
+                func()
         finally:
             ihook = self._fixturemanager.session.ihook
             ihook.pytest_fixture_post_finalizer(fixturedef=self)
@@ -795,7 +790,6 @@ def __repr__(self):
         return ("<FixtureDef name=%r scope=%r baseid=%r >" %
                 (self.argname, self.scope, self.baseid))
 
-
 def pytest_fixture_setup(fixturedef, request):
     """ Execution of fixture setup. """
     kwargs = {}
@@ -821,7 +815,7 @@ def pytest_fixture_setup(fixturedef, request):
     my_cache_key = request.param_index
     try:
         result = call_fixture_func(fixturefunc, request, kwargs)
-    except TEST_OUTCOME:
+    except Exception:
         fixturedef.cached_result = (None, my_cache_key, sys.exc_info())
         raise
     fixturedef.cached_result = (result, my_cache_key, None)
@@ -839,16 +833,17 @@ def __init__(self, scope, params, autouse=False, ids=None, name=None):
     def __call__(self, function):
         if isclass(function):
             raise ValueError(
-                "class fixtures not supported (may be in the future)")
+                    "class fixtures not supported (may be in the future)")
         function._pytestfixturefunction = self
         return function
 
 
+
 def fixture(scope="function", params=None, autouse=False, ids=None, name=None):
     """ (return a) decorator to mark a fixture factory function.
 
-    This decorator can be used (with or without parameters) to define a
-    fixture function.  The name of the fixture function can later be
+    This decorator can be used (with or or without parameters) to define
+    a fixture function.  The name of the fixture function can later be
     referenced to cause its invocation ahead of running tests: test
     modules or classes can use the pytest.mark.usefixtures(fixturename)
     marker.  Test functions can directly use fixture names as input
@@ -867,25 +862,25 @@ def fixture(scope="function", params=None, autouse=False, ids=None, name=None):
                 reference is needed to activate the fixture.
 
     :arg ids: list of string ids each corresponding to the params
-                so that they are part of the test id. If no ids are provided
-                they will be generated automatically from the params.
+       so that they are part of the test id. If no ids are provided
+       they will be generated automatically from the params.
 
     :arg name: the name of the fixture. This defaults to the name of the
-                decorated function. If a fixture is used in the same module in
-                which it is defined, the function name of the fixture will be
-                shadowed by the function arg that requests the fixture; one way
-                to resolve this is to name the decorated function
-                ``fixture_<fixturename>`` and then use
-                ``@pytest.fixture(name='<fixturename>')``.
+               decorated function. If a fixture is used in the same module in
+               which it is defined, the function name of the fixture will be
+               shadowed by the function arg that requests the fixture; one way
+               to resolve this is to name the decorated function
+               ``fixture_<fixturename>`` and then use
+               ``@pytest.fixture(name='<fixturename>')``.
 
     Fixtures can optionally provide their values to test functions using a ``yield`` statement,
     instead of ``return``. In this case, the code block after the ``yield`` statement is executed
     as teardown code regardless of the test outcome. A fixture function must yield exactly once.
     """
-    if callable(scope) and params is None and autouse is False:
+    if callable(scope) and params is None and autouse == False:
         # direct decoration
         return FixtureFunctionMarker(
-            "function", params, autouse, name=name)(scope)
+                "function", params, autouse, name=name)(scope)
     if params is not None and not isinstance(params, (list, tuple)):
         params = list(params)
     return FixtureFunctionMarker(scope, params, autouse, ids=ids, name=name)
@@ -900,7 +895,7 @@ def yield_fixture(scope="function", params=None, autouse=False, ids=None, name=N
     if callable(scope) and params is None and not autouse:
         # direct decoration
         return FixtureFunctionMarker(
-            "function", params, autouse, ids=ids, name=name)(scope)
+                "function", params, autouse, ids=ids, name=name)(scope)
     else:
         return FixtureFunctionMarker(scope, params, autouse, ids=ids, name=name)
 
@@ -959,9 +954,14 @@ def __init__(self, session):
         self._nodeid_and_autousenames = [("", self.config.getini("usefixtures"))]
         session.config.pluginmanager.register(self, "funcmanage")
 
