update CHANGELOG.md for 0.13.2

`spack module loads` and `spack module find` previously failed if any upstream modules were missing.  This prevented it from being used with upstreams (or, really, any spack instance) that blacklisted modules.

This PR makes module finding is now more lenient (especially for blacklisted modules).

- `spack module find` now does not report an error if the spec is blacklisted
  - instead, it prints a single warning if any modules will be omitted from the loads file
  - It comments the missing modules out of the loads file so the user can see what's missing
  - Debug messages are also printed so users can check this with `spack -d...`

- also added tests for new functionality

.codecov.yml

@@ -4,33 +4,13 @@ coverage:
   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"
+      default: yes
 
 ignore:
   - lib/spack/spack/test/.*
-  - lib/spack/env/.*
   - lib/spack/docs/.*
   - lib/spack/external/.*
+  - share/spack/qa/.*
+  - share/spack/spack-completion.bash
 
 comment: off

.coveragerc

@@ -7,7 +7,6 @@ branch = True
 source = lib
 omit =
      lib/spack/spack/test/*
-     lib/spack/env/*
      lib/spack/docs/*
      lib/spack/external/*
 

.dockerignore

@@ -0,0 +1,11 @@
+.git/*
+opt/spack/*
+
+/etc/spack/*
+!/etc/spack/defaults
+
+share/spack/dotkit/*
+share/spack/lmod/*
+share/spack/modules/*
+lib/spack/spack/test/*
+

.flake8

@@ -1,21 +1,32 @@
 # -*- conf -*-
 # flake8 settings for Spack core files.
 #
-# These exceptions ar for Spack core files. We're slightly more lenient
+# These exceptions are for Spack core files. We're slightly more lenient
 # with packages.  See .flake8_packages for that.
 #
-# Let people line things up nicely:
+# E1: Indentation
 # - E129: visually indented line with same indent as next logical line
+#
+# E2: Whitespace
 # - E221: multiple spaces before operator
 # - E241: multiple spaces after ','
 # - E272: multiple spaces before keyword
 #
-# Let people use terse Python features:
-# - E731: lambda expressions
+# E7: Statement
+# - E731: do not assign a lambda expression, use a def
+#
+# W5: Line break warning
+# - W503: line break before binary operator
+# - W504: line break after binary operator
 #
 # These are required to get the package.py files to test clean:
 # - F999: syntax error in doctest
 #
+# N8: PEP8-naming
+# - N801: class names should use CapWords convention
+# - N813: camelcase imported as lowercase
+# - N814: camelcase imported as constant
+#
 [flake8]
-ignore = E129,E221,E241,E272,E731,F999
+ignore = E129,E221,E241,E272,E731,W503,W504,F999,N801,N813,N814
 max-line-length = 79

.flake8_packages

@@ -7,16 +7,18 @@
 # 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
+# Note that we also add *per-line* exemptions for certain patterns 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:
+# F4: Import
 # - F405: `name` may be undefined, or undefined from star imports: `module`
-# - F821: undefined name `name` (needed for cmake, configure, etc.)
+#
+# F8: Name
+# - F821: undefined name `name`
 #
 [flake8]
-ignore = E129,E221,E241,E272,E731,F999,F405,F821
+ignore = E129,E221,E241,E272,E731,W503,W504,F405,F821,F999,N801,N813,N814
 max-line-length = 79

.github/CODE_OF_CONDUCT.md

@@ -1,4 +1,4 @@
-# Contributor Covenant Code of Conduct
+# Spack Community Code of Conduct
 
 ## Our Pledge
 
@@ -30,7 +30,7 @@ Project maintainers have the right and responsibility to remove, edit, or reject
 
 ## 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.
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the Spack project or its community. Examples of representing the 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 the project may be further defined and clarified by Spack maintainers.
 
 ## Enforcement
 

.github/CONTRIBUTING.md

@@ -0,0 +1,8 @@
+# Contributing to Spack
+
+All contributions to Spack must be made under both the Apache License,
+Version 2.0 (Apache-2.0) and the MIT license (MIT).
+
+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.

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,49 @@
+---
+name: Bug report 
+about: Report a bug in the core of Spack (command not working as expected, etc.) 
+labels: bug
+---
+
+
+*Explain, in a clear and concise way, the command you ran and the result you were trying to achieve.
+Example: "I ran Spack find to list all the installed packages and..."*
+
+
+
+### Steps to reproduce the issue
+
+```console
+$ spack <command1> <spec>
+$ spack <command2> <spec>
+...
+```
+
+### Error Message
+
+If Spack reported an error, provide the error message. If it did not report an error
+but the output appears incorrect, provide the incorrect output. If there was no error
+message and no output but the result is incorrect, describe how it does not match
+what you expect. To provide more information you might re-run the commands with 
+the additional -d/--stacktrace flags:
+```console
+$ spack -d --stacktrace <command1> <spec>
+$ spack -d --stacktrace <command2> <spec>
+...
+```
+that activate the full debug output. 
+
+
+### 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!

.github/ISSUE_TEMPLATE/build_error.md

@@ -0,0 +1,78 @@
+---
+name: Build error 
+about: Some package in Spack didn't build correctly  
+labels: "build-error"
+---
+
+*Thanks for taking the time to report this build failure. To proceed with the
+report please:*
+1. Title the issue "Installation issue: <name-of-the-package>".
+2. Provide the information required below.
+3. Remove the template instructions before posting the issue.
+
+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!
+
+
+---
+
+### Steps to reproduce the issue
+
+```console
+$ spack install <spec> # Fill in the exact spec you are using
+... # and the relevant part of the error message
+```
+
+### Platform and user environment
+
+Please report your OS here:
+```commandline
+$ uname -a 
+Linux nuvolari 4.15.0-29-generic #31-Ubuntu SMP Tue Jul 17 15:39:52 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
+$ lsb_release -d
+Description:	Ubuntu 18.04.1 LTS
+``` 
+and, if relevant, post or attach:
+
+- `packages.yaml`
+- `compilers.yaml`
+
+to the issue
+
+### Additional information
+
+Sometimes the issue benefits from additional details. In these cases there are
+a few things we can suggest doing. First of all, you can post the full output of:
+```console
+$ spack spec --install-status <spec>
+...
+```
+to show people whether Spack installed a faulty software or if it was not able to
+build it at all. 
+
+If your build didn't make it past the configure stage, Spack as also commands to parse 
+logs and report error and warning messages:
+```console
+$ spack log-parse --show=errors,warnings <file-to-parse>
+```
+You might want to run this command on the `config.log` or any other similar file
+found in the stage directory: 
+```console
+$ spack location -s <spec>
+```
+In case in `config.log` there are other settings that you think might be the cause 
+of the build failure, you can consider attaching the file to this issue.
+
+Rebuilding the package with the following options:
+```console
+$ spack -d install -j 1 <spec>
+...
+```
+will provide additional debug information. After the failure you will find two files in the current directory:
+
+1. `spack-cc-<spec>.in`, which contains details on the command given in input 
+    to Spack's compiler wrapper  
+1. `spack-cc-<spec>.out`, which contains the command used to compile / link the 
+    failed object after Spack's compiler wrapper did its processing 
+
+You can post or attach those files to provide maintainers with more information on what
+is causing the failure.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,28 @@
+---
+name: Feature request 
+about: Suggest adding a feature that is not yet in Spack  
+labels: feature
+
+---
+
+*Please add a concise summary of your suggestion here.*
+
+### Rationale
+
+*Is your feature request related to a problem? Please describe it!*
+
+### Description
+
+*Describe the solution you'd like and the alternatives you have considered.*
+
+
+### Additional information
+*Add any other context about the feature request here.*
+
+
+-----
+
+
+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!

.github/actions/add-maintainers-as-reviewers/Dockerfile

@@ -0,0 +1,6 @@
+FROM python:3.7-alpine
+
+RUN pip install pygithub
+
+ADD entrypoint.py /entrypoint.py
+ENTRYPOINT ["/entrypoint.py"]

.github/actions/add-maintainers-as-reviewers/entrypoint.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+#
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Maintainer review action.
+
+This action checks which packages have changed in a PR, and adds their
+maintainers to the pull request for review.
+"""
+
+import json
+import os
+import re
+import subprocess
+
+from github import Github
+
+
+def spack(*args):
+    """Run the spack executable with arguments, and return the output split.
+
+    This does just enough to run `spack pkg` and `spack maintainers`, the
+    two commands used by this action.
+    """
+    github_workspace = os.environ['GITHUB_WORKSPACE']
+    spack = os.path.join(github_workspace, 'bin', 'spack')
+    output = subprocess.check_output([spack] + list(args))
+    split = re.split(r'\s*', output.decode('utf-8').strip())
+    return [s for s in split if s]
+
+
+def main():
+    # get these first so that we'll fail early
+    token = os.environ['GITHUB_TOKEN']
+    event_path = os.environ['GITHUB_EVENT_PATH']
+
+    with open(event_path) as file:
+        data = json.load(file)
+
+    # make sure it's a pull_request event
+    assert 'pull_request' in data
+
+    # only request reviews on open, edit, or reopen
+    action = data['action']
+    if action not in ('opened', 'edited', 'reopened'):
+        return
+
+    # get data from the event payload
+    pr_data             = data['pull_request']
+    base_branch_name    = pr_data['base']['ref']
+    full_repo_name      = pr_data['base']['repo']['full_name']
+    pr_number           = pr_data['number']
+    requested_reviewers = pr_data['requested_reviewers']
+    author              = pr_data['user']['login']
+
+    # get a list of packages that this PR modified
+    changed_pkgs = spack(
+        'pkg', 'changed', '--type', 'ac', '%s...' % base_branch_name)
+
+    # get maintainers for all modified packages
+    maintainers = set()
+    for pkg in changed_pkgs:
+        pkg_maintainers = set(spack('maintainers', pkg))
+        maintainers |= pkg_maintainers
+
+    # remove any maintainers who are already on the PR, and the author,
+    # as you can't review your own PR)
+    maintainers -= set(requested_reviewers)
+    maintainers -= set([author])
+
+    if not maintainers:
+        return
+
+    # request reviews from each maintainer
+    gh = Github(token)
+    repo = gh.get_repo(full_repo_name)
+    pr = repo.get_pull(pr_number)
+    pr.create_review_request(list(maintainers))
+
+
+if __name__ == "__main__":
+    main()

.gitignore

@@ -1,6 +1,7 @@
 /db
 /var/spack/stage
 /var/spack/cache
+/var/spack/environments
 /var/spack/repos/*/index.yaml
 /var/spack/repos/*/lock
 *.pyc
@@ -19,7 +20,10 @@
 *.swp
 /htmlcov
 .coverage
-#*
+\#*
 .#*
-/.cache
+lib/spack/spack/test/.cache
 /bin/spackc
+*.in.log
+*.out.log
+*.orig

.gitlab-ci.yml

@@ -0,0 +1,14 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+generate ci jobs:
+  script:
+    - "./bin/generate-gitlab-ci-yml.sh"
+  tags:
+    - "spack-pre-ci"
+  artifacts:
+    paths:
+      - ci-generation
+    when: always

.mailmap

@@ -3,6 +3,7 @@ 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>
@@ -48,6 +49,7 @@ 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>

.readthedocs.yml

@@ -0,0 +1,9 @@
+version: 2
+
+sphinx:
+  configuration: lib/spack/docs/conf.py
+
+python:
+  version: 3.7
+  install:
+    - requirements: lib/spack/docs/requirements.txt

.travis.yml

@@ -11,119 +11,166 @@ branches:
 #=============================================================================
 # Build matrix
 #=============================================================================
+
+dist: xenial
+
 jobs:
   fast_finish: true
   include:
-    - stage: 'flake8'
-      python: '2.7'
+    - stage: 'style checks'
+      python: '3.8'
       os: linux
       language: python
       env: TEST_SUITE=flake8
-    - stage: 'unit tests + documentation'
-      python: '2.6'
+# Shell integration with module files
+    - python: '3.8'
       os: linux
       language: python
-      env: TEST_SUITE=unit
+      env: [ TEST_SUITE=bootstrap ]
+    - stage: 'unit tests + documentation'
+      python: '2.6'
+      dist: trusty
+      os: linux
+      language: python
+      env: [ TEST_SUITE=unit, COVERAGE=true ]
     - 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
+    - python: '3.7'
+      os: linux
+      language: python
+      env: TEST_SUITE=unit
+    - python: '3.8'
       os: linux
       language: python
       env: [ TEST_SUITE=unit, COVERAGE=true ]
-    - os: osx
-      language: generic
-      env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7, COVERAGE=true ]
-    - python: '2.7'
+    - python: '3.8'
       os: linux
       language: python
       env: TEST_SUITE=doc
+    - os: osx
+      language: generic
+      env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7, COVERAGE=true ]
+      if: type != pull_request
 # mpich (AutotoolsPackage)
     - stage: 'build tests'
       python: '2.7'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=mpich' ]
+      env: [ TEST_SUITE=build, 'SPEC=mpich' ]
 # astyle (MakefilePackage)
-    - python: '2.7'
+    - python: '3.8'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=astyle' ]
+      env: [ TEST_SUITE=build, 'SPEC=astyle' ]
 # tut (WafPackage)
-    - python: '2.7'
+    - python: '3.8'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=tut' ]
+      env: [ TEST_SUITE=build, 'SPEC=tut' ]
 # py-setuptools (PythonPackage)
-    - python: '2.7'
+    - python: '3.8'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=py-setuptools' ]
+      env: [ TEST_SUITE=build, 'SPEC=py-setuptools' ]
 # perl-dbi (PerlPackage)
-#    - python: '2.7'
+#    - python: '3.8'
 #      os: linux
 #      language: python
-#      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=perl-dbi' ]
+#      env: [ TEST_SUITE=build, 'SPEC=perl-dbi' ]
 # openjpeg (CMakePackage + external cmake)
-    - python: '2.7'
+    - python: '3.8'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=openjpeg' ]
+      env: [ TEST_SUITE=build, 'SPEC=openjpeg' ]
 # r-rcpp (RPackage + external R)
-    - python: '2.7'
+    - python: '3.8'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=r-rcpp' ]
+      env: [ TEST_SUITE=build, 'SPEC=r-rcpp' ]
 # mpich (AutotoolsPackage)
-    - python: '3.6'
+    - python: '3.8'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=mpich' ]
+      env: [ TEST_SUITE=build, 'SPEC=mpich' ]
+    - python: '3.8'
+      stage: 'docker build'
+      os: linux
+      language: python
+      env: TEST_SUITE=docker
+  allow_failures:
+    - env: TEST_SUITE=docker
+
+stages:
+  - 'style checks'
+  - 'unit tests + documentation'
+  - 'build tests'
+  - name: 'docker build'
+    if: type = push AND branch IN (develop, master)
+
 
 #=============================================================================
 # Environment
 #=============================================================================
-# Use new Travis infrastructure (Docker can't sudo yet)
-sudo: false
 
 # Docs need graphviz to build
 addons:
+  # for Linux builds, we use APT
   apt:
     packages:
+      - ccache
+      - cmake
       - gfortran
-      - mercurial
       - graphviz
       - gnupg2
-      - cmake
+      - kcov
+      - mercurial
+      - ninja-build
+      - perl
+      - perl-base
+      - realpath
       - r-base
       - r-base-core
       - r-base-dev
-      - perl
-      - perl-base
+      - zsh
+  # for Mac builds, we use Homebrew
+  homebrew:
+    packages:
+      - python@2
+      - gcc
+      - gnupg2
+      - ccache
+      - dash
+      - kcov
+    update: true
 
-cache: pip
+# ~/.ccache needs to be cached directly as Travis is not taking care of it
+# (possibly because we use 'language: python' and not 'language: c')
+cache:
+  pip: true
+  ccache: true
+  directories:
+    - ~/.mirror
+    - ~/.ccache
 
 # 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 [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions gcc    > /dev/null || brew install gcc;    fi
-  - if [[ "$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
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+        pip2 install --upgrade pip;
+        pip2 install virtualenv;
+        virtualenv venv;
+        source venv/bin/activate;
+    fi
+  - ccache -M 2G && ccache -z
 
 # Install various dependencies
 install:
@@ -132,7 +179,10 @@ install:
   - pip install --upgrade setuptools
   - pip install --upgrade codecov
   - pip install --upgrade flake8
-  - if [[ "$TEST_SUITE" == "doc" ]]; then pip install --upgrade -r lib/spack/docs/requirements.txt; fi
+  - pip install --upgrade pep8-naming
+  - if [[ "$TEST_SUITE" == "doc" ]]; then
+        pip install --upgrade -r lib/spack/docs/requirements.txt;
+    fi
 
 before_script:
   # Need this for the git tests to succeed.
@@ -140,18 +190,33 @@ before_script:
   - git config --global user.name "Test User"
 
   # Need this to be able to compute the list of changed files
-  - git fetch origin develop:develop
+  - git fetch origin ${TRAVIS_BRANCH}:${TRAVIS_BRANCH}
 
-  # Set up external dependencies for build tests, because the take too long to compile
-  - if [[ "$TEST_SUITE" == "build" ]]; then cp share/spack/qa/configuration/packages.yaml etc/spack/packages.yaml; fi
+  # Set up external deps for build tests, b/c they take too long to compile
+  - if [[ "$TEST_SUITE" == "build" ]]; then
+        cp share/spack/qa/configuration/*.yaml etc/spack/;
+    fi
 
 #=============================================================================
 # Building
 #=============================================================================
-script: share/spack/qa/run-$TEST_SUITE-tests
+services:
+  - docker
+
+script:
+  - share/spack/qa/run-$TEST_SUITE-tests
 
 after_success:
-  - codecov --env PY_VERSION
+  - ccache -s
+  - case "$TEST_SUITE" in
+        unit)
+            if [[ "$COVERAGE" == "true" ]]; then
+                codecov --env PYTHON_VERSION
+                        --required
+                        --flags "${TEST_SUITE}${TRAVIS_OS_NAME}";
+            fi
+            ;;
+    esac
 
 #=============================================================================
 # Notifications

CHANGELOG.md

@@ -0,0 +1,302 @@
+# v0.13.2 (2019-12-04)
+
+This release contains major performance improvements for Spack environments, as
+well as some bugfixes and minor changes.
+
+* allow missing modules if they are blacklisted (#13540)
+* speed up environment activation (#13557)
+* mirror path works for unknown versions (#13626)
+* environments: don't try to modify run-env if a spec is not installed (#13589)
+* use semicolons instead of newlines in module/python command (#13904)
+* verify.py: os.path.exists exception handling (#13656)
+* Document use of the maintainers field (#13479)
+* bugfix with config caching (#13755)
+* hwloc: added 'master' version pointing at the HEAD of the master branch (#13734)
+* config option to allow gpg warning suppression (#13744)
+* fix for relative symlinks when relocating binary packages (#13727)
+* allow binary relocation of strings in relative binaries (#13724)
+
+# v0.13.1 (2019-11-05)
+
+This is a bugfix release on top of `v0.13.0`.  Specific fixes include:
+
+* `spack find` now displays variants and other spec constraints
+* bugfix: uninstall should find concrete specs by DAG hash (#13598)
+* environments: make shell modifications partially unconditional (#13523)
+* binary distribution: relocate text files properly in relative binaries (#13578)
+* bugfix: fetch prefers to fetch local mirrors over remote resources (#13545)
+* environments: only write when necessary (#13546)
+* bugfix: spack.util.url.join() now handles absolute paths correctly (#13488)
+* sbang: use utf-8 for encoding when patching (#13490)
+* Specs with quoted flags containing spaces are parsed correctly (#13521)
+* targets: print a warning message before downgrading (#13513)
+* Travis CI: Test Python 3.8 (#13347)
+* Documentation: Database.query methods share docstrings (#13515)
+* cuda: fix conflict statements for x86-64 targets (#13472)
+* cpu: fix clang flags for generic x86_64 (#13491)
+* syaml_int type should use int.__repr__ rather than str.__repr__ (#13487)
+* elpa: prefer 2016.05.004 until sse/avx/avx2 issues are resolved (#13530)
+* trilinos: temporarily constrain netcdf@:4.7.1 (#13526)
+
+# v0.13.0 (2019-10-25)
+
+`v0.13.0` is our biggest Spack release yet, with *many* new major features.
+From facility deployment to improved environments, microarchitecture
+support, and auto-generated build farms, this release has features for all of
+our users.
+
+Spack grew by over 700 packages in the past year, and the project now has
+over 450 contributors.  Thanks to all of you for making this release possible.
+
+## Major new core features
+- Chaining: use dependencies from external "upstream" Spack instances
+- Environments now behave more like virtualenv/conda
+  - Each env has a *view*: a directory with all packages symlinked in
+  - Activating an environment sets `PATH`, `LD_LIBRARY_PATH`, `CPATH`,
+    `CMAKE_PREFIX_PATH`, `PKG_CONFIG_PATH`, etc. to point to this view.
+- Spack detects and builds specifically for your microarchitecture
+  - named, understandable targets like `skylake`, `broadwell`, `power9`, `zen2`
+  - Spack knows which compilers can build for which architectures
+  - Packages can easily query support for features like `avx512` and `sse3`
+  - You can pick a target with, e.g. `spack install foo target=icelake`
+- Spack stacks: combinatorial environments for facility deployment
+  - Environments can now build cartesian products of specs (with `matrix:`)
+  - Conditional syntax support to exclude certain builds from the stack
+- Projections: ability to build easily navigable symlink trees environments
+- Support no-source packages (BundlePackage) to aggregate related packages
+- Extensions: users can write custom commands that live outside of Spack repo
+- Support ARM and Fujitsu compilers
+
+## CI/build farm support
+- `spack release-jobs` can detect `package.py` changes and generate
+    `.gitlab-ci.yml` to create binaries for an environment or stack
+	in parallel (initial support -- will change in future release).
+- Results of build pipelines can be uploaded to a CDash server.
+- Spack can now upload/fetch from package mirrors in Amazon S3
+
+## New commands/options
+- `spack mirror create --all` downloads *all* package sources/resources/patches
+- `spack dev-build` runs phases of the install pipeline on the working directory
+- `spack deprecate` permanently symlinks an old, unwanted package to a new one
+- `spack verify` chcecks that packages' files match what was originally installed
+- `spack find --json` prints `JSON` that is easy to parse with, e.g. `jq`
+- `spack find --format FORMAT` allows you to flexibly print package metadata
+- `spack spec --json` prints JSON version of `spec.yaml`
+
+## Selected improvements
+- Auto-build requested compilers if they do not exist
+- Spack automatically adds `RPATHs` needed to make executables find compiler
+    runtime libraries (e.g., path to newer `libstdc++` in `icpc` or `g++`)
+- setup-env.sh is now compatible with Bash, Dash, and Zsh
+- Spack now caps build jobs at min(16, ncores) by default
+- `spack compiler find` now also throttles number of spawned processes
+- Spack now writes stage directories directly to `$TMPDIR` instead of
+    symlinking stages within `$spack/var/spack/cache`.
+- Improved and more powerful `spec` format strings
+- You can pass a `spec.yaml` file anywhere in the CLI you can type a spec.
+- Many improvements to binary caching
+- Gradually supporting new features from Environment Modules v4
+- `spack edit` respects `VISUAL` environment variable
+- Simplified package syntax for specifying build/run environment modifications
+- Numerous improvements to support for environments across Spack commands
+- Concretization improvements
+
+## Documentation
+- Multi-lingual documentation (Started a Japanese translation)
+- Tutorial now has its own site at spack-tutorial.readthedocs.io
+  - This enables us to keep multiple versions of the tutorial around
+
+## Deprecations
+- Spack no longer supports dotkit (LLNL's homegrown, now deprecated module tool)
+- `spack build`, `spack configure`, `spack diy` deprecated in favor of
+    `spack dev-build` and `spack install`
+
+## Important package changes
+- 3,563 total packages (718 added since 0.12.1)
+- Spack now defaults to Python 3 (previously preferred 2.7 by default)
+- Much improved ARM support thanks to Fugaku (RIKEN) and SNL teams
+- Support new special versions: master, trunk, and head (in addition to develop)
+- Better finding logic for libraries and headers
+
+
+# v0.12.1 (2018-11-13)
+
+This is a minor bugfix release, with a minor fix in the tutorial and a `flake8` fix.
+
+Bugfixes
+* Add `r` back to regex strings in binary distribution
+* Fix gcc install version in the tutorial
+
+
+# v0.12.0 (2018-11-13)
+
+## Major new features
+- Spack environments
+- `spack.yaml` and `spack.lock` files for tracking dependencies
+- Custom configurations via command line
+- Better support for linking Python packages into view directories
+- Packages have more control over compiler flags via flag handlers
+- Better support for module file generation
+- Better support for Intel compilers, Intel MPI, etc.
+- Many performance improvements, improved startup time
+
+## License
+- As of this release, all of Spack is permissively licensed under Apache-2.0 or MIT, at the user's option.
+- Consents from over 300 contributors were obtained to make this relicense possible.
+- Previous versions were distributed under the LGPL license, version 2.1.
+
+## New packages
+Over 2,900 packages (800 added since last year)
+
+Spack would not be possible without our community.  Thanks to all of our
+[contributors](https://github.com/spack/spack/graphs/contributors) for the
+new features and packages in this release!
+
+
+# v0.11.2 (2018-02-07)
+
+This release contains the following fixes:
+
+* Fixes for `gfortran` 7 compiler detection (#7017)
+* Fixes for exceptions thrown during module generation (#7173)
+
+
+# v0.11.1 (2018-01-19)
+
+This release contains bugfixes for compiler flag handling.  There were issues in `v0.11.0` that caused some packages to be built without proper optimization.
+
+Fixes:
+* Issue #6999: FFTW installed with Spack 0.11.0 gets built without optimisations
+
+Includes:
+* PR #6415: Fixes for flag handling behavior
+* PR #6960: Fix type issues with setting flag handlers
+* 880e319: Upstream fixes to `list_url` in various R packages
+
+
+# v0.11.0 (2018-01-17)
+
+Spack v0.11.0 contains many improvements since v0.10.0.
+Below is a summary of the major features, broken down by category.
+
+## New packages
+- Spack now has 2,178 packages (from 1,114 in v0.10.0)
+- Many more Python packages (356) and R packages (471)
+- 48 Exascale Proxy Apps (try `spack list -t proxy-app`)
+
+
+## Core features for users
+- Relocatable binary packages (`spack buildcache`, #4854)
+- Spack now fully supports Python 3 (#3395)
+- Packages can be tagged and searched by tags (#4786)
+- Custom module file templates using Jinja (#3183)
+- `spack bootstrap` command now sets up a basic module environment (#3057)
+- Simplified and better organized help output (#3033)
+- Improved, less redundant `spack install` output (#5714, #5950)
+- Reworked `spack dependents` and `spack dependencies` commands (#4478)
+
+
+## Major new features for packagers
+- Multi-valued variants (#2386)
+- New `conflicts()` directive (#3125)
+- New dependency type: `test` dependencies (#5132)
+- Packages can require their own patches on dependencies (#5476)
+  - `depends_on(..., patches=<patch list>)`
+- Build interface for passing linker information through Specs (#1875)
+  - Major packages that use blas/lapack now use this interface
+- Flag handlers allow packages more control over compiler flags (#6415)
+- Package subclasses support many more build systems:
+  - autotools, perl, qmake, scons, cmake, makefile, python, R, WAF
+  - package-level support for installing Intel HPC products (#4300)
+- `spack blame` command shows contributors to packages (#5522)
+- `spack create` now guesses many more build systems (#2707)
+- Better URL parsing to guess package version URLs (#2972)
+- Much improved `PythonPackage` support (#3367)
+
+
+## Core
+- Much faster concretization (#5716, #5783)
+- Improved output redirection (redirecting build output works properly #5084)
+- Numerous improvements to internal structure and APIs
+
+
+## Tutorials & Documentation
+- Many updates to documentation
+- [New tutorial material from SC17](https://spack.readthedocs.io/en/latest/tutorial.html)
+  - configuration
+  - build systems
+  - build interface
+  - working with module generation
+- Documentation on docker workflows and best practices
+
+
+## Selected improvements and bug fixes
+- No longer build Python eggs -- installations are plain directories (#3587)
+- Improved filtering of system paths from build PATHs and RPATHs (#2083, #3910)
+- Git submodules are properly handled on fetch (#3956)
+- Can now set default number of parallel build jobs in `config.yaml`
+- Improvements to `setup-env.csh` (#4044)
+- Better default compiler discovery on Mac OS X (#3427)
+  - clang will automatically mix with gfortran
+- Improved compiler detection on Cray machines (#3075)
+- Better support for IBM XL compilers
+- Better tab completion
+- Resume gracefully after prematurely terminated partial installs (#4331)
+- Better mesa support (#5170)
+
+
+Spack would not be possible without our community.  Thanks to all of our
+[contributors](https://github.com/spack/spack/graphs/contributors) for the
+new features and packages in this release!
+
+
+# v0.10.0 (2017-01-17)
+
+This is Spack `v0.10.0`.  With this release, we will start to push Spack
+releases more regularly.  This is the last Spack release without
+automated package testing.  With the next release, we will begin to run
+package tests in addition to unit tests.
+
+Spack has grown rapidly from 422 to
+[1,114 packages](https://spack.readthedocs.io/en/v0.10.0/package_list.html),
+thanks to the hard work of over 100 contributors.  Below is a condensed
+version of all the changes since `v0.9.1`.
+
+### Packages
+- Grew from 422 to 1,114 packages
+  - Includes major updates like X11, Qt
+  - Expanded HPC, R, and Python ecosystems
+
+### Core
+- Major speed improvements for spack find and concretization
+- Completely reworked architecture support
+  - Platforms can have front-end and back-end OS/target combinations
+  - Much better support for Cray and BG/Q cross-compiled environments
+- Downloads are now cached locally
+- Support installations in deeply nested directories: patch long shebangs using `sbang`
+
+### Basic usage
+- Easier global configuration via config.yaml
+  - customize install, stage, and cache locations
+- Hierarchical configuration scopes: default, site, user
+  - Platform-specific scopes allow better per-platform defaults
+- Ability to set `cflags`, `cxxflags`, `fflags` on the command line
+- YAML-configurable support for both Lmod and tcl modules in mainline
+- `spack install` supports --dirty option for emergencies
+
+### For developers
+- Support multiple dependency types: `build`, `link`, and `run`
+- Added `Package` base classes for custom build systems
+  - `AutotoolsPackage`, `CMakePackage`, `PythonPackage`, etc.
+  - `spack create` now guesses many more build systems
+- Development environment integration with `spack setup`
+- New interface to pass linking information via `spec` objects
+  - Currently used for `BLAS`/`LAPACK`/`SCALAPACK` libraries
+  - Polymorphic virtual dependency attributes: `spec['blas'].blas_libs`
+
+### Testing & Documentation
+- Unit tests run continuously on Travis CI for Mac and Linux
+- Switched from `nose` to `pytest` for unit tests.
+  - Unit tests take 1 minute now instead of 8
+- Massively expanded documentation
+- Docs are now hosted on [spack.readthedocs.io](http://spack.readthedocs.io)

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.

COPYRIGHT

@@ -0,0 +1,93 @@
+Intellectual Property Notice
+------------------------------
+
+Spack is licensed under the Apache License, Version 2.0 (LICENSE-APACHE
+or http://www.apache.org/licenses/LICENSE-2.0) or the MIT license,
+(LICENSE-MIT or http://opensource.org/licenses/MIT), at your option.
+
+Copyrights and patents in the Spack project are retained by contributors.
+No copyright assignment is required to contribute to Spack.
+
+Spack was originally distributed under the LGPL-2.1 license. Consent from
+contributors to relicense to Apache-2.0/MIT is documented at
+https://github.com/spack/spack/issues/9137.
+
+
+SPDX usage
+------------
+
+Individual files contain SPDX tags instead of the full license text.
+This enables machine processing of license information based on the SPDX
+License Identifiers that are available here: https://spdx.org/licenses/
+
+Files that are dual-licensed as Apache-2.0 OR MIT contain the following
+text in the license header:
+
+    SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+External Packages
+-------------------
+Spack bundles its external dependencies in lib/spack/external.  These
+packages are covered by various permissive licenses.  A summary listing
+follows.  See the license included with each package for full details.
+
+PackageName: argparse
+PackageHomePage: https://pypi.python.org/pypi/argparse
+PackageLicenseDeclared: Python-2.0
+
+PackageName: ctest_log_parser
+PackageHomePage: https://github.com/Kitware/CMake
+PackageLicenseDeclared: BSD-3-Clause
+
+PackageName: distro
+PackageHomePage: https://pypi.python.org/pypi/distro
+PackageLicenseDeclared: Apache-2.0
+
+PackageName: functools
+PackageHomePage: https://github.com/python/cpython/blob/2.7/Lib/functools.py
+PackageLicenseDeclared: Python-2.0
+
+PackageName: jinja2
+PackageHomePage: https://pypi.python.org/pypi/Jinja2
+PackageLicenseDeclared: BSD-3-Clause
+
+PackageName: jsonschema
+PackageHomePage: https://pypi.python.org/pypi/jsonschema
+PackageLicenseDeclared: MIT
+
+PackageName: markupsafe
+PackageHomePage: https://pypi.python.org/pypi/MarkupSafe
+PackageLicenseDeclared: BSD-3-Clause
+
+PackageName: orderddict
+Homepage: https://pypi.org/project/ordereddict/
+PackageLicenseDeclared: MIT
+
+PackageName: py
+PackageHomePage: https://pypi.python.org/pypi/py
+PackageLicenseDeclared: MIT
+
+PackageName: pyqver
+PackageHomePage: https://github.com/ghewgill/pyqver
+PackageLicenseDeclared: BSD-3-Clause
+
+PackageName: pytest
+PackageHomePage: https://pypi.python.org/pypi/pytest
+PackageLicenseDeclared: MIT
+
+PackageName: ruamel.yaml
+PackageHomePage: https://yaml.readthedocs.io/
+PackageLicenseDeclared: MIT
+
+PackageName: six
+PackageHomePage: https://pypi.python.org/pypi/six
+PackageLicenseDeclared: MIT
+
+PackageName: macholib
+PackageHomePage: https://macholib.readthedocs.io/en/latest/index.html
+PackageLicenseDeclared: MIT
+
+PackageName: altgraph
+PackageHomePage: https://altgraph.readthedocs.io/en/latest/index.html
+PackageLicenseDeclared: MIT

LICENSE

@@ -1,503 +0,0 @@
-		  GNU LESSER GENERAL PUBLIC LICENSE
-		       Version 2.1, February 1999
-
- 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 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.]
-
-			    Preamble
-
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-   responsibility for the accuracy, completeness, or usefulness of any
-   information, apparatus, product, or process disclosed, or
-   represents that its use would not infringe privately-owned rights.
-
-C. Also, reference herein to any specific commercial products,
-   process, or services by trade name, trademark, manufacturer or
-   otherwise does not necessarily constitute or imply its endorsement,
-   recommendation, or favoring by the United States Government or
-   Lawrence Livermore National Security, LLC. The views and opinions
-   of authors expressed herein do not necessarily state or reflect
-   those of the United States Government or Lawrence Livermore
-   National Security, LLC, and shall not be used for advertising or
-   product endorsement purposes.
-
-See the LICENSE file for the precise terms and conditions for copying,
-distribution and modification.
-
-########################################################################
+The views and opinions of authors expressed herein do not necessarily
+state or reflect those of the United States Government or Lawrence
+Livermore National Security, LLC, and shall not be used for advertising
+or product endorsement purposes.

README.md

@@ -26,49 +26,43 @@ Then:
 
     $ git clone https://github.com/spack/spack.git
     $ cd spack/bin
-    $ ./spack install libelf
+    $ ./spack install zlib
 
 Documentation
 ----------------
 
-[**Full documentation**](http://spack.readthedocs.io/) for Spack is
-the first place to look.
+[**Full documentation**](http://spack.readthedocs.io/) is available, or
+run `spack help` or `spack help --all`.
 
-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.
+Tutorial
+----------------
 
-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.
+We maintain a
+[**hands-on tutorial**](http://spack.readthedocs.io/en/latest/tutorial.html).
+It covers basic to advanced usage, packaging, developer features, and large HPC
+deployments.  You can do all of the exercises on your own laptop using a
+Docker container.
 
-Get Involved!
+Feel free to use these materials to teach users at your organization
+about Spack.
+
+Community
 ------------------------
 
 Spack is an open source project.  Questions, discussion, and
 contributions are welcome. Contributions can be anything from new
-packages to bugfixes, or even new core features.
+packages to bugfixes, documentation, or even new core features.
 
-### Mailing list
+Resources:
 
-If you are interested in contributing to spack, join the mailing list.
-We're using Google Groups for this:
-
-  * [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
+* **Slack workspace**: [spackpm.slack.com](https://spackpm.slack.com).
+  To get an invitation, [**click here**](https://spackpm.herokuapp.com).
+* **Mailing list**: [groups.google.com/d/forum/spack](https://groups.google.com/d/forum/spack)
+* **Twitter**: [@spackpm](https://twitter.com/spackpm). Be sure to
+  `@mention` us!
 
+Contributing
+------------------------
 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
@@ -86,6 +80,13 @@ branching model.  The ``develop`` branch contains the latest
 contributions, and ``master`` is always tagged and points to the latest
 stable release.
 
+Code of Conduct
+------------------------
+
+Please note that Spack has a
+[**Code of Conduct**](.github/CODE_OF_CONDUCT.md). By participating in
+the Spack community, you agree to abide by its rules.
+
 Authors
 ----------------
 Many thanks go to Spack's [contributors](https://github.com/spack/spack/graphs/contributors).
@@ -101,11 +102,21 @@ If you are referencing Spack in a publication, please cite the following paper:
    [**The Spack Package Manager: Bringing Order to HPC Software Chaos**](http://www.computer.org/csdl/proceedings/sc/2015/3723/00/2807623.pdf).
    In *Supercomputing 2015 (SC’15)*, Austin, Texas, November 15-20 2015. LLNL-CONF-669890.
 
-Release
+License
 ----------------
-Spack is released under an LGPL license.  For more details see the
-NOTICE and LICENSE files.
 
-``LLNL-CODE-647188``
+Spack is distributed under the terms of both the MIT license and the
+Apache License (Version 2.0). Users may choose either license, at their
+option.
 
