Update commands auto completion

`spack test` has a spurious '[+] ' in the output:

```
lib/spack/spack/test/install.py .........[+] ......
```

Output is properly suppressed:

```
lib/spack/spack/test/install.py ...............
```

.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:
+        threshold: 0.3%
 
 ignore:
   - lib/spack/spack/test/.*
-  - lib/spack/env/.*
   - lib/spack/docs/.*
   - lib/spack/external/.*
+  - share/spack/qa/.*
 
 comment: off

.coveragerc

@@ -7,9 +7,9 @@ branch = True
 source = lib
 omit =
      lib/spack/spack/test/*
-     lib/spack/env/*
      lib/spack/docs/*
      lib/spack/external/*
+     share/spack/qa/*
 
 [report]
 # Regexes for lines to exclude from consideration

.dockerignore

@@ -1,6 +1,11 @@
-.git
-opt/spack
-share/spack/docker/Dockerfile
-share/spack/docker/build-image.sh
-share/spack/docker/run-image.sh
-share/spack/docker/push-image.sh
+.git/*
+opt/spack/*
+
+/etc/spack/*
+!/etc/spack/defaults
+
+share/spack/dotkit/*
+share/spack/lmod/*
+share/spack/modules/*
+lib/spack/spack/test/*
+

.flake8

@@ -1,24 +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
 #
-# Exempt to allow decorator classes to be lowercase, but follow otherwise:
-# - N801: CapWords for class names.
+# 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,N801,W503,W504
+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,W503,W504
+ignore = E129,E221,E241,E272,E731,W503,W504,F405,F821,F999,N801,N813,N814
 max-line-length = 79

.gitattributes

@@ -0,0 +1 @@
+*.py diff=python

.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/ISSUE_TEMPLATE/bug_report.md

@@ -1,7 +1,7 @@
 ---
 name: Bug report 
 about: Report a bug in the core of Spack (command not working as expected, etc.) 
-
+labels: bug
 ---
 
 
@@ -24,10 +24,10 @@ If Spack reported an error, provide the error message. If it did not report an e
 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 -sd flags:
+the additional -d/--stacktrace flags:
 ```console
-$ spack -sd <command1> <spec>
-$ spack -sd <command2> <spec>
+$ spack -d --stacktrace <command1> <spec>
+$ spack -d --stacktrace <command2> <spec>
 ...
 ```
 that activate the full debug output. 
@@ -46,4 +46,4 @@ We encourage you to try, as much as possible, to reduce your problem to the mini
 
 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!
+Other than that, thanks for taking the time to contribute to Spack!

.github/ISSUE_TEMPLATE/build_error.md

@@ -1,7 +1,7 @@
 ---
 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

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,6 +1,7 @@
 ---
 name: Feature request 
 about: Suggest adding a feature that is not yet in Spack  
+labels: feature
 
 ---
 

.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 2013-2020 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()

.github/workflows/linux_build_tests.yaml

@@ -0,0 +1,57 @@
+name: linux builds
+
+on:
+  push:
+    branches:
+    - master
+    - develop
+  pull_request:
+    branches:
+    - master
+    - develop
+    paths-ignore:
+      # Don't run if we only modified packages in the built-in repository
+      - 'var/spack/repos/builtin/**'
+      - '!var/spack/repos/builtin/packages/lz4/**'
+      - '!var/spack/repos/builtin/packages/mpich/**'
+      - '!var/spack/repos/builtin/packages/tut/**'
+      - '!var/spack/repos/builtin/packages/py-setuptools/**'
+      - '!var/spack/repos/builtin/packages/openjpeg/**'
+      - '!var/spack/repos/builtin/packages/r-rcpp/**'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        package: [lz4, mpich, tut, py-setuptools, openjpeg, r-rcpp]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Cache ccache's store
+      uses: actions/cache@v1
+      with:
+        path: ~/.ccache
+        key: ccache-build-${{ matrix.package }}
+        restore-keys: |
+          ccache-build-${{ matrix.package }}
+    - name: Setup Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+    - name: Install System Packages
+      run: |
+        sudo apt-get -yqq install ccache gfortran perl perl-base r-base r-base-core r-base-dev findutils openssl libssl-dev libpciaccess-dev
+        R --version
+        perl --version
+    - name: Copy Configuration
+      run: |
+        ccache -M 300M && ccache -z
+        # Set up external deps for build tests, b/c they take too long to compile
+        cp share/spack/qa/configuration/*.yaml etc/spack/
+    - name: Run the build test
+      run: |
+        . share/spack/setup-env.sh
+        SPEC=${{ matrix.package }} share/spack/qa/run-build-tests
+        ccache -s

.github/workflows/minimum_python_versions.yaml

@@ -0,0 +1,30 @@
+name: python version check
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+      - develop
+jobs:
+  validate:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Setup Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install Python Packages
+      run: |
+        pip install --upgrade pip
+        pip install --upgrade vermin
+    - name: Minimum Version (Spack's Core)
+      run: vermin --backport argparse -t=2.6- -t=3.5- -v lib/spack/spack/ lib/spack/llnl/ bin/
+    - name: Minimum Version (Repositories)
+      run: vermin --backport argparse -t=2.6- -t=3.5- -v var/spack/repos