+
     def getfixtureinfo(self, node, func, cls, funcargs=True):
         if funcargs and not hasattr(node, "nofuncargs"):
-            argnames = getfuncargnames(func, cls=cls)
+            if cls is not None:
+                startindex = 1
+            else:
+                startindex = None
+            argnames = getfuncargnames(func, startindex)
         else:
             argnames = ()
         usefixtures = getattr(func, "usefixtures", None)
@@ -985,8 +985,8 @@ def pytest_plugin_registered(self, plugin):
             # by their test id)
             if p.basename.startswith("conftest.py"):
                 nodeid = p.dirpath().relto(self.config.rootdir)
-                if p.sep != nodes.SEP:
-                    nodeid = nodeid.replace(p.sep, nodes.SEP)
+                if p.sep != "/":
+                    nodeid = nodeid.replace(p.sep, "/")
         self.parsefactories(plugin, nodeid)
 
     def _getautousenames(self, nodeid):
@@ -996,7 +996,7 @@ def _getautousenames(self, nodeid):
             if nodeid.startswith(baseid):
                 if baseid:
                     i = len(baseid)
-                    nextchar = nodeid[i:i + 1]
+                    nextchar = nodeid[i:i+1]
                     if nextchar and nextchar not in ":/":
                         continue
                 autousenames.extend(basenames)
@@ -1041,14 +1041,9 @@ def pytest_generate_tests(self, metafunc):
             if faclist:
                 fixturedef = faclist[-1]
                 if fixturedef.params is not None:
-                    parametrize_func = getattr(metafunc.function, 'parametrize', None)
-                    func_params = getattr(parametrize_func, 'args', [[None]])
-                    func_kwargs = getattr(parametrize_func, 'kwargs', {})
+                    func_params = getattr(getattr(metafunc.function, 'parametrize', None), 'args', [[None]])
                     # skip directly parametrized arguments
-                    if "argnames" in func_kwargs:
-                        argnames = parametrize_func.kwargs["argnames"]
-                    else:
-                        argnames = func_params[0]
+                    argnames = func_params[0]
                     if not isinstance(argnames, (tuple, list)):
                         argnames = [x.strip() for x in argnames.split(",") if x.strip()]
                     if argname not in func_params and argname not in argnames:
@@ -1073,9 +1068,7 @@ def parsefactories(self, node_or_obj, nodeid=NOTSET, unittest=False):
         self._holderobjseen.add(holderobj)
         autousenames = []
         for name in dir(holderobj):
-            # The attribute can be an arbitrary descriptor, so the attribute
-            # access below can raise. safe_getatt() ignores such exceptions.
-            obj = safe_getattr(holderobj, name, None)
+            obj = getattr(holderobj, name, None)
             # fixture functions have a pytest_funcarg__ prefix (pre-2.3 style)
             # or are "@pytest.fixture" marked
             marker = getfixturemarker(obj)
@@ -1086,7 +1079,7 @@ def parsefactories(self, node_or_obj, nodeid=NOTSET, unittest=False):
                     continue
                 marker = defaultfuncargprefixmarker
                 from _pytest import deprecated
-                self.config.warn('C1', deprecated.FUNCARG_PREFIX.format(name=name), nodeid=nodeid)
+                self.config.warn('C1', deprecated.FUNCARG_PREFIX.format(name=name))
                 name = name[len(self._argprefix):]
             elif not isinstance(marker, FixtureFunctionMarker):
                 # magic globals  with __getattr__ might have got us a wrong
@@ -1136,5 +1129,6 @@ def getfixturedefs(self, argname, nodeid):
 
     def _matchfactories(self, fixturedefs, nodeid):
         for fixturedef in fixturedefs:
-            if nodes.ischildnode(fixturedef.baseid, nodeid):
+            if nodeid.startswith(fixturedef.baseid):
                 yield fixturedef
+

lib/spack/external/_pytest/freeze_support.py

@@ -2,7 +2,9 @@
 Provides a function to report all internal modules for using freezing tools
 pytest
 """
-from __future__ import absolute_import, division, print_function
+
+def pytest_namespace():
+    return {'freeze_includes': freeze_includes}
 
 
 def freeze_includes():

lib/spack/external/_pytest/helpconfig.py

@@ -1,61 +1,25 @@
 """ version info, help messages, tracing configuration.  """
-from __future__ import absolute_import, division, print_function
-
 import py
 import pytest
-from _pytest.config import PrintHelp
-import os
-import sys
-from argparse import Action
-
-
-class HelpAction(Action):
-    """This is an argparse Action that will raise an exception in
-    order to skip the rest of the argument parsing when --help is passed.
-    This prevents argparse from quitting due to missing required arguments
-    when any are defined, for example by ``pytest_addoption``.
-    This is similar to the way that the builtin argparse --help option is
-    implemented by raising SystemExit.
-    """
-
-    def __init__(self,
-                 option_strings,
-                 dest=None,
-                 default=False,
-                 help=None):
-        super(HelpAction, self).__init__(
-            option_strings=option_strings,
-            dest=dest,
-            const=True,
-            default=default,
-            nargs=0,
-            help=help)
-
-    def __call__(self, parser, namespace, values, option_string=None):
-        setattr(namespace, self.dest, self.const)
-
-        # We should only skip the rest of the parsing after preparse is done
-        if getattr(parser._parser, 'after_preparse', False):
-            raise PrintHelp
-
+import os, sys
 