-![Analytics](https://ga-beacon.appspot.com/UA-101208306-3/welcome-page?pixel)
+All new contributions must be made under both the MIT and Apache-2.0
+licenses.
+
+See [LICENSE-MIT](https://github.com/spack/spack/blob/develop/LICENSE-MIT),
+[LICENSE-APACHE](https://github.com/spack/spack/blob/develop/LICENSE-APACHE),
+[COPYRIGHT](https://github.com/spack/spack/blob/develop/COPYRIGHT), and
+[NOTICE](https://github.com/spack/spack/blob/develop/NOTICE) for details.
+
+SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+LLNL-CODE-647188

bin/generate-gitlab-ci-yml.sh

@@ -0,0 +1,91 @@
+#! /usr/bin/env bash
+
+# Remember where we are initially, it's the repo cloned by gitlab-ci
+original_directory=$(pwd)
+. "${original_directory}/share/spack/setup-env.sh"
+
+# Create a temporary working directory
+temp_dir=$(mktemp -d)
+trap 'rm -rf "$temp_dir"' INT TERM QUIT EXIT
+
+if [ -z "${DOWNSTREAM_CI_REPO}" ] ; then
+    echo "ERROR: missing variable: DOWNSTREAM_CI_REPO" >&2
+    exit 1
+fi
+
+if [ -z "${SPACK_RELEASE_ENVIRONMENT_PATH}" ] ; then
+    echo "ERROR: missing variable: SPACK_RELEASE_ENVIRONMENT_PATH" >&2
+    exit 1
+fi
+
+if [ -z "${CDASH_AUTH_TOKEN}" ] ; then
+    echo "WARNING: missing variable: CDASH_AUTH_TOKEN" >&2
+else
+    token_file="${temp_dir}/cdash_auth_token"
+    echo ${CDASH_AUTH_TOKEN} > ${token_file}
+fi
+
+if [ -z "${SPACK_RELEASE_ENVIRONMENT_REPO}" ] ; then
+    echo "Assuming spack repo contains environment" >&2
+    env_repo_dir=${original_directory}
+else
+    echo "Cloning ${SPACK_RELEASE_ENVIRONMENT_REPO} into ${temp_dir}/envrepo" >&2
+    cd ${temp_dir}
+    git clone ${SPACK_RELEASE_ENVIRONMENT_REPO} envrepo
+    cd envrepo
+    env_repo_dir=$(pwd)
+fi
+
+current_branch="$CI_COMMIT_REF_NAME"
+
+# Because want to see generated gitlab-ci file as an artifact,
+# we need to write it within the spack repo cloned by gitlab-ci.
+gen_ci_dir="${original_directory}/ci-generation"
+gen_ci_file="${gen_ci_dir}/.gitlab-ci.yml"
+mkdir -p ${gen_ci_dir}
+
+env_dir="${env_repo_dir}/${SPACK_RELEASE_ENVIRONMENT_PATH}"
+
+if [ ! -f "${env_dir}/spack.yaml" ] ; then
+    echo "ERROR: Cannot find spack environment file in ${env_dir}"
+    exit 1
+fi
+
+cd $env_dir
+
+# The next commands generates the .gitlab-ci.yml (and optionally creates a
+# buildgroup in cdash)
+RELEASE_JOBS_ARGS=("--output-file" "${gen_ci_file}")
+if [ ! -z "${token_file}" ]; then
+    RELEASE_JOBS_ARGS+=("--cdash-credentials" "${token_file}")
+fi
+
+spack release-jobs "${RELEASE_JOBS_ARGS[@]}"
+
+if [[ $? -ne 0 ]]; then
+    echo "spack release-jobs command failed"
+    exit 1
+fi
+
+cd "$original_directory"
+mv .git "$temp_dir/original-git-dir"
+git init .
+
+git config user.email "robot@spack.io"
+git config user.name "Spack Build Bot"
+
+cp ${gen_ci_file} "${original_directory}/.gitlab-ci.yml"
+git add .
+
+echo "git commit"
+commit_message="Auto-generated commit testing"
+commit_message="${commit_message} ${current_branch} (${CI_COMMIT_SHA})"
+git commit --message="${commit_message}"
+
+echo "git push"
+git remote add origin "$DOWNSTREAM_CI_REPO"
+git push --force origin "master:multi-ci-${current_branch}"
+
+rm -rf .git
+mv "$temp_dir/original-git-dir" .git
+git reset --hard HEAD

bin/rebuild-index.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+set -x
+
+SPACK_BIN_DIR="${CI_PROJECT_DIR}/bin"
+export PATH="${SPACK_BIN_DIR}:${PATH}"
+
+spack buildcache update-index -d "$MIRROR_URL"

bin/rebuild-package.sh

@@ -0,0 +1,399 @@
+#!/bin/bash
+
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+###
+### This script represents a gitlab-ci job, corresponding to a single release
+### spec.  As such this script must first decide whether or not the spec it
+### has been assigned is up to date on the remote binary mirror.  If it is
+### not (i.e. the source code has changed in a way that caused a change in the
+### full_hash of the spec), this script will build the package, create a
+### binary cache for it, and then push all related files to the remote binary
+### mirror.  This script also optionally communicates with a remote CDash
+### instance to share status on the package build process.
+###
+### The following environment variables are (possibly) used within this script
+### in order for the various elements function properly.
+###
+### First are two defaults we rely on from gitlab:
+###
+### CI_PROJECT_DIR
+### CI_JOB_NAME
+###
+### The following must be set up in the variables section of gitlab:
+###
+### AWS_ACCESS_KEY_ID
+### AWS_SECRET_ACCESS_KEY
+### SPACK_SIGNING_KEY
+###
+### SPACK_S3_UPLOAD_MIRROR_URL         // only required in the short term for the cloud case
+###
+### The following variabes are defined by the ci generation process and are
+### required:
+###
+### SPACK_ENABLE_CDASH
+### SPACK_ROOT_SPEC
+### SPACK_MIRROR_URL
+### SPACK_JOB_SPEC_PKG_NAME
+### SPACK_COMPILER_ACTION
+###
+### Finally, these variables are optionally defined by the ci generation
+### process, and may or may not be present:
+###
+### SPACK_CDASH_BASE_URL
+### SPACK_CDASH_PROJECT
+### SPACK_CDASH_PROJECT_ENC
+### SPACK_CDASH_BUILD_NAME
+### SPACK_CDASH_SITE
+### SPACK_RELATED_BUILDS
+### SPACK_JOB_SPEC_BUILDGROUP
+###
+
+shopt -s expand_aliases
+
+export FORCE_UNSAFE_CONFIGURE=1
+
+TEMP_DIR="${CI_PROJECT_DIR}/jobs_scratch_dir"
+
+JOB_LOG_DIR="${TEMP_DIR}/logs"
+SPEC_DIR="${TEMP_DIR}/specs"
+LOCAL_MIRROR="${CI_PROJECT_DIR}/local_mirror"
+BUILD_CACHE_DIR="${LOCAL_MIRROR}/build_cache"
+SPACK_BIN_DIR="${CI_PROJECT_DIR}/bin"
+
+if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then
+    CDASH_UPLOAD_URL="${SPACK_CDASH_BASE_URL}/submit.php?project=${SPACK_CDASH_PROJECT_ENC}"
+    DEP_JOB_RELATEBUILDS_URL="${SPACK_CDASH_BASE_URL}/api/v1/relateBuilds.php"
+    declare -a JOB_DEPS_PKG_NAMES
+fi
+
+export SPACK_ROOT=${CI_PROJECT_DIR}
+# export PATH="${SPACK_BIN_DIR}:${PATH}"
+export GNUPGHOME="${CI_PROJECT_DIR}/opt/spack/gpg"
+
+. "${CI_PROJECT_DIR}/share/spack/setup-env.sh"
+
+mkdir -p ${JOB_LOG_DIR}
+mkdir -p ${SPEC_DIR}
+
+cleanup() {
+    set +x
+
+    if [ -z "$exit_code" ] ; then
+
+        exit_code=$1
+        if [ -z "$exit_code" ] ; then
+            exit_code=0
+        fi
+
+        restore_io
+
+        if [ "$( type -t finalize )" '=' 'function' ] ; then
+            finalize "$JOB_LOG_DIR/cdash_log.txt"
+        fi
+
+        # We can clean these out later on, once we have a good sense for
+        # how the logging infrastructure is working
+        # rm -rf "$JOB_LOG_DIR"
+    fi
+
+    \exit $exit_code
+}
+
+alias exit='cleanup'
+
+begin_logging() {
+    trap "cleanup 1; \\exit \$exit_code" INT TERM QUIT
+    trap "cleanup 0; \\exit \$exit_code" EXIT
+
+    rm -rf "$JOB_LOG_DIR/cdash_log.txt"
+
+    # NOTE: Here, some redirects are set up
+    exec 3>&1 # fd 3 is now a dup of stdout
+    exec 4>&2 # fd 4 is now a dup of stderr
+
+    # stdout and stderr are joined and redirected to the log
+    exec &> "$JOB_LOG_DIR/cdash_log.txt"
+
+    set -x
+}
+
+restore_io() {
+    exec  >&-
+    exec 2>&-
+
+    exec  >&3
+    exec 2>&4
+
+    exec 3>&-
+    exec 4>&-
+}
+
+finalize() {
+    # If you define a finalize function:
+    #  - it will always be called at the very end of the script
+    #  - the log file will be passed in as the first argument, and
+    #  - the code in this function will not be logged.
+    echo "The full log file is located at $1"
+    # TODO: send this log data to cdash!
+}
+
+check_error()
+{
+    local last_exit_code=$1
+    local last_cmd=$2
+    if [[ ${last_exit_code} -ne 0 ]]; then
+        echo "${last_cmd} exited with code ${last_exit_code}"
+        echo "TERMINATING JOB"
+        exit 1
+    else
+        echo "${last_cmd} completed successfully"
+    fi
+}
+
+extract_build_id()
+{
+    LINES_TO_SEARCH=$1
+    regex="buildSummary\.php\?buildid=([[:digit:]]+)"
+    SINGLE_LINE_OUTPUT=$(echo ${LINES_TO_SEARCH} | tr -d '\n')
+
+    if [[ ${SINGLE_LINE_OUTPUT} =~ ${regex} ]]; then
+        echo "${BASH_REMATCH[1]}"
+    else
+        echo "NONE"
+    fi
+}
+
+get_relate_builds_post_data()
+{
+  cat <<EOF
+{
+  "project": "${1}",
+  "buildid": ${2},
+  "relatedid": ${3},
+  "relationship": "depends on"
+}
+EOF
+}
+
+gen_full_specs_for_job_and_deps() {
+    SPEC_YAML_PATH="${SPEC_DIR}/${SPACK_JOB_SPEC_PKG_NAME}.yaml"
+    local spec_names_to_save="${SPACK_JOB_SPEC_PKG_NAME}"
+
+    if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then
+        IFS=';' read -ra DEPS <<< "${SPACK_RELATED_BUILDS}"
+        for i in "${DEPS[@]}"; do
+            depPkgName="${i}"
+            spec_names_to_save="${spec_names_to_save} ${depPkgName}"
+            JOB_DEPS_PKG_NAMES+=("${depPkgName}")
+        done
+    fi
+
+    if [ "${SPACK_COMPILER_ACTION}" == "FIND_ANY" ]; then
+        # This corresponds to a bootstrapping phase where we need to
+        # rely on any available compiler to build the package (i.e. the
+        # compiler needed to be stripped from the spec), and thus we need
+        # to concretize the root spec again.
+        spack -d buildcache save-yaml --specs "${spec_names_to_save}" --root-spec "${SPACK_ROOT_SPEC}" --yaml-dir "${SPEC_DIR}"
+    else
+        # in this case, either we're relying on Spack to install missing compiler
+        # bootstrapped in a previous phase, or else we only had one phase (like a
+        # site which already knows what compilers are available on it's runners),
+        # so we don't want to concretize that root spec again.  The reason we need
+        # this in the first case (bootstrapped compiler), is that we can't concretize
+        # a spec at this point if we're going to ask spack to "install_missing_compilers".
+        tmp_dir=$(mktemp -d)
+        TMP_YAML_PATH="${tmp_dir}/root.yaml"
+        ROOT_SPEC_YAML=$(spack python -c "import base64 ; import zlib ; print(str(zlib.decompress(base64.b64decode('${SPACK_ROOT_SPEC}')).decode('utf-8')))")
+        echo "${ROOT_SPEC_YAML}" > "${TMP_YAML_PATH}"
+        spack -d buildcache save-yaml --specs "${spec_names_to_save}" --root-spec-yaml "${TMP_YAML_PATH}" --yaml-dir "${SPEC_DIR}"
+        rm -rf ${tmp_dir}
+    fi
+}
+
+begin_logging
+
+echo "Running job for spec: ${CI_JOB_NAME}"
+
+# This should create the directory we referred to as GNUPGHOME earlier
+spack gpg list
+
+# Importing the secret key using gpg2 directly should allow to
+# sign and verify both
+set +x
+KEY_IMPORT_RESULT=`echo ${SPACK_SIGNING_KEY} | base64 --decode | gpg2 --import`
+check_error $? "gpg2 --import"
+set -x
+
+spack gpg list --trusted
+spack gpg list --signing
+
+# To have spack install missing compilers, we need to add a custom
+# configuration scope, then we pass that to the package installation
+# command
+CUSTOM_CONFIG_SCOPE_DIR="${TEMP_DIR}/config_scope"
+mkdir -p "${CUSTOM_CONFIG_SCOPE_DIR}"
+CUSTOM_CONFIG_SCOPE_ARG=""
+
+if [ "${SPACK_COMPILER_ACTION}" == "INSTALL_MISSING" ]; then
+    echo "Make sure bootstrapped compiler will be installed"
+    custom_config_file_path="${CUSTOM_CONFIG_SCOPE_DIR}/config.yaml"
+      cat <<CONFIG_STUFF > "${custom_config_file_path}"
+config:
+  install_missing_compilers: true
+CONFIG_STUFF
+    CUSTOM_CONFIG_SCOPE_ARG="-C ${CUSTOM_CONFIG_SCOPE_DIR}"
+    # Configure the binary mirror where, if needed, this jobs compiler
+    # was installed in binary pacakge form, then tell spack to
+    # install_missing_compilers.
+elif [ "${SPACK_COMPILER_ACTION}" == "FIND_ANY" ]; then
+    echo "Just find any available compiler"
+    spack compiler find
+else
+    echo "No compiler action to be taken"
+fi
+
+# Finally, list the compilers spack knows about
+echo "Compiler Configurations:"
+spack config get compilers
+
+# Write full-deps yamls for this job spec and its dependencies
+gen_full_specs_for_job_and_deps
+
+# Make the build_cache directory if it doesn't exist
+mkdir -p "${BUILD_CACHE_DIR}"
+
+# Get buildcache name so we can write a CDash build id file in the right place.
+# If we're unable to get the buildcache name, we may have encountered a problem
+# concretizing the spec, or some other issue that will eventually cause the job
+# to fail.
+JOB_BUILD_CACHE_ENTRY_NAME=`spack -d buildcache get-buildcache-name --spec-yaml "${SPEC_YAML_PATH}"`
+if [[ $? -ne 0 ]]; then
+    echo "ERROR, unable to get buildcache entry name for job ${CI_JOB_NAME}"
+    exit 1
+fi
+
+if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then
+    # Whether we have to build the spec or download it pre-built, we expect to find
+    # the cdash build id file sitting in this location afterwards.
+    JOB_CDASH_ID_FILE="${BUILD_CACHE_DIR}/${JOB_BUILD_CACHE_ENTRY_NAME}.cdashid"
+fi
+
+# Finally, we can check the spec we have been tasked with build against
+# the built binary on the remote mirror to see if it needs to be rebuilt
+spack -d buildcache check --spec-yaml "${SPEC_YAML_PATH}" --mirror-url "${SPACK_MIRROR_URL}" --rebuild-on-error
+
+if [[ $? -ne 0 ]]; then
+    # Configure mirror
+    spack mirror add local_artifact_mirror "file://${LOCAL_MIRROR}"
+
+    if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then
+        JOB_CDASH_ID="NONE"
+
+        # Install package, using the buildcache from the local mirror to
+        # satisfy dependencies.
+        BUILD_ID_LINE=`spack -d -k -v "${CUSTOM_CONFIG_SCOPE_ARG}" install --keep-stage --cdash-upload-url "${CDASH_UPLOAD_URL}" --cdash-build "${SPACK_CDASH_BUILD_NAME}" --cdash-site "${SPACK_CDASH_SITE}" --cdash-track "${SPACK_JOB_SPEC_BUILDGROUP}" -f "${SPEC_YAML_PATH}" | grep "buildSummary\\.php"`
+        check_error $? "spack install"
+
+        # By parsing the output of the "spack install" command, we can get the
+        # buildid generated for us by CDash
+        JOB_CDASH_ID=$(extract_build_id "${BUILD_ID_LINE}")
+
+        # Write the .cdashid file to the buildcache as well
+        echo "${JOB_CDASH_ID}" >> ${JOB_CDASH_ID_FILE}
+    else
+        spack -d -k -v "${CUSTOM_CONFIG_SCOPE_ARG}" install --keep-stage -f "${SPEC_YAML_PATH}"
+    fi
+
+    # Copy some log files into an artifact location, once we have a way
+    # to provide a spec.yaml file to more spack commands (e.g. "location")
+    # stage_dir=$(spack location --stage-dir -f "${SPEC_YAML_PATH}")
+    # build_log_file=$(find -L "${stage_dir}" | grep "spack-build\\.out")
+    # config_log_file=$(find -L "${stage_dir}" | grep "config\\.log")
+    # cp "${build_log_file}" "${JOB_LOG_DIR}/"
+    # cp "${config_log_file}" "${JOB_LOG_DIR}/"
+
+    # Create buildcache entry for this package, reading the spec from the yaml
+    # file.
+    spack -d buildcache create --spec-yaml "${SPEC_YAML_PATH}" -a -f -d "${LOCAL_MIRROR}" --no-rebuild-index
+    check_error $? "spack buildcache create"
+
+    # TODO: The upload-s3 command should eventually be replaced with something
+    # like: "spack buildcache put <mirror> <spec>", when that subcommand is
+    # properly implemented.
+    if [ ! -z "${SPACK_S3_UPLOAD_MIRROR_URL}" ] ; then
+        spack -d upload-s3 spec --base-dir "${LOCAL_MIRROR}" --spec-yaml "${SPEC_YAML_PATH}" --endpoint-url "${SPACK_S3_UPLOAD_MIRROR_URL}"
+        check_error $? "spack upload-s3 spec"
+    else
+        spack -d buildcache copy --base-dir "${LOCAL_MIRROR}" --spec-yaml "${SPEC_YAML_PATH}" --destination-url "${SPACK_MIRROR_URL}"
+    fi
+else
+    echo "spec ${CI_JOB_NAME} is already up to date on remote mirror, downloading it"
+
+    # Configure remote mirror so we can download buildcache entry
+    spack mirror add remote_binary_mirror ${SPACK_MIRROR_URL}
+
+    # Now download it
+    BUILDCACHE_DL_ARGS=("--spec-yaml" "${SPEC_YAML_PATH}" "--path" "${BUILD_CACHE_DIR}/" )
+    if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then
+        BUILDCACHE_DL_ARGS+=( "--require-cdashid" )
+    fi
+    spack -d buildcache download "${BUILDCACHE_DL_ARGS[@]}"
+    check_error $? "spack buildcache download"
+fi
+
+# The next step is to relate this job to the jobs it depends on
+if [ "${SPACK_ENABLE_CDASH}" == "True" ] ; then
+    if [ -f "${JOB_CDASH_ID_FILE}" ]; then
+        JOB_CDASH_BUILD_ID=$(<${JOB_CDASH_ID_FILE})
+
+        if [ "${JOB_CDASH_BUILD_ID}" == "NONE" ]; then
+            echo "ERROR: unable to read this jobs id from ${JOB_CDASH_ID_FILE}"
+            exit 1
+        fi
+
+        # Now get CDash ids for dependencies and "relate" each dependency build
+        # with this jobs build
+        for DEP_PKG_NAME in "${JOB_DEPS_PKG_NAMES[@]}"; do
+            echo "Getting cdash id for dependency --> ${DEP_PKG_NAME} <--"
+            DEP_SPEC_YAML_PATH="${SPEC_DIR}/${DEP_PKG_NAME}.yaml"
+            DEP_JOB_BUILDCACHE_NAME=`spack -d buildcache get-buildcache-name --spec-yaml "${DEP_SPEC_YAML_PATH}"`
+
+            if [[ $? -eq 0 ]]; then
+                DEP_JOB_ID_FILE="${BUILD_CACHE_DIR}/${DEP_JOB_BUILDCACHE_NAME}.cdashid"
+                echo "DEP_JOB_ID_FILE path = ${DEP_JOB_ID_FILE}"
+
+                if [ -f "${DEP_JOB_ID_FILE}" ]; then
+                    DEP_JOB_CDASH_BUILD_ID=$(<${DEP_JOB_ID_FILE})
+                    echo "File ${DEP_JOB_ID_FILE} contained value ${DEP_JOB_CDASH_BUILD_ID}"
+                    echo "Relating builds -> ${SPACK_CDASH_BUILD_NAME} (buildid=${JOB_CDASH_BUILD_ID}) depends on ${DEP_PKG_NAME} (buildid=${DEP_JOB_CDASH_BUILD_ID})"
+                    relateBuildsPostBody="$(get_relate_builds_post_data "${SPACK_CDASH_PROJECT}" ${JOB_CDASH_BUILD_ID} ${DEP_JOB_CDASH_BUILD_ID})"
+                    relateBuildsResult=`curl "${DEP_JOB_RELATEBUILDS_URL}" -H "Content-Type: application/json" -H "Accept: application/json" -d "${relateBuildsPostBody}"`
+                    echo "Result of curl request: ${relateBuildsResult}"
+                else
+                    echo "ERROR: Did not find expected .cdashid file for dependency: ${DEP_JOB_ID_FILE}"
+                    exit 1
+                fi
+            else
+                echo "ERROR: Unable to get buildcache entry name for ${DEP_SPEC_NAME}"
+                exit 1
+            fi
+        done
+    else
+        echo "ERROR: Did not find expected .cdashid file ${JOB_CDASH_ID_FILE}"
+        exit 1
+    fi
+fi
+
+# Show the size of the buildcache and a list of what's in it, directly
+# in the gitlab log output
+(
+    restore_io
+    du -sh ${BUILD_CACHE_DIR}
+    find ${BUILD_CACHE_DIR} -maxdepth 3 -type d -ls
+)
+
+echo "End of rebuild package script"

bin/sbang

@@ -1,28 +1,10 @@
 #!/bin/bash
-##############################################################################
-# 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
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # `sbang`: Run scripts with long shebang lines.
 #

bin/spack

@@ -1,28 +1,26 @@
-#!/usr/bin/env python
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+#!/bin/sh
+# -*- python -*-
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+# This file is bilingual. The following shell code finds our preferred python.
+# Following line is a shell no-op, and starts a multi-line Python comment.
+# See https://stackoverflow.com/a/47886254
+""":"
+# prefer python3, then python, then python2
+for cmd in python3 python python2; do
+   command -v > /dev/null $cmd && exec $cmd $0 "$@"
+done
+
+echo "==> Error: spack could not find a python interpreter!" >&2
+exit 1
+":"""
+# Line above is a shell no-op, and ends a python multi-line comment.
+# The code above runs this file with our preferred python interpreter.
+
 from __future__ import print_function
 
 import os
@@ -43,38 +41,23 @@ 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)
+# Here we delete ruamel.yaml in case it has been already imported from site
+# (see #9206 for a broader description of the issue).
+#
+# Briefly: ruamel.yaml produces a .pth file when installed with pip that
+# makes the site installed package the preferred one, even though sys.path
+# is modified to point to another version of ruamel.yaml.
+if 'ruamel.yaml' in sys.modules:
+    del sys.modules['ruamel.yaml']
 
-# Quick and dirty check to clean orphaned .pyc files left over from
-# previous revisions.  These files were present in earlier versions of
-# Spack, were removed, but shadow system modules that Spack still
-# 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')
-]
-
-for pyc_file in orphaned_pyc_files:
-    if not os.path.exists(pyc_file):
-        continue
-    try:
-        os.remove(pyc_file)
-    except OSError as e:
-        print("WARNING: Spack may fail mysteriously. "
-              "Couldn't remove orphaned .pyc file: %s" % pyc_file)
+if 'ruamel' in sys.modules:
+    del sys.modules['ruamel']
 
 # Once we've set up the system path, run the spack main method
 import spack.main  # noqa

bin/spack-python

@@ -1,28 +1,10 @@
 #!/bin/sh
-##############################################################################
-# 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
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # spack-python
 #

etc/spack/defaults/config.yaml

@@ -18,41 +18,60 @@ 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
+    - $spack/share/spack/templates
+
+
+  # Default directory layout
+  install_path_scheme: "${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}"
+
 
   # Locations where different types of modules should be installed.
   module_roots:
     tcl:    $spack/share/spack/modules
     lmod:   $spack/share/spack/lmod
-    dotkit: $spack/share/spack/dotkit
 
 
   # Temporary locations Spack can try to use for builds.
   #
-  # Spack will use the first one it finds that exists and is writable.
-  # You can use $tempdir to refer to the system default temp directory
-  # (as returned by tempfile.gettempdir()).
+  # Recommended options are given below.
   #
-  # A value of $spack/var/spack/stage indicates that Spack should run
-  # builds directly inside its install directory without staging them in
-  # temporary space.
+  # Builds can be faster in temporary directories on some (e.g., HPC) systems.
+  # Specifying `$tempdir` will ensure use of the default temporary directory
+  # (i.e., ``$TMP` or ``$TMPDIR``).
   #
-  # The build stage can be purged with `spack purge --stage`.
+  # Another option that prevents conflicts and potential permission issues is
+  # to specify `~/.spack/stage`, which ensures each user builds in their home
+  # directory.
+  #
+  # A more traditional path uses the value of `$spack/var/spack/stage`, which
+  # builds directly inside Spack's instance without staging them in a
+  # temporary space.  Problems with specifying a path inside a Spack instance
+  # are that it precludes its use as a system package and its ability to be
+  # pip installable.
+  #
+  # In any case, if the username is not already in the path, Spack will append
+  # the value of `$user` in an attempt to avoid potential conflicts between
+  # users in shared temporary spaces.
+  #
+  # The build stage can be purged with `spack clean --stage` and
+  # `spack clean -a`, so it is important that the specified directory uniquely
+  # identifies Spack staging to avoid accidentally wiping out non-Spack work.
   build_stage:
-    - $tempdir
-    - /nfs/tmp2/$user
-    - $spack/var/spack/stage
+    - $tempdir/$user/spack-stage
+    - ~/.spack/stage
+  # - $spack/var/spack/stage
 
 
-  # Cache directory already downloaded source tarballs and archived
-  # repositories. This can be purged with `spack purge --downloads`.
+  # Cache directory for already downloaded source tarballs and archived
+  # repositories. This can be purged with `spack clean --downloads`.
   source_cache: $spack/var/spack/cache
 
 
   # Cache directory for miscellaneous files, like the package index.
-  # This can be purged with `spack purge --misc-cache`
+  # This can be purged with `spack clean --misc-cache`
   misc_cache: ~/.spack/cache
 
 
@@ -61,6 +80,20 @@ config:
   verify_ssl: true
 
 
+  # Suppress gpg warnings from binary package verification
+  # Only suppresses warnings, gpg failure will still fail the install
+  # Potential rationale to set True: users have already explicitly trusted the
+  # gpg key they are using, and may not want to see repeated warnings that it
+  # is self-signed or something of the sort.
+  suppress_gpg_warnings: false
+
+
+  # If set to true, Spack will attempt to build any compiler on the spec
+  # that is not already available. If set to False, Spack will only use
+  # compilers already configured in compilers.yaml
+  install_missing_compilers: False
+
+
   # If set to true, Spack will always check checksums after downloading
   # archives. If false, Spack skips the checksum step.
   checksum: true
@@ -71,7 +104,50 @@ config:
   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
+  # The language the build environment will use. This will produce English
+  # compiler messages by default, so the log parser can highlight errors.
+  # If set to C, it will use English (see man locale).
+  # If set to the empty string (''), it will use the language from the
+  # user's environment.
+  build_language: C
+
+
+  # When set to true, concurrent instances of Spack will use locks to
+  # avoid modifying the install tree, database file, etc. If false, Spack
+  # will disable all locking, but you must NOT run concurrent instances
+  # of Spack.  For filesystems that don't support locking, you should set
+  # this to false and run one Spack at a time, but otherwise we recommend
+  # enabling locks.
+  locks: true
+
+
+  # The maximum number of jobs to use when running `make` in parallel,
+  # always limited by the number of cores available. For instance:
+  # - If set to 16 on a 4 cores machine `spack install` will run `make -j4`
+  # - If set to 16 on a 18 cores machine `spack install` will run `make -j16`
+  # If not set, Spack will use all available cores up to 16.
+  # build_jobs: 16
+
+
+  # If set to true, Spack will use ccache to cache C compiles.
+  ccache: false
+
+
+  # How long to wait to lock the Spack installation database. This lock is used
+  # when Spack needs to manage its own package metadata and all operations are
+  # expected to complete within the default time limit. The timeout should
+  # therefore generally be left untouched.
+  db_lock_timeout: 120
+
+
+  # How long to wait when attempting to modify a package (e.g. to install it).
+  # This value should typically be 'null' (never time out) unless the Spack
+  # instance only ever has a single user at a time, and only if the user
+  # anticipates that a significant delay indicates that the lock attempt will
+  # never succeed.
+  package_lock_timeout: null
+
+  # Control whether Spack embeds RPATH or RUNPATH attributes in ELF binaries.
+  # Has no effect on macOS. DO NOT MIX these within the same install tree.
+  # See the Spack documentation for details.
+  shared_linking: 'rpath'

etc/spack/defaults/darwin/modules.yaml

@@ -0,0 +1,23 @@
+# -------------------------------------------------------------------------
+# This is the default configuration for Spack's module file generation.
+#
+# Settings here are versioned with Spack and are intended to provide
+# sensible defaults out of the box. Spack maintainers should edit this
+# file to keep it current.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/modules.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/modules.yaml
+# -------------------------------------------------------------------------
+modules:
+  prefix_inspections:
+    lib:
+      - DYLD_LIBRARY_PATH
+      - DYLD_FALLBACK_LIBRARY_PATH
+    lib64:
+      - DYLD_LIBRARY_PATH
+      - DYLD_FALLBACK_LIBRARY_PATH

etc/spack/defaults/darwin/packages.yaml

@@ -16,3 +16,12 @@
 packages:
   all:
     compiler: [clang, gcc, intel]
+    providers:
+      elf: [libelf]
+      unwind: [apple-libunwind]
+  apple-libunwind:
+    paths:
+    # Apple bundles libunwind version 35.3 with macOS 10.9 and later,
+    # although the version number used here isn't critical
+      apple-libunwind@35.3: /usr
+    buildable: False

etc/spack/defaults/linux/modules.yaml

@@ -0,0 +1,21 @@
+# -------------------------------------------------------------------------
+# This is the default configuration for Spack's module file generation.
+#
+# Settings here are versioned with Spack and are intended to provide
+# sensible defaults out of the box. Spack maintainers should edit this
+# file to keep it current.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/modules.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/modules.yaml
+# -------------------------------------------------------------------------
+modules:
+  prefix_inspections:
+    lib:
+      - LD_LIBRARY_PATH
+    lib64:
+      - LD_LIBRARY_PATH

etc/spack/defaults/modules.yaml

@@ -16,7 +16,6 @@
 modules:
   enable:
     - tcl
-    - dotkit
   prefix_inspections:
     bin:
       - PATH
@@ -28,16 +27,16 @@ modules:
       - ACLOCAL_PATH
     lib:
       - LIBRARY_PATH
-      - LD_LIBRARY_PATH
     lib64:
       - LIBRARY_PATH
-      - LD_LIBRARY_PATH
     include:
       - CPATH
     lib/pkgconfig:
       - PKG_CONFIG_PATH
     lib64/pkgconfig:
       - PKG_CONFIG_PATH
+    share/pkgconfig:
+      - PKG_CONFIG_PATH
     '':
       - CMAKE_PREFIX_PATH
 

etc/spack/defaults/packages.yaml

@@ -15,23 +15,34 @@
 # -------------------------------------------------------------------------
 packages:
   all:
-    compiler: [gcc, intel, pgi, clang, xl, nag]
+    compiler: [gcc, intel, pgi, clang, xl, nag, fj]
     providers:
+      D: [ldc]
       awk: [gawk]
       blas: [openblas]
       daal: [intel-daal]
       elf: [elfutils]
+      fftw-api: [fftw]
+      gl: [mesa+opengl, opengl]
+      glx: [mesa+glx, opengl]
+      glu: [mesa-glu, openglu]
       golang: [gcc]
       ipp: [intel-ipp]
-      java: [jdk]
+      java: [openjdk, jdk, ibm-java]
+      jpeg: [libjpeg-turbo, libjpeg]
       lapack: [openblas]
+      mariadb-client: [mariadb-c-client, mariadb]
       mkl: [intel-mkl]
       mpe: [mpe2]
       mpi: [openmpi, mpich]
+      mysql-client: [mysql, mariadb-c-client]
       opencl: [pocl]
-      openfoam: [openfoam-com, openfoam-org, foam-extend]
       pil: [py-pillow]
+      pkgconfig: [pkgconf, pkg-config]
       scalapack: [netlib-scalapack]
       szip: [libszip, libaec]
       tbb: [intel-tbb]
-      jpeg: [libjpeg-turbo, libjpeg]
+      unwind: [libunwind]
+    permissions:
+      read: world
+      write: user

lib/spack/docs/.gitignore

@@ -1,5 +1,7 @@
-package_list.rst
+package_list.html
 command_index.rst
 spack*.rst
 llnl*.rst
 _build
+.spack-env
+spack.lock

lib/spack/docs/Makefile

@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    = -E
+SPHINXOPTS    = -W
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build
@@ -17,7 +17,7 @@ ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext apidoc
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext apidoc dashdoc
 
 all: html
 
@@ -83,7 +83,7 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
 clean:
-	-rm -f package_list.rst command_index.rst
+	-rm -f command_index.rst
 	-rm -rf $(BUILDDIR)/* $(APIDOC_FILES)
 
 html:
@@ -196,3 +196,9 @@ doctest:
 	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/doctest/output.txt."
+
+dashdoc:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/dashdoc
+	doc2dash -A -v -n spack -d $(BUILDDIR)/ -f -I index.html -j $(BUILDDIR)/dashdoc
+	@echo
+	@echo "Build finished. The Docset is in $(BUILDDIR)/dashdoc."

lib/spack/docs/_spack_root

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

lib/spack/docs/_themes/sphinx_rtd_theme/__init__.py

@@ -1,17 +0,0 @@
-"""Sphinx ReadTheDocs theme.
-
-From https://github.com/ryan-roemer/sphinx-bootstrap-theme.
-
-"""
-import os
-
-VERSION = (0, 1, 8)
-
-__version__ = ".".join(str(v) for v in VERSION)
-__version_full__ = __version__
-
-
-def get_html_theme_path():
-    """Return list of HTML theme paths."""
-    cur_dir = os.path.abspath(os.path.dirname(os.path.dirname(__file__)))
-    return cur_dir

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

@@ -1,23 +0,0 @@
-<div role="navigation" aria-label="breadcrumbs navigation">
-  <ul class="wy-breadcrumbs">
-    <li><a href="{{ pathto(master_doc) }}">Docs</a> &raquo;</li>
-      {% for doc in parents %}
-          <li><a href="{{ doc.link|e }}">{{ doc.title }}</a> &raquo;</li>
-      {% endfor %}
-    <li>{{ title }}</li>
-      <li class="wy-breadcrumbs-aside">
-        {% if pagename != "search" %}
-          {% if display_github %}
-            <a href="https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/blob/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ source_suffix }}" class="fa fa-github"> Edit on GitHub</a>
-          {% elif display_bitbucket %}
-            <a href="https://bitbucket.org/{{ bitbucket_user }}/{{ bitbucket_repo }}/src/{{ bitbucket_version}}{{ conf_py_path }}{{ pagename }}{{ source_suffix }}" class="fa fa-bitbucket"> Edit on Bitbucket</a>
-          {% elif show_source and source_url_prefix %}
-            <a href="{{ source_url_prefix }}{{ pagename }}{{ source_suffix }}">View page source</a>
-          {% elif show_source and has_source and sourcename %}
-            <a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> View page source</a>
-          {% endif %}
-        {% endif %}
-      </li>
-  </ul>
-  <hr/>
-</div>

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

@@ -1,40 +0,0 @@
-<footer>
-  {% if next or prev %}
-    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
-      {% if next %}
-        <a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
-      {% endif %}
-      {% if prev %}
-        <a href="{{ prev.link|e }}" class="btn btn-neutral" title="{{ prev.title|striptags|e }}" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
-      {% endif %}
-    </div>
-  {% endif %}
-
-  <hr/>
-
-  <div role="contentinfo">
-    <p>
-    {%- if show_copyright %}
-      {%- if hasdoc('copyright') %}
-        {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
-      {%- else %}
-        {% trans copyright=copyright|e %}&copy; Copyright {{ copyright }}.{% endtrans %}
-      {%- endif %}
-    {%- endif %}
-
-    <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.
-
-    {%- if last_updated %}
-      <br/>
-      {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
-    {%- endif %}
-    </p>
-  </div>
-
-  {%- if show_sphinx %}
-  {% trans %}Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>{% endtrans %}.
-  {%- endif %}
-
-</footer>