.gitignore

@@ -20,9 +20,10 @@
 *.swp
 /htmlcov
 .coverage
-#*
+\#*
 .#*
 lib/spack/spack/test/.cache
 /bin/spackc
 *.in.log
 *.out.log
+*.orig

.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

@@ -12,182 +12,120 @@ branches:
 # Build matrix
 #=============================================================================
 
-# Adding the keyword dist to permit an `allow_failures` section
-# under `matrix.include`. More information here:
-#
-# https://docs.travis-ci.com/user/customizing-the-build/#Rows-that-are-Allowed-to-Fail
-dist: trusty
+dist: xenial
 
 jobs:
   fast_finish: true
   include:
     - stage: 'style checks'
-      python: '2.7'
-      sudo: required
+      python: '3.8'
       os: linux
       language: python
       env: TEST_SUITE=flake8
-    - stage: 'flake8 + documentation'
-      python: '2.7'
+# Shell integration with module files
+    - python: '3.8'
       os: linux
       language: python
-      env: TEST_SUITE=doc
-    - stage: 'unit tests'
+      env: [ TEST_SUITE=bootstrap ]
+    - stage: 'unit tests + documentation'
       python: '2.6'
-      sudo: required
+      dist: trusty
       os: linux
       language: python
-      env: TEST_SUITE=unit
+      env: [ TEST_SUITE=unit, COVERAGE=true ]
     - python: '2.7'
-      sudo: required
       os: linux
       language: python
-      env: TEST_SUITE=unit
-    - python: '3.4'
-      sudo: required
-      os: linux
-      language: python
-      env: TEST_SUITE=unit
+      env: [ TEST_SUITE=unit, COVERAGE=true ]
     - python: '3.5'
-      sudo: required
       os: linux
       language: python
       env: TEST_SUITE=unit
     - python: '3.6'
-      sudo: required
       os: linux
       language: python
       env: TEST_SUITE=unit
     - python: '3.7'
-      sudo: required
       os: linux
-      dist: xenial
       language: python
       env: TEST_SUITE=unit
-    - python: '3.6'
-      sudo: required
+    - python: '3.8'
+      os: linux
+      language: python
+      env: [ TEST_SUITE=unit, COVERAGE=true ]
+    - python: '3.8'
       os: linux
       language: python
       env: TEST_SUITE=doc
     - os: osx
       language: generic
-      env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7 ]
-# mpich (AutotoolsPackage)
-    - stage: 'build tests'
-      python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, 'SPEC=mpich' ]
-# astyle (MakefilePackage)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, 'SPEC=astyle' ]
-# tut (WafPackage)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, 'SPEC=tut' ]
-# py-setuptools (PythonPackage)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, 'SPEC=py-setuptools' ]
-# perl-dbi (PerlPackage)
-#    - python: '2.7'
-#      os: linux
-#      language: python
-#      env: [ TEST_SUITE=build, 'SPEC=perl-dbi' ]
-# openjpeg (CMakePackage + external cmake)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, 'SPEC=openjpeg' ]
-# r-rcpp (RPackage + external R)
-    - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, 'SPEC=r-rcpp' ]
-# mpich (AutotoolsPackage)
-    - python: '3.6'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=build, 'SPEC=mpich' ]
-    - stage: 'docker build'
-      sudo: required
-      os: linux
-      language: generic
-      env: TEST_SUITE=docker
-  allow_failures:
-    - dist: xenial
-    - env: TEST_SUITE=docker
-    # temporary Python 2.6 exception while we figure out why Travis is hanging
-    - python: '2.6'
+      env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7, COVERAGE=true ]
+      if: type != pull_request
 
 stages:
   - 'style checks'
   - 'unit tests + documentation'
-  - 'build tests'
-  - name: 'docker build'
-    if: type = push AND branch IN (develop, master)
-
-
-stages:
-  - 'flake8 + documentation'
-  - 'unit tests'
-  - 'build tests'
-  - name: 'unit tests - osx'
-    if: type IN (cron)
 
 
 #=============================================================================
 # 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
 
+# ~/.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;
-        export HOMEBREW_NO_AUTO_UPDATE=1;
-        rm /usr/local/include/c++ ;
-        brew ls --versions python@2 > /dev/null || brew install python@2;
-        brew ls --versions gcc      > /dev/null || brew install gcc;
-        brew ls --versions gnupg2   > /dev/null || brew install gnupg2;
         pip2 install --upgrade pip;
         pip2 install virtualenv;
         virtualenv venv;
         source venv/bin/activate;
     fi
+  - ccache -M 2G && ccache -z
 
 # Install various dependencies
 install:
   - pip install --upgrade pip
   - pip install --upgrade six
   - pip install --upgrade setuptools
-  - pip install --upgrade codecov
+  - pip install --upgrade codecov coverage==4.5.4
   - pip install --upgrade flake8
   - pip install --upgrade pep8-naming
   - if [[ "$TEST_SUITE" == "doc" ]]; then
@@ -200,43 +138,25 @@ 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
-
-  # 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/packages.yaml etc/spack/packages.yaml;
-    fi
+  - git fetch origin ${TRAVIS_BRANCH}:${TRAVIS_BRANCH}
 