 def pytest_addoption(parser):
     group = parser.getgroup('debugconfig')
     group.addoption('--version', action="store_true",
-                    help="display pytest lib version and import information.")
-    group._addoption("-h", "--help", action=HelpAction, dest="help",
-                     help="show help message and configuration info")
-    group._addoption('-p', action="append", dest="plugins", default=[],
-                     metavar="name",
-                     help="early-load given plugin (multi-allowed). "
-                     "To avoid loading of plugins, use the `no:` prefix, e.g. "
-                     "`no:doctest`.")
+            help="display pytest lib version and import information.")
+    group._addoption("-h", "--help", action="store_true", dest="help",
+            help="show help message and configuration info")
+    group._addoption('-p', action="append", dest="plugins", default = [],
+               metavar="name",
+               help="early-load given plugin (multi-allowed). "
+                    "To avoid loading of plugins, use the `no:` prefix, e.g. "
+                    "`no:doctest`.")
     group.addoption('--traceconfig', '--trace-config',
-                    action="store_true", default=False,
-                    help="trace considerations of conftest.py files."),
+               action="store_true", default=False,
+               help="trace considerations of conftest.py files."),
     group.addoption('--debug',
-                    action="store_true", dest="debug", default=False,
-                    help="store internal tracing debug information in 'pytestdebug.log'.")
+               action="store_true", dest="debug", default=False,
+               help="store internal tracing debug information in 'pytestdebug.log'.")
     group._addoption(
         '-o', '--override-ini', nargs='*', dest="override_ini",
         action="append",
@@ -70,10 +34,10 @@ def pytest_cmdline_parse():
         path = os.path.abspath("pytestdebug.log")
         debugfile = open(path, 'w')
         debugfile.write("versions pytest-%s, py-%s, "
-                        "python-%s\ncwd=%s\nargs=%s\n\n" % (
-                            pytest.__version__, py.__version__,
-                            ".".join(map(str, sys.version_info)),
-                            os.getcwd(), config._origargs))
+                "python-%s\ncwd=%s\nargs=%s\n\n" %(
+            pytest.__version__, py.__version__,
+            ".".join(map(str, sys.version_info)),
+            os.getcwd(), config._origargs))
         config.trace.root.setwriter(debugfile.write)
         undo_tracing = config.pluginmanager.enable_tracing()
         sys.stderr.write("writing pytestdebug information to %s\n" % path)
@@ -87,12 +51,11 @@ def unset_tracing():
 
         config.add_cleanup(unset_tracing)
 
-
 def pytest_cmdline_main(config):
     if config.option.version:
         p = py.path.local(pytest.__file__)
         sys.stderr.write("This is pytest version %s, imported from %s\n" %
-                         (pytest.__version__, p))
+            (pytest.__version__, p))
         plugininfo = getpluginversioninfo(config)
         if plugininfo:
             for line in plugininfo:
@@ -104,7 +67,6 @@ def pytest_cmdline_main(config):
         config._ensure_unconfigure()
         return 0
 
-
 def showhelp(config):
     reporter = config.pluginmanager.get_plugin('terminalreporter')
     tw = reporter._tw
@@ -120,7 +82,7 @@ def showhelp(config):
         if type is None:
             type = "string"
         spec = "%s (%s)" % (name, type)
-        line = "  %-24s %s" % (spec, help)
+        line = "  %-24s %s" %(spec, help)
         tw.line(line[:tw.fullwidth])
 
     tw.line()
@@ -149,7 +111,6 @@ def showhelp(config):
     ('pytest_plugins', 'list of plugin names to load'),
 ]
 
-
 def getpluginversioninfo(config):
     lines = []
     plugininfo = config.pluginmanager.list_plugin_distinfo()
@@ -161,12 +122,11 @@ def getpluginversioninfo(config):
             lines.append("  " + content)
     return lines
 
-
 def pytest_report_header(config):
     lines = []
     if config.option.debug or config.option.traceconfig:
         lines.append("using: pytest-%s pylib-%s" %
-                     (pytest.__version__, py.__version__))
+            (pytest.__version__,py.__version__))
 
         verinfo = getpluginversioninfo(config)
         if verinfo:
@@ -180,5 +140,5 @@ def pytest_report_header(config):
                 r = plugin.__file__
             else:
                 r = repr(plugin)
-            lines.append("    %-20s: %s" % (name, r))
+            lines.append("    %-20s: %s" %(name, r))
     return lines