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

@@ -1,181 +0,0 @@
-{# TEMPLATE VAR SETTINGS #}
-{%- set url_root = pathto('', 1) %}
-{%- if url_root == '#' %}{% set url_root = '' %}{% endif %}
-{%- if not embedded and docstitle %}
-  {%- set titlesuffix = " — "|safe + docstitle|e %}
-{%- else %}
-  {%- set titlesuffix = "" %}
-{%- endif %}
-
-<!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
-<head>
-  <meta charset="utf-8">
-  {{ metatags }}
-  <meta name="viewport" content="width=device-width, initial-scale=1.0">
-  {% block htmltitle %}
-  <title>{{ title|striptags|e }}{{ titlesuffix }}</title>
-  {% endblock %}
-
-  {# FAVICON #}
-  {% if favicon %}
-    <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
-  {% endif %}
-
-  {# CSS #}
-
-  {# OPENSEARCH #}
-  {% if not embedded %}
-    {% if use_opensearch %}
-      <link rel="search" type="application/opensearchdescription+xml" title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}" href="{{ pathto('_static/opensearch.xml', 1) }}"/>
-    {% endif %}
-
-  {% endif %}
-
-  {# RTD hosts this file, so just load on non RTD builds #}
-  {% if not READTHEDOCS %}
-    <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
-  {% endif %}
-
-  {% for cssfile in css_files %}
-    <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
-  {% endfor %}
-
-  {% for cssfile in extra_css_files %}
-    <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
-  {% endfor %}
-
-  {%- block linktags %}
-    {%- if hasdoc('about') %}
-        <link rel="author" title="{{ _('About these documents') }}"
-              href="{{ pathto('about') }}"/>
-    {%- endif %}
-    {%- if hasdoc('genindex') %}
-        <link rel="index" title="{{ _('Index') }}"
-              href="{{ pathto('genindex') }}"/>
-    {%- endif %}
-    {%- if hasdoc('search') %}
-        <link rel="search" title="{{ _('Search') }}" href="{{ pathto('search') }}"/>
-    {%- endif %}
-    {%- if hasdoc('copyright') %}
-        <link rel="copyright" title="{{ _('Copyright') }}" href="{{ pathto('copyright') }}"/>
-    {%- endif %}
-    <link rel="top" title="{{ docstitle|e }}" href="{{ pathto('index') }}"/>
-    {%- if parents %}
-        <link rel="up" title="{{ parents[-1].title|striptags|e }}" href="{{ parents[-1].link|e }}"/>
-    {%- endif %}
-    {%- if next %}
-        <link rel="next" title="{{ next.title|striptags|e }}" href="{{ next.link|e }}"/>
-    {%- endif %}
-    {%- if prev %}
-        <link rel="prev" title="{{ prev.title|striptags|e }}" href="{{ prev.link|e }}"/>
-    {%- endif %}
-  {%- endblock %}
-  {%- block extrahead %} {% endblock %}
-
-  {# Keep modernizr in head - http://modernizr.com/docs/#installing #}
-  <script src="_static/js/modernizr.min.js"></script>
-
-</head>
-
-<body class="wy-body-for-nav" role="document">
-
-  <div class="wy-grid-for-nav">
-
-    {# SIDE NAV, TOGGLES ON MOBILE #}
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-nav-search">
-        {% block sidebartitle %}
-
-        {% if logo and theme_logo_only %}
-          <a href="{{ pathto(master_doc) }}">
-        {% else %}
-          <a href="{{ pathto(master_doc) }}" class="icon icon-home"> {{ project }}
-        {% endif %}
-
-        {% if logo %}
-          {# Not strictly valid HTML, but it's the only way to display/scale it properly, without weird scripting or heaps of work #}
-          <img src="{{ pathto('_static/' + logo, 1) }}" class="logo" />
-        {% endif %}
-        </a>
-
-        {% include "searchbox.html" %}
-
-        {% endblock %}
-      </div>
-
-      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-        {% block menu %}
-          {% set toctree = toctree(maxdepth=4, collapse=False, includehidden=True) %}
-          {% if toctree %}
-              {{ toctree }}
-          {% else %}
-              <!-- Local TOC -->
-              <div class="local-toc">{{ toc }}</div>
-          {% endif %}
-        {% endblock %}
-      </div>
-      &nbsp;
-    </nav>
-
-    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
-
-      {# MOBILE NAV, TRIGGLES SIDE NAV ON TOGGLE #}
-      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
-        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-        <a href="{{ pathto(master_doc) }}">{{ project }}</a>
-      </nav>
-
-
-      {# PAGE CONTENT #}
-      <div class="wy-nav-content">
-        <div class="rst-content">
-          {% include "breadcrumbs.html" %}
-          <div role="main" class="document">
-            {% block body %}{% endblock %}
-          </div>
-          {% include "footer.html" %}
-        </div>
-      </div>
-
-    </section>
-
-  </div>
-  {% include "versions.html" %}
-
-  {% if not embedded %}
-
-    <script type="text/javascript">
-        var DOCUMENTATION_OPTIONS = {
-            URL_ROOT:'{{ url_root }}',
-            VERSION:'{{ release|e }}',
-            COLLAPSE_INDEX:false,
-            FILE_SUFFIX:'{{ '' if no_search_suffix else file_suffix }}',
-            HAS_SOURCE:  {{ has_source|lower }}
-        };
-    </script>
-    {%- for scriptfile in script_files %}
-      <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
-    {%- endfor %}
-
-  {% endif %}
-
-  {# RTD hosts this file, so just load on non RTD builds #}
-  {% if not READTHEDOCS %}
-    <script type="text/javascript" src="{{ pathto('_static/js/theme.js', 1) }}"></script>
-  {% endif %}
-
-  {# STICKY NAVIGATION #}
-  {% if theme_sticky_navigation %}
-  <script type="text/javascript">
-      jQuery(function () {
-          SphinxRtdTheme.StickyNav.enable();
-      });
-  </script>
-  {% endif %}
-
-  {%- block footer %} {% endblock %}
-
-</body>
-</html>

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

@@ -1,205 +0,0 @@
-{#
-    basic/layout.html
-    ~~~~~~~~~~~~~~~~~
-
-    Master layout template for Sphinx themes.
-
-    :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
-    :license: BSD, see LICENSE for details.
-#}
-{%- block doctype -%}
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-{%- endblock %}
-{%- set reldelim1 = reldelim1 is not defined and ' &raquo;' or reldelim1 %}
-{%- set reldelim2 = reldelim2 is not defined and ' |' or reldelim2 %}
-{%- set render_sidebar = (not embedded) and (not theme_nosidebar|tobool) and
-                         (sidebars != []) %}
-{%- set url_root = pathto('', 1) %}
-{# XXX necessary? #}
-{%- if url_root == '#' %}{% set url_root = '' %}{% endif %}
-{%- if not embedded and docstitle %}
-  {%- set titlesuffix = " &mdash; "|safe + docstitle|e %}
-{%- else %}
-  {%- set titlesuffix = "" %}
-{%- endif %}
-
-{%- macro relbar() %}
-    <div class="related">
-      <h3>{{ _('Navigation') }}</h3>
-      <ul>
-        {%- for rellink in rellinks %}
-        <li class="right" {% if loop.first %}style="margin-right: 10px"{% endif %}>
-          <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
-             {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
-          {%- if not loop.first %}{{ reldelim2 }}{% endif %}</li>
-        {%- endfor %}
-        {%- block rootrellink %}
-        <li><a href="{{ pathto(master_doc) }}">{{ shorttitle|e }}</a>{{ reldelim1 }}</li>
-        {%- endblock %}
-        {%- for parent in parents %}
-          <li><a href="{{ parent.link|e }}" {% if loop.last %}{{ accesskey("U") }}{% endif %}>{{ parent.title }}</a>{{ reldelim1 }}</li>
-        {%- endfor %}
-        {%- block relbaritems %} {% endblock %}
-      </ul>
-    </div>
-{%- endmacro %}
-
-{%- macro sidebar() %}
-      {%- if render_sidebar %}
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-          {%- block sidebarlogo %}
-          {%- if logo %}
-            <p class="logo"><a href="{{ pathto(master_doc) }}">
-              <img class="logo" src="{{ pathto('_static/' + logo, 1) }}" alt="Logo"/>
-            </a></p>
-          {%- endif %}
-          {%- endblock %}
-          {%- if sidebars != None %}
-            {#- new style sidebar: explicitly include/exclude templates #}
-            {%- for sidebartemplate in sidebars %}
-            {%- include sidebartemplate %}
-            {%- endfor %}
-          {%- else %}
-            {#- old style sidebars: using blocks -- should be deprecated #}
-            {%- block sidebartoc %}
-            {%- include "localtoc.html" %}
-            {%- endblock %}
-            {%- block sidebarrel %}
-            {%- include "relations.html" %}
-            {%- endblock %}
-            {%- block sidebarsourcelink %}
-            {%- include "sourcelink.html" %}
-            {%- endblock %}
-            {%- if customsidebar %}
-            {%- include customsidebar %}
-            {%- endif %}
-            {%- block sidebarsearch %}
-            {%- include "searchbox.html" %}
-            {%- endblock %}
-          {%- endif %}
-        </div>
-      </div>
-      {%- endif %}
-{%- endmacro %}
-
-{%- macro script() %}
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '{{ url_root }}',
-        VERSION:     '{{ release|e }}',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '{{ '' if no_search_suffix else file_suffix }}',
-        HAS_SOURCE:  {{ has_source|lower }}
-      };
-    </script>
-    {%- for scriptfile in script_files %}
-    <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
-    {%- endfor %}
-{%- endmacro %}
-
-{%- macro css() %}
-    <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
-    <link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" />
-    {%- for cssfile in css_files %}
-    <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
-    {%- endfor %}
-{%- endmacro %}
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset={{ encoding }}" />
-    {{ metatags }}
-    {%- block htmltitle %}
-    <title>{{ title|striptags|e }}{{ titlesuffix }}</title>
-    {%- endblock %}
-    {{ css() }}
-    {%- if not embedded %}
-    {{ script() }}
-    {%- if use_opensearch %}
-    <link rel="search" type="application/opensearchdescription+xml"
-          title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}"
-          href="{{ pathto('_static/opensearch.xml', 1) }}"/>
-    {%- endif %}
-    {%- if favicon %}
-    <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
-    {%- endif %}
-    {%- endif %}
-{%- block linktags %}
-    {%- if hasdoc('about') %}
-    <link rel="author" title="{{ _('About these documents') }}" href="{{ pathto('about') }}" />
-    {%- endif %}
-    {%- if hasdoc('genindex') %}
-    <link rel="index" title="{{ _('Index') }}" href="{{ pathto('genindex') }}" />
-    {%- endif %}
-    {%- if hasdoc('search') %}
-    <link rel="search" title="{{ _('Search') }}" href="{{ pathto('search') }}" />
-    {%- endif %}
-    {%- if hasdoc('copyright') %}
-    <link rel="copyright" title="{{ _('Copyright') }}" href="{{ pathto('copyright') }}" />
-    {%- endif %}
-    <link rel="top" title="{{ docstitle|e }}" href="{{ pathto('index') }}" />
-    {%- if parents %}
-    <link rel="up" title="{{ parents[-1].title|striptags|e }}" href="{{ parents[-1].link|e }}" />
-    {%- endif %}
-    {%- if next %}
-    <link rel="next" title="{{ next.title|striptags|e }}" href="{{ next.link|e }}" />
-    {%- endif %}
-    {%- if prev %}
-    <link rel="prev" title="{{ prev.title|striptags|e }}" href="{{ prev.link|e }}" />
-    {%- endif %}
-{%- endblock %}
-{%- block extrahead %} {% endblock %}
-  </head>
-  <body>
-{%- block header %}{% endblock %}
-
-{%- block relbar1 %}{{ relbar() }}{% endblock %}
-
-{%- block content %}
-  {%- block sidebar1 %} {# possible location for sidebar #} {% endblock %}
-
-    <div class="document">
-  {%- block document %}
-      <div class="documentwrapper">
-      {%- if render_sidebar %}
-        <div class="bodywrapper">
-      {%- endif %}
-          <div class="body">
-            {% block body %} {% endblock %}
-          </div>
-      {%- if render_sidebar %}
-        </div>
-      {%- endif %}
-      </div>
-  {%- endblock %}
-
-  {%- block sidebar2 %}{{ sidebar() }}{% endblock %}
-      <div class="clearer"></div>
-    </div>
-{%- endblock %}
-
-{%- block relbar2 %}{{ relbar() }}{% endblock %}
-
-{%- block footer %}
-    <div class="footer">
-    {%- if show_copyright %}
-      {%- if hasdoc('copyright') %}
-        {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
-      {%- else %}
-        {% trans copyright=copyright|e %}&copy; Copyright {{ copyright }}.{% endtrans %}
-      {%- endif %}
-    {%- endif %}
-    {%- if last_updated %}
-      {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
-    {%- endif %}
-    {%- if show_sphinx %}
-      {% trans sphinx_version=sphinx_version|e %}Created using <a href="http://sphinx-doc.org/">Sphinx</a> {{ sphinx_version }}.{% endtrans %}
-    {%- endif %}
-    </div>
-    <p>asdf asdf asdf asdf 22</p>
-{%- endblock %}
-  </body>
-</html>
-

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

@@ -1,50 +0,0 @@
-{#
-    basic/search.html
-    ~~~~~~~~~~~~~~~~~
-
-    Template for the search page.
-
-    :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
-    :license: BSD, see LICENSE for details.
-#}
-{%- extends "layout.html" %}
-{% set title = _('Search') %}
-{% set script_files = script_files + ['_static/searchtools.js'] %}
-{% block footer %}
-  <script type="text/javascript">
-    jQuery(function() { Search.loadIndex("{{ pathto('searchindex.js', 1) }}"); });
-  </script>
-  {# this is used when loading the search index using $.ajax fails,
-     such as on Chrome for documents on localhost #}
-  <script type="text/javascript" id="searchindexloader"></script>
-  {{ super() }}
-{% endblock %}
-{% block body %}
-  <noscript>
-  <div id="fallback" class="admonition warning">
-    <p class="last">
-      {% trans %}Please activate JavaScript to enable the search
-      functionality.{% endtrans %}
-    </p>
-  </div>
-  </noscript>
-
-  {% if search_performed %}
-    <h2>{{ _('Search Results') }}</h2>
-    {% if not search_results %}
-      <p>{{ _('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.') }}</p>
-    {% endif %}
-  {% endif %}
-  <div id="search-results">
-  {% if search_results %}
-    <ul>
-    {% for href, caption, context in search_results %}
-      <li>
-        <a href="{{ pathto(item.href) }}">{{ caption }}</a>
-        <p class="context">{{ context|e }}</p>
-      </li>
-    {% endfor %}
-    </ul>
-  {% endif %}
-  </div>
-{% endblock %}

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

@@ -1,9 +0,0 @@
-{%- if builder != 'singlehtml' %}
-<div role="search">
-  <form id="rtd-search-form" class="wy-form" action="{{ pathto('search') }}" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
-    <input type="hidden" name="check_keywords" value="yes" />
-    <input type="hidden" name="area" value="default" />
-  </form>
-</div>
-{%- endif %}

lib/spack/docs/_themes/sphinx_rtd_theme/static/css/badge_only.css

@@ -1,2 +0,0 @@
-.fa:before{-webkit-font-smoothing:antialiased}.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-weight:normal;font-style:normal;src:url("../font/fontawesome_webfont.eot");src:url("../font/fontawesome_webfont.eot?#iefix") format("embedded-opentype"),url("../font/fontawesome_webfont.woff") format("woff"),url("../font/fontawesome_webfont.ttf") format("truetype"),url("../font/fontawesome_webfont.svg#FontAwesome") format("svg")}.fa:before{display:inline-block;font-family:FontAwesome;font-style:normal;font-weight:normal;line-height:1;text-decoration:inherit}a .fa{display:inline-block;text-decoration:inherit}li .fa{display:inline-block}li .fa-large:before,li .fa-large:before{width:1.875em}ul.fas{list-style-type:none;margin-left:2em;text-indent:-0.8em}ul.fas li .fa{width:0.8em}ul.fas li .fa-large:before,ul.fas li .fa-large:before{vertical-align:baseline}.fa-book:before{content:""}.icon-book:before{content:""}.fa-caret-down:before{content:""}.icon-caret-down:before{content:""}.fa-caret-up:before{content:""}.icon-caret-up:before{content:""}.fa-caret-left:before{content:""}.icon-caret-left:before{content:""}.fa-caret-right:before{content:""}.icon-caret-right:before{content:""}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;border-top:solid 10px #343131;font-family:"Lato","proxima-nova","Helvetica Neue",Arial,sans-serif;z-index:400}.rst-versions a{color:#2980B9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27AE60;*zoom:1}.rst-versions .rst-current-version:before,.rst-versions .rst-current-version:after{display:table;content:""}.rst-versions .rst-current-version:after{clear:both}.rst-versions .rst-current-version .fa{color:#fcfcfc}.rst-versions .rst-current-version .fa-book{float:left}.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#E74C3C;color:#fff}.rst-versions .rst-current-version.rst-active-old-version{background-color:#F1C40F;color:#000}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:gray;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:solid 1px #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px}.rst-versions.rst-badge .icon-book{float:none}.rst-versions.rst-badge .fa-book{float:none}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .fa-book{float:left}.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge .rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width: 768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}img{width:100%;height:auto}}
-/*# sourceMappingURL=badge_only.css.map */

lib/spack/docs/_themes/sphinx_rtd_theme/static/css/badge_only.css.map

@@ -1,7 +0,0 @@
-{
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lib/spack/docs/_themes/sphinx_rtd_theme/static/js/theme.js

@@ -1,113 +0,0 @@
-function toggleCurrent (elem) {
-    var parent_li = elem.closest('li');
-    parent_li.siblings('li.current').removeClass('current');
-    parent_li.siblings().find('li.current').removeClass('current');
-    parent_li.find('> ul li.current').removeClass('current');
-    parent_li.toggleClass('current');
-}
-
-$(document).ready(function() {
-    // Shift nav in mobile when clicking the menu.
-    $(document).on('click', "[data-toggle='wy-nav-top']", function() {
-        $("[data-toggle='wy-nav-shift']").toggleClass("shift");
-        $("[data-toggle='rst-versions']").toggleClass("shift");
-    });
-    // Nav menu link click operations
-    $(document).on('click', ".wy-menu-vertical .current ul li a", function() {
-        var target = $(this);
-        // Close menu when you click a link.
-        $("[data-toggle='wy-nav-shift']").removeClass("shift");
-        $("[data-toggle='rst-versions']").toggleClass("shift");
-        // Handle dynamic display of l3 and l4 nav lists
-        toggleCurrent(target);
-        if (typeof(window.SphinxRtdTheme) != 'undefined') {
-            window.SphinxRtdTheme.StickyNav.hashChange();
-        }
-    });
-    $(document).on('click', "[data-toggle='rst-current-version']", function() {
-        $("[data-toggle='rst-versions']").toggleClass("shift-up");
-    });
-    // Make tables responsive
-    $("table.docutils:not(.field-list)").wrap("<div class='wy-table-responsive'></div>");
-
-    // Add expand links to all parents of nested ul
-    $('.wy-menu-vertical ul').siblings('a').each(function () {
-        var link = $(this);
-            expand = $('<span class="toctree-expand"></span>');
-        expand.on('click', function (ev) {
-            toggleCurrent(link);
-            ev.stopPropagation();
-            return false;
-        });
-        link.prepend(expand);
-    });
-});
-
-// Sphinx theme state
-window.SphinxRtdTheme = (function (jquery) {
-    var stickyNav = (function () {
-        var navBar,
-            win,
-            winScroll = false,
-            linkScroll = false,
-            winPosition = 0,
-            enable = function () {
-                init();
-                reset();
-                win.on('hashchange', reset);
-
-                // Set scrolling
-                win.on('scroll', function () {
-                    if (!linkScroll) {
-                        winScroll = true;
-                    }
-                });
-                setInterval(function () {
-                    if (winScroll) {
-                        winScroll = false;
-                        var newWinPosition = win.scrollTop(),
-                            navPosition = navBar.scrollTop(),
-                            newNavPosition = navPosition + (newWinPosition - winPosition);
-                        navBar.scrollTop(newNavPosition);
-                        winPosition = newWinPosition;
-                    }
-                }, 25);
-            },
-            init = function () {
-                navBar = jquery('nav.wy-nav-side:first');
-                win = jquery(window);
-            },
-            reset = function () {
-                // Get anchor from URL and open up nested nav
-                var anchor = encodeURI(window.location.hash);
-                if (anchor) {
-                    try {
-                        var link = $('.wy-menu-vertical')
-                            .find('[href="' + anchor + '"]');
-                        $('.wy-menu-vertical li.toctree-l1 li.current')
-                            .removeClass('current');
-                        link.closest('li.toctree-l2').addClass('current');
-                        link.closest('li.toctree-l3').addClass('current');
-                        link.closest('li.toctree-l4').addClass('current');
-                    }
-                    catch (err) {
-                        console.log("Error expanding nav for anchor", err);
-                    }
-                }
-            },
-            hashChange = function () {
-                linkScroll = true;
-                win.one('hashchange', function () {
-                    linkScroll = false;
-                });
-            };
-        jquery(init);
-        return {
-            enable: enable,
-            hashChange: hashChange
-        };
-    }());
-    return {
-        StickyNav: stickyNav
-    };
-}($));

lib/spack/docs/_themes/sphinx_rtd_theme/theme.conf

@@ -1,9 +0,0 @@
-[theme]
-inherit = basic
-stylesheet = css/theme.css
-
-[options]
-typekit_id = hiw1hhg
-analytics_id = 
-sticky_navigation = False
-logo_only =

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

@@ -1,37 +0,0 @@
-{% if READTHEDOCS %}
-{# Add rst-badge after rst-versions for small badge style. #}
-  <div class="rst-versions" data-toggle="rst-versions" role="note" aria-label="versions">
-    <span class="rst-current-version" data-toggle="rst-current-version">
-      <span class="fa fa-book"> Read the Docs</span>
-      v: {{ current_version }}
-      <span class="fa fa-caret-down"></span>
-    </span>
-    <div class="rst-other-versions">
-      <dl>
-        <dt>Versions</dt>
-        {% for slug, url in versions %}
-          <dd><a href="{{ url }}">{{ slug }}</a></dd>
-        {% endfor %}
-      </dl>
-      <dl>
-        <dt>Downloads</dt>
-        {% for type, url in downloads %}
-          <dd><a href="{{ url }}">{{ type }}</a></dd>
-        {% endfor %}
-      </dl>
-      <dl>
-        <dt>On Read the Docs</dt>
-          <dd>
-            <a href="//{{ PRODUCTION_DOMAIN }}/projects/{{ slug }}/?fromdocs={{ slug }}">Project Home</a>
-          </dd>
-          <dd>
-            <a href="//{{ PRODUCTION_DOMAIN }}/builds/{{ slug }}/?fromdocs={{ slug }}">Builds</a>
-          </dd>
-      </dl>
-      <hr/>
-      Free document hosting provided by <a href="http://www.readthedocs.org">Read the Docs</a>.
-
-    </div>
-  </div>
-{% endif %}
-

lib/spack/docs/basic_usage.rst

@@ -1,3 +1,8 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _basic-usage:
 
 ===========
@@ -34,12 +39,15 @@ available.  You can see a list of available package names at the
 ``spack list``
 ^^^^^^^^^^^^^^
 
-The ``spack list`` command prints out a list of all of the packages
-Spack can install:
+The ``spack list`` command prints out a list of all of the packages Spack
+can install:
 
 .. command-output:: spack list
+   :ellipsis: 10
 
-The packages are listed by name in alphabetical order.
+There are thosands of them, so we've truncated the output above, but you
+can find a :ref:`full list here <package-list>`.
+Packages are listed by name in alphabetical order.
 A pattern to match with no wildcards, ``*`` or ``?``,
 will be treated as though it started and ended with
 ``*``, so ``util`` is equivalent to ``*util*``.  All patterns will be treated
@@ -269,6 +277,86 @@ the tarballs in question to it (see :ref:`mirrors`):
 
        $ spack install galahad
 
+-----------------------------
+Deprecating insecure packages
+-----------------------------
+
+``spack deprecate`` allows for the removal of insecure packages with
+minimal impact to their dependents.
+
+.. warning::
+
+  The ``spack deprecate`` command is designed for use only in
+  extraordinary circumstances. This is a VERY big hammer to be used
+  with care.
+
+The ``spack deprecate`` command will remove one package and replace it
+with another by replacing the deprecated package's prefix with a link
+to the deprecator package's prefix.
+
+.. warning::
+
+  The ``spack deprecate`` command makes no promises about binary
+  compatibility. It is up to the user to ensure the deprecator is
+  suitable for the deprecated package.
+
+Spack tracks concrete deprecated specs and ensures that no future packages
+concretize to a deprecated spec.
+
+The first spec given to the ``spack deprecate`` command is the package
+to deprecate. It is an abstract spec that must describe a single
+installed package. The second spec argument is the deprecator
+spec. By default it must be an abstract spec that describes a single
+installed package, but with the ``-i/--install-deprecator`` it can be
+any abstract spec that Spack will install and then use as the
+deprecator. The ``-I/--no-install-deprecator`` option will ensure
+the default behavior.
+
+By default, ``spack deprecate`` will deprecate all dependencies of the
+deprecated spec, replacing each by the dependency of the same name in
+the deprecator spec. The ``-d/--dependencies`` option will ensure the
+default, while the ``-D/--no-dependencies`` option will deprecate only
+the root of the deprecate spec in favor of the root of the deprecator
+spec.
+
+``spack deprecate`` can use symbolic links or hard links. The default
+behavior is symbolic links, but the ``-l/--link-type`` flag can take
+options ``hard`` or ``soft``.
+
+-----------------------
+Verifying installations
+-----------------------
+
+The ``spack verify`` command can be used to verify the validity of
+Spack-installed packages any time after installation.
+
+At installation time, Spack creates a manifest of every file in the
+installation prefix. For links, Spack tracks the mode, ownership, and
+destination. For directories, Spack tracks the mode, and
+ownership. For files, Spack tracks the mode, ownership, modification
+time, hash, and size. The Spack verify command will check, for every
+file in each package, whether any of those attributes have changed. It
+will also check for newly added files or deleted files from the
+installation prefix. Spack can either check all installed packages
+using the `-a,--all` or accept specs listed on the command line to
+verify.
+
+The ``spack verify`` command can also verify for individual files that
+they haven't been altered since installation time. If the given file
+is not in a Spack installation prefix, Spack will report that it is
+not owned by any package. To check individual files instead of specs,
+use the ``-f,--files`` option.
+
+Spack installation manifests are part of the tarball signed by Spack
+for binary package distribution. When installed from a binary package,
+Spack uses the packaged installation manifest instead of creating one
+at install time.
+
+The ``spack verify`` command also accepts the ``-l,--local`` option to
+check only local packages (as opposed to those used transparently from
+``upstream`` spack instances) and the ``-j,--json`` option to output
+machine-readable json data for any errors.
+
 -------------------------
 Seeing installed packages
 -------------------------
@@ -326,11 +414,17 @@ Packages are divided into groups according to their architecture and
 compiler.  Within each group, Spack tries to keep the view simple, and
 only shows the version of installed packages.
 
-``spack find`` can filter the package list based on the package name, spec, or
-a number of properties of their installation status.  For example, missing
-dependencies of a spec can be shown with ``--missing``, packages which were
-explicitly installed with ``spack install <package>`` can be singled out with
-``--explicit`` and those which have been pulled in only as dependencies with
+""""""""""""""""""""""""""""""""
+Viewing more metadata
+""""""""""""""""""""""""""""""""
+
+``spack find`` can filter the package list based on the package name,
+spec, or a number of properties of their installation status.  For
+example, missing dependencies of a spec can be shown with
+``--missing``, deprecated packages can be included with
+``--deprecated``, packages which were explicitly installed with
+``spack install <package>`` can be singled out with ``--explicit`` and
+those which have been pulled in only as dependencies with
 ``--implicit``.
 
 In some cases, there may be different configurations of the *same*
@@ -383,8 +477,8 @@ use ``spack find --paths``:
        callpath@1.0.2        ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318
    ...
 
-And, finally, you can restrict your search to a particular package
-by supplying its name:
+You can restrict your search to a particular package by supplying its
+name:
 
 .. code-block:: console
 
@@ -394,6 +488,10 @@ by supplying its name:
        libelf@0.8.12  ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.12
        libelf@0.8.13  ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.13
 
+""""""""""""""""""""""""""""""""
+Spec queries
+""""""""""""""""""""""""""""""""
+
 ``spack find`` actually does a lot more than this.  You can use
 *specs* to query for specific configurations and builds of each
 package. If you want to find only libelf versions greater than version
@@ -421,6 +519,109 @@ with the 'debug' compile-time option enabled.
 
 The full spec syntax is discussed in detail in :ref:`sec-specs`.
 
+
+""""""""""""""""""""""""""""""""
+Machine-readable output
+""""""""""""""""""""""""""""""""
+
+If you only want to see very specific things about installed packages,
+Spack has some options for you.  ``spack find --format`` can be used to
+output only specific fields:
+
+.. code-block:: console
+
+   $ spack find --format "{name}-{version}-{hash}"
+   autoconf-2.69-icynozk7ti6h4ezzgonqe6jgw5f3ulx4
+   automake-1.16.1-o5v3tc77kesgonxjbmeqlwfmb5qzj7zy
+   bzip2-1.0.6-syohzw57v2jfag5du2x4bowziw3m5p67
+   bzip2-1.0.8-zjny4jwfyvzbx6vii3uuekoxmtu6eyuj
+   cmake-3.15.1-7cf6onn52gywnddbmgp7qkil4hdoxpcb
+   ...
+
+or:
+
+.. code-block:: console
+
+   $ spack find --format "{hash:7}"
+   icynozk
+   o5v3tc7
+   syohzw5
+   zjny4jw
+   7cf6onn
+   ...
+
+This uses the same syntax as described in documentation for
+:meth:`~spack.spec.Spec.format` -- you can use any of the options there.
+This is useful for passing metadata about packages to other command-line
+tools.
+
+Alternately, if you want something even more machine readable, you can
+output each spec as JSON records using ``spack find --json``.  This will
+output metadata on specs and all dependencies as json:
+
+.. code-block:: console
+
+    $ spack find --json sqlite@3.28.0
+    [
+     {
+      "name": "sqlite",
+      "hash": "3ws7bsihwbn44ghf6ep4s6h4y2o6eznv",
+      "version": "3.28.0",
+      "arch": {
+       "platform": "darwin",
+       "platform_os": "mojave",
+       "target": "x86_64"
+      },
+      "compiler": {
+       "name": "clang",
+       "version": "10.0.0-apple"
+      },
+      "namespace": "builtin",
+      "parameters": {
+       "fts": true,
+       "functions": false,
+       "cflags": [],
+       "cppflags": [],
+       "cxxflags": [],
+       "fflags": [],
+       "ldflags": [],
+       "ldlibs": []
+      },
+      "dependencies": {
+       "readline": {
+        "hash": "722dzmgymxyxd6ovjvh4742kcetkqtfs",
+        "type": [
+         "build",
+         "link"
+        ]
+       }
+      }
+     },
+     ...
+    ]
+
+You can use this with tools like `jq <https://stedolan.github.io/jq/>`_ to quickly create JSON records
+structured the way you want:
+
+.. code-block:: console
+
+    $ spack find --json sqlite@3.28.0 | jq -C '.[] | { name, version, hash }'
+    {
+      "name": "sqlite",
+      "version": "3.28.0",
+      "hash": "3ws7bsihwbn44ghf6ep4s6h4y2o6eznv"
+    }
+    {
+      "name": "readline",
+      "version": "7.0",
+      "hash": "722dzmgymxyxd6ovjvh4742kcetkqtfs"
+    }
+    {
+      "name": "ncurses",
+      "version": "6.1",
+      "hash": "zvaa4lhlhilypw5quj3akyd3apbq5gap"
+    }
+
 .. _sec-specs:
 
 --------------------
@@ -596,6 +797,9 @@ name or compiler specifier to their left in the spec.
 If the compiler spec is omitted, Spack will choose a default compiler
 based on site policies.
 
+
+.. _basic-variants:
+
 ^^^^^^^^
 Variants
 ^^^^^^^^
@@ -665,10 +869,10 @@ compile line.
 Notice that the value of the compiler flags must be quoted if it
 contains any spaces. Any of ``cppflags=-O3``, ``cppflags="-O3"``,
 ``cppflags='-O3'``, and ``cppflags="-O3 -fPIC"`` are acceptable, but
-``cppflags=-O3 -fPIC`` is not. Additionally, if they value of the
+``cppflags=-O3 -fPIC`` is not. Additionally, if the value of the
 compiler flags is not the last thing on the line, it must be followed
 by a space. The commmand ``spack install libelf cppflags="-O3"%intel``
-will be interpreted as an attempt to set `cppflags="-O3%intel"``.
+will be interpreted as an attempt to set ``cppflags="-O3%intel"``.
 
 The six compiler flags are injected in the order of implicit make commands
 in GNU Autotools. If all flags are set, the order is
@@ -681,11 +885,12 @@ Compiler environment variables and additional RPATHs
 
 In the exceptional case a compiler requires setting special environment
 variables, like an explicit library load path. These can bet set in an
-extra section in the compiler configuration.  The user can also specify
-additional ``RPATHs`` that the compiler will add to all executables
-generated by that compiler.  This is useful for forcing certain compilers
-to RPATH their own runtime libraries, so that executables will run
-without the need to set ``LD_LIBRARY_PATH``.
+extra section in the compiler configuration (the supported environment
+modification commands are: ``set``, ``unset``, ``append-path``, and
+``prepend-path``). The user can also specify additional ``RPATHs`` that the
+compiler will add to all executables generated by that compiler.  This is
+useful for forcing certain compilers to RPATH their own runtime libraries, so
+that executables will run without the need to set ``LD_LIBRARY_PATH``.
 
 .. code-block:: yaml
 
@@ -698,28 +903,140 @@ without the need to set ``LD_LIBRARY_PATH``.
           f77: /opt/gcc/bin/gfortran
           fc: /opt/gcc/bin/gfortran
         environment:
+          unset:
+            BAD_VARIABLE: # The colon is required but the value must be empty
           set:
-            LD_LIBRARY_PATH : /opt/gcc/lib
+            GOOD_VARIABLE_NUM: 1
+            GOOD_VARIABLE_STR: good
+          prepend-path:
+            PATH: /path/to/binutils
+          append-path:
+            LD_LIBRARY_PATH: /opt/gcc/lib
         extra_rpaths:
         - /path/to/some/compiler/runtime/directory
         - /path/to/some/other/compiler/runtime/directory
 
+
+.. note::
+
+   The section `environment` is interpreted as an ordered dictionary, which
+   means two things. First, environment modification are applied in the order
+   they are specified in the configuration file. Second, you cannot express
+   environment modifications that require mixing different commands, i.e. you
+   cannot `set` one variable, than `prepend-path` to another one, and than
+   again `set` a third one.
+
 ^^^^^^^^^^^^^^^^^^^^^^^
 Architecture specifiers
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-The architecture can be specified by using the reserved
-words ``target`` and/or ``os`` (``target=x86-64 os=debian7``). You can also
-use the triplet form of platform, operating system and processor.
+Each node in the dependency graph of a spec has an architecture attribute.
+This attribute is a triplet of platform, operating system and processor.
+You can specify the elements either separately, by using
+the reserved keywords ``platform``, ``os`` and ``target``:
+
+.. code-block:: console
+
+   $ spack install libelf platform=linux
+   $ spack install libelf os=ubuntu18.04
+   $ spack install libelf target=broadwell
+
+or together by using the reserved keyword ``arch``:
 
 .. code-block:: console
 
    $ spack install libelf arch=cray-CNL10-haswell
 
-Users on non-Cray systems won't have to worry about specifying the architecture.
-Spack will autodetect what kind of operating system is on your machine as well
-as the processor. For more information on how the architecture can be
-used on Cray machines, see :ref:`cray-support`
+Normally users don't have to bother specifying the architecture if they
+are installing software for their current host, as in that case the
+values will be detected automatically.  If you need fine-grained control
+over which packages use which targets (or over *all* packages' default
+target), see :ref:`concretization-preferences`.
+
+.. admonition:: Cray machines
+
+  The situation is a little bit different for Cray machines and a detailed
+  explanation on how the architecture can be set on them can be found at :ref:`cray-support`
+
+.. _support-for-microarchitectures:
+
+"""""""""""""""""""""""""""""""""""""""
+Support for specific microarchitectures
+"""""""""""""""""""""""""""""""""""""""
+
+Spack knows how to detect and optimize for many specific microarchitectures
+(including recent Intel, AMD and IBM chips) and encodes this information in
+the ``target`` portion of the architecture specification. A complete list of
+the microarchitectures known to Spack can be obtained in the following way:
+
+.. command-output:: spack arch --known-targets
+
+When a spec is installed Spack matches the compiler being used with the
+microarchitecture being targeted to inject appropriate optimization flags
+at compile time. Giving a command such as the following:
+
+.. code-block:: console
+
+   $ spack install zlib%gcc@9.0.1 target=icelake
+
+will produce compilation lines similar to:
+
+.. code-block:: console
+
+   $ /usr/bin/gcc-9 -march=icelake-client -mtune=icelake-client -c ztest10532.c
+   $ /usr/bin/gcc-9 -march=icelake-client -mtune=icelake-client -c -fPIC -O2 ztest10532.
+   ...
+
+where the flags ``-march=icelake-client -mtune=icelake-client`` are injected
+by Spack based on the requested target and compiler.
+
+If Spack knows that the requested compiler can't optimize for the current target
+or can't build binaries for that target at all, it will exit with a meaningful error message:
+
+.. code-block:: console
+
+   $ spack install zlib%gcc@5.5.0 target=icelake
+   ==> Error: cannot produce optimized binary for micro-architecture "icelake" with gcc@5.5.0 [supported compiler versions are 8:]
+
+When instead an old compiler is selected on a recent enough microarchitecture but there is
+no explicit ``target`` specification, Spack will optimize for the best match it can find instead
+of failing:
+
+.. code-block:: console
+
+   $ spack arch
+   linux-ubuntu18.04-broadwell
+
+   $ spack spec zlib%gcc@4.8
+   Input spec
+   --------------------------------
+   zlib%gcc@4.8
+
+   Concretized
+   --------------------------------
+   zlib@1.2.11%gcc@4.8+optimize+pic+shared arch=linux-ubuntu18.04-haswell
+
+   $ spack spec zlib%gcc@9.0.1
+   Input spec
+   --------------------------------
+   zlib%gcc@9.0.1
+
+   Concretized
+   --------------------------------
+   zlib@1.2.11%gcc@9.0.1+optimize+pic+shared arch=linux-ubuntu18.04-broadwell
+
+In the snippet above, for instance, the microarchitecture was demoted to ``haswell`` when
+compiling with ``gcc@4.8`` since support to optimize for ``broadwell`` starts from ``gcc@4.9:``.
+
+Finally if Spack has no information to match compiler and target, it will
+proceed with the installation but avoid injecting any microarchitecture
+specific flags.
+
+.. warning::
+
+   Currently Spack doesn't print any warning to the user if it has no information
+   on which optimization flags should be used for a given compiler. This behavior
+   might change in the future.
 
 .. _sec-virtual-dependencies:
 
@@ -950,41 +1267,43 @@ directly when you run ``python``:
    ImportError: No module named numpy
    >>>
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Extensions & Environment Modules
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^
+Using Extensions
+^^^^^^^^^^^^^^^^
 
-There are two ways to get ``numpy`` working in Python.  The first is
-to use :ref:`shell-support`.  You can simply ``use`` or ``load`` the
+There are three ways to get ``numpy`` working in Python.  The first is
+to use :ref:`shell-support`.  You can simply ``load`` the
 module for the extension, and it will be added to the ``PYTHONPATH``
-in your current shell.
-
-For tcl modules:
+in your current shell:
 
 .. code-block:: console
 
    $ spack load python
    $ spack load py-numpy
 
-or, for dotkit:
-
-.. code-block:: console
-
-   $ spack use python
-   $ spack use py-numpy
-
 Now ``import numpy`` will succeed for as long as you keep your current
 session open.
 