 #=============================================================================
 # Building
 #=============================================================================
-services:
-  - docker
-
 script:
   - share/spack/qa/run-$TEST_SUITE-tests
-  - if [[ "$TEST_SUITE" == "docker build" ]]; then
-        login_attempted=0; login_success=0;
-        for config in share/spack/docker/config/* ; do
-            source "$config" ;
-            ./share/spack/docker/build-image.sh;
-            if [ "$TRAVIS_EVENT_TYPE" != "pull_request" ]; then
-                if [ "$login_attempted" '=' '0' ]; then
-                    if echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin; then
-                        login_success=1;
-                    fi;
-                    login_attempted=1;
-                fi;
-                if [ "$login_success" '=' '1' ]; then
-                    ./share/spack/docker/push-image.sh;
-                fi
+
+after_success:
+  - ccache -s
+  - case "$TEST_SUITE" in
+        unit)
+            if [[ "$COVERAGE" == "true" ]]; then
+                codecov --env PYTHON_VERSION
+                        --required
+                        --flags "${TEST_SUITE}${TRAVIS_OS_NAME}";
             fi
-        done;
-    fi
-  - if [[ "$TEST_SUITE" == "unit" || "$TEST_SUITE" == "build" ]]; then
-        codecov --env PYTHON_VERSION
-                --required --flags "${TEST_SUITE}${TRAVIS_OS_NAME}";
-    fi
+            ;;
+    esac
 
 #=============================================================================
 # Notifications

CHANGELOG.md

@@ -0,0 +1,451 @@
+# v0.14.2 (2019-04-15)
+
+This is a minor release on the `0.14` series. It includes performance
+improvements and bug fixes:
+
+* Improvements to how `spack install` handles foreground/background (#15723)
+* Major performance improvements for reading the package DB (#14693, #15777)
+* No longer check for the old `index.yaml` database file (#15298)
+* Properly activate environments with '-h' in the name (#15429)
+* External packages have correct `.prefix` in environments/views (#15475)
+* Improvements to computing env modifications from sourcing files (#15791)
+* Bugfix on Cray machines when getting `TERM` env variable (#15630)
+* Avoid adding spurious `LMOD` env vars to Intel modules (#15778)
+* Don't output [+] for mock installs run during tests (#15609)
+
+# v0.14.1 (2019-03-20)
+
+This is a bugfix release on top of `v0.14.0`.  Specific fixes include:
+
+* several bugfixes for parallel installation (#15339, #15341, #15220, #15197)
+* `spack load` now works with packages that have been renamed (#14348)
+* bugfix for `suite-sparse` installation (#15326)
+* deduplicate identical suffixes added to module names (#14920)
+* fix issues with `configure_args` during module refresh (#11084)
+* increased test coverage and test fixes (#15237, #15354, #15346)
+* remove some unused code (#15431)
+
+# v0.14.0 (2020-02-23)
+
+`v0.14.0` is a major feature release, with 3 highlighted features:
+
+1. **Distributed builds.** Multiple Spack instances will now coordinate
+   properly with each other through locks. This works on a single node
+   (where you've called `spack` several times) or across multiple nodes
+   with a shared filesystem. For example, with SLURM, you could build
+   `trilinos` and its dependencies on 2 24-core nodes, with 3 Spack
+   instances per node and 8 build jobs per instance, with `srun -N 2 -n 6
+   spack install -j 8 trilinos`. This requires a filesystem with locking
+   enabled, but not MPI or any other library for parallelism.
+
+2.  **Build pipelines.** You can also build in parallel through Gitlab
+   CI. Simply create a Spack environment and push it to Gitlab to build
+   on Gitlab runners. Pipeline support is now integreated into a single
+   `spack ci` command, so setting it up is easier than ever.  See the
+   [Pipelines section](https://spack.readthedocs.io/en/v0.14.0/pipelines.html)
+   in the docs.
+
+3. **Container builds.** The new `spack containerize` command allows you
+   to create a Docker or Singularity recipe from any Spack environment.
+   There are options to customize the build if you need them. See the
+   [Container Images section](https://spack.readthedocs.io/en/latest/containers.html)
+   in the docs.
+
+In addition, there are several other new commands, many bugfixes and
+improvements, and `spack load` no longer requires modules, so you can use
+it the same way on your laptop or on your supercomputer.
+
+Spack grew by over 300 packages since our last release in November 2019,
+and the project grew to over 500 contributors.  Thanks to all of you for
+making yet another great release possible. Detailed notes below.
+
+## Major new core features
+* Distributed builds: spack instances coordinate and build in parallel (#13100)
+* New `spack ci` command to manage CI pipelines (#12854)
+* Generate container recipes from environments: `spack containerize` (#14202)
+* `spack load` now works without using modules (#14062, #14628)
+* Garbage collect old/unused installations with `spack gc` (#13534)
+* Configuration files all set environment modifications the same way (#14372,
+  [docs](https://spack.readthedocs.io/en/v0.14.0/configuration.html#environment-modifications))
+* `spack commands --format=bash` auto-generates completion (#14393, #14607)
+* Packages can specify alternate fetch URLs in case one fails (#13881)
+
+## Improvements
+* Improved locking for concurrency with environments (#14676, #14621, #14692)
+* `spack test` sends args to `pytest`, supports better listing (#14319)
+* Better support for aarch64 and cascadelake microarch (#13825, #13780, #13820)
+* Archspec is now a separate library (see https://github.com/archspec/archspec)
+* Many improvements to the `spack buildcache` command (#14237, #14346,
+  #14466, #14467, #14639, #14642, #14659, #14696, #14698, #14714, #14732,
+  #14929, #15003, #15086, #15134)
+
+## Selected Bugfixes
+* Compilers now require an exact match on version (#8735, #14730, #14752)
+* Bugfix for patches that specified specific versions (#13989)
+* `spack find -p` now works in environments (#10019, #13972)
+* Dependency queries work correctly in `spack find` (#14757)
+* Bugfixes for locking upstream Spack instances chains (#13364)
+* Fixes for PowerPC clang optimization flags (#14196)
+* Fix for issue with compilers and specific microarchitectures (#13733, #14798)
+
+## New commands and options
+* `spack ci` (#12854)
+* `spack containerize` (#14202)
+* `spack gc` (#13534)
+* `spack load` accepts `--only package`, `--only dependencies` (#14062, #14628)
+* `spack commands --format=bash` (#14393)
+* `spack commands --update-completion` (#14607)
+* `spack install --with-cache` has new option: `--no-check-signature` (#11107)
+* `spack test` now has `--list`, `--list-long`, and `--list-names` (#14319)
+* `spack install --help-cdash` moves CDash help out of the main help (#13704)
+
+## Deprecations
+* `spack release-jobs` has been rolled into `spack ci`
+* `spack bootstrap` will be removed in a future version, as it is no longer
+  needed to set up modules (see `spack load` improvements above)
+
+## Documentation
+* New section on building container images with Spack (see
+  [docs](https://spack.readthedocs.io/en/latest/containers.html))
+* New section on using `spack ci` command to build pipelines (see
+  [docs](https://spack.readthedocs.io/en/latest/pipelines.html))
+* Document how to add conditional dependencies (#14694)
+* Document how to use Spack to replace Homebrew/Conda (#13083, see
+  [docs](https://spack.readthedocs.io/en/latest/workflows.html#using-spack-to-replace-homebrew-conda))
+
+## Important package changes
+* 3,908 total packages (345 added since 0.13.0)
+* Added first cut at a TensorFlow package (#13112)
+* We now build R without "recommended" packages, manage them w/Spack (#12015)
+* Elpa and OpenBLAS now leverage microarchitecture support (#13655, #14380)
+* Fix `octave` compiler wrapper usage (#14726)
+* Enforce that packages in `builtin` aren't missing dependencies (#13949)
+
+
+# v0.13.4 (2020-02-07)
+
+This release contains several bugfixes:
+
+* bugfixes for invoking python in various environments (#14349, #14496, #14569)
+* brought tab completion up to date (#14392)
+* bugfix for removing extensions from views in order (#12961)
+* bugfix for nondeterministic hashing for specs with externals (#14390)
+
+# v0.13.3 (2019-12-23)
+
+This release contains more major performance improvements for Spack
+environments, as well as bugfixes for mirrors and a `python` issue with
+RHEL8.
+
+* mirror bugfixes: symlinks, duplicate patches, and exception handling (#13789)
+* don't try to fetch `BundlePackages` (#13908)
+* avoid re-fetching patches already added to a mirror (#13908)
+* avoid re-fetching alread added patches (#13908)
+* avoid re-fetching alread added patches (#13908)
+* allow repeated invocations of `spack mirror create` on the same dir (#13908)
+* bugfix for RHEL8 when `python` is unavailable (#14252)
+* improve concretization performance in environments (#14190)
+* improve installation performance in environments (#14263)
+
+# 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)

COPYRIGHT

@@ -68,10 +68,6 @@ 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
@@ -83,3 +79,11 @@ 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-MIT

@@ -1,4 +1,4 @@
-Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
 Spack Project Developers. See the top-level COPYRIGHT file for details.
 