-^^^^^^^^^^^^^^^^^^^^^
-Activating Extensions
-^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Activating Extensions in a View
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-It is often desirable to have certain packages *always* available as
-part of a Python installation.  Spack offers a more permanent solution
-for this case.  Instead of requiring users to load particular
-environment modules, you can *activate* the package within the Python
-installation:
+The second way to use extensions is to create a view, which merges the
+python installation along with the extensions into a single prefix.
+See :ref:`filesystem-views` for a more in-depth description of views and
+:ref:`cmd-spack-view` for usage of the ``spack view`` command.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Activating Extensions Globally
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As an alternative to creating a merged prefix with Python and its extensions,
+and prior to support for views, Spack has provided a means to install the
+extension into the Spack installation prefix for the extendee. This has
+typically been useful since extendable packages typically search their own
+installation path for addons by default.
+
+Global activations are performed with the ``spack activate`` command:
 
 .. _cmd-spack-activate:
 
@@ -1044,11 +1363,11 @@ the ``py-numpy`` into the prefix of the ``python`` package.  To the
 python interpreter, it looks like ``numpy`` is installed in the
 ``site-packages`` directory.
 
-The only limitation of activation is that you can only have a *single*
+The only limitation of global activation is that you can only have a *single*
 version of an extension activated at a time.  This is because multiple
 versions of the same extension would conflict if symbolically linked
 into the same prefix.  Users who want a different version of a package
-can still get it by using environment modules, but they will have to
+can still get it by using environment modules or views, but they will have to
 explicitly load their preferred version.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -1093,22 +1412,43 @@ several variants:
 Filesystem requirements
 -----------------------
 
-Spack currently needs to be run from a filesystem that supports
+By default, Spack needs to be run from a filesystem that supports
 ``flock`` locking semantics.  Nearly all local filesystems and recent
-versions of NFS support this, but parallel filesystems may be mounted
-without ``flock`` support enabled.  You can determine how your
-filesystems are mounted with ``mount -p``.  The output for a Lustre
+versions of NFS support this, but parallel filesystems or NFS volumes may
+be configured without ``flock`` support enabled.  You can determine how
+your filesystems are mounted with ``mount``.  The output for a Lustre
 filesystem might look like this:
 
 .. code-block:: console
 
-   $ mount -l | grep lscratch
-   pilsner-mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
-   porter-mds1-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
+   $ mount | grep lscratch
+   mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,lazystatfs,flock)
+   mds2-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,lazystatfs,flock)
 
-Note the ``flock`` option on both Lustre mounts.  If you do not see
-this or a similar option for your filesystem, you may need ot ask your
-system administrator to enable ``flock``.
+Note the ``flock`` option on both Lustre mounts.
+
+If you do not see this or a similar option for your filesystem, you have
+a few options. First, you can move your Spack installation to a
+filesystem that supports locking. Second, you could ask your system
+administrator to enable ``flock`` for your filesystem.
+
+If none of those work, you can disable locking in one of two ways:
+
+  1. Run Spack with the ``-L`` or ``--disable-locks`` option to disable
+     locks on a call-by-call basis.
+  2. Edit :ref:`config.yaml <config-yaml>` and set the ``locks`` option
+     to ``false`` to always disable locking.
+
+.. warning::
+
+   If you disable locking, concurrent instances of Spack will have no way
+   to avoid stepping on each other.  You must ensure that there is only
+   **one** instance of Spack running at a time.  Otherwise, Spack may end
+   up with a corrupted database file, or you may not be able to see all
+   installed packages in commands like ``spack find``.
+
+   If you are unfortunate enough to run into this situation, you may be
+   able to fix it by running ``spack reindex``.
 
 This issue typically manifests with the error below:
 

lib/spack/docs/binary_caches.rst

@@ -1,7 +1,12 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _binary_caches:
 
 ============
-Build caches
+Build Caches
 ============
 
 Some sites may encourage users to set up their own test environments

lib/spack/docs/build_settings.rst

@@ -1,14 +1,20 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _build-settings:
 
-======================================
-Build customization
-======================================
+===================
+Build Customization
+===================
 
 Spack allows you to customize how your software is built through the
 ``packages.yaml`` file.  Using it, you can make Spack prefer particular
-implementations of virtual dependencies (e.g., compilers, MPI, or BLAS),
+implementations of virtual dependencies (e.g., MPI or BLAS/LAPACK),
 or you can make it prefer to build with particular compilers.  You can
-also tell Spack to use *external* installations of certain software.
+also tell Spack to use *external* software installations already
+present on your system.
 
 At a high level, the ``packages.yaml`` file is structured like this:
 
@@ -23,14 +29,14 @@ At a high level, the ``packages.yaml`` file is structured like this:
      all:
        # settings that apply to all packages.
 
-So you can either set build preferences *specifically* for one package,
-or you can specify that certain settings should apply to all packages.
+So you can either set build preferences specifically for *one* package,
+or you can specify that certain settings should apply to *all* packages.
 The types of settings you can customize are described in detail below.
 
 Spack's build defaults are in the default
 ``etc/spack/defaults/packages.yaml`` file.  You can override them in
 ``~/.spack/packages.yaml`` or ``etc/spack/packages.yaml``. For more
-details on how this works, see :ref:`configuration-scopes`
+details on how this works, see :ref:`configuration-scopes`.
 
 .. _sec-external-packages:
 
@@ -56,11 +62,22 @@ directory. Here's an example of an external configuration:
          openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug
          openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel
 
-This example lists three installations of OpenMPI, one built with gcc,
-one built with gcc and debug information, and another built with Intel.
+This example lists three installations of OpenMPI, one built with GCC,
+one built with GCC and debug information, and another built with Intel.
 If Spack is asked to build a package that uses one of these MPIs as a
-dependency, it will use the the pre-installed OpenMPI in
-the given directory. Packages.yaml can also be used to specify modules
+dependency, it will use the pre-installed OpenMPI in
+the given directory. Note that the specified path is the top-level
+install prefix, not the ``bin`` subdirectory.
+
+``packages.yaml`` can also be used to specify modules to load instead
+of the installation prefixes.  The following example says that module
+``CMake/3.7.2`` provides cmake version 3.7.2.
+
+.. code-block:: yaml
+
+   cmake:
+     modules:
+       cmake@3.7.2: CMake/3.7.2
 
 Each ``packages.yaml`` begins with a ``packages:`` token, followed
 by a list of package names.  To specify externals, add a ``paths`` or ``modules``
@@ -77,9 +94,9 @@ though the package and compiler may not ever 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
-external packages.  In the above example, if an OpenMPI 1.8.4 became
-available Spack may choose to start building and linking with that version
-rather than continue using the pre-installed OpenMPI versions.
+external packages.  In the above example, since newer versions of OpenMPI
+are available, Spack will choose to start building and linking with the
+latest version rather than continue using the pre-installed OpenMPI versions.
 
 To prevent this, the ``packages.yaml`` configuration also allows packages
 to be flagged as non-buildable.  The previous example could be modified to
@@ -115,12 +132,12 @@ Concretization Preferences
 --------------------------
 
 Spack can be configured to prefer certain compilers, package
-versions, depends_on, and variants during concretization.
+versions, dependencies, and variants during concretization.
 The preferred configuration can be controlled via the
-``~/.spack/packages.yaml`` file for user configuations, or the
+``~/.spack/packages.yaml`` file for user configurations, or the
 ``etc/spack/packages.yaml`` site configuration.
 
-Here's an example packages.yaml file that sets preferred packages:
+Here's an example ``packages.yaml`` file that sets preferred packages:
 
 .. code-block:: yaml
 
@@ -131,25 +148,26 @@ Here's an example packages.yaml file that sets preferred packages:
      gperftools:
        version: [2.2, 2.4, 2.3]
      all:
-       compiler: [gcc@4.4.7, gcc@4.6:, intel, clang, pgi]
+       compiler: [gcc@4.4.7, 'gcc@4.6:', intel, clang, pgi]
+       target: [sandybridge]
        providers:
-         mpi: [mvapich, mpich, openmpi]
+         mpi: [mvapich2, mpich, openmpi]
 
 At a high level, this example is specifying how packages should be
-concretized.  The opencv package should prefer using gcc 4.9 and
+concretized.  The opencv package should prefer using GCC 4.9 and
 be built with debug options.  The gperftools package should prefer version
-2.2 over 2.4.  Every package on the system should prefer mvapich for
-its MPI and gcc 4.4.7 (except for opencv, which overrides this by preferring gcc 4.9).
+2.2 over 2.4.  Every package on the system should prefer mvapich2 for
+its MPI and GCC 4.4.7 (except for opencv, which overrides this by preferring GCC 4.9).
 These options are used to fill in implicit defaults.  Any of them can be overwritten
 on the command line if explicitly requested.
 
-Each packages.yaml file begins with the string ``packages:`` and
+Each ``packages.yaml`` file begins with the string ``packages:`` and
 package names are specified on the next level. The special string ``all``
-applies settings to each package. Underneath each package name is
-one or more components: ``compiler``, ``variants``, ``version``,
-or ``providers``.  Each component has an ordered list of spec
-``constraints``, with earlier entries in the list being preferred over
-later entries.
+applies settings to *all* packages. Underneath each package name is one
+or more components: ``compiler``, ``variants``, ``version``,
+``providers``, and ``target``.  Each component has an ordered list of
+spec ``constraints``, with earlier entries in the list being preferred
+over later entries.
 
 Sometimes a package installation may have constraints that forbid
 the first concretization rule, in which case Spack will use the first
@@ -164,5 +182,54 @@ gcc to pgi will thus be preferred over the xlc compiler.
 
 The syntax for the ``provider`` section differs slightly from other
 concretization rules.  A provider lists a value that packages may
-``depend_on`` (e.g, mpi) and a list of rules for fulfilling that
+``depend_on`` (e.g, MPI) and a list of rules for fulfilling that
 dependency.
+
+.. _package_permissions:
+
+-------------------
+Package Permissions
+-------------------
+
+Spack can be configured to assign permissions to the files installed
+by a package.
+
+In the ``packages.yaml`` file under ``permissions``, the attributes
+``read``, ``write``, and ``group`` control the package
+permissions. These attributes can be set per-package, or for all
+packages under ``all``. If permissions are set under ``all`` and for a
+specific package, the package-specific settings take precedence.
+
+The ``read`` and ``write`` attributes take one of ``user``, ``group``,
+and ``world``.
+
+.. code-block:: yaml
+
+  packages:
+    all:
+      permissions:
+        write: group
+        group: spack
+    my_app:
+      permissions:
+        read: group
+        group: my_team
+
+The permissions settings describe the broadest level of access to
+installations of the specified packages. The execute permissions of
+the file are set to the same level as read permissions for those files
+that are executable. The default setting for ``read`` is ``world``,
+and for ``write`` is ``user``. In the example above, installations of
+``my_app`` will be installed with user and group permissions but no
+world permissions, and owned by the group ``my_team``. All other
+packages will be installed with user and group write privileges, and
+world read privileges. Those packages will be owned by the group
+``spack``.
+
+The ``group`` attribute assigns a Unix-style group to a package. All
+files installed by the package will be owned by the assigned group,
+and the sticky group bit will be set on the install prefix and all
+directories inside the install prefix. This will ensure that even
+manually placed files within the install prefix are owned by the
+assigned group. If no group is assigned, Spack will allow the OS
+default behavior to go as expected.

lib/spack/docs/build_systems.rst

@@ -0,0 +1,90 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+.. _build-systems:
+
+=============
+Build Systems
+=============
+
+Spack defines a number of classes which understand how to use common
+`build systems  <https://en.wikipedia.org/wiki/List_of_build_automation_software>`_
+(Makefiles, CMake, etc.). Spack package definitions can inherit these
+classes in order to streamline their builds.
+
+This guide provides information specific to each particular build system.
+It assumes that you've read the :ref:`packaging-guide` and expands
+on these ideas for each distinct build system that Spack supports:
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Make-based
+
+   build_systems/makefilepackage
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Make-incompatible
+
+   build_systems/sconspackage
+   build_systems/wafpackage
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Build-script generation
+
+   build_systems/autotoolspackage
+   build_systems/cmakepackage
+   build_systems/mesonpackage
+   build_systems/qmakepackage
+   build_systems/sippackage
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Language-specific
+
+   build_systems/octavepackage
+   build_systems/perlpackage
+   build_systems/pythonpackage
+   build_systems/rpackage
+   build_systems/rubypackage
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Other
+
+   build_systems/cudapackage
+   build_systems/intelpackage
+   build_systems/custompackage
+
+For reference, the :py:mod:`Build System API docs <spack.build_systems>`
+provide a list of build systems and methods/attributes that can be
+overridden. If you are curious about the implementation of a particular
+build system, you can view the source code by running:
+
+.. code-block:: console
+
+   $ spack edit --build-system autotools
+
+
+This will open up the ``AutotoolsPackage`` definition in your favorite
+editor. In addition, if you are working with a less common build system
+like QMake, SCons, or Waf, it may be useful to see examples of other
+packages. You can quickly find examples by running:
+
+.. code-block:: console
+
+   $ cd var/spack/repos/builtin/packages
+   $ grep -l QMakePackage */package.py
+
+
+You can then view these packages with ``spack edit``.
+
+This guide is intended to supplement the
+:py:mod:`Build System API docs <spack.build_systems>` with examples of
+how to override commonly used methods. It also provides rules of thumb
+and suggestions for package developers who are unfamiliar with a
+particular build system.

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lib/spack/docs/build_systems/autotoolspackage.rst

@@ -0,0 +1,305 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _autotoolspackage:
+
+----------------
+AutotoolsPackage
+----------------
+
+Autotools is a GNU build system that provides a build-script generator.
+By running the platform-independent ``./configure`` script that comes
+with the package, you can generate a platform-dependent Makefile.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``AutotoolsPackage`` base class comes with the following phases:
+
+#. ``autoreconf`` - generate the configure script
+#. ``configure`` - generate the Makefiles
+#. ``build`` - build the package
+#. ``install`` - install the package
+
+Most of the time, the ``autoreconf`` phase will do nothing, but if the
+package is missing a ``configure`` script, ``autoreconf`` will generate
+one for you.
+
+The other phases run:
+
+.. code-block:: console
+
+   $ ./configure --prefix=/path/to/installation/prefix
+   $ make
+   $ make check  # optional
+   $ make install
+   $ make installcheck  # optional
+
+
+Of course, you may need to add a few arguments to the ``./configure``
+line.
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+The most important file for an Autotools-based package is the ``configure``
+script. This script is automatically generated by Autotools and generates
+the appropriate Makefile when run.
+
+.. warning::
+
+   Watch out for fake Autotools packages!
+
+   Autotools is a very popular build system, and many people are used to the
+   classic steps to install a package:
+
+   .. code-block:: console
+
+      $ ./configure
+      $ make
+      $ make install
+
+
+   For this reason, some developers will write their own ``configure``
+   scripts that have nothing to do with Autotools. These packages may
+   not accept the same flags as other Autotools packages, so it is
+   better to use the ``Package`` base class and create a
+   :ref:`custom build system <custompackage>`. You can tell if a package
+   uses Autotools by running ``./configure --help`` and comparing the output
+   to other known Autotools packages. You should also look for files like:
+
+   * ``configure.ac``
+   * ``configure.in``
+   * ``Makefile.am``
+
+   Packages that don't use Autotools aren't likely to have these files.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Whether or not your package requires Autotools to install depends on
+how the source code is distributed. Most of the time, when developers
+distribute tarballs, they will already contain the ``configure`` script
+necessary for installation. If this is the case, your package does not
+require any Autotools dependencies.
+
+However, a basic rule of version control systems is to never commit
+code that can be generated. The source code repository itself likely
+does not have a ``configure`` script. Developers typically write
+(or auto-generate) a ``configure.ac`` script that contains configuration
+preferences and a ``Makefile.am`` script that contains build instructions.
+Then, ``autoconf`` is used to convert ``configure.ac`` into ``configure``,
+while ``automake`` is used to convert ``Makefile.am`` into ``Makefile.in``.
+``Makefile.in`` is used by ``configure`` to generate a platform-dependent
+``Makefile`` for you. The following diagram provides a high-level overview
+of the process:
+
+.. figure:: Autoconf-automake-process.*
+   :target: https://commons.wikimedia.org/w/index.php?curid=15581407
+
+   `GNU autoconf and automake process for generating makefiles <https://commons.wikimedia.org/wiki/File:Autoconf-automake-process.svg>`_
+   by `Jdthood` under `CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0/deed.en>`_
+
+If a ``configure`` script is not present in your tarball, you will
+need to generate one yourself. Luckily, Spack already has an ``autoreconf``
+phase to do most of the work for you. By default, the ``autoreconf``
+phase runs:
+
+.. code-block:: console
+
+   $ libtoolize
+   $ aclocal
+   $ autoreconf --install --verbose --force
+
+All you need to do is add a few Autotools dependencies to the package.
+Most stable releases will come with a ``configure`` script, but if you
+check out a commit from the ``develop`` branch, you would want to add:
+
+.. code-block:: python
+
+   depends_on('autoconf', type='build', when='@develop')
+   depends_on('automake', type='build', when='@develop')
+   depends_on('libtool',  type='build', when='@develop')
+   depends_on('m4',       type='build', when='@develop')
+
+In some cases, developers might need to distribute a patch that modifies
+one of the files used to generate ``configure`` or ``Makefile.in``.
+In this case, these scripts will need to be regenerated. It is
+preferable to regenerate these manually using the patch, and then
+create a new patch that directly modifies ``configure``. That way,
+Spack can use the secondary patch and additional build system
+dependencies aren't necessary.
+
+""""""""""""""""
+force_autoreconf
+""""""""""""""""
+
+If for whatever reason you really want to add the original patch
+and tell Spack to regenerate ``configure``, you can do so using the
+following setting:
+
+.. code-block:: python
+
+   force_autoreconf = True
+
+This line tells Spack to wipe away the existing ``configure`` script
+and generate a new one. If you only need to do this for a single
+version, this can be done like so:
+
+.. code-block:: python
+
+   @property
+   def force_autoreconf(self):
+       return self.version == Version('1.2.3'):
+
+^^^^^^^^^^^^^^^^^^^^^^^
+Finding configure flags
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Once you have a ``configure`` script present, the next step is to
+determine what option flags are available. These flags can be found
+by running:
+
+.. code-block:: console
+
+   $ ./configure --help
+
+``configure`` will display a list of valid flags separated into
+some or all of the following sections:
+
+* Configuration
+* Installation directories
+* Fine tuning of the installation directories
+* Program names
+* X features
+* System types
+* **Optional Features**
+* **Optional Packages**
+* **Some influential environment variables**
+
+For the most part, you can ignore all but the last 3 sections.
+The "Optional Features" sections lists flags that enable/disable
+features you may be interested in. The "Optional Packages" section
+often lists dependencies and the flags needed to locate them. The
+"environment variables" section lists environment variables that the
+build system uses to pass flags to the compiler and linker.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Addings flags to configure
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For most of the flags you encounter, you will want a variant to
+optionally enable/disable them. You can then optionally pass these
+flags to the ``configure`` call by overriding the ``configure_args``
+function like so:
+
+.. code-block:: python
+
+   def configure_args(self):
+       args = []
+
+       if '+mpi' in self.spec:
+           args.append('--enable-mpi')
+       else:
+           args.append('--disable-mpi')
+
+       return args
+
+Note that we are explicitly disabling MPI support if it is not
+requested. This is important, as many Autotools packages will enable
+options by default if the dependencies are found, and disable them
+otherwise. We want Spack installations to be as deterministic as possible.
+If two users install a package with the same variants, the goal is that
+both installations work the same way. See `here <https://www.linux.com/news/best-practices-autotools>`__
+and `here <https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Automagic_dependencies>`__
+for a rationale as to why these so-called "automagic" dependencies
+are a problem.
+
+By default, Autotools installs packages to ``/usr``. We don't want this,
+so Spack automatically adds ``--prefix=/path/to/installation/prefix``
+to your list of ``configure_args``. You don't need to add this yourself.
+
+^^^^^^^^^^^^^^^^
+Helper functions
+^^^^^^^^^^^^^^^^
+
+You may have noticed that most of the Autotools flags are of the form
+``--enable-foo``, ``--disable-bar``, ``--with-baz=<prefix>``, or
+``--without-baz``. Since these flags are so common, Spack provides a
+couple of helper functions to make your life easier.
+
+TODO: document ``with_or_without`` and ``enable_or_disable``.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Configure script in a sub-directory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Occasionally, developers will hide their source code and ``configure``
+script in a subdirectory like ``src``. If this happens, Spack won't
+be able to automatically detect the build system properly when running
+``spack create``. You will have to manually change the package base
+class and tell Spack where the ``configure`` script resides. You can
+do this like so:
+
+.. code-block:: python
+
+   configure_directory = 'src'
+
+^^^^^^^^^^^^^^^^^^^^^^
+Building out of source
+^^^^^^^^^^^^^^^^^^^^^^
+
+Some packages like ``gcc`` recommend building their software in a
+different directory than the source code to prevent build pollution.
+This can be done using the ``build_directory`` variable:
+
+.. code-block:: python
+
+   build_directory = 'spack-build'
+
+By default, Spack will build the package in the same directory that
+contains the ``configure`` script
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build and install targets
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For most Autotools packages, the usual:
+
+.. code-block:: console
+
+   $ configure
+   $ make
+   $ make install
+
+is sufficient to install the package. However, if you need to run
+make with any other targets, for example, to build an optional
+library or build the documentation, you can add these like so:
+
+.. code-block:: python
+
+   build_targets = ['all', 'docs']
+   install_targets = ['install', 'docs']
+
+^^^^^^^
+Testing
+^^^^^^^
+
+Autotools-based packages typically provide unit testing via the
+``check`` and ``installcheck`` targets. If you build your software
+with ``spack install --test=root``, Spack will check for the presence
+of a ``check`` or ``test`` target in the Makefile and run
+``make check`` for you. After installation, it will check for an
+``installcheck`` target and run ``make installcheck`` if it finds one.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the Autotools build system, see:
+https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html

lib/spack/docs/build_systems/cmakepackage.rst

@@ -0,0 +1,279 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _cmakepackage:
+
+------------
+CMakePackage
+------------
+
+Like Autotools, CMake is a widely-used build-script generator. Designed
+by Kitware, CMake is the most popular build system for new C, C++, and
+Fortran projects, and many older projects are switching to it as well.
+
+Unlike Autotools, CMake can generate build scripts for builders other
+than Make: Ninja, Visual Studio, etc. It is therefore cross-platform,
+whereas Autotools is Unix-only.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``CMakePackage`` base class comes with the following phases:
+
+#. ``cmake`` - generate the Makefile
+#. ``build`` - build the package
+#. ``install`` - install the package
+
+By default, these phases run:
+
+.. code-block:: console
+
+   $ mkdir spack-build
+   $ cd spack-build
+   $ cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/installation/prefix
+   $ make
+   $ make test  # optional
+   $ make install
+
+
+A few more flags are passed to ``cmake`` by default, including flags
+for setting the build type and flags for locating dependencies. Of
+course, you may need to add a few arguments yourself.
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+A CMake-based package can be identified by the presence of a
+``CMakeLists.txt`` file. This file defines the build flags that can be
+passed to the cmake invocation, as well as linking instructions. If
+you are familiar with CMake, it can prove very useful for determining
+dependencies and dependency version requirements.
+
+One thing to look for is the ``cmake_minimum_required`` function:
+
+.. code-block:: cmake
+
+   cmake_minimum_required(VERSION 2.8.12)
+
+
+This means that CMake 2.8.12 is the earliest release that will work.
+You should specify this in a ``depends_on`` statement.
+
+CMake-based packages may also contain ``CMakeLists.txt`` in subdirectories.
+This modularization helps to manage complex builds in a hierarchical
+fashion. Sometimes these nested ``CMakeLists.txt`` require additional
+dependencies not mentioned in the top-level file.
+
+There's also usually a ``cmake`` or ``CMake`` directory containing
+additional macros, find scripts, etc. These may prove useful in
+determining dependency version requirements.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Every package that uses the CMake build system requires a ``cmake``
+dependency. Since this is always the case, the ``CMakePackage`` base
+class already contains:
+
+.. code-block:: python
+
+   depends_on('cmake', type='build')
+
+
+If you need to specify a particular version requirement, you can
+override this in your package:
+
+.. code-block:: python
+
+   depends_on('cmake@2.8.12:', type='build')
+
+
+^^^^^^^^^^^^^^^^^^^
+Finding cmake flags
+^^^^^^^^^^^^^^^^^^^
+
+To get a list of valid flags that can be passed to ``cmake``, run the
+following command in the directory that contains ``CMakeLists.txt``:
+
+.. code-block:: console
+
+   $ cmake . -LAH
+
+
+CMake will start by checking for compilers and dependencies. Eventually
+it will begin to list build options. You'll notice that most of the
+build options at the top are prefixed with ``CMAKE_``. You can safely
+ignore most of these options as Spack already sets them for you. This
+includes flags needed to locate dependencies, RPATH libraries, set the
+installation directory, and set the build type.
+
+The rest of the flags are the ones you should consider adding to your
+package. They often include flags to enable/disable support for certain
+features and locate specific dependencies. One thing you'll notice that
+makes CMake different from Autotools is that CMake has an understanding
+of build flag hierarchy. That is, certain flags will not display unless
+their parent flag has been selected. For example, flags to specify the
+``lib`` and ``include`` directories for a package might not appear
+unless CMake found the dependency it was looking for. You may need to
+manually specify certain flags to explore the full depth of supported
+build flags, or check the ``CMakeLists.txt`` yourself.
+
+^^^^^^^^^^^^^^^^^^^^^
+Adding flags to cmake
+^^^^^^^^^^^^^^^^^^^^^
+
+To add additional flags to the ``cmake`` call, simply override the
+``cmake_args`` function:
+
+.. code-block:: python
+
+   def cmake_args(self):
+       args = []
+
+       if '+hdf5' in self.spec:
+           args.append('-DDETECT_HDF5=ON')
+       else:
+           args.append('-DDETECT_HDF5=OFF')
+
+       return args
+
+
+^^^^^^^^^^
+Generators
+^^^^^^^^^^
+
+CMake and Autotools are build-script generation tools; they "generate"
+the Makefiles that are used to build a software package. CMake actually
+supports multiple generators, not just Makefiles. Another common
+generator is Ninja. To switch to the Ninja generator, simply add:
+
+.. code-block:: python
+
+   generator = 'Ninja'
+
+
+``CMakePackage`` defaults to "Unix Makefiles". If you switch to the
+Ninja generator, make sure to add:
+
+.. code-block:: python
+
+   depends_on('ninja', type='build')
+
+to the package as well. Aside from that, you shouldn't need to do
+anything else. Spack will automatically detect that you are using
+Ninja and run:
+
+.. code-block:: console
+
+   $ cmake .. -G Ninja
+   $ ninja
+   $ ninja install
+
+Spack currently only supports "Unix Makefiles" and "Ninja" as valid
+generators, but it should be simple to add support for alternative
+generators. For more information on CMake generators, see:
+https://cmake.org/cmake/help/latest/manual/cmake-generators.7.html
+
+^^^^^^^^^^^^^^^^
+CMAKE_BUILD_TYPE
+^^^^^^^^^^^^^^^^
+
+Every CMake-based package accepts a ``-DCMAKE_BUILD_TYPE`` flag to
+dictate which level of optimization to use. In order to ensure
+uniformity across packages, the ``CMakePackage`` base class adds
+a variant to control this:
+
+.. code-block:: python
+
+   variant('build_type', default='RelWithDebInfo',
+           description='CMake build type',
+           values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'))
+
+However, not every CMake package accepts all four of these options.
+Grep the ``CMakeLists.txt`` file to see if the default values are
+missing or replaced. For example, the
+`dealii <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/dealii/package.py>`_
+package overrides the default variant with:
+
+.. code-block:: python
+
+   variant('build_type', default='DebugRelease',
+           description='The build type to build',
+           values=('Debug', 'Release', 'DebugRelease'))
+
+For more information on ``CMAKE_BUILD_TYPE``, see:
+https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+CMakeLists.txt in a sub-directory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Occasionally, developers will hide their source code and ``CMakeLists.txt``
+in a subdirectory like ``src``. If this happens, Spack won't
+be able to automatically detect the build system properly when running
+``spack create``. You will have to manually change the package base
+class and tell Spack where ``CMakeLists.txt`` resides. You can do this
+like so:
+
+.. code-block:: python
+
+   root_cmakelists_dir = 'src'
+
+
+Note that this path is relative to the root of the extracted tarball,
+not to the ``build_directory``. It defaults to the current directory.
+
+^^^^^^^^^^^^^^^^^^^^^^
+Building out of source
+^^^^^^^^^^^^^^^^^^^^^^
+
+By default, Spack builds every ``CMakePackage`` in a ``spack-build``
+sub-directory. If, for whatever reason, you would like to build in a
+different sub-directory, simply override ``build_directory`` like so:
+
+.. code-block:: python
+
+   build_directory = 'my-build'
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build and install targets
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For most CMake packages, the usual:
+
+.. code-block:: console
+
+   $ cmake
+   $ make
+   $ make install
+
+is sufficient to install the package. However, if you need to run
+make with any other targets, for example, to build an optional
+library or build the documentation, you can add these like so:
+
+.. code-block:: python
+
+   build_targets = ['all', 'docs']
+   install_targets = ['install', 'docs']
+
+^^^^^^^
+Testing
+^^^^^^^
+
+CMake-based packages typically provide unit testing via the
+``test`` target. If you build your software with ``--test=root``,
+Spack will check for the presence of a ``test`` target in the
+Makefile and run ``make test`` for you. If you want to run a
+different test instead, simply override the ``check`` method.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the CMake build system, see:
+https://cmake.org/cmake/help/latest/

lib/spack/docs/build_systems/cudapackage.rst

@@ -0,0 +1,43 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _cudapackage:
+
+-----------
+CudaPackage
+-----------
+
+Different from other packages, ``CudaPackage`` does not represent a build
+system. Instead its goal is to simplify and unify usage of ``CUDA`` in other
+packages.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Provided variants and dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+``CudaPackage`` provides ``cuda`` variant (default to ``off``) to enable/disable
+``CUDA``, and ``cuda_arch`` variant to optionally specify the architecture.
+It also declares dependencies on the ``CUDA`` package ``depends_on('cuda@...')``
+based on the architecture as well as specifies conflicts for certain compiler versions.
+
+^^^^^
+Usage
+^^^^^
+
+In order to use it, just add another base class to your package, for example:
+
+.. code-block:: python
+
+    class MyPackage(CMakePackage, CudaPackage):
+        ...
+        def cmake_args(self):
+            spec = self.spec
+            if '+cuda' in spec:
+                options.append('-DWITH_CUDA=ON')
+                cuda_arch = spec.variants['cuda_arch'].value
+                if cuda_arch is not None:
+                    options.append('-DCUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch[0]))
+            else:
+                options.append('-DWITH_CUDA=OFF')

lib/spack/docs/build_systems/custompackage.rst

@@ -0,0 +1,209 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _custompackage:
+
+--------------------
+Custom Build Systems
+--------------------
+
+While the build systems listed above should meet your needs for the
+vast majority of packages, some packages provide custom build scripts.
+This guide is intended for the following use cases:
+
+* Packaging software with its own custom build system
+* Adding support for new build systems
+
+If you want to add support for a new build system, a good place to
+start is to look at the definitions of other build systems. This guide
+focuses mostly on how Spack's build systems work.
+
+In this guide, we will be using the
+`perl <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/perl/package.py>`_ and
+`cmake <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cmake/package.py>`_
+packages as examples. ``perl``'s build system is a hand-written
+``Configure`` shell script, while ``cmake`` bootstraps itself during
+installation. Both of these packages require custom build systems.
+
+^^^^^^^^^^
+Base class
+^^^^^^^^^^
+
+If your package does not belong to any of the aforementioned build
+systems that Spack already supports, you should inherit from the
+``Package`` base class. ``Package`` is a simple base class with a
+single phase: ``install``. If your package is simple, you may be able
+to simply write an ``install`` method that gets the job done. However,
+if your package is more complex and installation involves multiple
+steps, you should add separate phases as mentioned in the next section.
+
+If you are creating a new build system base class, you should inherit
+from ``PackageBase``. This is the superclass for all build systems in
+Spack.
+
+^^^^^^
+Phases
+^^^^^^
+
+The most important concept in Spack's build system support is the idea
+of phases. Each build system defines a set of phases that are necessary
+to install the package. They usually follow some sort of "configure",
+"build", "install" guideline, but any of those phases may be missing
+or combined with another phase.
+
+If you look at the ``perl`` package, you'll see:
+
+.. code-block:: python
+
+   phases = ['configure', 'build', 'install']
+
+Similarly, ``cmake`` defines:
+
+.. code-block:: python
+
+   phases = ['bootstrap', 'build', 'install']
+
+If we look at the ``cmake`` example, this tells Spack's ``PackageBase``
+class to run the ``bootstrap``, ``build``, and ``install`` functions
+in that order. It is now up to you to define these methods.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Phase and phase_args functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If we look at ``perl``, we see that it defines a ``configure`` method:
+
+.. code-block:: python
+
+   def configure(self, spec, prefix):
+       configure = Executable('./Configure')
+       configure(*self.configure_args())
+
+There is also a corresponding ``configure_args`` function that handles
+all of the arguments to pass to ``Configure``, just like in
+``AutotoolsPackage``. Comparatively, the ``build`` and ``install``
+phases are pretty simple:
+
+.. code-block:: python
+
+   def build(self, spec, prefix):
+       make()
+
+   def install(self, spec, prefix):
+       make('install')
+
+The ``cmake`` package looks very similar, but with a ``bootstrap``
+function instead of ``configure``:
+
+.. code-block:: python
+
+   def bootstrap(self, spec, prefix):
+       bootstrap = Executable('./bootstrap')
+       bootstrap(*self.bootstrap_args())
+
+   def build(self, spec, prefix):
+       make()
+
+   def install(self, spec, prefix):
+       make('install')
+
+Again, there is a ``boostrap_args`` function that determines the
+correct bootstrap flags to use.
+
+^^^^^^^^^^^^^^^^^^^^
+run_before/run_after
+^^^^^^^^^^^^^^^^^^^^
+
+Occasionally, you may want to run extra steps either before or after
+a given phase. This applies not just to custom build systems, but to
+existing build systems as well. You may need to patch a file that is
+generated by configure, or install extra files in addition to what
+``make install`` copies to the installation prefix. This is where
+``@run_before`` and ``@run_after`` come in.
+
+These Python decorators allow you to write functions that are called
+before or after a particular phase. For example, in ``perl``, we see:
+
+.. code-block:: python
+
+   @run_after('install')
+   def install_cpanm(self):
+       spec = self.spec
+
+       if '+cpanm' in spec:
+           with working_dir(join_path('cpanm', 'cpanm')):
+               perl = spec['perl'].command
+               perl('Makefile.PL')
+               make()
+               make('install')
+
+This extra step automatically installs ``cpanm`` in addition to the
+base Perl installation.
+
+^^^^^^^^^^^^^^^^^^^^^
+on_package_attributes
+^^^^^^^^^^^^^^^^^^^^^
+
+The ``run_before``/``run_after`` logic discussed above becomes
+particularly powerful when combined with the ``@on_package_attributes``
+decorator. This decorator allows you to conditionally run certain
+functions depending on the attributes of that package. The most
+common example is conditional testing. Many unit tests are prone to
+failure, even when there is nothing wrong with the installation.
+Unfortunately, non-portable unit tests and tests that are
+"supposed to fail" are more common than we would like. Instead of
+always running unit tests on installation, Spack lets users
+conditionally run tests with the ``--test=root`` flag.
+
+If we wanted to define a function that would conditionally run
+if and only if this flag is set, we would use the following line:
+
+.. code-block:: python
+
+   @on_package_attributes(run_tests=True)
+
+^^^^^^^
+Testing
+^^^^^^^
+
+Let's put everything together and add unit tests to our package.
+In the ``perl`` package, we can see:
+
+.. code-block:: python
+
+   @run_after('build')
+   @on_package_attributes(run_tests=True)
+   def test(self):
+       make('test')
+
+As you can guess, this runs ``make test`` *after* building the package,
+if and only if testing is requested. Again, this is not specific to
+custom build systems, it can be added to existing build systems as well.
+
+Ideally, every package in Spack will have some sort of test to ensure
+that it was built correctly. It is up to the package authors to make
+sure this happens. If you are adding a package for some software and
+the developers list commands to test the installation, please add these
+tests to your ``package.py``.
+
+.. warning::
+
+   The order of decorators matters. The following ordering:
+
+   .. code-block:: python
+
+      @run_after('install')
+      @on_package_attributes(run_tests=True)
+
+   works as expected. However, if you reverse the ordering:
+
+   .. code-block:: python
+
+      @on_package_attributes(run_tests=True)
+      @run_after('install')
+
+   the tests will always be run regardless of whether or not
+   ``--test=root`` is requested. See https://github.com/spack/spack/issues/3833
+   for more information