 Permission is hereby granted, free of charge, to any person obtaining a

README.md

@@ -1,6 +1,7 @@
 # <img src="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo.svg" width="64" valign="middle" alt="Spack"/> Spack
 
 [![Build Status](https://travis-ci.org/spack/spack.svg?branch=develop)](https://travis-ci.org/spack/spack)
+[![Linux Builds](https://github.com/spack/spack/workflows/linux%20builds/badge.svg)](https://github.com/spack/spack/actions)
 [![codecov](https://codecov.io/gh/spack/spack/branch/develop/graph/badge.svg)](https://codecov.io/gh/spack/spack)
 [![Read the Docs](https://readthedocs.org/projects/spack/badge/?version=latest)](https://spack.readthedocs.io)
 [![Slack](https://spackpm.herokuapp.com/badge.svg)](https://spackpm.herokuapp.com)
@@ -26,55 +27,43 @@ 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.
-
-### Twitter
-
-You can follow [@spackpm](https://twitter.com/spackpm) on Twitter for
-updates. Also, feel free to `@mention` us in in questions or comments
-about your own experience with Spack.
-
-### 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
@@ -92,6 +81,13 @@ 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).
@@ -122,6 +118,6 @@ See [LICENSE-MIT](https://github.com/spack/spack/blob/develop/LICENSE-MIT),
 [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)`
+SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-``LLNL-CODE-647188``
+LLNL-CODE-647188

bin/sbang

@@ -1,6 +1,6 @@
 #!/bin/bash
 #
-# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2020 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)
@@ -103,10 +103,10 @@ interpreter_f="${interpreter_v[0]}"
 
 # Invoke any interpreter found, or raise an error if none was found.
 if [[ -n "$interpreter_f" ]]; then
-    if [[ "${interpreter_f##*/}" = "perl" ]]; then
-        exec $interpreter_v -x "$@"
+    if [[ "${interpreter_f##*/}" = "perl"* ]]; then
+        exec $interpreter -x "$@"
     else
-        exec $interpreter_v "$@"
+        exec $interpreter "$@"
     fi
 else
     echo "error: sbang found no interpreter in $script"

bin/spack

@@ -1,10 +1,26 @@
-#!/usr/bin/env python
+#!/bin/sh
+# -*- python -*-
 #
-# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2020 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 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
@@ -35,7 +51,7 @@ sys.path.insert(0, spack_external_libs)
 # (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 tough sys.path
+# 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']

bin/spack-python

@@ -1,6 +1,6 @@
 #!/bin/sh
 #
-# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2020 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)

etc/spack/defaults/config.yaml

@@ -16,7 +16,7 @@
 config:
   # This is the path to the root of the Spack install tree.
   # You can use $spack here to refer to the root of the spack instance.
-  install_tree: $spack/opt/spack
+  install_tree: ~/.spack/opt/spack
 
 
   # Locations where templates should be found
@@ -30,31 +30,44 @@ config:
 
   # 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
+    tcl:    ~/.spack/share/spack/modules
+    lmod:   ~/.spack/share/spack/lmod
 
 
   # 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 clean --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 for already downloaded source tarballs and archived
   # repositories. This can be purged with `spack clean --downloads`.
-  source_cache: $spack/var/spack/cache
+  source_cache: ~/.spack/var/spack/cache
 
 
   # Cache directory for miscellaneous files, like the package index.
@@ -67,6 +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
@@ -94,10 +121,12 @@ config:
   locks: true
 
 
-  # 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 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.
@@ -108,7 +137,7 @@ config:
   # 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
+  db_lock_timeout: 3
 
 
   # How long to wait when attempting to modify a package (e.g. to install it).
@@ -117,3 +146,8 @@ config:
   # 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/modules.yaml

@@ -16,7 +16,6 @@
 modules:
   enable:
     - tcl
-    - dotkit
   prefix_inspections:
     bin:
       - PATH
@@ -36,6 +35,8 @@ modules:
       - PKG_CONFIG_PATH
     lib64/pkgconfig:
       - PKG_CONFIG_PATH
+    share/pkgconfig:
+      - PKG_CONFIG_PATH
     '':
       - CMAKE_PREFIX_PATH
 

etc/spack/defaults/packages.yaml

@@ -15,7 +15,7 @@
 # -------------------------------------------------------------------------
 packages:
   all:
-    compiler: [gcc, intel, pgi, clang, xl, nag]
+    compiler: [gcc, intel, pgi, clang, xl, nag, fj]
     providers:
       D: [ldc]
       awk: [gawk]
@@ -23,24 +23,28 @@ packages:
       daal: [intel-daal]
       elf: [elfutils]
       fftw-api: [fftw]
-      gl: [mesa, opengl]
+      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]
+      sycl: [hipsycl]
       szip: [libszip, libaec]
       tbb: [intel-tbb]
       unwind: [libunwind]
+      sycl: [hipsycl]
     permissions:
       read: world
       write: user

etc/spack/defaults/upstreams.yaml

@@ -0,0 +1,7 @@
+upstreams:
+   global:
+     install_tree: $spack/opt/spack
+     modules:
+       tcl:    $spack/share/spack/modules
+       lmod:   $spack/share/spack/lmod
+       dotkit: $spack/share/spack/dotkit

lib/spack/docs/.gitignore

@@ -3,3 +3,5 @@ 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

lib/spack/docs/_spack_root

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

lib/spack/docs/basic_usage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -39,12 +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
@@ -229,6 +232,50 @@ remove dependent packages *before* removing their dependencies or use the
 
 .. _nondownloadable:
 