lib/spack/docs/build_systems/makefilepackage.rst

@@ -0,0 +1,309 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _makefilepackage:
+
+---------------
+MakefilePackage
+---------------
+
+The most primitive build system a package can use is a plain Makefile.
+Makefiles are simple to write for small projects, but they usually
+require you to edit the Makefile to set platform and compiler-specific
+variables.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``MakefilePackage`` base class comes with 3 phases:
+
+#. ``edit`` - edit the Makefile
+#. ``build`` - build the project
+#. ``install`` - install the project
+
+By default, ``edit`` does nothing, but you can override it to replace
+hard-coded Makefile variables. The ``build`` and ``install`` phases
+run:
+
+.. code-block:: console
+
+   $ make
+   $ make install
+
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+The main file that matters for a ``MakefilePackage`` is the Makefile.
+This file will be named one of the following ways:
+
+* GNUmakefile (only works with GNU Make)
+* Makefile (most common)
+* makefile
+
+Some Makefiles also *include* other configuration files. Check for an
+``include`` directive in the Makefile.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Spack assumes that the operating system will have a valid ``make`` utility
+installed already, so you don't need to add a dependency on ``make``.
+However, if the package uses a ``GNUmakefile`` or the developers recommend
+using GNU Make, you should add a dependency on ``gmake``:
+
+.. code-block:: python
+
+   depends_on('gmake', type='build')
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Types of Makefile packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Most of the work involved in packaging software that uses Makefiles
+involves overriding or replacing hard-coded variables. Many packages
+make the mistake of hard-coding compilers, usually for GCC or Intel.
+This is fine if you happen to be using that particular compiler, but
+Spack is designed to work with *any* compiler, and you need to ensure
+that this is the case.
+
+Depending on how the Makefile is designed, there are 4 common strategies
+that can be used to set or override the appropriate variables:
+
+"""""""""""""""""""""
+Environment variables
+"""""""""""""""""""""
+
+Make has multiple types of
+`assignment operators <https://www.gnu.org/software/make/manual/make.html#Setting>`_.
+Some Makefiles use ``=`` to assign variables. The only way to override
+these variables is to edit the Makefile or override them on the
+command-line. However, Makefiles that use ``?=`` for assignment honor
+environment variables. Since Spack already sets ``CC``, ``CXX``, ``F77``,
+and ``FC``, you won't need to worry about setting these variables. If
+there are any other variables you need to set, you can do this in the
+``edit`` method:
+
+.. code-block:: python
+
+   def edit(self, spec, prefix):
+       env['PREFIX'] = prefix
+       env['BLASLIB'] = spec['blas'].libs.ld_flags
+
+
+`cbench <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cbench/package.py>`_
+is a good example of a simple package that does this, while
+`esmf <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/esmf/package.py>`_
+is a good example of a more complex package.
+
+""""""""""""""""""""""
+Command-line arguments
+""""""""""""""""""""""
+
+If the Makefile ignores environment variables, the next thing to try
+is command-line arguments. You can do this by overriding the
+``build_targets`` attribute. If you don't need access to the spec,
+you can do this like so:
+
+.. code-block:: python
+
+   build_targets = ['CC=cc']
+
+
+If you do need access to the spec, you can create a property like so:
+
+.. code-block:: python
+
+   @property
+   def build_targets(self):
+       spec = self.spec
+
+       return [
+           'CC=cc',
+           'BLASLIB={0}'.format(spec['blas'].libs.ld_flags),
+       ]
+
+
+`cloverleaf <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cloverleaf/package.py>`_
+is a good example of a package that uses this strategy.
+
+"""""""""""""
+Edit Makefile
+"""""""""""""
+
+Some Makefiles are just plain stubborn and will ignore command-line
+variables. The only way to ensure that these packages build correctly
+is to directly edit the Makefile. Spack provides a ``FileFilter`` class
+and a ``filter_file`` method to help with this. For example:
+
+.. code-block:: python
+
+   def edit(self, spec, prefix):
+       makefile = FileFilter('Makefile')
+
+       makefile.filter('CC = gcc',  'CC = cc')
+       makefile.filter('CXX = g++', 'CC = c++')
+
+
+`stream <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/stream/package.py>`_
+is a good example of a package that involves editing a Makefile to set
+the appropriate variables.
+
+"""""""""""
+Config file
+"""""""""""
+
+More complex packages often involve Makefiles that *include* a
+configuration file. These configuration files are primarily composed
+of variables relating to the compiler, platform, and the location of
+dependencies or names of libraries. Since these config files are
+dependent on the compiler and platform, you will often see entire
+directories of examples for common compilers and architectures. Use
+these examples to help determine what possible values to use.
+
+If the config file is long and only contains one or two variables
+that need to be modified, you can use the technique above to edit
+the config file. However, if you end up needing to modify most of
+the variables, it may be easier to write a new file from scratch.
+
+If each variable is independent of each other, a dictionary works
+well for storing variables:
+
+.. code-block:: python
+
+   def edit(self, spec, prefix):
+       config = {
+           'CC': 'cc',
+           'MAKE': 'make',
+       }
+
+       if '+blas' in spec:
+           config['BLAS_LIBS'] = spec['blas'].libs.joined()
+
+       with open('make.inc', 'w') as inc:
+           for key in config:
+               inc.write('{0} = {1}\n'.format(key, config[key]))
+
+
+`elk <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/elk/package.py>`_
+is a good example of a package that uses a dictionary to store
+configuration variables.
+
+If the order of variables is important, it may be easier to store
+them in a list:
+
+.. code-block:: python
+
+   def edit(self, spec, prefix):
+       config = [
+           'INSTALL_DIR = {0}'.format(prefix),
+           'INCLUDE_DIR = $(INSTALL_DIR)/include',
+           'LIBRARY_DIR = $(INSTALL_DIR)/lib',
+       ]
+
+       with open('make.inc', 'w') as inc:
+           for var in config:
+               inc.write('{0}\n'.format(var))
+
+
+`hpl <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/hpl/package.py>`_
+is a good example of a package that uses a list to store
+configuration variables.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Variables to watch out for
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following is a list of common variables to watch out for. The first
+two sections are
+`implicit variables <https://www.gnu.org/software/make/manual/html_node/Implicit-Variables.html>`_
+defined by Make and will always use the same name, while the rest are
+user-defined variables and may vary from package to package.
+
+* **Compilers**
+
+  This includes variables such as ``CC``, ``CXX``, ``F77``, ``F90``,
+  and ``FC``, as well as variables related to MPI compiler wrappers,
+  like ``MPICC`` and friends.
+
+* **Compiler flags**
+
+  This includes variables for specific compilers, like ``CFLAGS``,
+  ``CXXFLAGS``, ``F77FLAGS``, ``F90FLAGS``, ``FCFLAGS``, and ``CPPFLAGS``.
+  These variables are often hard-coded to contain flags specific to a
+  certain compiler. If these flags don't work for every compiler,
+  you may want to consider filtering them.
+
+* **Variables that enable or disable features**
+
+  This includes variables like ``MPI``, ``OPENMP``, ``PIC``, and
+  ``DEBUG``. These flags often require you to create a variant
+  so that you can either build with or without MPI support, for
+  example. These flags are often compiler-dependent. You should
+  replace them with the appropriate compiler flags, such as
+  ``self.compiler.openmp_flag`` or ``self.compiler.pic_flag``.
+
+* **Platform flags**
+
+  These flags control the type of architecture that the executable
+  is compiler for. Watch out for variables like ``PLAT`` or ``ARCH``.
+
+* **Dependencies**
+
+  Look out for variables that sound like they could be used to
+  locate dependencies, such as ``JAVA_HOME``, ``JPEG_ROOT``, or
+  ``ZLIBDIR``. Also watch out for variables that control linking,
+  such as ``LIBS``, ``LDFLAGS``, and ``INCLUDES``. These variables
+  need to be set to the installation prefix of a dependency, or
+  to the correct linker flags to link to that dependency.
+
+* **Installation prefix**
+
+  If your Makefile has an ``install`` target, it needs some way of
+  knowing where to install. By default, many packages install to
+  ``/usr`` or ``/usr/local``. Since many Spack users won't have
+  sudo privileges, it is imperative that each package is installed
+  to the proper prefix. Look for variables like ``PREFIX`` or
+  ``INSTALL``.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Makefiles in a sub-directory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Not every package places their Makefile in the root of the package
+tarball. If the Makefile is in a sub-directory like ``src``, you
+can tell Spack where to locate it like so:
+
+.. code-block:: python
+
+   build_directory = 'src'
+
+
+^^^^^^^^^^^^^^^^^^^
+Manual installation
+^^^^^^^^^^^^^^^^^^^
+
+Not every Makefile includes an ``install`` target. If this is the
+case, you can override the default ``install`` method to manually
+install the package:
+
+.. code-block:: python
+
+   def install(self, spec, prefix):
+       mkdir(prefix.bin)
+       install('foo', prefix.bin)
+       install_tree('lib', prefix.lib)
+
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on reading and writing Makefiles, see:
+https://www.gnu.org/software/make/manual/make.html

lib/spack/docs/build_systems/mesonpackage.rst

@@ -0,0 +1,134 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _mesonpackage:
+
+------------
+MesonPackage
+------------
+
+Much like Autotools and CMake, Meson is a build system.  But it is
+meant to be both fast and as user friendly as possible.  GNOME's goal
+is to port modules to use the Meson build system.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``MesonPackage`` base class comes with the following phases:
+
+#. ``meson`` - generate ninja files
+#. ``build`` - build the project
+#. ``install`` - install the project
+
+By default, these phases run:
+
+.. code-block:: console
+
+   $ mkdir spack-build
+   $ cd spack-build
+   $ meson .. --prefix=/path/to/installation/prefix
+   $ ninja
+   $ ninja test  # optional
+   $ ninja install
+
+
+Any of these phases can be overridden in your package as necessary.
+There is also a ``check`` method that looks for a ``test`` target
+in the build file. If a ``test`` target exists and the user runs:
+
+.. code-block:: console
+
+   $ spack install --test=root <meson-package>
+
+
+Spack will run ``ninja test`` after the build phase.
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+Packages that use the Meson build system can be identified by the
+presence of a ``meson.build`` file. This file declares things
+like build instructions and dependencies.
+
+One thing to look for is the ``meson_version`` key that gets passed
+to the ``project`` function:
+
+.. code-block:: none
+   :emphasize-lines: 10
+
+   project('gtk+', 'c',
+        version: '3.94.0',
+        default_options: [
+          'buildtype=debugoptimized',
+          'warning_level=1',
+          # We only need c99, but glib needs GNU-specific features
+          # https://github.com/mesonbuild/meson/issues/2289
+          'c_std=gnu99',
+        ],
+        meson_version: '>= 0.43.0',
+        license: 'LGPLv2.1+')
+
+
+This means that Meson 0.43.0 is the earliest release that will work.
+You should specify this in a ``depends_on`` statement.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+At the bare minimum, packages that use the Meson build system need
+``meson`` and ```ninja``` dependencies. Since this is always the case,
+the ``MesonPackage`` base class already contains:
+
+.. code-block:: python
+
+   depends_on('meson', type='build')
+   depends_on('ninja', type='build')
+
+
+If you need to specify a particular version requirement, you can
+override this in your package:
+
+.. code-block:: python
+
+   depends_on('meson@0.43.0:', type='build')
+   depends_on('ninja', type='build')
+
+
+^^^^^^^^^^^^^^^^^^^
+Finding meson flags
+^^^^^^^^^^^^^^^^^^^
+
+To get a list of valid flags that can be passed to ``meson``, run the
+following command in the directory that contains ``meson.build``:
+
+.. code-block:: console
+
+   $ meson setup --help
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to meson
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you need to pass any arguments to the ``meson`` call, you can
+override the ``meson_args`` method like so:
+
+.. code-block:: python
+
+   def meson_args(self):
+       return ['--default-library=both']
+
+
+This method can be used to pass flags as well as variables.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the Meson build system, see:
+https://mesonbuild.com/index.html

lib/spack/docs/build_systems/octavepackage.rst

@@ -0,0 +1,52 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _octavepackage:
+
+-------------
+OctavePackage
+-------------
+
+Octave has its own build system for installing packages.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``OctavePackage`` base class has a single phase:
+
+#. ``install`` - install the package
+
+By default, this phase runs the following command:
+
+.. code-block:: console
+
+   $ octave '--eval' 'pkg prefix <prefix>; pkg install <archive_file>'
+
+
+Beware that uninstallation is not implemented at the moment. After uninstalling
+a package via Spack, you also need to manually uninstall it from Octave via
+``pkg uninstall <package_name>``.
+
+^^^^^^^^^^^^^^^^^^^^^^^
+Finding Octave packages
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Most Octave packages are listed at https://octave.sourceforge.io/packages.php.
+
+^^^^^^^^^^^^
+Dependencies
+^^^^^^^^^^^^
+
+Usually, the homepage of a package will list dependencies, i.e.
+``Dependencies:	Octave >= 3.6.0 struct >= 1.0.12``. The same information should
+be available in the ``DESCRIPTION`` file in the root of each archive.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External Documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the Octave build system, see:
+https://octave.org/doc/v4.4.0/Installing-and-Removing-Packages.html

lib/spack/docs/build_systems/perlpackage.rst

@@ -0,0 +1,212 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _perlpackage:
+
+-----------
+PerlPackage
+-----------
+
+Much like Octave, Perl has its own language-specific
+build system.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``PerlPackage`` base class comes with 3 phases that can be overridden:
+
+#. ``configure`` - configure the package
+#. ``build`` - build the package
+#. ``install`` - install the package
+
+Perl packages have 2 common modules used for module installation:
+
+"""""""""""""""""""""""
+``ExtUtils::MakeMaker``
+"""""""""""""""""""""""
+
+The ``ExtUtils::MakeMaker`` module is just what it sounds like, a module
+designed to generate Makefiles. It can be identified by the presence of
+a ``Makefile.PL`` file, and has the following installation steps:
+
+.. code-block:: console
+
+   $ perl Makefile.PL INSTALL_BASE=/path/to/installation/prefix
+   $ make
+   $ make test  # optional
+   $ make install
+
+
+"""""""""""""""""
+``Module::Build``
+"""""""""""""""""
+
+The ``Module::Build`` module is a pure-Perl build system, and can be
+identified by the presence of a ``Build.PL`` file. It has the following
+installation steps:
+
+.. code-block:: console
+
+   $ perl Build.PL --install_base /path/to/installation/prefix
+   $ ./Build
+   $ ./Build test  # optional
+   $ ./Build install
+
+
+If both ``Makefile.PL`` and ``Build.PL`` files exist in the package,
+Spack will use ``Makefile.PL`` by default. If your package uses a
+different module, ``PerlPackage`` will need to be extended to support
+it.
+
+``PerlPackage`` automatically detects which build steps to use, so there
+shouldn't be much work on the package developer's side to get things
+working.
+
+^^^^^^^^^^^^^^^^^^^^^
+Finding Perl packages
+^^^^^^^^^^^^^^^^^^^^^
+
+Most Perl modules are hosted on CPAN - The Comprehensive Perl Archive
+Network. If you need to find a package for ``XML::Parser``, for example,
+you should search for "CPAN XML::Parser".
+
+Some CPAN pages are versioned. Check for a link to the
+"Latest Release" to make sure you have the latest version.
+
+^^^^^^^^^^^^
+Package name
+^^^^^^^^^^^^
+
+When you use ``spack create`` to create a new Perl package, Spack will
+automatically prepend ``perl-`` to the front of the package name. This
+helps to keep Perl modules separate from other packages. The same
+naming scheme is used for other language extensions, like Python and R.
+
+^^^^^^^^^^^
+Description
+^^^^^^^^^^^
+
+Most CPAN pages have a short description under "NAME" and a longer
+description under "DESCRIPTION". Use whichever you think is more
+useful while still being succinct.
+
+^^^^^^^^
+Homepage
+^^^^^^^^
+
+In the top-right corner of the CPAN page, you'll find a "permalink"
+for the package. This should be used instead of the current URL, as
+it doesn't contain the version number and will always link to the
+latest release.
+
+^^^
+URL
+^^^
+
+If you haven't found it already, the download URL is on the right
+side of the page below the permalink. Search for "Download".
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Every ``PerlPackage`` obviously depends on Perl at build and run-time,
+so ``PerlPackage`` contains:
+
+.. code-block:: python
+
+   extends('perl')
+
+   depends_on('perl', type=('build', 'run'))
+
+
+If your package requires a specific version of Perl, you should
+specify this.
+
+Although newer versions of Perl include ``ExtUtils::MakeMaker`` and
+``Module::Build`` as "core" modules, you may want to add dependencies
+on ``perl-extutils-makemaker`` and ``perl-module-build`` anyway. Many
+people add Perl as an external package, and we want the build to work
+properly. If your package uses ``Makefile.PL`` to build, add:
+
+.. code-block:: python
+
+   depends_on('perl-extutils-makemaker', type='build')
+
+
+If your package uses ``Build.PL`` to build, add:
+
+.. code-block:: python
+
+   depends_on('perl-module-build', type='build')
+
+
+^^^^^^^^^^^^^^^^^
+Perl dependencies
+^^^^^^^^^^^^^^^^^
+
+Below the download URL, you will find a "Dependencies" link, which
+takes you to a page listing all of the dependencies of the package.
+Packages listed as "Core module" don't need to be added as dependencies,
+but all direct dependencies should be added. Don't add dependencies of
+dependencies. These should be added as dependencies to the dependency,
+not to your package.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to configure
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Packages that have non-Perl dependencies often use command-line
+variables to specify their installation directory. You can pass
+arguments to ``Makefile.PL`` or ``Build.PL`` by overriding
+``configure_args`` like so:
+
+.. code-block:: python
+
+   def configure_args(self):
+       expat = self.spec['expat'].prefix
+
+       return [
+           'EXPATLIBPATH={0}'.format(expat.lib),
+           'EXPATINCPATH={0}'.format(expat.include),
+       ]
+
+
+^^^^^^^^^^^^^^^^^^^^^
+Alternatives to Spack
+^^^^^^^^^^^^^^^^^^^^^
+
+If you need to maintain a stack of Perl modules for a user and don't
+want to add all of them to Spack, a good alternative is ``cpanm``.
+If Perl is already installed on your system, it should come with a
+``cpan`` executable. To install ``cpanm``, run the following command:
+
+.. code-block:: console
+
+   $ cpan App::cpanminus
+
+
+Now, you can install any Perl module you want by running:
+
+.. code-block:: console
+
+   $ cpanm Module::Name
+
+
+Obviously, these commands can only be run if you have root privileges.
+Furthermore, ``cpanm`` is not capable of installing non-Perl dependencies.
+If you need to install to your home directory or need to install a module
+with non-Perl dependencies, Spack is a better option.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+You can find more information on installing Perl modules from source
+at: http://www.perlmonks.org/?node_id=128077
+
+More generic Perl module installation instructions can be found at:
+http://www.cpan.org/modules/INSTALL.html

lib/spack/docs/build_systems/pythonpackage.rst

@@ -0,0 +1,747 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _pythonpackage:
+
+-------------
+PythonPackage
+-------------
+
+Python packages and modules have their own special build system.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``PythonPackage`` base class provides the following phases that
+can be overridden:
+
+* ``build``
+* ``build_py``
+* ``build_ext``
+* ``build_clib``
+* ``build_scripts``
+* ``clean``
+* ``install``
+* ``install_lib``
+* ``install_headers``
+* ``install_scripts``
+* ``install_data``
+* ``sdist``
+* ``register``
+* ``bdist``
+* ``bdist_dumb``
+* ``bdist_rpm``
+* ``bdist_wininst``
+* ``upload``
+* ``check``
+
+These are all standard ``setup.py`` commands and can be found by running:
+
+.. code-block:: console
+
+   $ python setup.py --help-commands
+
+
+By default, only the ``build`` and ``install`` phases are run:
+
+#. ``build`` - build everything needed to install
+#. ``install`` - install everything from build directory
+
+If for whatever reason you need to run more phases, simply modify your
+``phases`` list like so:
+
+.. code-block:: python
+
+   phases = ['build_ext', 'install', 'bdist']
+
+
+Each phase provides a function ``<phase>`` that runs:
+
+.. code-block:: console
+
+   $ python -s setup.py --no-user-cfg <phase>
+
+
+Each phase also has a ``<phase_args>`` function that can pass arguments to
+this call. All of these functions are empty except for the ``install_args``
+function, which passes ``--prefix=/path/to/installation/prefix``. There is
+also some additional logic specific to setuptools and eggs.
+
+If you need to run a phase that is not a standard ``setup.py`` command,
+you'll need to define a function for it like so:
+
+.. code-block:: python
+
+   phases = ['configure', 'build', 'install']
+
+   def configure(self, spec, prefix):
+       self.setup_py('configure')
+
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+Python packages can be identified by the presence of a ``setup.py`` file.
+This file is used by package managers like ``pip`` to determine a
+package's dependencies and the version of dependencies required, so if
+the ``setup.py`` file is not accurate, the package will not build properly.
+For this reason, the ``setup.py`` file should be fairly reliable. If the
+documentation and ``setup.py`` disagree on something, the ``setup.py``
+file should be considered to be the truth. As dependencies are added or
+removed, the documentation is much more likely to become outdated than
+the ``setup.py``.
+
+^^^^^^^^^^^^^^^^^^^^^^^
+Finding Python packages
+^^^^^^^^^^^^^^^^^^^^^^^
+
+The vast majority of Python packages are hosted on PyPI - The Python
+Package Index. ``pip`` only supports packages hosted on PyPI, making
+it the only option for developers who want a simple installation.
+Search for "PyPI <package-name>" to find the download page. Note that
+some pages are versioned, and the first result may not be the newest
+version. Click on the "Latest Version" button to the top right to see
+if a newer version is available. The download page is usually at:
+https://pypi.org/project/<package-name>
+
+^^^^^^^^^^^
+Description
+^^^^^^^^^^^
+
+The top of the PyPI downloads page contains a description of the
+package. The first line is usually a short description, while there
+may be a several line "Project Description" that follows. Choose whichever
+is more useful. You can also get these descriptions on the command-line
+using:
+
+.. code-block:: console
+
+   $ python setup.py --description
+   $ python setup.py --long-description
+
+
+^^^^^^^^
+Homepage
+^^^^^^^^
+
+Package developers use ``setup.py`` to upload new versions to PyPI.
+The ``setup`` method often passes metadata like ``homepage`` to PyPI.
+This metadata is displayed on the left side of the download page.
+Search for the text "Homepage" under "Project links" to find it. You
+should use this page instead of the PyPI page if they differ. You can
+also get the homepage on the command-line by running:
+
+.. code-block:: console
+
+   $ python setup.py --url
+
+
+^^^
+URL
+^^^
+
+You may have noticed that Spack allows you to add multiple versions of
+the same package without adding multiple versions of the download URL.
+It does this by guessing what the version string in the URL is and
+replacing this with the requested version. Obviously, if Spack cannot
+guess the version correctly, or if non-version-related things change
+in the URL, Spack cannot substitute the version properly.
+
+Once upon a time, PyPI offered nice, simple download URLs like:
+https://pypi.python.org/packages/source/n/numpy/numpy-1.13.1.zip
+
+As you can see, the version is 1.13.1. It probably isn't hard to guess
+what URL to use to download version 1.12.0, and Spack was perfectly
+capable of performing this calculation.
+
+However, PyPI switched to a new download URL format:
+https://pypi.python.org/packages/c0/3a/40967d9f5675fbb097ffec170f59c2ba19fc96373e73ad47c2cae9a30aed/numpy-1.13.1.zip#md5=2c3c0f4edf720c3a7b525dacc825b9ae
+
+and more recently:
+https://files.pythonhosted.org/packages/b0/2b/497c2bb7c660b2606d4a96e2035e92554429e139c6c71cdff67af66b58d2/numpy-1.14.3.zip
+
+As you can imagine, it is impossible for Spack to guess what URL to
+use to download version 1.12.0 given this URL. There is a solution,
+however. PyPI offers a new hidden interface for downloading
+Python packages that does not include a hash in the URL:
+https://pypi.io/packages/source/n/numpy/numpy-1.13.1.zip
+
+This URL redirects to the files.pythonhosted.org URL. The general syntax for
+this pypi.io URL is:
+https://pypi.io/packages/source/<first-letter-of-name>/<name>/<name>-<version>.<extension>
+
+Please use the pypi.io URL instead of the pypi.python.org URL. If both
+``.tar.gz`` and ``.zip`` versions are available, ``.tar.gz`` is preferred.
+If some releases offer both ``.tar.gz`` and ``.zip`` versions, but some
+only offer ``.zip`` versions, use ``.zip``.
+
+"""""""""""""""
+PyPI vs. GitHub
+"""""""""""""""
+
+Many packages are hosted on PyPI, but are developed on GitHub and other
+version control systems. The tarball can be downloaded from either
+location, but PyPI is preferred for the following reasons:
+
+#. PyPI contains the bare minimum of files to install the package.
+
+   You may notice that the tarball you download from PyPI does not
+   have the same checksum as the tarball you download from GitHub.
+   When a developer uploads a new release to PyPI, it doesn't contain
+   every file in the repository, only the files necessary to install
+   the package. PyPI tarballs are therefore smaller.
+
+#. PyPI is the official source for package managers like ``pip``.
+
+   Let's be honest, ``pip`` is much more popular than Spack. If the
+   GitHub tarball contains a file not present in the PyPI tarball that
+   causes a bug, the developers may not realize this for quite some
+   time. If the bug was in a file contained in the PyPI tarball, users
+   would notice the bug much more quickly.
+
+#. GitHub release may be a beta version.
+
+   When a developer releases a new version of a package on GitHub,
+   it may not be intended for most users. Until that release also
+   makes its way to PyPI, it should be assumed that the release is
+   not yet ready for general use.
+
+#. The checksum for a GitHub release may change.
+
+   Unfortunately, some developers have a habit of patching releases
+   without incrementing the version number. This results in a change
+   in tarball checksum. Package managers like Spack that use checksums
+   to verify the integrity of a download tarball grind to a halt when
+   the checksum for a known version changes. Most of the time, the
+   change is intentional, and contains a needed bug fix. However,
+   sometimes the change indicates a download source that has been
+   compromised, and a tarball that contains a virus. If this happens,
+   you must contact the developers to determine which is the case.
+   PyPI is nice because it makes it physically impossible to
+   re-release the same version of a package with a different checksum.
+
+There are some reasons to prefer downloading from GitHub:
+
+#. The GitHub tarball may contain unit tests
+
+   As previously mentioned, the PyPI tarball contains the bare minimum
+   of files to install the package. Unless explicitly specified by the
+   developers, it will not contain development files like unit tests.
+   If you desire to run the unit tests during installation, you should
+   use the GitHub tarball instead.
+
+#. Spack does not yet support ``spack versions`` and ``spack checksum``
+   with PyPI URLs
+
+   These commands work just fine with GitHub URLs. This is a minor
+   annoyance, not a reason to prefer GitHub over PyPI.
+
+If you really want to run these unit tests, no one will stop you from
+submitting a PR for a new package that downloads from GitHub.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are a few dependencies common to the ``PythonPackage`` build system.
+
+""""""
+Python
+""""""
+
+Obviously, every ``PythonPackage`` needs Python at build-time to run
+``python setup.py build && python setup.py install``. Python is also
+needed at run-time if you want to import the module. Due to backwards
+incompatible changes between Python 2 and 3, it is very important to
+specify which versions of Python are supported. If the documentation
+mentions that Python 3 is required, this can be specified as:
+
+.. code-block:: python
+
+   depends_on('python@3:', type=('build', 'run')
+
+
+If Python 2 is required, this would look like:
+
+.. code-block:: python
+
+   depends_on('python@:2', type=('build', 'run')
+
+
+If Python 2.7 is the only version that works, you can use:
+
+.. code-block:: python
+
+   depends_on('python@2.7:2.8', type=('build', 'run')
+
+
+The documentation may not always specify supported Python versions.
+Another place to check is in the ``setup.py`` file. Look for a line
+containing ``python_requires``. An example from
+`py-numpy <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-numpy/package.py>`_
+looks like:
+
+.. code-block:: python
+
+   python_requires='>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*'
+
+
+More commonly, you will find a version check at the top of the file:
+
+.. code-block:: python
+
+   if sys.version_info[:2] < (2, 7) or (3, 0) <= sys.version_info[:2] < (3, 4):
+       raise RuntimeError("Python version 2.7 or >= 3.4 required.")
+
+
+This can be converted to Spack's spec notation like so:
+
+.. code-block:: python
+
+   depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
+
+""""""""""
+setuptools
+""""""""""
+
+Originally, the Python language had a single build system called
+distutils, which is built into Python. Distutils provided a common
+framework for package authors to describe their project and how it
+should be built. However, distutils was not without limitations.
+Most notably, there was no way to list a project's dependencies
+with distutils. Along came setuptools, a non-builtin build system
+designed to overcome the limitations of distutils. Both projects
+use a similar API, making the transition easy while adding much
+needed functionality. Today, setuptools is used in around 75% of
+the Python packages in Spack.
+
+Since setuptools isn't built-in to Python, you need to add it as a
+dependency. To determine whether or not a package uses setuptools,
+search the file for an import statement like:
+
+.. code-block:: python
+
+   import setuptools
+
+
+or:
+
+.. code-block:: python
+
+   from setuptools import setup
+
+
+Some packages are designed to work with both setuptools and distutils,
+so you may find something like:
+
+.. code-block:: python
+
+   try:
+       from setuptools import setup
+   except ImportError:
+       from distutils.core import setup
+
+
+This uses setuptools if available, and falls back to distutils if not.
+In this case, you would still want to add a setuptools dependency, as
+it offers us more control over the installation.
+
+Unless specified otherwise, setuptools is usually a build-only dependency.
+That is, it is needed to install the software, but is not needed at
+run-time. This can be specified as:
+
+.. code-block:: python
+
+   depends_on('py-setuptools', type='build')
+
+
+""""""
+cython
+""""""
+
+Compared to compiled languages, interpreted languages like Python can
+be quite a bit slower. To work around this, some Python developers
+rewrite computationally demanding sections of code in C, a process
+referred to as "cythonizing". In order to build these package, you
+need to add a build dependency on cython:
+
+.. code-block:: python
+
+   depends_on('py-cython', type='build')
+
+
+Look for references to "cython" in the ``setup.py`` to determine
+whether or not this is necessary. Cython may be optional, but
+even then you should list it as a required dependency. Spack is
+designed to compile software, and is meant for HPC facilities
+where speed is crucial. There is no reason why someone would not
+want an optimized version of a library instead of the pure-Python
+version.
+
+^^^^^^^^^^^^^^^^^^^
+Python dependencies
+^^^^^^^^^^^^^^^^^^^
+
+When you install a package with ``pip``, it reads the ``setup.py``
+file in order to determine the dependencies of the package.
+If the dependencies are not yet installed, ``pip`` downloads them
+and installs them for you. This may sound convenient, but Spack
+cannot rely on this behavior for two reasons:
+
+#. Spack needs to be able to install packages on air-gapped networks.
+
+   If there is no internet connection, ``pip`` can't download the
+   package dependencies. By explicitly listing every dependency in
+   the ``package.py``, Spack knows what to download ahead of time.
+
+#. Duplicate installations of the same dependency may occur.
+
+   Spack supports *activation* of Python extensions, which involves
+   symlinking the package installation prefix to the Python installation
+   prefix. If your package is missing a dependency, that dependency
+   will be installed to the installation directory of the same package.
+   If you try to activate the package + dependency, it may cause a
+   problem if that package has already been activated.
+
+For these reasons, you must always explicitly list all dependencies.
+Although the documentation may list the package's dependencies,
+often the developers assume people will use ``pip`` and won't have to
+worry about it. Always check the ``setup.py`` to find the true
+dependencies.
+
+If the package relies on ``distutils``, it may not explicitly list its
+dependencies. Check for statements like:
+
+.. code-block:: python
+
+   try:
+       import numpy
+   except ImportError:
+       raise ImportError("numpy must be installed prior to installation")
+
+
+Obviously, this means that ``py-numpy`` is a dependency.
+
+If the package uses ``setuptools``, check for the following clues:
+
+* ``install_requires``
+
+  These packages are required for installation.
+
+* ``extra_requires``
+
+  These packages are optional dependencies that enable additional
+  functionality. You should add a variant that optionally adds these
+  dependencies.
+
+* ``test_requires``
+
+  These are packages that are required to run the unit tests for the
+  package. These dependencies can be specified using the
+  ``type='test'`` dependency type.
+
+In the root directory of the package, you may notice a
+``requirements.txt`` file. It may look like this file contains a list
+of all of the package's dependencies. Don't be fooled. This file is
+used by tools like Travis to install the pre-requisites for the
+package... and a whole bunch of other things. It often contains
+dependencies only needed for unit tests, like:
+
+* mock
+* nose
+* pytest
+
+It can also contain dependencies for building the documentation, like
+sphinx. If you can't find any information about the package's
+dependencies, you can take a look in ``requirements.txt``, but be sure
+not to add test or documentation dependencies.
+
+""""""""""
+setuptools
+""""""""""
+
+Setuptools is a bit of a special case. If a package requires setuptools
+at run-time, how do they express this? They could add it to
+``install_requires``, but setuptools is imported long before this and
+needed to read this line. And since you can't install the package
+without setuptools, the developers assume that setuptools will already
+be there, so they never mention when it is required. We don't want to
+add run-time dependencies if they aren't needed, so you need to
+determine whether or not setuptools is needed. Grep the installation
+directory for any files containing a reference to ``setuptools`` or
+``pkg_resources``. Both modules come from ``py-setuptools``.
+``pkg_resources`` is particularly common in scripts in ``prefix/bin``.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to setup.py
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The default build and install phases should be sufficient to install
+most packages. However, you may want to pass additional flags to
+either phase.
+
+You can view the available options for a particular phase with:
+
+.. code-block:: console
+
+   $ python setup.py <phase> --help
+
+
+Each phase provides a ``<phase_args>`` function that can be used to
+pass arguments to that phase. For example,
+`py-numpy <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-numpy/package.py>`_
+adds:
+
+.. code-block:: python
+
+   def build_args(self, spec, prefix):
+       args = []
+
+       # From NumPy 1.10.0 on it's possible to do a parallel build.
+       if self.version >= Version('1.10.0'):
+           # But Parallel build in Python 3.5+ is broken.  See:
+           # https://github.com/spack/spack/issues/7927
+           # https://github.com/scipy/scipy/issues/7112
+           if spec['python'].version < Version('3.5'):
+               args = ['-j', str(make_jobs)]
+
+       return args
+
+
+^^^^^^^
+Testing
+^^^^^^^
+
+``PythonPackage`` provides a couple of options for testing packages.
+
+""""""""""""
+Import tests
+""""""""""""
+
+Just because a package successfully built does not mean that it built
+correctly. The most reliable test of whether or not the package was
+correctly installed is to attempt to import all of the modules that
+get installed. To get a list of modules, run the following command
+in the source directory:
+
+.. code-block:: console
+
+   $ python
+   >>> import setuptools
+   >>> setuptools.find_packages()
+   ['numpy', 'numpy._build_utils', 'numpy.compat', 'numpy.core', 'numpy.distutils', 'numpy.doc', 'numpy.f2py', 'numpy.fft', 'numpy.lib', 'numpy.linalg', 'numpy.ma', 'numpy.matrixlib', 'numpy.polynomial', 'numpy.random', 'numpy.testing', 'numpy.core.code_generators', 'numpy.distutils.command', 'numpy.distutils.fcompiler']
+
+
+Large, complex packages like ``numpy`` will return a long list of
+packages, while other packages like ``six`` will return an empty list.
+``py-six`` installs a single ``six.py`` file. In Python packaging lingo,
+a "package" is a directory containing files like:
+
+.. code-block:: none
+
+   foo/__init__.py
+   foo/bar.py
+   foo/baz.py
+
+
+whereas a "module" is a single Python file. Since ``find_packages``
+only returns packages, you'll have to determine the correct module
+names yourself. You can now add these packages and modules to the
+package like so:
+
+.. code-block:: python
+
+   import_modules = ['six']
+
+
+When you run ``spack install --test=root py-six``, Spack will attempt
+to import the ``six`` module after installation.
+
+These tests most often catch missing dependencies and non-RPATHed
+libraries. Make sure not to add modules/packages containing the word
+"test", as these likely won't end up in installation directory.
+
+""""""""""
+Unit tests
+""""""""""
+
+The package you want to install may come with additional unit tests.
+By default, Spack runs:
+
+.. code-block:: console
+
+   $ python setup.py test
+
+
+if it detects that the ``setup.py`` file supports a ``test`` phase.
+You can add additional build-time or install-time tests by overriding
+``test`` and ``installtest``, respectively. For example, ``py-numpy``
+adds:
+
+.. code-block:: python
+
+   def install_test(self):
+        with working_dir('..'):
+            python('-c', 'import numpy; numpy.test("full", verbose=2)')
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Setup file in a sub-directory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In order to be compatible with package managers like ``pip``, the package
+is required to place its ``setup.py`` in the root of the tarball. However,
+not every Python package cares about ``pip`` or PyPI. If you are installing
+a package that is not hosted on PyPI, you may find that it places its
+``setup.py`` in a sub-directory. To handle this, add the directory containing
+``setup.py`` to the package like so:
+
+.. code-block:: python
+
+   build_directory = 'source'
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Alternate names for setup.py
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As previously mentioned, packages need to call their setup script ``setup.py``
+in order to be compatible with package managers like ``pip``. However, some
+packages like
+`py-meep <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-meep/package.py>`_  and
+`py-adios <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-adios/package.py>`_
+come with multiple setup scripts, one for a serial build and another for a
+parallel build. You can override the default name to use like so:
+
+.. code-block:: python
+
+   def setup_file(self):
+       return 'setup-mpi.py' if '+mpi' in self.spec else 'setup.py'
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+PythonPackage vs. packages that use Python
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are many packages that make use of Python, but packages that depend
+on Python are not necessarily ``PythonPackages``.
+
+"""""""""""""""""""""""
+Choosing a build system
+"""""""""""""""""""""""
+
+First of all, you need to select a build system. ``spack create`` usually
+does this for you, but if for whatever reason you need to do this manually,
+choose ``PythonPackage`` if and only if the package contains a ``setup.py``
+file.
+
+"""""""""""""""""""""""
+Choosing a package name
+"""""""""""""""""""""""
+
+Selecting the appropriate package name is a little more complicated
+than choosing the build system. By default, ``spack create`` will
+prepend ``py-`` to the beginning of the package name if it detects
+that the package uses the ``PythonPackage`` build system. However, there
+are occasionally packages that use ``PythonPackage`` that shouldn't
+start with ``py-``. For example:
+
+* busco
+* easybuild
+* httpie
+* mercurial
+* scons
+* snakemake
+
+The thing these packages have in common is that they are command-line
+tools that just so happen to be written in Python. Someone who wants
+to install ``mercurial`` with Spack isn't going to realize that it is
+written in Python, and they certainly aren't going to assume the package
+is called ``py-mercurial``. For this reason, we manually renamed the
+package to ``mercurial``.
+
+Likewise, there are occasionally packages that don't use the
+``PythonPackage`` build system but should still be prepended with ``py-``.
+For example:
+
+* py-genders
+* py-py2cairo
+* py-pygobject
+* py-pygtk
+* py-pyqt
+* py-pyserial
+* py-sip
+* py-xpyb
+
+These packages are primarily used as Python libraries, not as
+command-line tools. You may see C/C++ packages that have optional
+Python language-bindings, such as:
+
+* antlr
+* cantera
+* conduit
+* pagmo
+* vtk
+
+Don't prepend these kind of packages with ``py-``. When in doubt,
+think about how this package will be used. Is it primarily a Python
+library that will be imported in other Python scripts? Or is it a
+command-line tool, or C/C++/Fortran program with optional Python
+modules? The former should be prepended with ``py-``, while the
+latter should not.
+
+""""""""""""""""""""""
+extends vs. depends_on
+""""""""""""""""""""""
+
+This is very similar to the naming dilemma above, with a slight twist.
+As mentioned in the :ref:`Packaging Guide <packaging_extensions>`,
+``extends`` and ``depends_on`` are very similar, but ``extends`` adds
+the ability to *activate* the package. Activation involves symlinking
+everything in the installation prefix of the package to the installation
+prefix of Python. This allows the user to import a Python module without
+having to add that module to ``PYTHONPATH``.
+
+When deciding between ``extends`` and ``depends_on``, the best rule of
+thumb is to check the installation prefix. If Python libraries are
+installed to ``prefix/lib/python2.7/site-packages`` (where 2.7 is the
+MAJOR.MINOR version of Python you used to install the package), then
+you should use ``extends``. If Python libraries are installed elsewhere
+or the only files that get installed reside in ``prefix/bin``, then
+don't use ``extends``, as symlinking the package wouldn't be useful.
+
+^^^^^^^^^^^^^^^^^^^^^
+Alternatives to Spack
+^^^^^^^^^^^^^^^^^^^^^
+
+PyPI has hundreds of thousands of packages that are not yet in Spack,
+and ``pip`` may be a perfectly valid alternative to using Spack. The
+main advantage of Spack over ``pip`` is its ability to compile
+non-Python dependencies. It can also build cythonized versions of a
+package or link to an optimized BLAS/LAPACK library like MKL,
+resulting in calculations that run orders of magnitude faster.
+Spack does not offer a significant advantage to other python-management
+systems for installing and using tools like flake8 and sphinx.
+But if you need packages with non-Python dependencies like
+numpy and scipy, Spack will be very valuable to you.
+
+Anaconda is another great alternative to Spack, and comes with its own
+``conda`` package manager. Like Spack, Anaconda is capable of compiling
+non-Python dependencies. Anaconda contains many Python packages that
+are not yet in Spack, and Spack contains many Python packages that are
+not yet in Anaconda. The main advantage of Spack over Anaconda is its
+ability to choose a specific compiler and BLAS/LAPACK or MPI library.
+Spack also has better platform support for supercomputers. On the
+other hand, Anaconda offers Windows support.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on Python packaging, see:
+https://packaging.python.org/

lib/spack/docs/build_systems/qmakepackage.rst

@@ -0,0 +1,116 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _qmakepackage:
+
+------------
+QMakePackage
+------------
+
+Much like Autotools and CMake, QMake is a build-script generator
+designed by the developers of Qt. In its simplest form, Spack's
+``QMakePackage`` runs the following steps:
+
+.. code-block:: console
+
+   $ qmake
+   $ make
+   $ make check  # optional
+   $ make install
+
+
+QMake does not appear to have a standardized way of specifying
+the installation directory, so you may have to set environment
+variables or edit ``*.pro`` files to get things working properly.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``QMakePackage`` base class comes with the following phases:
+
+#. ``qmake`` - generate Makefiles
+#. ``build`` - build the project
+#. ``install`` - install the project
+
+By default, these phases run:
+
+.. code-block:: console
+
+   $ qmake
+   $ make
+   $ make install
+
+
+Any of these phases can be overridden in your package as necessary.
+There is also a ``check`` method that looks for a ``check`` target
+in the Makefile. If a ``check`` target exists and the user runs:
+
+.. code-block:: console
+
+   $ spack install --test=root <qmake-package>
+
+
+Spack will run ``make check`` after the build phase.
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+Packages that use the QMake build system can be identified by the
+presence of a ``<project-name>.pro`` file. This file declares things
+like build instructions and dependencies.
+
+One thing to look for is the ``minQtVersion`` function:
+
+.. code-block:: none
+
+   minQtVersion(5, 6, 0)
+
+
+This means that Qt 5.6.0 is the earliest release that will work.
+You should specify this in a ``depends_on`` statement.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+At the bare minimum, packages that use the QMake build system need a
+``qt`` dependency. Since this is always the case, the ``QMakePackage``
+base class already contains:
+
+.. code-block:: python
+
+   depends_on('qt', type='build')
+
+
+If you want to specify a particular version requirement, or need to
+link to the ``qt`` libraries, you can override this in your package:
+
+.. code-block:: python
+
+   depends_on('qt@5.6.0:')
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to qmake
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you need to pass any arguments to the ``qmake`` call, you can
+override the ``qmake_args`` method like so:
+
+.. code-block:: python
+
+   def qmake_args(self):
+       return ['-recursive']
+
+
+This method can be used to pass flags as well as variables.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the QMake build system, see:
+http://doc.qt.io/qt-5/qmake-manual.html

lib/spack/docs/build_systems/rpackage.rst

@@ -0,0 +1,366 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _rpackage:
+
+--------
+RPackage
+--------
+
+Like Python, R has its own built-in build system.
+
+The R build system is remarkably uniform and well-tested.
+This makes it one of the easiest build systems to create
+new Spack packages for.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``RPackage`` base class has a single phase:
+
+#. ``install`` - install the package
+
+By default, this phase runs the following command:
+
+.. code-block:: console
+
+   $ R CMD INSTALL --library=/path/to/installation/prefix/rlib/R/library .
+
+
+^^^^^^^^^^^^^^^^^^
+Finding R packages
+^^^^^^^^^^^^^^^^^^
+
+The vast majority of R packages are hosted on CRAN - The Comprehensive
+R Archive Network. If you are looking for a particular R package, search
+for "CRAN <package-name>" and you should quickly find what you want.
+If it isn't on CRAN, try Bioconductor, another common R repository.
+
+For the purposes of this tutorial, we will be walking through
+`r-caret <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/r-caret/package.py>`_
+as an example. If you search for "CRAN caret", you will quickly find what
+you are looking for at https://cran.r-project.org/package=caret.
+https://cran.r-project.org is the main CRAN website. However, CRAN also
+has a https://cloud.r-project.org site that automatically redirects to
+`mirrors around the world <https://cloud.r-project.org/mirrors.html>`_.
+For stability and performance reasons, we will use https://cloud.r-project.org/package=caret.
+If you search for "Package source", you will find the download URL for
+the latest release. Use this URL with ``spack create`` to create a new
+package.
+
+^^^^^^^^^^^^
+Package name
+^^^^^^^^^^^^
+
+The first thing you'll notice is that Spack prepends ``r-`` to the front
+of the package name. This is how Spack separates R package extensions
+from the rest of the packages in Spack. Without this, we would end up
+with package name collisions more frequently than we would like. For
+instance, there are already packages for both:
+
+* ``ape`` and ``r-ape``
+* ``curl`` and ``r-curl``
+* ``gmp`` and ``r-gmp``
+* ``jpeg`` and ``r-jpeg``
+* ``openssl`` and ``r-openssl``
+* ``uuid`` and ``r-uuid``
+* ``xts`` and ``r-xts``
+
+Many popular programs written in C/C++ are later ported to R as a
+separate project.
+
+^^^^^^^^^^^
+Description
+^^^^^^^^^^^
+
+The first thing you'll need to add to your new package is a description.
+The top of the homepage for ``caret`` lists the following description:
+
+   caret: Classification and Regression Training
+
+   Misc functions for training and plotting classification and regression models.
+
+You can either use the short description (first line), long description
+(second line), or both depending on what you feel is most appropriate.
+
+^^^^^^^^
+Homepage
+^^^^^^^^
+
+If you look at the bottom of the page, you'll see:
+
+   Linking:
+
+   Please use the canonical form https://CRAN.R-project.org/package=caret to link to this page.
+
+Please uphold the wishes of the CRAN admins and use
+https://cloud.r-project.org/package=caret as the homepage instead of
+https://cloud.r-project.org/web/packages/caret/index.html. The latter may
+change without notice.
+
+^^^
+URL
+^^^
+
+As previously mentioned, the download URL for the latest release can be
+found by searching "Package source" on the homepage.
+
+^^^^^^^^
+List URL
+^^^^^^^^
+
+CRAN maintains a single webpage containing the latest release of every
+single package: https://cloud.r-project.org/src/contrib/
+
+Of course, as soon as a new release comes out, the version you were using
+in your package is no longer available at that URL. It is moved to an
+archive directory. If you search for "Old sources", you will find:
+https://cloud.r-project.org/src/contrib/Archive/caret
+
+If you only specify the URL for the latest release, your package will
+no longer be able to fetch that version as soon as a new release comes
+out. To get around this, add the archive directory as a ``list_url``.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As an extension of the R ecosystem, your package will obviously depend
+on R to build and run. Normally, we would use ``depends_on`` to express
+this, but for R packages, we use ``extends``. ``extends`` is similar to
+``depends_on``, but adds an additional feature: the ability to "activate"
+the package by symlinking it to the R installation directory. Since
+every R package needs this, the ``RPackage`` base class contains:
+
+.. code-block:: python
+
+   extends('r')
+   depends_on('r', type=('build', 'run'))
+
+
+Take a close look at the homepage for ``caret``. If you look at the
+"Depends" section, you'll notice that ``caret`` depends on "R (≥ 3.2.0)".
+You should add this to your package like so:
+
+.. code-block:: python
+
+   depends_on('r@3.2.0:', type=('build', 'run'))
+
+
+^^^^^^^^^^^^^^
+R dependencies
+^^^^^^^^^^^^^^
+
+R packages are often small and follow the classic Unix philosophy
+of doing one thing well. They are modular and usually depend on
+several other packages. You may find a single package with over a
+hundred dependencies. Luckily, CRAN packages are well-documented
+and list all of their dependencies in the following sections:
+
+* Depends
+* Imports
+* LinkingTo
+
+As far as Spack is concerned, all 3 of these dependency types
+correspond to ``type=('build', 'run')``, so you don't have to worry
+about the details. If you are curious what they mean,
+https://github.com/spack/spack/issues/2951 has a pretty good summary:
+
+   ``Depends`` is required and will cause those R packages to be *attached*,
+   that is, their APIs are exposed to the user. ``Imports`` *loads* packages
+   so that *the package* importing these packages can access their APIs,
+   while *not* being exposed to the user. When a user calls ``library(foo)``
+   s/he *attaches* package ``foo`` and all of the packages under ``Depends``.
+   Any function in one of these package can be called directly as ``bar()``.
+   If there are conflicts, user can also specify ``pkgA::bar()`` and
+   ``pkgB::bar()`` to distinguish between them. Historically, there was only
+   ``Depends`` and ``Suggests``, hence the confusing names. Today, maybe
+   ``Depends`` would have been named ``Attaches``.
+
+   The ``LinkingTo`` is not perfect and there was recently an extensive
+   discussion about API/ABI among other things on the R-devel mailing
+   list among very skilled R developers:
+
+   * https://stat.ethz.ch/pipermail/r-devel/2016-December/073505.html
+   * https://stat.ethz.ch/pipermail/r-devel/2017-January/073647.html
+
+Some packages also have a fourth section:
+
+* Suggests
+
+These are optional, rarely-used dependencies that a user might find
+useful. You should **NOT** add these dependencies to your package.
+R packages already have enough dependencies as it is, and adding
+optional dependencies can really slow down the concretization
+process. They can also introduce circular dependencies.
+
+A fifth rarely used section is:
+
+* Enhances
+
+This means that the package can be used as an optional dependency
+for another package. Again, these packages should **NOT** be listed
+as dependencies.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Core, recommended, and non-core packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you look at "Depends", "Imports", and "LinkingTo", you will notice
+3 different types of packages:
+
+"""""""""""""
+Core packages
+"""""""""""""
+
+If you look at the ``caret`` homepage, you'll notice a few dependencies
+that don't have a link to the package, like ``methods``, ``stats``, and
+``utils``. These packages are part of the core R distribution and are
+tied to the R version installed. You can basically consider these to be
+"R itself". These are so essential to R that it would not make sense for
+them to be updated via CRAN. If you did, you would basically get a different
+version of R. Thus, they're updated when R is updated.
+
+You can find a list of these core libraries at:
+https://github.com/wch/r-source/tree/trunk/src/library
+
+""""""""""""""""""""
+Recommended packages
+""""""""""""""""""""
+
+When you install R, there is an option called ``--with-recommended-packages``.
+This flag causes the R installation to include a few "Recommended" packages
+(legacy term). They are for historical reasons quite tied to the core R
+distribution, developed by the R core team or people closely related to it.
+The R core distribution "knows" about these package, but they are indeed
+distributed via CRAN. Because they're distributed via CRAN, they can also be
+updated between R version releases.
+
+Spack explicitly adds the ``--without-recommended-packages`` flag to prevent
+the installation of these packages. Due to the way Spack handles package
+activation (symlinking packages to the R installation directory),
+pre-existing recommended packages will cause conflicts for already-existing
+files. We could either not include these recommended packages in Spack and
+require them to be installed through ``--with-recommended-packages``, or
+we could not install them with R and let users choose the version of the
+package they want to install. We chose the latter.
+
+Since these packages are so commonly distributed with the R system, many
+developers may assume these packages exist and fail to list them as
+dependencies. Watch out for this.
+
+You can find a list of these recommended packages at:
+https://github.com/wch/r-source/blob/trunk/share/make/vars.mk
+
+"""""""""""""""""
+Non-core packages
+"""""""""""""""""
+
+These are packages that are neither "core" nor "recommended". There are more
+than 10,000 of these packages hosted on CRAN alone.
+
+For each of these package types, if you see that a specific version is
+required, for example, "lattice (≥ 0.20)", please add this information to
+the dependency:
+
+.. code-block:: python
+
+   depends_on('r-lattice@0.20:', type=('build', 'run'))
+
+
+^^^^^^^^^^^^^^^^^^
+Non-R dependencies
+^^^^^^^^^^^^^^^^^^
+
+Some packages depend on non-R libraries for linking. Check out the
+`r-stringi <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/r-stringi/package.py>`_
+package for an example: https://cloud.r-project.org/package=stringi.
+If you search for the text "SystemRequirements", you will see:
+
+   ICU4C (>= 52, optional)
+
+This is how non-R dependencies are listed. Make sure to add these
+dependencies. The default dependency type should suffice.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to the installation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Some R packages provide additional flags that can be passed to
+``R CMD INSTALL``, often to locate non-R dependencies.
+`r-rmpi <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/r-rmpi/package.py>`_
+is an example of this, and flags for linking to an MPI library. To pass
+these to the installation command, you can override ``configure_args``
+like so:
+
+.. code-block:: python
+
+   def configure_args(self, spec, prefix):
+       mpi_name = spec['mpi'].name
+
+       # The type of MPI. Supported values are:
+       # OPENMPI, LAM, MPICH, MPICH2, or CRAY
+       if mpi_name == 'openmpi':
+           Rmpi_type = 'OPENMPI'
+       elif mpi_name == 'mpich':
+           Rmpi_type = 'MPICH2'
+       else:
+           raise InstallError('Unsupported MPI type')
+
+       return [
+           '--with-Rmpi-type={0}'.format(Rmpi_type),
+           '--with-mpi={0}'.format(spec['mpi'].prefix),
+       ]
+
+
+There is a similar ``configure_vars`` function that can be overridden
+to pass variables to the build.
+
+^^^^^^^^^^^^^^^^^^^^^
+Alternatives to Spack
+^^^^^^^^^^^^^^^^^^^^^
+
+CRAN hosts over 10,000 R packages, most of which are not in Spack. Many
+users may not need the advanced features of Spack, and may prefer to
+install R packages the normal way:
+
+.. code-block:: console
+
+   $ R
+   > install.packages("ggplot2")
+
+
+R will search CRAN for the ``ggplot2`` package and install all necessary
+dependencies for you. If you want to update all installed R packages to
+the latest release, you can use:
+
+.. code-block:: console
+
+   > update.packages(ask = FALSE)
+
+
+This works great for users who have internet access, but those on an
+air-gapped cluster will find it easier to let Spack build a download
+mirror and install these packages for you.
+
+Where Spack really shines is its ability to install non-R dependencies
+and link to them properly, something the R installation mechanism
+cannot handle.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on installing R packages, see:
+https://stat.ethz.ch/R-manual/R-devel/library/utils/html/INSTALL.html
+
+For more information on writing R packages, see:
+https://cloud.r-project.org/doc/manuals/r-release/R-exts.html
+
+In particular,
+https://cloud.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies
+has a great explanation of the difference between Depends, Imports,
+and LinkingTo.

lib/spack/docs/build_systems/rubypackage.rst

@@ -0,0 +1,16 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _rubypackage:
+
+-----------
+RubyPackage
+-----------
+
+Like Perl, Python, and R, Ruby has its own build system for
+installing Ruby gems.
+
+This build system is a work-in-progress. See
+https://github.com/spack/spack/pull/3127 for more information.

lib/spack/docs/build_systems/sconspackage.rst

@@ -0,0 +1,306 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _sconspackage:
+
+------------
+SConsPackage
+------------
+
+SCons is a general-purpose build system that does not rely on
+Makefiles to build software. SCons is written in Python, and handles
+all building and linking itself.
+
+As far as build systems go, SCons is very non-uniform. It provides a
+common framework for developers to write build scripts, but the build
+scripts themselves can vary drastically. Some developers add subcommands
+like:
+
+.. code-block:: console
+
+   $ scons clean
+   $ scons build
+   $ scons test
+   $ scons install
+
+
+Others don't add any subcommands. Some have configuration options that
+can be specified through variables on the command line. Others don't.
+
+^^^^^^
+Phases
+^^^^^^
+
+As previously mentioned, SCons allows developers to add subcommands like
+``build`` and ``install``, but by default, installation usually looks like:
+
+.. code-block:: console
+
+   $ scons
+   $ scons install
+
+
+To facilitate this, the ``SConsPackage`` base class provides the
+following phases:
+
+#. ``build`` - build the package
+#. ``install`` - install the package
+
+Package developers often add unit tests that can be invoked with
+``scons test`` or ``scons check``. Spack provides a ``test`` method
+to handle this. Since we don't know which one the package developer
+chose, the ``test`` method does nothing by default, but can be easily
+overridden like so:
+
+.. code-block:: python
+
+   def test(self):
+       scons('check')
+
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+SCons packages can be identified by their ``SConstruct`` files. These
+files handle everything from setting up subcommands and command-line
+options to linking and compiling.
+
+One thing to look for is the ``EnsureSConsVersion`` function:
+
+.. code-block:: none
+
+   EnsureSConsVersion(2, 3, 0)
+
+
+This means that SCons 2.3.0 is the earliest release that will work.
+You should specify this in a ``depends_on`` statement.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+At the bare minimum, packages that use the SCons build system need a
+``scons`` dependency. Since this is always the case, the ``SConsPackage``
+base class already contains:
+
+.. code-block:: python
+
+   depends_on('scons', type='build')
+
+
+If you want to specify a particular version requirement, you can override
+this in your package:
+
+.. code-block:: python
+
+   depends_on('scons@2.3.0:', type='build')
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Finding available options
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The first place to start when looking for a list of valid options to
+build a package is ``scons --help``. Some packages like
+`kahip <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/kahip/package.py>`_
+don't bother overwriting the default SCons help message, so this isn't
+very useful, but other packages like
+`serf <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/serf/package.py>`_
+print a list of valid command-line variables:
+
+.. code-block:: console
+
+   $ scons --help
+   scons: Reading SConscript files ...
+   Checking for GNU-compatible C compiler...yes
+   scons: done reading SConscript files.
+
+   PREFIX: Directory to install under ( /path/to/PREFIX )
+       default: /usr/local
+       actual: /usr/local
+
+   LIBDIR: Directory to install architecture dependent libraries under ( /path/to/LIBDIR )
+       default: $PREFIX/lib
+       actual: /usr/local/lib
+
+   APR: Path to apr-1-config, or to APR's install area ( /path/to/APR )
+       default: /usr
+       actual: /usr
+
+   APU: Path to apu-1-config, or to APR's install area ( /path/to/APU )
+       default: /usr
+       actual: /usr
+
+   OPENSSL: Path to OpenSSL's install area ( /path/to/OPENSSL )
+       default: /usr
+       actual: /usr
+
+   ZLIB: Path to zlib's install area ( /path/to/ZLIB )
+       default: /usr
+       actual: /usr
+
+   GSSAPI: Path to GSSAPI's install area ( /path/to/GSSAPI )
+       default: None
+       actual: None
+
+   DEBUG: Enable debugging info and strict compile warnings (yes|no)
+       default: False
+       actual: False
+
+   APR_STATIC: Enable using a static compiled APR (yes|no)
+       default: False
+       actual: False
+
+   CC: Command name or path of the C compiler
+       default: None
+       actual: gcc
+
+   CFLAGS: Extra flags for the C compiler (space-separated)
+       default: None
+       actual:
+
+   LIBS: Extra libraries passed to the linker, e.g. "-l<library1> -l<library2>" (space separated)
+       default: None
+       actual: None
+
+   LINKFLAGS: Extra flags for the linker (space-separated)
+       default: None
+       actual:
+
+   CPPFLAGS: Extra flags for the C preprocessor (space separated)
+       default: None
+       actual: None
+
+   Use scons -H for help about command-line options.
+
+
+More advanced packages like
+`cantera <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cantera/package.py>`_
+use ``scons --help`` to print a list of subcommands:
+
+.. code-block:: console
+
+   $ scons --help
+   scons: Reading SConscript files ...
+
+   SCons build script for Cantera
+
+   Basic usage:
+       'scons help' - print a description of user-specifiable options.
+
+       'scons build' - Compile Cantera and the language interfaces using
+                       default options.
+
+       'scons clean' - Delete files created while building Cantera.
+
+       '[sudo] scons install' - Install Cantera.
+
+       '[sudo] scons uninstall' - Uninstall Cantera.
+
+       'scons test' - Run all tests which did not previously pass or for which the
+                      results may have changed.
+
+       'scons test-reset' - Reset the passing status of all tests.
+
+       'scons test-clean' - Delete files created while running the tests.
+
+       'scons test-help' - List available tests.
+
+       'scons test-NAME' - Run the test named "NAME".
+
+       'scons <command> dump' - Dump the state of the SCons environment to the
+                                screen instead of doing <command>, e.g.
+                                'scons build dump'. For debugging purposes.
+
+       'scons samples' - Compile the C++ and Fortran samples.
+
+       'scons msi' - Build a Windows installer (.msi) for Cantera.
+
+       'scons sphinx' - Build the Sphinx documentation
+
+       'scons doxygen' - Build the Doxygen documentation
+
+
+You'll notice that cantera provides a ``scons help`` subcommand. Running
+``scons help`` prints a list of valid command-line variables.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to scons
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Now that you know what arguments the project accepts, you can add them to
+the package build phase. This is done by overriding ``build_args`` like so:
+
+.. code-block:: python
+
+   def build_args(self, spec, prefix):
+       args = [
+         'PREFIX={0}'.format(prefix),
+         'ZLIB={0}'.format(spec['zlib'].prefix),
+       ]
+
+       if '+debug' in spec:
+           args.append('DEBUG=yes')
+       else:
+           args.append('DEBUG=no')
+
+       return args
+
+
+``SConsPackage`` also provides an ``install_args`` function that you can
+override to pass additional arguments to ``scons install``.
+
+^^^^^^^^^^^^^^^^^
+Compiler wrappers
+^^^^^^^^^^^^^^^^^
+
+By default, SCons builds all packages in a separate execution environment,
+and doesn't pass any environment variables from the user environment.
+Even changes to ``PATH`` are not propagated unless the package developer
+does so.
+
+This is particularly troublesome for Spack's compiler wrappers, which depend
+on environment variables to manage dependencies and linking flags. In many
+cases, SCons packages are not compatible with Spack's compiler wrappers,
+and linking must be done manually.
+
+First of all, check the list of valid options for anything relating to
+environment variables. For example, cantera has the following option:
+
+.. code-block:: none
+
+   * env_vars: [ string ]
+       Environment variables to propagate through to SCons. Either the
+       string "all" or a comma separated list of variable names, e.g.
+       'LD_LIBRARY_PATH,HOME'.
+       - default: 'LD_LIBRARY_PATH,PYTHONPATH'
+
+
+In the case of cantera, using ``env_vars=all`` allows us to use
+Spack's compiler wrappers. If you don't see an option related to
+environment variables, try using Spack's compiler wrappers by passing
+``spack_cc``, ``spack_cxx``, and ``spack_fc`` via the ``CC``, ``CXX``,
+and ``FC`` arguments, respectively. If you pass them to the build and
+you see an error message like:
+
+.. code-block:: none
+
+   Spack compiler must be run from Spack! Input 'SPACK_PREFIX' is missing.
+
+
+you'll know that the package isn't compatible with Spack's compiler
+wrappers. In this case, you'll have to use the path to the actual
+compilers, which are stored in ``self.compiler.cc`` and friends.
+Note that this may involve passing additional flags to the build to
+locate dependencies, a task normally done by the compiler wrappers.
+serf is an example of a package with this limitation.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the SCons build system, see:
+http://scons.org/documentation.html

lib/spack/docs/build_systems/sippackage.rst

@@ -0,0 +1,141 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _sippackage:
+
+----------
+SIPPackage
+----------
+
+SIP is a tool that makes it very easy to create Python bindings for C and C++
+libraries. It was originally developed to create PyQt, the Python bindings for
+the Qt toolkit, but can be used to create bindings for any C or C++ library.
+
+SIP comprises a code generator and a Python module. The code generator
+processes a set of specification files and generates C or C++ code which is
+then compiled to create the bindings extension module. The SIP Python module
+provides support functions to the automatically generated code.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``SIPPackage`` base class comes with the following phases:
+
+#. ``configure`` - configure the package
+#. ``build`` - build the package
+#. ``install`` - install the package
+
+By default, these phases run:
+
+.. code-block:: console
+
+   $ python configure.py --bindir ... --destdir ...
+   $ make
+   $ make install
+
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+Each SIP package comes with a custom ``configure.py`` build script,
+written in Python. This script contains instructions to build the project.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+``SIPPackage`` requires several dependencies. Python is needed to run
+the ``configure.py`` build script, and to run the resulting Python
+libraries. Qt is needed to provide the ``qmake`` command. SIP is also
+needed to build the package. SIP is an unusual dependency in that it
+must be installed in the same installation directory as the package,
+so instead of a ``depends_on``, we use a ``resource``. All of these
+dependencies are automatically added via the base class
+
+.. code-block:: python
+
+   extends('python')
+
+   depends_on('qt', type='build')
+
+   resource(name='sip',
+            url='https://www.riverbankcomputing.com/static/Downloads/sip/4.19.18/sip-4.19.18.tar.gz',
+            sha256='c0bd863800ed9b15dcad477c4017cdb73fa805c25908b0240564add74d697e1e',
+            destination='.')
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to ``configure.py``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Each phase comes with a ``<phase_args>`` function that can be used to pass
+arguments to that particular phase. For example, if you need to pass
+arguments to the configure phase, you can use:
+
+.. code-block:: python
+
+   def configure_args(self, spec, prefix):
+       return ['--no-python-dbus']
+
+
+A list of valid options can be found by running ``python configure.py --help``.
+
+^^^^^^^
+Testing
+^^^^^^^
+
+Just because a package successfully built does not mean that it built
+correctly. The most reliable test of whether or not the package was
+correctly installed is to attempt to import all of the modules that
+get installed. To get a list of modules, run the following command
+in the site-packages directory:
+
+.. code-block:: console
+
+   $ python
+   >>> import setuptools
+   >>> setuptools.find_packages()
+   ['QtPy5']
+
+
+Large, complex packages like ``QtPy5`` will return a long list of
+packages, while other packages may return an empty list. These packages
+only install a single ``foo.py`` file. In Python packaging lingo,
+a "package" is a directory containing files like:
+
+.. code-block:: none
+
+   foo/__init__.py
+   foo/bar.py
+   foo/baz.py
+
+
+whereas a "module" is a single Python file. Since ``find_packages``
+only returns packages, you'll have to determine the correct module
+names yourself. You can now add these packages and modules to the
+package like so:
+
+.. code-block:: python
+
+   import_modules = ['PyQt5']
+
+
+When you run ``spack install --test=root py-pyqt5``, Spack will attempt
+to import the ``PyQt5`` module after installation.
+
+These tests most often catch missing dependencies and non-RPATHed
+libraries.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the SIP build system, see:
+
+* https://www.riverbankcomputing.com/software/sip/intro
+* https://www.riverbankcomputing.com/static/Docs/sip/
+* https://wiki.python.org/moin/SIP

lib/spack/docs/build_systems/wafpackage.rst

@@ -0,0 +1,129 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _wafpackage:
+
+----------
+WafPackage
+----------
+
+Like SCons, Waf is a general-purpose build system that does not rely
+on Makefiles to build software.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``WafPackage`` base class comes with the following phases:
+
+#. ``configure`` - configure the project
+#. ``build`` - build the project
+#. ``install`` - install the project
+
+By default, these phases run:
+
+.. code-block:: console
+
+   $ python waf configure --prefix=/path/to/installation/prefix
+   $ python waf build
+   $ python waf install
+
+
+Each of these are standard Waf commands and can be found by running:
+
+.. code-block:: console
+
+   $ python waf --help
+
+
+Each phase provides a ``<phase>`` function that runs:
+
+.. code-block:: console
+
+   $ python waf -j<jobs> <phase>
+
+
+where ``<jobs>`` is the number of parallel jobs to build with. Each phase
+also has a ``<phase_args>`` function that can pass arguments to this call.
+All of these functions are empty except for the ``configure_args``
+function, which passes ``--prefix=/path/to/installation/prefix``.
+
+^^^^^^^
+Testing
+^^^^^^^
+
+``WafPackage`` also provides ``test`` and ``installtest`` methods,
+which are run after the ``build`` and ``install`` phases, respectively.
+By default, these phases do nothing, but you can override them to
+run package-specific unit tests. For example, the
+`py-py2cairo <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-py2cairo/package.py>`_
+package uses:
+
+.. code-block:: python
+
+   def installtest(self):
+       with working_dir('test'):
+           pytest = which('py.test')
+           pytest()
+
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+Each Waf package comes with a custom ``waf`` build script, written in
+Python. This script contains instructions to build the project.
+
+The package also comes with a ``wscript`` file. This file is used to
+override the default ``configure``, ``build``, and ``install`` phases
+to customize the Waf project. It also allows developers to override
+the default ``./waf --help`` message. Check this file to find useful
+information about dependencies and the minimum versions that are
+supported.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+``WafPackage`` does not require ``waf`` to build. ``waf`` is only
+needed to create the ``./waf`` script. Since ``./waf`` is a Python
+script, Python is needed to build the project. ``WafPackage`` adds
+the following dependency automatically:
+
+.. code-block:: python
+
+   depends_on('python@2.5:', type='build')
+
+
+Waf only supports Python 2.5 and up.
+
+^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to waf
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+As previously mentioned, each phase comes with a ``<phase_args>``
+function that can be used to pass arguments to that particular
+phase. For example, if you need to pass arguments to the build
+phase, you can use:
+
+.. code-block:: python
+
+   def build_args(self, spec, prefix):
+       args = []
+
+       if self.run_tests:
+           args.append('--test')
+
+       return args
+
+
+A list of valid options can be found by running ``./waf --help``.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the Waf build system, see:
+https://waf.io/book/

lib/spack/docs/chain.rst

@@ -0,0 +1,96 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. chain:
+
+============================
+Chaining Spack Installations
+============================
+
+You can point your Spack installation to another installation to use any
+packages that are installed there. To register the other Spack instance,
+you can add it as an entry to ``upstreams.yaml``:
+
+.. code-block:: yaml
+
+  upstreams:
+    spack-instance-1:
+      install_tree: /path/to/other/spack/opt/spack
+    spack-instance-2:
+      install_tree: /path/to/another/spack/opt/spack
+
+``install_tree`` must point to the ``opt/spack`` directory inside of the
+Spack base directory.
+
+Once the upstream Spack instance has been added, ``spack find`` will
+automatically check the upstream instance when querying installed packages,
+and new package installations for the local Spack install will use any
+dependencies that are installed in the upstream instance.
+
+This other instance of Spack has no knowledge of the local Spack instance
+and may not have the same permissions or ownership as the local Spack instance.
+This has the following consequences:
+
+#. Upstream Spack instances are not locked. Therefore it is up to users to
+   make sure that the local instance is not using an upstream instance when it
+   is being modified.
+
+#. Users should not uninstall packages from the upstream instance. Since the
+   upstream instance doesn't know about the local instance, it cannot prevent
+   the uninstallation of packages which the local instance depends on.
+
+Other details about upstream installations:
+
+#. If a package is installed both locally and upstream, the local installation
+   will always be used as a dependency. This can occur if the local Spack
+   installs a package which is not present in the upstream, but later on the
+   upstream Spack instance also installs that package.
+
+#. If an upstream Spack instance registers and installs an external package,
+   the local Spack instance will treat this the same as a Spack-installed
+   package. This feature will only work if the upstream Spack instance
+   includes the upstream functionality (i.e. if its commit is after March
+   27, 2019).
+
+---------------------------------------
+Using Multiple Upstream Spack Instances
+---------------------------------------
+
+A single Spack instance can use multiple upstream Spack installations. Spack
+will search upstream instances in the order you list them in your
+configuration. If your installation refers to instances X and Y, in that order,
+then instance X must list Y as an upstream in its own ``upstreams.yaml``.
+
+-----------------------------------
+Using Modules for Upstream Packages
+-----------------------------------
+
+The local Spack instance does not generate modules for packages which are
+installed upstream. The local Spack instance can be configured to use the
+modules generated by the upstream Spack instance.
+
+There are two requirements to use the modules created by an upstream Spack
+instance: firstly the upstream instance must do a ``spack module tcl refresh``,
+which generates an index file that maps installed packages to their modules;
+secondly, the local Spack instance must add a ``modules`` entry to the
+configuration:
+
+.. code-block:: yaml
+
+  upstreams:
+    spack-instance-1:
+      install_tree: /path/to/other/spack/opt/spack
+      modules:
+        tcl: /path/to/other/spack/share/spack/modules
+
+Each time new packages are installed in the upstream Spack instance, the
+upstream Spack maintainer should run ``spack module tcl refresh`` (or the
+corresponding command for the type of module they intend to use).
+
+.. note::
+
+   Spack can generate modules that :ref:`automatically load
+   <autoloading-dependencies>` the modules of dependency packages. Spack cannot
+   currently do this for modules in upstream packages.

lib/spack/docs/command_index.in

@@ -1,9 +1,9 @@
-=============
-Command Index
-=============
+=================
+Command Reference
+=================
 
-This is an alphabetical list of commands with links to the places they
-appear in the documentation.
+This is a reference for all commands in the Spack command line interface.
+The same information is available through :ref:`spack-help`.
 
-.. hlist::
-   :columns: 3
+Commands that also have sections in the main documentation have a link to
+"More documentation".

lib/spack/docs/conf.py

@@ -1,28 +1,9 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # flake8: noqa
-##############################################################################
-# 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
-##############################################################################
 # -*- coding: utf-8 -*-
 #
 # Spack documentation build configuration file, created by
@@ -39,55 +20,45 @@
 import sys
 import os
 import re
-import shutil
 import subprocess
 from glob import glob
-from sphinx.apidoc import main as sphinx_apidoc
+
+from sphinx.ext.apidoc import main as sphinx_apidoc
 
 # -- Spack customizations -----------------------------------------------------
-
 # 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('../external'))
+sys.path.insert(0, os.path.abspath('_spack_root/lib/spack/external'))
+
 if sys.version_info[0] < 3:
-    sys.path.insert(0, os.path.abspath('../external/yaml/lib'))
+    sys.path.insert(
+        0, os.path.abspath('_spack_root/lib/spack/external/yaml/lib'))
 else:
-    sys.path.insert(0, os.path.abspath('../external/yaml/lib3'))
-sys.path.append(os.path.abspath('..'))
+    sys.path.insert(
+        0, os.path.abspath('_spack_root/lib/spack/external/yaml/lib3'))
+
+sys.path.append(os.path.abspath('_spack_root/lib/spack/'))
 
 # Add the Spack bin directory to the path so that we can use its output in docs.
-spack_root = '../../..'
-os.environ['SPACK_ROOT'] = spack_root
-os.environ['PATH'] += '%s%s/bin' % (os.pathsep, spack_root)
+os.environ['SPACK_ROOT'] = os.path.abspath('_spack_root')
+os.environ['PATH'] += "%s%s" % (os.pathsep, os.path.abspath('_spack_root/bin'))
 
 # Set an environment variable so that colify will print output like it would to
 # a terminal.
 os.environ['COLIFY_SIZE'] = '25x120'
+os.environ['COLUMNS'] = '120'
 
-#
-# Generate package list using spack command
-#
-with open('package_list.rst', 'w') as plist_file:
-    subprocess.Popen(
-        [spack_root + '/bin/spack', 'list', '--format=rst'], stdout=plist_file)
+# Generate full package list if needed
+subprocess.call([
+    'spack', 'list', '--format=html', '--update=package_list.html'])
 
-#
-# Find all the `cmd-spack-*` references and add them to a command index
-#
-command_names = []
-for filename in glob('*rst'):
-    with open(filename) as f:
-        for line in f:
-            match = re.match('.. _(cmd-spack-.*):', line)
-            if match:
-                command_names.append(match.group(1).strip())
-
-shutil.copy('command_index.in', 'command_index.rst')
-with open('command_index.rst', 'a') as index:
-    index.write('\n')
-    for cmd in sorted(command_names):
-        index.write('   * :ref:`%s`\n' % cmd)
+# Generate a command index if an update is needed
+subprocess.call([
+    'spack', 'commands',
+    '--format=rst',
+    '--header=command_index.in',
+    '--update=command_index.rst'] + glob('*rst'))
 
 #
 # Run sphinx-apidoc
@@ -97,35 +68,12 @@
 # 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'])
-
-#
-# Exclude everything in spack.__all__ from indexing.  All of these
-# symbols are imported from elsewhere in spack; their inclusion in
-# __all__ simply allows package authors to use `from spack import *`.
-# Excluding them ensures they're only documented in their "real" module.
-#
-# This also avoids issues where some of these symbols shadow core spack
-# modules.  Sphinx will complain about duplicate docs when this happens.
-#
-import fileinput, spack
-handling_spack = False
-for line in fileinput.input('spack.rst', inplace=1):
-    if handling_spack:
-        if not line.startswith('    :noindex:'):
-            print('    :noindex: %s' % ' '.join(spack.__all__))
-        handling_spack = False
-
-    if line.startswith('.. automodule::'):
-        handling_spack = (line == '.. automodule:: spack\n')
-
-    sys.stdout.write(line)
+sphinx_apidoc(apidoc_args + ['_spack_root/lib/spack/spack'])
+sphinx_apidoc(apidoc_args + ['_spack_root/lib/spack/llnl'])
 
 # Enable todo items
 todo_include_todos = True
@@ -142,12 +90,12 @@ def resolve_xref(self, env, fromdocname, builder, typ, target, node, contnode):
             env, fromdocname, builder, typ, target, node, contnode)
 
 def setup(sphinx):
-    sphinx.override_domain(PatchedPythonDomain)
+    sphinx.add_domain(PatchedPythonDomain, override=True)
 
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+needs_sphinx = '1.8'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
@@ -180,21 +128,29 @@ def setup(sphinx):
 
 # General information about the project.
 project = u'Spack'
-copyright = u'2013-2017, Lawrence Livermore National Laboratory.'
+copyright = u'2013-2019, 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))
+import spack
+version = '.'.join(str(s) for s in spack.spack_version_info[:2])
 # The full version, including alpha/beta/rc tags.
-release = str(spack.spack_version.up_to(2))
+release = spack.spack_version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #language = None
 
+# Places to look for .po/.mo files for doc translations
+#locale_dirs = []
+
+# Sphinx gettext settings
+gettext_compact = True
+gettext_uuid = False
+
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
 #today = ''
@@ -203,7 +159,7 @@ def setup(sphinx):
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ['_build', '_spack_root', '.spack-env']
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None
@@ -238,7 +194,7 @@ def setup(sphinx):
 html_theme_options = { 'logo_only' : True }
 
 # Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = ["_themes"]
+# html_theme_path = ["_themes"]
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
@@ -249,12 +205,12 @@ 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 = '_spack_root/share/spack/logo/spack-logo-white-text.svg'
 
 # 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
 # pixels large.
-html_favicon = '../../../share/spack/logo/favicon.ico'
+html_favicon = '_spack_root/share/spack/logo/favicon.ico'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

lib/spack/docs/config_yaml.rst

@@ -1,14 +1,19 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _config-yaml:
 
-====================================
-Basic settings in ``config.yaml``
-====================================
+==============
+Basic Settings
+==============
 
 Spack's basic configuration options are set in ``config.yaml``.  You can
 see the default settings by looking at
 ``etc/spack/defaults/config.yaml``:
 
-.. literalinclude:: ../../../etc/spack/defaults/config.yaml
+.. literalinclude:: _spack_root/etc/spack/defaults/config.yaml
    :language: yaml
 
 These settings can be overridden in ``etc/spack/config.yaml`` or
@@ -31,19 +36,18 @@ 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}``
+Secondly, it is also possible to modify the entire installation
+scheme. By default Spack uses
+``{architecture}/{compiler.name}-{compiler.version}/{name}-{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
+same as those understood by the :meth:`~spack.spec.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}'
+         install_path_scheme: '{name}/{version}/{hash:7}'
 
 would install packages into sub-directories using only the package
 name, version and a hash length of 7 characters.
@@ -70,7 +74,6 @@ the location for each type of module.  e.g.:
    module_roots:
      tcl:    $spack/share/spack/modules
      lmod:   $spack/share/spack/lmod
-     dotkit: $spack/share/spack/dotkit
 
 See :ref:`modules` for details.
 