+^^^^^^^^^^^^^^^^^^
+Garbage collection
+^^^^^^^^^^^^^^^^^^
+
+When Spack builds software from sources, if often installs tools that are needed
+just to build or test other software. These are not necessary at runtime.
+To support cases where removing these tools can be a benefit Spack provides
+the ``spack gc`` ("garbage collector") command, which will uninstall all unneeded packages:
+
+.. code-block:: console
+
+   $ spack find
+   ==> 24 installed packages
+   -- linux-ubuntu18.04-broadwell / gcc@9.0.1 ----------------------
+   autoconf@2.69    findutils@4.6.0  libiconv@1.16        libszip@2.1.1  m4@1.4.18    openjpeg@2.3.1  pkgconf@1.6.3  util-macros@1.19.1
+   automake@1.16.1  gdbm@1.18.1      libpciaccess@0.13.5  libtool@2.4.6  mpich@3.3.2  openssl@1.1.1d  readline@8.0   xz@5.2.4
+   cmake@3.16.1     hdf5@1.10.5      libsigsegv@2.12      libxml2@2.9.9  ncurses@6.1  perl@5.30.0     texinfo@6.5    zlib@1.2.11
+
+   $ spack gc
+   ==> The following packages will be uninstalled:
+
+       -- linux-ubuntu18.04-broadwell / gcc@9.0.1 ----------------------
+       vn47edz autoconf@2.69    6m3f2qn findutils@4.6.0  ubl6bgk libtool@2.4.6  pksawhz openssl@1.1.1d  urdw22a readline@8.0
+       ki6nfw5 automake@1.16.1  fklde6b gdbm@1.18.1      b6pswuo m4@1.4.18      k3s2csy perl@5.30.0     lp5ya3t texinfo@6.5
+       ylvgsov cmake@3.16.1     5omotir libsigsegv@2.12  leuzbbh ncurses@6.1    5vmfbrq pkgconf@1.6.3   5bmv4tg util-macros@1.19.1
+
+   ==> Do you want to proceed? [y/N] y
+
+   [ ... ]
+
+   $ spack find
+   ==> 9 installed packages
+   -- linux-ubuntu18.04-broadwell / gcc@9.0.1 ----------------------
+   hdf5@1.10.5  libiconv@1.16  libpciaccess@0.13.5  libszip@2.1.1  libxml2@2.9.9  mpich@3.3.2  openjpeg@2.3.1  xz@5.2.4  zlib@1.2.11
+
+In the example above Spack went through all the packages in the DB
+and removed everything that is not either:
+
+1. A package installed upon explicit request of the user
+2. A ``link`` or ``run`` dependency, even transitive, of one of the packages at point 1.
+
+You can check :ref:`cmd-spack-find-metadata` to see how to query for explicitly installed packages
+or :ref:`dependency-types` for a more thorough treatment of dependency types.
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 Non-Downloadable Tarballs
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -274,6 +321,86 @@ 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
 -------------------------
@@ -331,11 +458,19 @@ 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
+.. _cmd-spack-find-metadata:
+
+""""""""""""""""""""""""""""""""
+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*
@@ -388,8 +523,8 @@ 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
 
@@ -399,6 +534,10 @@ 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
@@ -426,6 +565,109 @@ 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:
 
 --------------------
@@ -673,10 +915,10 @@ 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
@@ -687,11 +929,13 @@ in GNU Autotools. If all flags are set, the order is
 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 supported environment
-modification commands are: ``set``, ``unset``, ``append-path``, and
-``prepend-path``). The user can also specify additional ``RPATHs`` that the
+Sometimes compilers require setting special environment variables to
+operate correctly. Spack handles these cases by allowing custom environment
+modifications in the ``environment`` attribute of the compiler configuration
+section. See also the :ref:`configuration_environment_variables` section
+of the configuration files docs for more information.
+
+It is also possible to 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``.
@@ -708,44 +952,130 @@ that executables will run without the need to set ``LD_LIBRARY_PATH``.
           fc: /opt/gcc/bin/gfortran
         environment:
           unset:
-            BAD_VARIABLE: # The colon is required but the value must be empty
+            - BAD_VARIABLE
           set:
             GOOD_VARIABLE_NUM: 1
             GOOD_VARIABLE_STR: good
-          prepend-path:
+          prepend_path:
             PATH: /path/to/binutils
-          append-path:
+          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:
 
@@ -980,33 +1310,41 @@ directly when you run ``python``:
 Using Extensions
 ^^^^^^^^^^^^^^^^
 
-There are three ways to get ``numpy`` working in Python.  The first is
-to use :ref:`shell-support`.  You can simply ``use`` or ``load`` the
-module for the extension, and it will be added to the ``PYTHONPATH``
-in your current shell.
-
-For tcl modules:
+There are four ways to get ``numpy`` working in Python.  The first is
+to use :ref:`shell-support`.  You can simply ``load`` the extension,
+and it will be added to the ``PYTHONPATH`` in your current shell:
 
 .. code-block:: console
 
    $ spack load python
    $ spack load py-numpy
 
-or, for dotkit:
+Now ``import numpy`` will succeed for as long as you keep your current
+session open.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Loading Extensions via Modules
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Instead of using Spack's environment modification capabilities through
+the ``spack load`` command, you can load numpy through your
+environment modules (using ``environment-modules`` or ``lmod``). This
+will also add the extension to the ``PYTHONPATH`` in your current
+shell.
 
 .. code-block:: console
 
-   $ spack use python
-   $ spack use py-numpy
+   $ module load <name of numpy module>
 
-Now ``import numpy`` will succeed for as long as you keep your current
-session open.
+If you do not know the name of the specific numpy module you wish to
+load, you can use the ``spack module tcl|lmod loads`` command to get
+the name of the module from the Spack spec.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Activating Extensions in a View
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The second way to use extensions is to create a view, which merges the
+Another 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.

lib/spack/docs/binary_caches.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_settings.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -58,16 +58,26 @@ directory. Here's an example of an external configuration:
    packages:
      openmpi:
        paths:
-         openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3
-         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
+         openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64: /opt/openmpi-1.4.3
+         openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64+debug: /opt/openmpi-1.4.3-debug
+         openmpi@1.6.5%intel@10.1 arch=linux-debian7-x86_64: /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.
 If Spack is asked to build a package that uses one of these MPIs as a
 dependency, it will use the pre-installed OpenMPI in
-the given directory. ``packages.yaml`` can also be used to specify modules
-to load instead of the installation prefixes.
+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``
@@ -97,9 +107,9 @@ be:
    packages:
      openmpi:
        paths:
-         openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7: /opt/openmpi-1.4.3
-         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
+         openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64: /opt/openmpi-1.4.3
+         openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64+debug: /opt/openmpi-1.4.3-debug
+         openmpi@1.6.5%intel@10.1 arch=linux-debian7-x86_64: /opt/openmpi-1.6.5-intel
        buildable: False
 
 The addition of the ``buildable`` flag tells Spack that it should never build
@@ -138,7 +148,8 @@ 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: [mvapich2, mpich, openmpi]
 
@@ -152,11 +163,11 @@ on the command line if explicitly requested.
 
 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

lib/spack/docs/build_systems.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -40,6 +40,7 @@ on these ideas for each distinct build system that Spack supports:
    build_systems/cmakepackage
    build_systems/mesonpackage
    build_systems/qmakepackage
+   build_systems/sippackage
 
 .. toctree::
    :maxdepth: 1
@@ -55,6 +56,7 @@ on these ideas for each distinct build system that Spack supports:
    :maxdepth: 1
    :caption: Other
 
+   build_systems/bundlepackage
    build_systems/cudapackage
    build_systems/intelpackage
    build_systems/custompackage

lib/spack/docs/build_systems/autotoolspackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/bundlepackage.rst

@@ -0,0 +1,52 @@
+.. Copyright 2013-2020 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)
+
+.. _bundlepackage:
+
+-------------
+BundlePackage
+-------------
+
+``BundlePackage`` represents a set of packages that are expected to work well
+together, such as a collection of commonly used software libraries.  The
+associated software is specified as bundle dependencies.
+
+
+^^^^^^^^
+Creation
+^^^^^^^^
+
+Be sure to specify the ``bundle`` template if you are using ``spack create``
+to generate a package from the template.  For example, use the following
+command to create a bundle package whose class name will be ``Mybundle``:
+
+.. code-block:: console
+
+    $ spack create --template bundle --name mybundle
+
+
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``BundlePackage`` base class does not provide any phases by default
+since the bundle does not represent a build system.
+
+
+^^^
+URL
+^^^
+
+The ``url`` property does not have meaning since there is no package-specific
+code to fetch.
+
+
+^^^^^^^
+Version
+^^^^^^^
+
+At least one ``version`` must be specified in order for the package to
+build.

lib/spack/docs/build_systems/cmakepackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/cudapackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/custompackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/intelpackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -120,7 +120,7 @@ version numbers seen with most other Spack packages. For example, we have:
    ...
    Preferred version:
        professional.2018.3    http:...
-  
+
    Safe versions:
        professional.2018.3    http:...
        ...
@@ -728,7 +728,7 @@ For packages that contain a compiler, follow `the previous section
 
    .. code-block:: console
 
-      $ spack install intel-mpi@2018.3.199 
+      $ spack install intel-mpi@2018.3.199
       $ spack install intel-mpi@2018.3.199  %intel@18
 
 4. To prepare the new packages for use with client packages,
@@ -802,7 +802,7 @@ by one of the following means:
   Configure the order of compilers in the appropriate ``packages.yaml`` file,
   under either an ``all:`` or client-package-specific entry, in a
   ``compiler:`` list. Consult the Spack documentation for
-  :ref:`Configuring Package Preferences <configs-tutorial-package-prefs>`
+  `Configuring Package Preferences <https://spack-tutorial.readthedocs.io/en/latest/tutorial_configuration.html#configuring-package-preferences>`_
   and
   :ref:`Concretization Preferences <concretization-preferences>`.
 
@@ -851,7 +851,7 @@ client packages, edit the ``packages.yaml`` file.  Customize, either in the
 the virtual packages and whose values are the Spack specs that satisfy the
 virtual package, in order of decreasing preference.  To learn more about the
 ``providers:`` settings, see the Spack tutorial for
-:ref:`Configuring Package Preferences <configs-tutorial-package-prefs>`
+`Configuring Package Preferences <https://spack-tutorial.readthedocs.io/en/latest/tutorial_configuration.html#configuring-package-preferences>`_
 and the section
 :ref:`Concretization Preferences <concretization-preferences>`.
 