@@ -79,41 +82,47 @@ See :ref:`modules` for details.
 --------------------
 
 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,
-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
-create build stages in temporary space.
+systems the home directory is a (slow) network file system.  On most systems,
+building in a temporary file system is faster.  Usually, there is also more
+space available in the temporary location than in the home directory.  If the
+username is not already in the path, Spack will append the value of ``$user`` to
+the selected ``build_stage`` path.
+
+.. warning:: We highly recommend specifying ``build_stage`` paths that
+   distinguish between staging and other activities to ensure 
+   ``spack clean`` does not inadvertently remove unrelated files.
+   Spack prepends ``spack-stage-`` to temporary staging directory names to
+   reduce this risk.  Using a combination of ``spack`` and or ``stage`` in
+   each specified path, as shown in the default settings and documented
+   examples, will add another layer of protection.
 
 By default, Spack's ``build_stage`` is configured like this:
 
 .. code-block:: yaml
 
    build_stage:
-    - $tempdir
-    - /nfs/tmp2/$user
-    - $spack/var/spack/stage
+    - $tempdir/$user/spack-stage
+    - ~/.spack/stage
 
-This is an ordered list of paths that Spack should search when trying to
+This can be an ordered list of paths that Spack should search when trying to
 find a temporary directory for the build stage.  The list is searched in
 order, and Spack will use the first directory to which it has write access.
-See :ref:`config-file-variables` for more on ``$tempdir`` and ``$spack``.
+
+Specifying `~/.spack/stage` first will ensure each user builds in their home
+directory.  The historic Spack stage path `$spack/var/spack/stage` will build
+directly inside the Spack instance.  See :ref:`config-file-variables` for more
+on ``$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.
-
-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
+``build_stage``.  After the 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>`.
 
 .. note::
 
-   The last item in the list is ``$spack/var/spack/stage``.  If this is the
-   only writable directory in the ``build_stage`` list, Spack will build
-   *directly* in ``$spack/var/spack/stage`` and will not link to temporary
-   space.
+   The build will fail if there is no writable directory in the ``build_stage``
+   list, where any user- and site-specific setting will be searched first.
 
 --------------------
 ``source_cache``
@@ -150,6 +159,17 @@ checksum, and will refuse to build packages that it cannot verify.  Set
 to ``false`` to disable these checks.  Disabling this can expose you to
 attacks.  Use at your own risk.
 
+--------------------
+``locks``
+--------------------
+
+When set to ``true``, concurrent instances of Spack will use locks to
+avoid modifying the install tree, database file, etc. If false, Spack
+will disable all locking, but you must **not** run concurrent instances
+of Spack.  For file systems that don't support locking, you should set
+this to ``false`` and run one Spack at a time, but otherwise we recommend
+enabling locks.
+
 --------------------
 ``dirty``
 --------------------
@@ -164,19 +184,66 @@ 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:
+
 --------------
 ``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.
+packages in parallel. The default parallelism is equal to the number of
+cores on your machine, up to 16. Parallelism cannot exceed the number of
+cores available on the host. For a build system that uses Makefiles, this
+means running:
+
+- ``make -j<build_jobs>``, when ``build_jobs`` is less than the number of
+  cores on the machine
+- ``make -j<ncores>``, when ``build_jobs`` is greater or equal to the
+  number of cores on the machine
 
-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.
+
+--------------------
+``ccache``
+--------------------
+
+When set to ``true`` Spack will use ccache to cache compiles. This is
+useful specifically in two cases: (1) when using ``spack setup``, and (2)
+when building the same package with many different variants. The default is
+``false``.
+
+When enabled, Spack will look inside your ``PATH`` for a ``ccache``
+executable and stop if it is not found. Some systems come with
+``ccache``, but it can also be installed using ``spack install
+ccache``. ``ccache`` comes with reasonable defaults for cache size
+and location. (See the *Configuration settings* section of ``man
+ccache`` to learn more about the default settings and how to change
+them). Please note that we currently disable ccache's ``hash_dir``
+feature to avoid an issue with the stage directory (see
+https://github.com/LLNL/spack/pull/3761#issuecomment-294352232).
+
+------------------
+``shared_linking``
+------------------
+
+Control whether Spack embeds ``RPATH`` or ``RUNPATH`` attributes in ELF binaries
+so that they can find their dependencies. Has no effect on macOS.
+Two options are allowed:
+
+ 1. ``rpath`` uses ``RPATH`` and forces the ``--disable-new-tags`` flag to be passed to the linker
+ 2. ``runpath`` uses ``RUNPATH`` and forces the ``--enable-new-tags`` flag to be passed to the linker
+
+``RPATH`` search paths have higher precedence than ``LD_LIBRARY_PATH``
+and ld.so will search for libraries in transitive ``RPATHs`` of
+parent objects.
+
+``RUNPATH`` search paths have lower precedence than ``LD_LIBRARY_PATH``,
+and ld.so will ONLY search for dependencies in the ``RUNPATH`` of
+the loading object.
+
+DO NOT MIX the two options within the same install tree.

lib/spack/docs/configuration.rst

@@ -1,8 +1,13 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _configuration:
 
-==============================
-Configuration Files in Spack
-==============================
+===================
+Configuration Files
+===================
 
 Spack has many configuration files.  Here is a quick list of them, in
 case you want to skip directly to specific docs:
@@ -14,9 +19,9 @@ case you want to skip directly to specific docs:
 * :ref:`packages.yaml <build-settings>`
 * :ref:`repos.yaml <repositories>`
 
--------------------------
+-----------
 YAML Format
--------------------------
+-----------
 
 Spack configuration files are written in YAML.  We chose YAML because
 it's human readable, but also versatile in that it supports dictionaries,
@@ -29,44 +34,52 @@ Here is an example ``config.yaml`` file:
    config:
      install_tree: $spack/opt/spack
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
-       - $tempdir
-       - /nfs/tmp2/$user
+       - $tempdir/$user/spack-stage
+       - ~/.spack/stage
 
-Each spack configuration files is nested under a top-level section
+Each Spack configuration file is nested under a top-level section
 corresponding to its name. So, ``config.yaml`` starts with ``config:``,
-and ``mirrors.yaml`` starts with ``mirrors:``, etc.
+``mirrors.yaml`` starts with ``mirrors:``, etc.
 
 .. _configuration-scopes:
 
--------------------------
+--------------------
 Configuration Scopes
--------------------------
+--------------------
 
 Spack pulls configuration data from files in several directories. There
-are four configuration scopes.  From lowest to highest:
+are six configuration scopes. From lowest to highest:
 
 #. **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
+#. **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.
+   root access on the machine. They override the defaults scope.
 
-#. **site**: Stored in ``$(prefix)/etc/spack/``.  Settings here affect
-   only *this instance* of Spack, and they override defaults.  The site
-   scope can can be used for per-project settings (one spack instance per
-   project) or for site-wide settings on a multi-user machine (e.g., for
-   a common spack instance).
+#. **site**: Stored in ``$(prefix)/etc/spack/``. Settings here affect
+   only *this instance* of Spack, and they override the defaults and system
+   scopes.  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
-   affect all instances of Spack and take the highest precedence.
+   affect all instances of Spack and take higher precedence than site,
+   system, or defaults scopes.
+
+#. **custom**: Stored in a custom directory specified by ``--config-scope``.
+   If multiple scopes are listed on the command line, they are ordered
+   from lowest to highest precedence.
+
+#. **command line**: Build settings specified on the command line take
+   precedence over all other scopes.
 
 Each configuration directory may contain several configuration files,
 such as ``config.yaml``, ``compilers.yaml``, or ``mirrors.yaml``.  When
@@ -75,76 +88,175 @@ lower-precedence settings.
 
 Commands that modify scopes (e.g., ``spack compilers``, ``spack repo``,
 etc.) take a ``--scope=<name>`` parameter that you can use to control
-which scope is modified.  By default they modify the highest-precedence
+which scope is modified.  By default, they modify the highest-precedence
 scope.
 
+.. _custom-scopes:
+
+^^^^^^^^^^^^^
+Custom scopes
+^^^^^^^^^^^^^
+
+In addition to the ``defaults``, ``system``, ``site``, and ``user``
+scopes, you may add configuration scopes directly on the command
+line with the ``--config-scope`` argument, or ``-C`` for short.
+
+For example, the following adds two configuration scopes, named
+``scopea`` and ``scopeb``, to a ``spack spec`` command:
+
+.. code-block:: console
+
+   $ spack -C ~/myscopes/scopea -C ~/myscopes/scopeb spec ncurses
+
+Custom scopes come *after* the ``spack`` command and *before* the
+subcommand, and they specify a single path to a directory full of
+configuration files. You can add the same configuration files to that
+directory that you can add to any other scope (``config.yaml``,
+``packages.yaml``, etc.).
+
+If multiple scopes are provided:
+
+#. Each must be preceded with the ``--config-scope`` or ``-C`` flag.
+#. They must be ordered from lowest to highest precedence.
+
+"""""""""""""""""""""""""""""""""""""""""""
+Example: scopes for release and development
+"""""""""""""""""""""""""""""""""""""""""""
+
+Suppose that you need to support simultaneous building of release and
+development versions of ``mypackage``, where ``mypackage`` -> ``A`` -> ``B``.
+You could create The following files:
+
+.. code-block:: yaml
+   :caption: ~/myscopes/release/packages.yaml
+
+   packages:
+       mypackage:
+           version: [1.7]
+       A:
+           version: [2.3]
+       B:
+           version: [0.8]
+
+.. code-block:: yaml
+   :caption: ~/myscopes/develop/packages.yaml
+
+   packages:
+       mypackage:
+           version: [develop]
+       A:
+           version: [develop]
+       B:
+           version: [develop]
+
+You can switch between ``release`` and ``develop`` configurations using
+configuration arguments.  You would type ``spack -C ~/myscopes/release``
+when you want to build the designated release versions of ``mypackage``,
+``A``, and ``B``, and you would type ``spack -C ~/myscopes/develop`` when
+you want to build all of these packages at the ``develop`` version.
+
+"""""""""""""""""""""""""""""""
+Example: swapping MPI providers
+"""""""""""""""""""""""""""""""
+
+Suppose that you need to build two software packages, ``packagea`` and
+``packageb``. ``packagea`` is Python 2-based and ``packageb`` is Python
+3-based. ``packagea`` only builds with OpenMPI and ``packageb`` only builds
+with MPICH. You can create different configuration scopes for use with
+``packagea`` and ``packageb``:
+
+.. code-block:: yaml
+   :caption: ~/myscopes/packgea/packages.yaml
+
+   packages:
+       python:
+           version: [2.7.11]
+       all:
+           providers:
+               mpi: [openmpi]
+
+.. code-block:: yaml
+   :caption: ~/myscopes/packageb/packages.yaml
+
+   packages:
+       python:
+           version: [3.5.2]
+       all:
+           providers:
+               mpi: [mpich]
+
+
 .. _platform-scopes:
 
--------------------------
-Platform-specific scopes
--------------------------
+------------------------
+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 each scope above, there can also be platform-specific settings.
+For example, on most platforms, GCC is the preferred compiler.
+However, on macOS (darwin), Clang often works for more packages,
+and is set as the default compiler. This configuration is set in
+``$(prefix)/etc/spack/defaults/darwin/packages.yaml``. It will take
+precedence over settings in the ``defaults`` scope, but can still be
+overridden by settings in ``system``, ``system/darwin``, ``site``,
+``site/darwin``, ``user``, ``user/darwin``, ``custom``, or
+``custom/darwin``. 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>``
+#. ``defaults``
+#. ``defaults/<platform>``
+#. ``system``
+#. ``system/<platform>``
+#. ``site``
+#. ``site/<platform>``
+#. ``user``
+#. ``user/<platform>``
+#. ``custom``
+#. ``custom/<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.
 
--------------------------
-Scope precedence
--------------------------
+----------------
+Scope Precedence
+----------------
 
 When spack queries for configuration parameters, it searches in
-higher-precedence scopes first.  So, settings in a higher-precedence file
-can override those with the same key in a lower-precedence one.  For
+higher-precedence scopes first. So, settings in a higher-precedence file
+can override those with the same key in a lower-precedence one. For
 list-valued settings, Spack *prepends* higher-precedence settings to
 lower-precedence settings. Completely ignoring higher-level configuration
 options is supported with the ``::`` notation for keys (see
 :ref:`config-overrides` below).
 
-^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^
 Simple keys
-^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^
 
-Let's look at an example of overriding a single key in a Spack file.  If
+Let's look at an example of overriding a single key in a Spack file. If
 your configurations look like this:
 
-**defaults** scope:
-
 .. code-block:: yaml
+   :caption: $(prefix)/etc/spack/defaults/config.yaml
 
    config:
      install_tree: $spack/opt/spack
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
-       - $tempdir
-       - /nfs/tmp2/$user
+       - $tempdir/$user/spack-stage
+       - ~/.spack/stage
 
-**site** scope:
 
 .. code-block:: yaml
+   :caption: ~/.spack/config.yaml
 
    config:
      install_tree: /some/other/directory
 
+
 Spack will only override ``install_tree`` in the ``config`` section, and
-will take the site preferences for other settings.  You can see the
+will take the site preferences for other settings. You can see the
 final, combined configuration with the ``spack config get <configtype>``
 command:
 
@@ -155,11 +267,11 @@ command:
    config:
      install_tree: /some/other/directory
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
-       - $tempdir
-       - /nfs/tmp2/$user
-   $ _
+       - $tempdir/$user/spack-stage
+       - ~/.spack/stage
+
 
 .. _config-overrides:
 
@@ -167,14 +279,14 @@ command:
 Overriding entire sections
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Above, the site ``config.yaml`` only overrides specific settings in the
-default ``config.yaml``.  Sometimes, it is useful to *completely*
-override lower-precedence settings.  To do this, you can use *two* colons
-at the end of a key in a configuration file.  For example, if the
-**site** ``config.yaml`` above looks like this:
+Above, the user ``config.yaml`` only overrides specific settings in the
+default ``config.yaml``. Sometimes, it is useful to *completely*
+override lower-precedence settings. To do this, you can use *two* colons
+at the end of a key in a configuration file. For example:
 
 .. code-block:: yaml
    :emphasize-lines: 1
+   :caption: ~/.spack/config.yaml
 
    config::
      install_tree: /some/other/directory
@@ -188,35 +300,36 @@ Spack will ignore all lower-precedence configuration under the
    config:
      install_tree: /some/other/directory
 
-^^^^^^^^^^^^^^^^^^^^^^
-List-valued settings
-^^^^^^^^^^^^^^^^^^^^^^
 
-Let's revisit the ``config.yaml`` example one more time.  The
+^^^^^^^^^^^^^^^^^^^^
+List-valued settings
+^^^^^^^^^^^^^^^^^^^^
+
+Let's revisit the ``config.yaml`` example one more time. The
 ``build_stage`` setting's value is an ordered list of directories:
 
-**defaults**
-
 .. code-block:: yaml
+   :caption: $(prefix)/etc/spack/defaults/config.yaml
 
    build_stage:
-     - $tempdir
-     - /nfs/tmp2/$user
+     - $tempdir/$user/spack-stage
+     - ~/.spack/stage
+
 
 Suppose the user configuration adds its *own* list of ``build_stage``
 paths:
 
-**user**
-
 .. code-block:: yaml
+   :caption: ~/.spack/config.yaml
 
    build_stage:
-     - /lustre-scratch/$user
+     - /lustre-scratch/$user/spack
      - ~/mystage
 
-Spack will first look at the paths in the site ``config.yaml``, then the
-paths in the user's ``~/.spack/config.yaml``.  The list in the
-higher-precedence scope is *prepended* to the defaults.  ``spack config
+
+Spack will first look at the paths in the defaults ``config.yaml``, then the
+paths in the user's ``~/.spack/config.yaml``. The list in the
+higher-precedence scope is *prepended* to the defaults. ``spack config
 get config`` shows the result:
 
 .. code-block:: console
@@ -226,27 +339,27 @@ get config`` shows the result:
    config:
      install_tree: /some/other/directory
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
-       - /lustre-scratch/$user
+       - /lustre-scratch/$user/spack
        - ~/mystage
-       - $tempdir
-       - /nfs/tmp2/$user
-   $ _
+       - $tempdir/$user/spack-stage
+       - ~/.spack/stage
+
 
 As in :ref:`config-overrides`, the higher-precedence scope can
-*completely* override the lower-precedence scope using `::`.  So if the
+*completely* override the lower-precedence scope using ``::``. So if the
 user config looked like this:
 
-**user**
-
 .. code-block:: yaml
    :emphasize-lines: 1
+   :caption: ~/.spack/config.yaml
 
    build_stage::
-     - /lustre-scratch/$user
+     - /lustre-scratch/$user/spack
      - ~/mystage
 
+
 The merged configuration would look like this:
 
 .. code-block:: console
@@ -256,57 +369,161 @@ The merged configuration would look like this:
    config:
      install_tree: /some/other/directory
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
-       - /lustre-scratch/$user
+       - /lustre-scratch/$user/spack
        - ~/mystage
-   $ _
+
 
 .. _config-file-variables:
 
-------------------------------
-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 ``$``. User path variables are indicated at the start of the path with
-``~`` or ``~user``. Let's discuss each in turn.
+Spack understands several variables which can be used in config file
+paths wherever they appear. There are three sets of these variables:
+Spack-specific variables, environment variables, and user path
+variables. Spack-specific variables and environment variables are both
+indicated by prefixing the variable name with ``$``. User path variables
+are indicated at the start of the path with ``~`` or ``~user``.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^
-Spack Specific Variables
+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.
-  * ``$user``: name of the current user
+* ``$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.
+``${varname}``. Their names are also case insensitive, meaning that
+``$SPACK`` works just as well as ``$spack``. These special variables are
+substituted first, so any environment variables with the same name will
+not be used.
 
 ^^^^^^^^^^^^^^^^^^^^^
-Environment Variables
+Environment variables
 ^^^^^^^^^^^^^^^^^^^^^
 
-Spack then uses ``os.path.expandvars`` to expand any remaining environment
-variables.
+After Spack-specific variables are evaluated, environment variables are
+expanded. These are formatted like Spack-specific variables, e.g.,
+``${varname}``. You can use this to insert environment variables in your
+Spack configuration.
 
-^^^^^^^^^^^^^^
-User Variables
-^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^
+User home directories
+^^^^^^^^^^^^^^^^^^^^^
 
-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.
+Spack performs Unix-style tilde expansion on paths in configuration
+files. This means that tilde (``~``) will expand to the current user's
+home directory, and ``~user`` will expand to a specified user's home
+directory. The ``~`` must appear at the beginning of the path, or Spack
+will not expand it.
+
+----------------------------
+Seeing Spack's Configuration
+----------------------------
+
+With so many scopes overriding each other, it can sometimes be difficult
+to understand what Spack's final configuration looks like.
+
+Spack provides two useful ways to view the final "merged" version of any
+configuration file: ``spack config get`` and ``spack config blame``.
+
+.. _cmd-spack-config-get:
+
+^^^^^^^^^^^^^^^^^^^^
+``spack config get``
+^^^^^^^^^^^^^^^^^^^^
+
+``spack config get`` shows a fully merged configuration file, taking into
+account all scopes. For example, to see the fully merged
+``config.yaml``, you can type:
+
+.. code-block:: console
+
+   $ spack config get config
+   config:
+     debug: false
+     checksum: true
+     verify_ssl: true
+     dirty: false
+     build_jobs: 8
+     install_tree: $spack/opt/spack
+     template_dirs:
+     - $spack/templates
+     directory_layout: {architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}
+     module_roots:
+       tcl: $spack/share/spack/modules
+       lmod: $spack/share/spack/lmod
+     build_stage:
+     - $tempdir/$user/spack-stage
+     - ~/.spack/stage
+     - $spack/var/spack/stage
+     source_cache: $spack/var/spack/cache
+     misc_cache: ~/.spack/cache
+     locks: true
+
+Likewise, this will show the fully merged ``packages.yaml``:
+
+.. code-block:: console
+
+   $ spack config get packages
+
+You can use this in conjunction with the ``-C`` / ``--config-scope`` argument to
+see how your scope will affect Spack's configuration:
+
+.. code-block:: console
+
+   $ spack -C /path/to/my/scope config get packages
+
+
+.. _cmd-spack-config-blame:
+
+^^^^^^^^^^^^^^^^^^^^^^
+``spack config blame``
+^^^^^^^^^^^^^^^^^^^^^^
+
+``spack config blame`` functions much like ``spack config get``, but it
+shows exactly which configuration file each preference came from. If you
+do not know why Spack is behaving a certain way, this can help you track
+down the problem:
+
+.. code-block:: console
+
+   $ spack --insecure -C ./my-scope -C ./my-scope-2 config blame config
+   ==> Warning: You asked for --insecure. Will NOT check SSL certificates.
+   ---                                                   config:
+   _builtin                                                debug: False
+   /home/myuser/spack/etc/spack/defaults/config.yaml:72    checksum: True
+   command_line                                            verify_ssl: False
+   ./my-scope-2/config.yaml:2                              dirty: False
+   _builtin                                                build_jobs: 8
+   ./my-scope/config.yaml:2                                install_tree: /path/to/some/tree
+   /home/myuser/spack/etc/spack/defaults/config.yaml:23    template_dirs:
+   /home/myuser/spack/etc/spack/defaults/config.yaml:24    - $spack/templates
+   /home/myuser/spack/etc/spack/defaults/config.yaml:28    directory_layout: {architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}
+   /home/myuser/spack/etc/spack/defaults/config.yaml:32    module_roots:
+   /home/myuser/spack/etc/spack/defaults/config.yaml:33      tcl: $spack/share/spack/modules
+   /home/myuser/spack/etc/spack/defaults/config.yaml:34      lmod: $spack/share/spack/lmod
+   /home/myuser/spack/etc/spack/defaults/config.yaml:49    build_stage:
+   /home/myuser/spack/etc/spack/defaults/config.yaml:50    - $tempdir/$user/spack-stage
+   /home/myuser/spack/etc/spack/defaults/config.yaml:51    - ~/.spack/stage
+   /home/myuser/spack/etc/spack/defaults/config.yaml:52    - $spack/var/spack/stage
+   /home/myuser/spack/etc/spack/defaults/config.yaml:57    source_cache: $spack/var/spack/cache
+   /home/myuser/spack/etc/spack/defaults/config.yaml:62    misc_cache: ~/.spack/cache
+   /home/myuser/spack/etc/spack/defaults/config.yaml:86    locks: True
+
+You can see above that the ``build_jobs`` and ``debug`` settings are
+built in and are not overridden by a configuration file. The
+``verify_ssl`` setting comes from the ``--insceure`` option on the
+command line. ``dirty`` and ``install_tree`` come from the custom
+scopes ``./my-scope`` and ``./my-scope-2``, and all other configuration
+options come from the default configuration files that ship with Spack.

lib/spack/docs/contribution_guide.rst

@@ -1,3 +1,8 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _contribution-guide:
 
 ==================
@@ -34,13 +39,30 @@ Continuous Integration
 
 Spack uses `Travis CI <https://travis-ci.org/spack/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. We currently perform 3 types of tests:
+against Python 2.6, 2.7, and 3.4-3.7 on both macOS and Linux. We currently
+perform 3 types of tests:
 
 ^^^^^^^^^^
 Unit Tests
@@ -80,6 +102,13 @@ tests, run:
 A more detailed list of available unit tests can be found by running
 ``spack test --long-list``.
 
+By default, ``pytest`` captures the output of all unit tests. If you add print
+statements to a unit test and want to see the output, simply run:
+
+.. code-block:: console
+
+   $ spack test -s -k architecture
+
 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
 adding new unit tests or strengthening existing tests.
@@ -87,7 +116,7 @@ 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 Coverage with the
+   runs the unit tests. Afterwards, it reports back to Codecov 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``.
@@ -154,20 +183,27 @@ 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 ``run-flake8-tests`` again
+will change if you add or delete lines, so simply run ``spack flake8`` again
 to update them.
 
 .. tip::
 
    Try fixing flake8 errors in reverse order. This eliminates the need for
-   multiple runs of ``flake8`` just to re-compute line numbers and makes it
-   much easier to fix errors directly off of the Travis output.
+   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.
 
 .. warning::
 
-   Flake8 requires setuptools in order to run. If you installed ``py-flake8``
-   with Spack, make sure to add ``py-setuptools`` to your ``PYTHONPATH``.
-   Otherwise, you will get an error message like:
+   Flake8 and ``pep8-naming`` require a number of dependencies in order
+   to run.  If you installed ``py-flake8`` and ``py-pep8-naming``, the
+   easiest way to ensure the right packages are on your ``PYTHONPATH`` is
+   to run::
+
+     spack activate py-flake8
+     spack activate pep8-naming
+
+   so that all of the dependencies are symlinked to a central
+   location. If you see an error message like:
 
    .. code-block:: console
 
@@ -176,6 +212,8 @@ 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
 ^^^^^^^^^^^^^^^^^^^
@@ -190,6 +228,7 @@ installed with Spack:
 
 * sphinx
 * sphinxcontrib-programoutput
+* sphinx-rtd-theme
 * graphviz
 * git
 * mercurial
@@ -199,18 +238,25 @@ installed with Spack:
 
    Sphinx has `several required dependencies <https://github.com/spack/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
-   ``spack activate py-sphinx`` so that all of the dependencies are symlinked
-   to a central location. If you see an error message like:
+   dependencies to your ``PYTHONPATH``. The easiest way to do this is to run:
 
    .. code-block:: console
 
-      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
+      $ spack activate py-sphinx
+      $ spack activate py-sphinx-rtd-theme
+      $ spack activate py-sphinxcontrib-programoutput
 
-   that means Sphinx couldn't find setuptools in your ``PYTHONPATH``.
+   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``.
 
 Once all of the dependencies are installed, you can try building the documentation:
 
@@ -225,11 +271,11 @@ your PR is accepted.
 
 .. note::
 
-   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 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 ``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
    at once.
 
 If you are editing the documentation, you should obviously be running the
@@ -277,6 +323,37 @@ 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

@@ -1,3 +1,8 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _developer_guide:
 
 ===============
@@ -119,7 +124,7 @@ etc.) but we wanted to make Spack *very* easy to use.  The simple layout
 spares users from the need to install Spack into a Python environment.
 Many users don't have write access to a Python installation, and installing
 an entire new instance of Python to bootstrap Spack would be very complicated.
-Users should not have to install install a big, complicated package to
+Users should not have to install a big, complicated package to
 use the thing that's supposed to spare them from the details of big,
 complicated packages.  The end result is that Spack works out of the
 box: clone it and add ``bin`` to your PATH and you're ready to go.
@@ -314,7 +319,7 @@ See the `Argparse documentation <https://docs.python.org/2.7/library/argparse.ht
 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
+``spack module lmod 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
@@ -483,7 +488,7 @@ supply ``--profile`` to Spack on the command line, before any subcommands.
 
 ``spack --profile`` output looks like this:
 
-.. command-output:: spack --profile graph dyninst
+.. command-output:: spack --profile graph hdf5
    :ellipsis: 25
 
 The bottom of the output shows the top most time consuming functions,

lib/spack/docs/docker_for_developers.rst

@@ -0,0 +1,41 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _docker_for_developers:
+
+=====================
+Docker for Developers
+=====================
+
+This guide is intended for people who want to use our prepared docker
+environments to work on developing Spack or working on spack packages. It is
+meant to serve as the companion documentation for the :ref:`packaging-guide`.
+
+--------
+Overview
+--------
+
+To get started, all you need is the latest version of ``docker``.
+
+.. code-block:: console
+
+    $ cd share/spack/docker
+    $ source config/ubuntu.bash
+    $ ./run-image.sh
+
+This command should drop you into an interactive shell where you can run spack
+within an isolated docker container running ubuntu.  The copy of spack being
+used should be tied to the working copy of your cloned git repo, so any changes
+you make should be immediately reflected in the running docker container.  Feel
+free to add or modify any packages or to hack on spack, itself.  Your contained
+copy of spack should immediately reflect all changes.
+
+To work within a container running a different linux distro, source one of the
+other environment files under ``config``.
+
+.. code-block:: console
+
+    $ source config/fedora.bash
+    $ ./run-image.sh

lib/spack/docs/environments.rst

@@ -0,0 +1,823 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _environments:
+
+============
+Environments
+============
+
+An environment is used to group together a set of specs for the
+purpose of building, rebuilding and deploying in a coherent fashion.
+Environments provide a number of advantages over the *à la carte*
+approach of building and loading individual Spack modules:
+
+#. Environments separate the steps of (a) choosing what to
+   install, (b) concretizing, and (c) installing.  This allows
+   Environments to remain stable and repeatable, even if Spack packages
+   are upgraded: specs are only re-concretized when the user
+   explicitly asks for it.  It is even possible to reliably
+   transport environments between different computers running
+   different versions of Spack!
+#. Environments allow several specs to be built at once; a more robust
+   solution than ad-hoc scripts making multiple calls to ``spack
+   install``.
+#. An Environment that is built as a whole can be loaded as a whole
+   into the user environment. An Environment can be built to maintain
+   a filesystem view of its packages, and the environment can load
+   that view into the user environment at activation time. Spack can
+   also generate a script to load all modules related to an
+   environment.
+
+Other packaging systems also provide environments that are similar in
+some ways to Spack environments; for example, `Conda environments
+<https://conda.io/docs/user-guide/tasks/manage-environments.html>`_ or
+`Python Virtual Environments
+<https://docs.python.org/3/tutorial/venv.html>`_.  Spack environments
+provide some distinctive features:
+
+#. A spec installed "in" an environment is no different from the same
+   spec installed anywhere else in Spack.  Environments are assembled
+   simply by collecting together a set of specs.
+#. Spack Environments may contain more than one spec of the same
+   package.
+
+Spack uses a "manifest and lock" model similar to `Bundler gemfiles
+<https://bundler.io/man/gemfile.5.html>`_ and other package
+managers. The user input file is named ``spack.yaml`` and the lock
+file is named ``spack.lock``
+
+------------------
+Using Environments
+------------------
+
+Here we follow a typical use case of creating, concretizing,
+installing and loading an environment.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Creating a named Environment
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+An environment is created by:
+
+.. code-block:: console
+
+   $ spack env create myenv
+
+Spack then creates the directory ``var/spack/environments/myenv``.
+
+.. note::
+
+   All named environments are stored in the ``var/spack/environments`` folder.
+
+In the ``var/spack/environments/myenv`` directory, Spack creates the
+file ``spack.yaml`` and the hidden directory ``.spack-env``.
+
+Spack stores metadata in the ``.spack-env`` directory. User
+interaction will occur through the ``spack.yaml`` file and the Spack
+commands that affect it. When the environment is concretized, Spack
+will create a file ``spack.lock`` with the concrete information for
+the environment.
+
+In addition to being the default location for the view associated with
+an Environment, the ``.spack-env`` directory also contains:
+
+  * ``repo/``: A repo consisting of the Spack packages used in this
+    environment.  This allows the environment to build the same, in
+    theory, even on different versions of Spack with different
+    packages!
+  * ``logs/``: A directory containing the build logs for the packages
+    in this Environment.
+
+Spack Environments can also be created from either a ``spack.yaml``
+manifest or a ``spack.lock`` lockfile. To create an Environment from a
+``spack.yaml`` manifest:
+
+.. code-block:: console
+
+   $ spack env create myenv spack.yaml
+
+To create an Environment from a ``spack.lock`` lockfile:
+
+.. code-block:: console
+
+   $ spack env create myenv spack.lock
+
+Either of these commands can also take a full path to the
+initialization file.
+
+A Spack Environment created from a ``spack.yaml`` manifest is
+guaranteed to have the same root specs as the original Environment,
+but may concretize differently. A Spack Environment created from a
+``spack.lock`` lockfile is guaranteed to have the same concrete specs
+as the original Environment. Either may obviously then differ as the
+user modifies it.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Activating an Environment
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To activate an environment, use the following command:
+
+.. code-block:: console
+
+   $ spack env activate myenv
+
+By default, the ``spack env activate`` will load the view associated
+with the Environment into the user environment. The ``-v,
+--with-view`` argument ensures this behavior, and the ``-V,
+--without-vew`` argument activates the environment without changing
+the user environment variables.
+
+The ``-p`` option to the ``spack env activate`` command modifies the
+user's prompt to begin with the environment name in brackets.
+
+.. code-block:: console
+
+   $ spack env activate -p myenv
+   [myenv] $ ...
+
+To deactivate an environment, use the command:
+
+.. code-block:: console
+
+   $ spack env deactivate
+
+or the shortcut alias
+
+.. code-block:: console
+
+   $ despacktivate
+
+If the environment was activated with its view, deactivating the
+environment will remove the view from the user environment.
+
+^^^^^^^^^^^^^^^^^^^^^^
+Anonymous Environments
+^^^^^^^^^^^^^^^^^^^^^^
+
+Any directory can be treated as an environment if it contains a file
+``spack.yaml``. To load an anonymous environment, use:
+
+.. code-block:: console
+
+   $ spack env activate -d /path/to/directory
+
+Spack commands that are environment sensitive will also act on the
+environment any time the current working directory contains a
+``spack.yaml`` file. Changing working directory to a directory
+containing a ``spack.yaml`` file is equivalent to the command:
+
+.. code-block:: console
+
+   $ spack env activate -d /path/to/dir --without-view
+
+Anonymous specs can be created in place using the command:
+
+.. code-block:: console
+
+   $ spack env create -d .
+
+In this case Spack simply creates a spack.yaml file in the requested
+directory.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Environment Sensitive Commands
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Spack commands are environment sensitive. For example, the ``find``
+command shows only the specs in the active Environment if an
+Environment has been activated. Similarly, the ``install`` and
+``uninstall`` commands act on the active environment.
+
+.. code-block:: console
+
+  $ spack find
+  ==> 0 installed packages
+
+  $ spack install zlib@1.2.11
+  ==> Installing zlib
+  ==> Searching for binary cache of zlib
+  ==> Warning: No Spack mirrors are currently configured
+  ==> No binary for zlib found: installing from source
+  ==> Fetching http://zlib.net/fossils/zlib-1.2.11.tar.gz
+  ######################################################################## 100.0%
+  ==> Staging archive: /spack/var/spack/stage/zlib-1.2.11-3r4cfkmx3wwfqeof4bc244yduu2mz4ur/zlib-1.2.11.tar.gz
+  ==> Created stage in /spack/var/spack/stage/zlib-1.2.11-3r4cfkmx3wwfqeof4bc244yduu2mz4ur
+  ==> No patches needed for zlib
+  ==> Building zlib [Package]
+  ==> Executing phase: 'install'
+  ==> Successfully installed zlib
+    Fetch: 0.36s.  Build: 11.58s.  Total: 11.93s.
+  [+] /spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/zlib-1.2.11-3r4cfkmx3wwfqeof4bc244yduu2mz4ur
+
+  $ spack env activate myenv
+
+  $ spack find
+  ==> In environment myenv
+  ==> No root specs
+
+  ==> 0 installed packages
+
+  $ spack install zlib@1.2.8
+  ==> Installing zlib
+  ==> Searching for binary cache of zlib
+  ==> Warning: No Spack mirrors are currently configured
+  ==> No binary for zlib found: installing from source
+  ==> Fetching http://zlib.net/fossils/zlib-1.2.8.tar.gz
+  ######################################################################## 100.0%
+  ==> Staging archive: /spack/var/spack/stage/zlib-1.2.8-y2t6kq3s23l52yzhcyhbpovswajzi7f7/zlib-1.2.8.tar.gz
+  ==> Created stage in /spack/var/spack/stage/zlib-1.2.8-y2t6kq3s23l52yzhcyhbpovswajzi7f7
+  ==> No patches needed for zlib
+  ==> Building zlib [Package]
+  ==> Executing phase: 'install'
+  ==> Successfully installed zlib
+    Fetch: 0.26s.  Build: 2.08s.  Total: 2.35s.
+  [+] /spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/zlib-1.2.8-y2t6kq3s23l52yzhcyhbpovswajzi7f7
+
+  $ spack find
+  ==> In environment myenv
+  ==> Root specs
+  zlib@1.2.8
+
+  ==> 1 installed package
+  -- linux-rhel7-x86_64 / gcc@4.9.3 -------------------------------
+  zlib@1.2.8
+
+  $ despacktivate
+  $ spack find
+  ==> 2 installed packages
+  -- linux-rhel7-x86_64 / gcc@4.9.3 -------------------------------
+  zlib@1.2.8  zlib@1.2.11
+
+Note that when we installed the abstract spec ``zlib@1.2.8``, it was
+presented as a root of the Environment. All explicitly installed
+packages will be listed as roots of the Environment.
+
+All of the Spack commands that act on the list of installed specs are
+Environment-sensitive in this way, including ``install``,
+``uninstall``, ``activate``, ``deactivate``, ``find``, ``extensions``,
+and more. In the :ref:`environment-configuration` section we will discuss
+Environment-sensitive commands further.
+
+^^^^^^^^^^^^^^^^^^^^^
+Adding Abstract Specs
+^^^^^^^^^^^^^^^^^^^^^
+
+An abstract spec is the user-specified spec before Spack has applied
+any defaults or dependency information.
+
+Users can add abstract specs to an Environment using the ``spack add``
+command. The most important component of an Environment is a list of
+abstract specs.
+
+Adding a spec adds to the manifest (the ``spack.yaml`` file) and to
+the roots of the Environment, but does not affect the concrete specs
+in the lockfile, nor does it install the spec.
+
+The ``spack add`` command is environment aware. It adds to the
+currently active environment. All environment aware commands can also
+be called using the ``spack -E`` flag to specify the environment.
+
+.. code-block:: console
+
+   $ spack activate myenv
+   $ spack add mpileaks
+
+or
+
+.. code-block:: console
+
+   $ spack -E myenv add python
+
+.. _environments_concretization:
+
+^^^^^^^^^^^^
+Concretizing
+^^^^^^^^^^^^
+
+Once some user specs have been added to an environment, they can be
+concretized. *By default specs are concretized separately*, one after
+the other. This mode of operation permits to deploy a full
+software stack where multiple configurations of the same package
+need to be installed alongside each other. Central installations done
+at HPC centers by system administrators or user support groups
+are a common case that fits in this behavior.
+Environments *can also be configured to concretize all
+the root specs in a self-consistent way* to ensure that
+each package in the environment comes with a single configuration. This
+mode of operation is usually what is required by software developers that
+want to deploy their development environment.
+
+Regardless of which mode of operation has been chosen, the following
+command will ensure all the root specs are concretized according to the
+constraints that are prescribed in the configuration:
+
+.. code-block:: console
+
+   [myenv]$ spack concretize
+
+In the case of specs that are not concretized together, the command
+above will concretize only the specs that were added and not yet
+concretized. Forcing a re-concretization of all the specs can be done
+instead with this command:
+
+.. code-block:: console
+
+   [myenv]$ spack concretize -f
+
+When the ``-f`` flag is not used to reconcretize all specs, Spack
+guarantees that already concretized specs are unchanged in the
+environment.
+
+The ``concretize`` command does not install any packages. For packages
+that have already been installed outside of the environment, the
+process of adding the spec and concretizing is identical to installing
+the spec assuming it concretizes to the exact spec that was installed
+outside of the environment.
+
+The ``spack find`` command can show concretized specs separately from
+installed specs using the ``-c`` (``--concretized``) flag.
+
+.. code-block:: console
+
+  [myenv]$ spack add zlib
+  [myenv]$ spack concretize
+  [myenv]$ spack find -c
+  ==> In environment myenv
+  ==> Root specs
+  zlib
+
+  ==> Concretized roots
+  -- linux-rhel7-x86_64 / gcc@4.9.3 -------------------------------
+  zlib@1.2.11
+
+  ==> 0 installed packages
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Installing an Environment
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In addition to installing individual specs into an Environment, one
+can install the entire Environment at once using the command
+
+.. code-block:: console
+
+   [myenv]$ spack install
+
+If the Environment has been concretized, Spack will install the
+concretized specs. Otherwise, ``spack install`` will first concretize
+the Environment and then install the concretized specs.
+
+As it installs, ``spack install`` creates symbolic links in the
+``logs/`` directory in the Environment, allowing for easy inspection
+of build logs related to that environment. The ``spack install``
+command also stores a Spack repo containing the ``package.py`` file
+used at install time for each package in the ``repos/`` directory in
+the Environment.
+
+^^^^^^^
+Loading
+^^^^^^^
+
+Once an environment has been installed, the following creates a load script for it:
+
+.. code-block:: console
+
+   $ spack env myenv loads -r
+
+This creates a file called ``loads`` in the environment directory.
+Sourcing that file in Bash will make the environment available to the
+user; and can be included in ``.bashrc`` files, etc.  The ``loads``
+file may also be copied out of the environment, renamed, etc.
+
+----------
+spack.yaml
+----------
+
+Spack environments can be customized at finer granularity by editing
+the ``spack.yaml`` manifest file directly.
+
+.. _environment-configuration:
+
+^^^^^^^^^^^^^^^^^^^^^^^^
+Configuring Environments
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+A variety of Spack behaviors are changed through Spack configuration
+files, covered in more detail in the :ref:`configuration`
+section.
+
+Spack Environments provide an additional level of configuration scope
+between the custom scope and the user scope discussed in the
+configuration documentation.
+
+There are two ways to include configuration information in a Spack Environment:
+
+#. Inline in the ``spack.yaml`` file
+
+#. Included in the ``spack.yaml`` file from another file.
+
+"""""""""""""""""""""
+Inline configurations
+"""""""""""""""""""""
+
+Inline Environment-scope configuration is done using the same yaml
+format as standard Spack configuration scopes, covered in the
+:ref:`configuration` section. Each section is contained under a
+top-level yaml object with it's name. For example, a ``spack.yaml``
+manifest file containing some package preference configuration (as in
+a ``packages.yaml`` file) could contain:
+
+.. code-block:: yaml
+
+   spack:
+     ...
+     packages:
+       all:
+         compiler: [intel]
+     ...
+
+This configuration sets the default compiler for all packages to
+``intel``.
+
+"""""""""""""""""""""""
+Included configurations
+"""""""""""""""""""""""
+
+Spack environments allow an ``include`` heading in their yaml
+schema. This heading pulls in external configuration files and applies
+them to the Environment.
+
+.. code-block:: yaml
+
+   spack:
+     include:
+     - relative/path/to/config.yaml
+     - /absolute/path/to/packages.yaml
+
+Environments can include files with either relative or absolute
+paths. Inline configurations take precedence over included
+configurations, so you don't have to change shared configuration files
+to make small changes to an individual Environment. Included configs
+listed later will have higher precedence, as the included configs are
+applied in order.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Manually Editing the Specs List
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The list of abstract/root specs in the Environment is maintained in
+the ``spack.yaml`` manifest under the heading ``specs``.
+
+.. code-block:: yaml
+
+   spack:
+       specs:
+         - ncview
+         - netcdf
+         - nco
+         - py-sphinx
+
+Appending to this list in the yaml is identical to using the ``spack
+add`` command from the command line. However, there is more power
+available from the yaml file.
+
+"""""""""""""""""""
+Spec concretization
+"""""""""""""""""""
+
+Specs can be concretized separately or together, as already
+explained in :ref:`environments_concretization`. The behavior active
+under any environment is determined by the ``concretization`` property:
+
+.. code-block:: yaml
+
+   spack:
+       specs:
+         - ncview
+         - netcdf
+         - nco
+         - py-sphinx
+       concretization: together
+
+which can currently take either one of the two allowed values ``together`` or ``separately``
+(the default).
+
+.. admonition:: Re-concretization of user specs
+
+   When concretizing specs together the entire set of specs will be
+   re-concretized after any addition of new user specs, to ensure that
+   the environment remains consistent. When instead the specs are concretized
+   separately only the new specs will be re-concretized after any addition.
+
+"""""""""""""
+Spec Matrices
+"""""""""""""
+
+Entries in the ``specs`` list can be individual abstract specs or a
+spec matrix.
+
+A spec matrix is a yaml object containing multiple lists of specs, and
+evaluates to the cross-product of those specs. Spec matrices also
+contain an ``excludes`` directive, which eliminates certain
+combinations from the evaluated result.
+
+The following two Environment manifests are identical:
+
+.. code-block:: yaml
+
+   spack:
+     specs:
+       - zlib %gcc@7.1.0
+       - zlib %gcc@4.9.3
+       - libelf %gcc@7.1.0
+       - libelf %gcc@4.9.3
+       - libdwarf %gcc@7.1.0
+       - cmake
+
+   spack:
+     specs:
+       - matrix:
+           - [zlib, libelf, libdwarf]
+           - ['%gcc@7.1.0', '%gcc@4.9.3']
+         exclude:
+           - libdwarf%gcc@4.9.3
+       - cmake
+
+Spec matrices can be used to install swaths of software across various
+toolchains.
+
+The concretization logic for spec matrices differs slightly from the
+rest of Spack. If a variant or dependency constraint from a matrix is
+invalid, Spack will reject the constraint and try again without
+it. For example, the following two Environment manifests will produce
+the same specs:
+
+.. code-block:: yaml
+
+   spack:
+     specs:
+       - matrix:
+           - [zlib, libelf, hdf5+mpi]
+           - [^mvapich2@2.2, ^openmpi@3.1.0]
+
+   spack:
+     specs:
+       - zlib
+       - libelf
+       - hdf5+mpi ^mvapich2@2.2
+       - hdf5+mpi ^openmpi@3.1.0
+
+This allows one to create toolchains out of combinations of
+constraints and apply them somewhat indiscriminately to packages,
+without regard for the applicability of the constraint.
+
+""""""""""""""""""""
+Spec List References
+""""""""""""""""""""
+
+The last type of possible entry in the specs list is a reference.
+
+The Spack Environment manifest yaml schema contains an additional
+heading ``definitions``. Under definitions is an array of yaml
+objects. Each object has one or two fields. The one required field is
+a name, and the optional field is a ``when`` clause.
+
+The named field is a spec list. The spec list uses the same syntax as
+the ``specs`` entry. Each entry in the spec list can be a spec, a spec
+matrix, or a reference to an earlier named list. References are
+specified using the ``$`` sigil, and are "splatted" into place
+(i.e. the elements of the referent are at the same level as the
+elements listed separately). As an example, the following two manifest
+files are identical.
+
+.. code-block:: yaml
+
+   spack:
+     definitions:
+       - first: [libelf, libdwarf]
+       - compilers: ['%gcc', '^intel']
+       - second:
+           - $first
+           - matrix:
+               - [zlib]
+               - [$compilers]
+     specs:
+       - $second
+       - cmake
+
+   spack:
+     specs:
+       - libelf
+       - libdwarf
+       - zlib%gcc
+       - zlib%intel
+       - cmake
+
+.. note::
+
+   Named spec lists in the definitions section may only refer
+   to a named list defined above itself. Order matters.
+
+In short files like the example, it may be easier to simply list the
+included specs. However for more complicated examples involving many
+packages across many toolchains, separately factored lists make
+Environments substantially more manageable.
+
+Additionally, the ``-l`` option to the ``spack add`` command allows
+one to add to named lists in the definitions section of the manifest
+file directly from the command line.
+
+The ``when`` directive can be used to conditionally add specs to a
+named list. The ``when`` directive takes a string of Python code
+referring to a restricted set of variables, and evaluates to a
+boolean. The specs listed are appended to the named list if the
+``when`` string evaluates to ``True``. In the following snippet, the
+named list ``compilers`` is ``['%gcc', '%clang', '%intel']`` on
+``x86_64`` systems and ``['%gcc', '%clang']`` on all other systems.
+
+.. code-block:: yaml
+
+   spack:
+     definitions:
+       - compilers: ['%gcc', '%clang']
+       - when: target == 'x86_64'
+         compilers: ['%intel']
+
+.. note::
+
+   Any definitions with the same named list with true ``when``
+   clauses (or absent ``when`` clauses) will be appended together
+
+The valid variables for a ``when`` clause are:
+
+#. ``platform``. The platform string of the default Spack
+   architecture on the system.
+
+#. ``os``. The os string of the default Spack architecture on
+   the system.
+
+#. ``target``. The target string of the default Spack
+   architecture on the system.
+
+#. ``architecture`` or ``arch``. The full string of the
+   default Spack architecture on the system.
+
+#. ``re``. The standard regex module in Python.
+
+#. ``env``. The user environment (usually ``os.environ`` in Python).
+
+#. ``hostname``. The hostname of the system (if ``hostname`` is an
+   executable in the user's PATH).
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Environment-managed Views
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Spack Environments can define filesystem views of their software,
+which are maintained as packages and can be installed and uninstalled from
+the Environment. Filesystem views provide an access point for packages
+from the filesystem for users who want to access those packages
+directly. For more information on filesystem views, see the section
+:ref:`filesystem-views`.
+
+Spack Environment managed views are updated every time the environment
+is written out to the lock file ``spack.lock``, so the concrete
+environment and the view are always compatible.
+
+"""""""""""""""""""""""""""""
+Configuring environment views
+"""""""""""""""""""""""""""""
+
+The Spack Environment manifest file has a top-level keyword
+``view``. Each entry under that heading is a view descriptor, headed
+by a name. The view descriptor contains the root of the view, and
+optionally the projections for the view, and ``select`` and
+``exclude`` lists for the view. For example, in the following manifest
+file snippet we define a view named ``mpis``, rooted at
+``/path/to/view`` in which all projections use the package name,
+version, and compiler name to determine the path for a given
+package. This view selects all packages that depend on MPI, and
+excludes those built with the PGI compiler at version 18.5.
+
+.. code-block:: yaml
+
+   spack:
+     ...
+     view:
+       mpis:
+         root: /path/to/view
+         select: [^mpi]
+         exclude: ['%pgi@18.5']
+         projections:
+           all: {name}/{version}-{compiler.name}
+
+For more information on using view projections, see the section on
+:ref:`adding_projections_to_views`. The default for the ``select`` and
+``exclude`` values is to select everything and exclude nothing. The
+default projection is the default view projection (``{}``).
+
+Any number of views may be defined under the ``view`` heading in a
+Spack Environment.
+
+There are two shorthands for environments with a single view. If the
+environment at ``/path/to/env`` has a single view, with a root at
+``/path/to/env/.spack-env/view``, with default selection and exclusion
+and the default projection, we can put ``view: True`` in the
+environment manifest. Similarly, if the environment has a view with a
+different root, but default selection, exclusion, and projections, the
+manifest can say ``view: /path/to/view``. These views are
+automatically named ``default``, so that
+
+.. code-block:: yaml
+
+   spack:
+     ...
+     view: True
+
+is equivalent to
+
+.. code-block:: yaml
+
+   spack:
+     ...
+     view:
+       default:
+         root: .spack-env/view
+
+and
+
+.. code-block:: yaml
+
+   spack:
+     ...
+     view: /path/to/view
+
+is equivalent to
+
+.. code-block:: yaml
+
+   spack:
+     ...
+     view:
+       default:
+         root: /path/to/view
+
+By default, Spack environments are configured with ``view: True`` in
+the manifest. Environments can be configured without views using
+``view: False``. For backwards compatibility reasons, environments
+with no ``view`` key are treated the same as ``view: True``.
+
+From the command line, the ``spack env create`` command takes an
+argument ``--with-view [PATH]`` that sets the path for a single, default
+view. If no path is specified, the default path is used (``view:
+True``). The argument ``--without-view`` can be used to create an
+environment without any view configured.
+
+The ``spack env view`` command can be used to change the manage views
+of an Environment. The subcommand ``spack env view enable`` will add a
+view named ``default`` to an environment. It takes an optional
+argument to specify the path for the new default view. The subcommand
+``spack env view disable`` will remove the view named ``default`` from
+an environment if one exists. The subcommand ``spack env view
+regenerate`` will regenerate the views for the environment. This will
+apply any updates in the environment configuration that have not yet
+been applied.
+
+""""""""""""""""""""""""""""
+Activating environment views
+""""""""""""""""""""""""""""
+
+The ``spack env activate`` command will put the default view for the
+environment into the user's path, in addition to activating the
+environment for Spack commands. The arguments ``-v,--with-view`` and
+``-V,--without-view`` can be used to tune this behavior. The default
+behavior is to activate with the environment view if there is one.
+
+The environment variables affected by the ``spack env activate``
+command and the paths that are used to update them are in the
+following table.
+
+=================== =========
+Variable            Paths
+=================== =========
+PATH                bin
+MANPATH             man, share/man
+ACLOCAL_PATH        share/aclocal
+LD_LIBRARY_PATH     lib, lib64
+LIBRARY_PATH        lib, lib64
+CPATH               include
+PKG_CONFIG_PATH     lib/pkgconfig, lib64/pkgconfig, share/pkgconfig
+CMAKE_PREFIX_PATH   .
+=================== =========
+
+Each of these paths are appended to the view root, and added to the
+relevant variable if the path exists. For this reason, it is not
+recommended to use non-default projections with the default view of an
+environment.
+
+The ``spack env deactivate`` command will remove the default view of
+the environment from the user's path.

lib/spack/docs/example_files/spack.yaml

@@ -0,0 +1,161 @@
+spack:
+  definitions:
+  - compiler-pkgs:
+    - 'llvm+clang@6.0.1 os=centos7'
+    - 'gcc@6.5.0 os=centos7'
+    - 'llvm+clang@6.0.1 os=ubuntu18.04'
+    - 'gcc@6.5.0 os=ubuntu18.04'
+  - pkgs:
+    - readline@7.0
+    # - xsdk@0.4.0
+  - compilers:
+    - '%gcc@5.5.0'
+    - '%gcc@6.5.0'
+    - '%gcc@7.3.0'
+    - '%clang@6.0.0'
+    - '%clang@6.0.1'
+  - oses:
+    - os=ubuntu18.04
+    - os=centos7
+
+  specs:
+  - matrix:
+    - [$pkgs]
+    - [$compilers]
+    - [$oses]
+    exclude:
+      - '%gcc@7.3.0 os=centos7'
+      - '%gcc@5.5.0 os=ubuntu18.04'
+
+  mirrors:
+    cloud_gitlab: https://mirror.spack.io
+
+  compilers:
+    # The .gitlab-ci.yml for this project picks a Docker container which does
+    # not have any compilers pre-built and ready to use, so we need to fake the
+    # existence of those here.
+    - compiler:
+        operating_system: centos7
+        modules: []
+        paths:
+          cc: /not/used
+          cxx: /not/used
+          f77: /not/used
+          fc: /not/used
+        spec: gcc@5.5.0
+        target: x86_64
+    - compiler:
+        operating_system: centos7
+        modules: []
+        paths:
+          cc: /not/used
+          cxx: /not/used
+          f77: /not/used
+          fc: /not/used
+        spec: gcc@6.5.0
+        target: x86_64
+    - compiler:
+        operating_system: centos7
+        modules: []
+        paths:
+          cc: /not/used
+          cxx: /not/used
+          f77: /not/used
+          fc: /not/used
+        spec: clang@6.0.0
+        target: x86_64
+    - compiler:
+        operating_system: centos7
+        modules: []
+        paths:
+          cc: /not/used
+          cxx: /not/used
+          f77: /not/used
+          fc: /not/used
+        spec: clang@6.0.1
+        target: x86_64
+
+    - compiler:
+        operating_system: ubuntu18.04
+        modules: []
+        paths:
+          cc: /not/used
+          cxx: /not/used
+          f77: /not/used
+          fc: /not/used
+        spec: clang@6.0.0
+        target: x86_64
+    - compiler:
+        operating_system: ubuntu18.04
+        modules: []
+        paths:
+          cc: /not/used
+          cxx: /not/used
+          f77: /not/used
+          fc: /not/used
+        spec: clang@6.0.1
+        target: x86_64
+    - compiler:
+        operating_system: ubuntu18.04
+        modules: []
+        paths:
+          cc: /not/used
+          cxx: /not/used
+          f77: /not/used
+          fc: /not/used
+        spec: gcc@6.5.0
+        target: x86_64
+    - compiler:
+        operating_system: ubuntu18.04
+        modules: []
+        paths:
+          cc: /not/used
+          cxx: /not/used
+          f77: /not/used
+          fc: /not/used
+        spec: gcc@7.3.0
+        target: x86_64
+
+  gitlab-ci:
+    bootstrap:
+      - name: compiler-pkgs
+        compiler-agnostic: true
+    mappings:
+      - # spack-cloud-ubuntu
+        match:
+          # these are specs, if *any* match the spec under consideration, this
+          # 'mapping' will be used to generate the CI job
+          - os=ubuntu18.04
+        runner-attributes:
+          # 'tags' and 'image' go directly onto the job, 'variables' will
+          # be added to what we already necessarily create for the job as
+          # a part of the CI workflow
+          tags:
+            - spack-k8s
+          image:
+            name: scottwittenburg/spack_builder_ubuntu_18.04
+            entrypoint: [""]
+      - # spack-cloud-centos
+        match:
+          # these are specs, if *any* match the spec under consideration, this
+          # 'mapping' will be used to generate the CI job
+          - 'os=centos7'
+        runner-attributes:
+          tags:
+            - spack-k8s
+          image:
+            name: scottwittenburg/spack_builder_centos_7
+            entrypoint: [""]
+
+  cdash:
+    build-group: Release Testing
+    url: http://cdash
+    project: Spack Testing
+    site: Spack Docker-Compose Workflow
+
+  repos: []
+  upstreams: {}
+  modules:
+    enable: []
+  packages: {}
+  config: {}

lib/spack/docs/extensions.rst

@@ -0,0 +1,128 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. extensions:
+
+=================
+Custom Extensions
+=================
+
+.. warning::
+
+   The support for extending Spack with custom commands is still experimental.
+   Users should expect APIs or prescribed directory structures to
+   change at any time.
+
+*Spack extensions* permit you to extend Spack capabilities by deploying your
+own custom commands or logic in an arbitrary location on your filesystem.
+This might be extremely useful e.g. to develop and maintain a command whose purpose is
+too specific to be considered for reintegration into the mainline or to
+evolve a command through its early stages before starting a discussion to merge
+it upstream.
+From Spack's point of view an extension is any path in your filesystem which
+respects a prescribed naming and layout for files:
+
+.. code-block:: console
+
+  spack-scripting/ # The top level directory must match the format 'spack-{extension_name}'
+  ├── pytest.ini # Optional file if the extension ships its own tests
+  ├── scripting # Folder that may contain modules that are needed for the extension commands
+  │   └── cmd # Folder containing extension commands
+  │       └── filter.py # A new command that will be available
+  ├── tests # Tests for this extension
+  │   ├── conftest.py
+  │   └── test_filter.py
+  └── templates # Templates that may be needed by the extension
+
+In the example above the extension named *scripting* adds an additional command (``filter``)
+and unit tests to verify its behavior. The code for this example can be
+obtained by cloning the corresponding git repository:
+
+.. TODO: write an ad-hoc "hello world" extension and make it part of the spack organization
+
+.. code-block:: console
+
+   $ pwd
+   /home/user
+   $ mkdir tmp && cd tmp
+   $ git clone https://github.com/alalazo/spack-scripting.git
+   Cloning into 'spack-scripting'...
+   remote: Counting objects: 11, done.
+   remote: Compressing objects: 100% (7/7), done.
+   remote: Total 11 (delta 0), reused 11 (delta 0), pack-reused 0
+   Receiving objects: 100% (11/11), done.
+
+As you can see by inspecting the sources, Python modules that are part of the extension
+can import any core Spack module.
+
+---------------------------------
+Configure Spack to Use Extensions
+---------------------------------
+
+To make your current Spack instance aware of extensions you should add their root
+paths to ``config.yaml``. In the case of our example this means ensuring that:
+
+.. code-block:: yaml
+
+   config:
+     extensions:
+     - /home/user/tmp/spack-scripting
+
+is part of your configuration file. Once this is setup any command that the extension provides
+will be available from the command line:
+
+.. code-block:: console
+
+   $ spack filter --help
+   usage: spack filter [-h] [--installed | --not-installed]
+                       [--explicit | --implicit] [--output OUTPUT]
+                       ...
+
+   filter specs based on their properties
+
+   positional arguments:
+     specs            specs to be filtered
+
+   optional arguments:
+     -h, --help       show this help message and exit
+     --installed      select installed specs
+     --not-installed  select specs that are not yet installed
+     --explicit       select specs that were installed explicitly
+     --implicit       select specs that are not installed or were installed implicitly
+     --output OUTPUT  where to dump the result
+
+The corresponding unit tests can be run giving the appropriate options to ``spack test``:
+
+.. code-block:: console
+
+   $ spack test --extension=scripting
+
+   ============================================================== test session starts ===============================================================
+   platform linux2 -- Python 2.7.15rc1, pytest-3.2.5, py-1.4.34, pluggy-0.4.0
+   rootdir: /home/mculpo/tmp/spack-scripting, inifile: pytest.ini
+   collected 5 items
+
+   tests/test_filter.py ...XX
+   ============================================================ short test summary info =============================================================
+   XPASS tests/test_filter.py::test_filtering_specs[flags3-specs3-expected3]
+   XPASS tests/test_filter.py::test_filtering_specs[flags4-specs4-expected4]
+
+   =========================================================== slowest 20 test durations ============================================================
+   3.74s setup    tests/test_filter.py::test_filtering_specs[flags0-specs0-expected0]
+   0.17s call     tests/test_filter.py::test_filtering_specs[flags3-specs3-expected3]
+   0.16s call     tests/test_filter.py::test_filtering_specs[flags2-specs2-expected2]
+   0.15s call     tests/test_filter.py::test_filtering_specs[flags1-specs1-expected1]
+   0.13s call     tests/test_filter.py::test_filtering_specs[flags4-specs4-expected4]
+   0.08s call     tests/test_filter.py::test_filtering_specs[flags0-specs0-expected0]
+   0.04s teardown tests/test_filter.py::test_filtering_specs[flags4-specs4-expected4]
+   0.00s setup    tests/test_filter.py::test_filtering_specs[flags4-specs4-expected4]
+   0.00s setup    tests/test_filter.py::test_filtering_specs[flags3-specs3-expected3]
+   0.00s setup    tests/test_filter.py::test_filtering_specs[flags1-specs1-expected1]
+   0.00s setup    tests/test_filter.py::test_filtering_specs[flags2-specs2-expected2]
+   0.00s teardown tests/test_filter.py::test_filtering_specs[flags2-specs2-expected2]
+   0.00s teardown tests/test_filter.py::test_filtering_specs[flags1-specs1-expected1]
+   0.00s teardown tests/test_filter.py::test_filtering_specs[flags0-specs0-expected0]
+   0.00s teardown tests/test_filter.py::test_filtering_specs[flags3-specs3-expected3]
+   ====================================================== 3 passed, 2 xpassed in 4.51 seconds =======================================================

lib/spack/docs/features.rst

@@ -1,3 +1,8 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 ================
 Feature Overview
 ================
@@ -55,14 +60,14 @@ Customize dependencies
 ----------------------
 
 Spack allows *dependencies* of a particular installation to be
-customized extensively.  Suppose that ``mpileaks`` depends indirectly
-on ``libelf`` and ``libdwarf``.  Using ``^``, users can add custom
+customized extensively.  Suppose that ``hdf5`` depends
+on ``openmpi`` and indirectly on ``hwloc``.  Using ``^``, users can add custom
 configurations for the dependencies:
 
 .. code-block:: console
 
-   # Install mpileaks and link it with specific versions of libelf and libdwarf
-   $ spack install mpileaks@1.1.2 %gcc@4.7.3 +debug ^libelf@0.8.12 ^libdwarf@20130729+debug
+   # Install hdf5 and link it with specific versions of openmpi and hwloc
+   $ spack install hdf5@1.10.1 %gcc@4.7.3 +debug ^openmpi+cuda fabrics=auto ^hwloc+gl
 
 ------------------------
 Non-destructive installs
@@ -125,8 +130,8 @@ creates a simple python file:
 It doesn't take much python coding to get from there to a working
 package:
 
-.. literalinclude:: ../../../var/spack/repos/builtin/packages/libelf/package.py
-   :lines: 25-
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/libelf/package.py
+   :lines: 6-
 
 Spack also provides wrapper functions around common commands like
 ``configure``, ``make``, and ``cmake`` to make writing packages

lib/spack/docs/getting_started.rst

@@ -1,3 +1,8 @@
+.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _getting_started:
 
 ===============
@@ -11,10 +16,11 @@ 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)
-2. A C/C++ compiler
-3. The ``git`` and ``curl`` commands.
-4. If using the ``gpg`` subcommand, ``gnupg2`` is required.
+#. Python 2 (2.6 or 2.7) or 3 (3.5 - 3.8) to run Spack
+#. A C/C++ compiler for building
+#. The ``make`` executable for building
+#. The ``git`` and ``curl`` commands for fetching
+#. 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
@@ -65,7 +71,7 @@ This automatically adds Spack to your ``PATH`` and allows the ``spack``
 command to be used to execute spack :ref:`commands <shell-support>` and
 :ref:`useful packaging commands <packaging-shell-support>`.
 
-If :ref:`environment-modules or dotkit <InstallEnvironmentModules>` is
+If :ref:`environment-modules <InstallEnvironmentModules>` is
 installed and available, the ``spack`` command can also load and unload
 :ref:`modules <modules>`.
 
@@ -163,7 +169,7 @@ compilers`` or ``spack compiler list``:
 Any of these compilers can be used to build Spack packages.  More on
 how this is done is in :ref:`sec-specs`.
 
-.. _spack-compiler-add:
+.. _cmd-spack-compiler-add:
 
 ^^^^^^^^^^^^^^^^^^^^^^
 ``spack compiler add``
@@ -171,7 +177,7 @@ how this is done is in :ref:`sec-specs`.
 
 An alias for ``spack compiler find``.
 
-.. _spack-compiler-find:
+.. _cmd-spack-compiler-find:
 
 ^^^^^^^^^^^^^^^^^^^^^^^
 ``spack compiler find``
@@ -184,7 +190,7 @@ where the compiler is installed.  For example:
 .. code-block:: console
 
    $ spack compiler find /usr/local/tools/ic-13.0.079
-   ==> Added 1 new compiler to ~/.spack/compilers.yaml
+   ==> Added 1 new compiler to ~/.spack/linux/compilers.yaml
        intel@13.0.079
 
 Or you can run ``spack compiler find`` with no arguments to force
@@ -196,13 +202,20 @@ installed, but you know that new compilers have been added to your
 
    $ module load gcc-4.9.0
    $ spack compiler find
-   ==> Added 1 new compiler to ~/.spack/compilers.yaml
+   ==> Added 1 new compiler to ~/.spack/linux/compilers.yaml
        gcc@4.9.0
 
 This loads the environment module for gcc-4.9.0 to add it to
 ``PATH``, and then it adds the compiler to Spack.
 
-.. _spack-compiler-info:
+.. note::
+
+   By default, spack does not fill in the ``modules:`` field in the
+   ``compilers.yaml`` file.  If you are using a compiler from a
+   module, then you should add this field manually.
+   See the section on :ref:`compilers-requiring-modules`.
+
+.. _cmd-spack-compiler-info:
 
 ^^^^^^^^^^^^^^^^^^^^^^^
 ``spack compiler info``
@@ -234,7 +247,7 @@ Manual compiler configuration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 If auto-detection fails, you can manually configure a compiler by
-editing your ``~/.spack/compilers.yaml`` file.  You can do this by running
+editing your ``~/.spack/<platform>/compilers.yaml`` file.  You can do this by running
 ``spack config edit compilers``, which will open the file in your ``$EDITOR``.
 
 Each compiler configuration in the file looks like this:
@@ -250,7 +263,7 @@ Each compiler configuration in the file looks like this:
          cxx: /usr/local/bin/icpc-15.0.024-beta
          f77: /usr/local/bin/ifort-15.0.024-beta
          fc: /usr/local/bin/ifort-15.0.024-beta
-       spec: intel@15.0.0:
+       spec: intel@15.0.0
 
 For compilers that do not support Fortran (like ``clang``), put
 ``None`` for ``f77`` and ``fc``:
@@ -320,6 +333,7 @@ by adding the following to your ``packages.yaml`` file:
      all:
        compiler: [gcc@4.9.3]
 
+.. _compilers-requiring-modules:
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Compilers Requiring Modules
@@ -455,18 +469,21 @@ Fortran.
    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 only thing left to do is to edit ``~/.spack/darwin/compilers.yaml`` to provide
    the path to ``gfortran``:
 
    .. code-block:: yaml
 
       compilers:
-        darwin-x86_64:
-          clang@7.3.0-apple:
-            cc: /usr/bin/clang
-            cxx: /usr/bin/clang++
-            f77: /path/to/bin/gfortran
-            fc: /path/to/bin/gfortran
+      - compiler:
+        ...
+        paths:
+          cc: /usr/bin/clang
+          cxx: /usr/bin/clang++
+          f77: /path/to/bin/gfortran
+          fc: /path/to/bin/gfortran
+        spec: clang@11.0.0-apple
+
 
    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
@@ -484,6 +501,9 @@ simple package.  For example:
 
    $ spack install zlib%gcc@5.3.0
 
+
+.. _vendor-specific-compiler-configuration:
+
 --------------------------------------
 Vendor-Specific Compiler Configuration
 --------------------------------------
@@ -574,11 +594,12 @@ flags to the ``icc`` command:
            operating_system: centos7
            paths:
              cc: /opt/intel-15.0.24/bin/icc-15.0.24-beta
-             cflags: -gcc-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/gcc
              cxx: /opt/intel-15.0.24/bin/icpc-15.0.24-beta
-             cxxflags: -gxx-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/g++
              f77: /opt/intel-15.0.24/bin/ifort-15.0.24-beta
              fc: /opt/intel-15.0.24/bin/ifort-15.0.24-beta
+           flags:
+             cflags: -gcc-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/gcc
+             cxxflags: -gxx-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/g++
              fflags: -gcc-name ~/spack/opt/spack/linux-centos7-x86_64/gcc-4.9.3-iy4rw.../bin/gcc
            spec: intel@15.0.24.4.9.3
 
@@ -805,7 +826,7 @@ encountered on a Macintosh during ``spack install julia-master``:
 
 .. code-block:: console
 
-   ==> Trying to clone git repository:
+   ==> Cloning git repository:
      https://github.com/JuliaLang/julia.git
      on branch master
    Cloning into 'julia'...
@@ -816,7 +837,7 @@ 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 tcl loads git`` to your ``.bashrc``.
 
 If this doesn't work, it is also possible to disable checking of SSL
 certificates by using:
@@ -861,7 +882,7 @@ or alternately:
 
 .. code-block:: console
 
-    $ spack module loads curl >>~/.bashrc
+    $ spack module tcl loads curl >>~/.bashrc
 
 or if environment modules don't work:
 
@@ -926,75 +947,38 @@ Once ``curl`` has been installed, you can similarly install the others.
 Environment Modules
 """""""""""""""""""
 
-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, Spack can
-build it for you!
+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:
 
-What follows are three steps describing how to install and use environment-modules with spack.
+.. code-block:: console
 
-#. Install ``environment-modules``.
+   $ spack bootstrap
 
-   * ``spack bootstrap`` will build ``environment-modules`` for you (and may build
-     other packages that are useful to the operation of Spack)
+.. 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.
 
-   * Install ``environment-modules`` using ``spack install`` with
-     ``spack install environment-modules~X`` (The ``~X`` variant builds without Xorg
-     dependencies, but ``environment-modules`` works fine too.)
+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:
 
-#. Add ``modulecmd`` to ``PATH`` and create a ``module`` command. 
+.. code-block:: console
 
-   * If you are using ``bash`` or ``ksh``, Spack can currently do this for you as well.
-     After installing ``environment-modules`` following the step
-     above, source Spack's shell integration script. This will automatically
-     detect the lack of ``modulecmd`` and ``module``, and use the installed
-     ``environment-modules`` from ``spack bootstrap`` or ``spack install``.
-     
-     .. code-block:: console
+   $ yum install environment-modules
 
-        # For bash/zsh users
-        $ export SPACK_ROOT=/path/to/spack
-        $ . $SPACK_ROOT/share/spack/setup-env.sh
+Once you have the tool installed and available in your path, you can source
+Spack's setup file:
 
+.. code-block:: console
 
-   * If you prefer to do it manually,  you can activate with the following 
-     script (or apply the updates to your ``.bashrc`` file manually):
+   $ source share/spack/setup-env.sh
 
-         .. code-block:: sh
+This activates :ref:`shell support <shell-support>` and makes commands like
+``spack load`` available for use.
 
-            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 is added to your ``.bashrc`` (or similar) files, enabling Environment
-      Modules when you log in.
-        
-#. Test that the ``module`` command is found with:
-
-   .. code-block:: console
-
-      $ module avail
-
-
-If ``tcl`` 8.0 or later is installed on  your system, you can prevent
-spack from rebuilding ``tcl`` as part of the ``environment-modules`` dependency
-stack by adding the following to your ``~/.spack/packages.yaml`` replacing
-version 8.5 with whatever version is installed on your system:
-
-   .. code-block:: yaml
-
-      packages:
-          tcl:
-              paths:
-                  tcl@8.5: /usr
-              buildable: False
 
 ^^^^^^^^^^^^^^^^^
 Package Utilities
@@ -1096,6 +1080,37 @@ 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 appearing to hang*). Virtual machines and cloud
+      instances are particularly likely to display this behavior.
+
+      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.
+
+      Another alternative is ``haveged``, which can be installed on
+      RHEL/CentOS machines as follows:
+
+      .. code-block:: console
+
+         $ sudo yum install haveged
+         $ sudo chkconfig haveged on
+
+      `This Digital Ocean tutorial
+      <https://www.digitalocean.com/community/tutorials/how-to-setup-additional-entropy-for-cloud-servers-using-haveged>`_
+      provides a good overview of sources of randomness.
+
 ^^^^^^^^^^^^
 Listing keys
 ^^^^^^^^^^^^
@@ -1226,6 +1241,13 @@ cray-mpich module into the environment. You can then be able to use whatever
 environment variables, libraries, etc, that are brought into the environment
 via module load.
 
+.. note::
+
+    For Cray-provided packages, it is best to use ``modules:`` instead of ``paths:``
+    in ``packages.yaml``, because the Cray Programming Environment heavily relies on
+    modules (e.g., loading the ``cray-mpich`` module adds MPI libraries to the
+    compiler wrapper link line).
+
 You can set the default compiler that Spack can use for each compiler type.
 If you want to use the Cray defaults, then set them under ``all:`` in packages.yaml.
 In the compiler field, set the compiler specs in your order of preference.
@@ -1262,3 +1284,17 @@ for each compiler type for each cray modules. This ensures that for each
 compiler on our system we can use that external module.
 
 For more on external packages check out the section :ref:`sec-external-packages`.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Using Linux containers on Cray machines
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Spack uses environment variables particular to the Cray programming
+environment to determine which systems are Cray platforms. These
+environment variables may be propagated into containers that are not
+using the Cray programming environment.
+
+To ensure that Spack does not autodetect the Cray programming
+environment, unset the environment variable ``CRAYPE_VERSION``. This
+will cause Spack to treat a linux container on a Cray system as a base
+linux distro.