@@ -972,7 +972,7 @@ a *virtual* ``mkl`` package is declared in Spack.
   .. code-block:: python
 
     self.spec['blas'].headers.include_flags
-    
+
   and to generate linker options (``-L<dir> -llibname ...``), use the same as above,
 
   .. code-block:: python

lib/spack/docs/build_systems/makefilepackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/mesonpackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -54,6 +54,28 @@ 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
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -67,6 +89,28 @@ the ``MesonPackage`` base class already contains:
    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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^

lib/spack/docs/build_systems/octavepackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/perlpackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/pythonpackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/qmakepackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/rpackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -42,7 +42,11 @@ 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/web/packages/caret/index.html.
+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.
@@ -93,8 +97,8 @@ If you look at the bottom of the page, you'll see:
    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://CRAN.R-project.org/package=caret as the homepage instead of
-https://cran.r-project.org/web/packages/caret/index.html. The latter may
+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.
 
 ^^^
@@ -109,12 +113,12 @@ List URL
 ^^^^^^^^
 
 CRAN maintains a single webpage containing the latest release of every
-single package: https://cran.r-project.org/src/contrib/
+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://cran.r-project.org/src/contrib/Archive/caret
+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
@@ -138,12 +142,12 @@ every R package needs this, the ``RPackage`` base class contains:
 
 
 Take a close look at the homepage for ``caret``. If you look at the
-"Depends" section, you'll notice that ``caret`` depends on "R (≥ 2.10)".
+"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@2.10:', type=('build', 'run'))
+   depends_on('r@3.2.0:', type=('build', 'run'))
 
 
 ^^^^^^^^^^^^^^
@@ -162,7 +166,7 @@ and list all of their dependencies in the following sections:
 
 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 them. If you are curious what they mean,
+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*,
@@ -193,6 +197,14 @@ 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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -208,8 +220,8 @@ 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 so it would not make sense that
-they could be updated via CRAN. If so, you would basically get a different
+"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:
@@ -265,7 +277,7 @@ 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://CRAN.R-project.org/package=stringi.
+package for an example: https://cloud.r-project.org/package=stringi.
 If you search for the text "SystemRequirements", you will see:
 
    ICU4C (>= 52, optional)
@@ -344,3 +356,11 @@ 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

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/sconspackage.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/build_systems/sippackage.rst

@@ -0,0 +1,141 @@
+.. Copyright 2013-2020 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

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/chain.rst

@@ -0,0 +1,96 @@
+.. Copyright 2013-2020 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/conf.py

@@ -1,4 +1,4 @@
-# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2020 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)
@@ -20,67 +20,45 @@
 import sys
 import os
 import re
-import shutil
 import subprocess
 from glob import glob
 
-# Since Sphinx 1.7, sphinx.apidoc has been moved to sphinx.ext.apidoc
-# sphinx.apidoc is deprecated and will be removed in Sphinx 2.0
-try:
-    from sphinx.ext.apidoc import main as sphinx_apidoc
-except ImportError:
-    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'
-
-#
-# Generate package list using spack command
-#
-with open('package_list.html', 'w') as plist_file:
-    subprocess.Popen(
-        [spack_root + '/bin/spack', 'list', '--format=html'],
-        stdout=plist_file)
-
-#
-# Find all the `cmd-spack-*` references and add them to a command index
-#
-import spack
-import spack.cmd
-command_names = spack.cmd.all_commands()
-documented_commands = set()
-for filename in glob('*rst'):
-    with open(filename) as f:
-        for line in f:
-            match = re.match('.. _cmd-(spack-.*):', line)
-            if match:
-                documented_commands.add(match.group(1).strip())
-
 os.environ['COLUMNS'] = '120'
-shutil.copy('command_index.in', 'command_index.rst')
-with open('command_index.rst', 'a') as index:
-    subprocess.Popen(
-        [spack_root + '/bin/spack', 'commands', '--format=rst'] + list(
-            documented_commands),
-        stdout=index)
+
+# Generate full package list if needed
+subprocess.call([
+    'spack', 'list', '--format=html', '--update=package_list.html'])
+
+# 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
@@ -90,13 +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'])
+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
@@ -113,12 +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.
@@ -151,13 +128,14 @@ def setup(sphinx):
 
 # General information about the project.
 project = u'Spack'
-copyright = u'2013-2018, 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.
+import spack
 version = '.'.join(str(s) for s in spack.spack_version_info[:2])
 # The full version, including alpha/beta/rc tags.
 release = spack.spack_version
@@ -166,6 +144,13 @@ def setup(sphinx):
 # 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 = ''
@@ -174,7 +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
@@ -191,7 +176,25 @@ def setup(sphinx):
 #show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+# We use our own extension of the default style with a few modifications
+from pygments.style import Style
+from pygments.styles.default import DefaultStyle
+from pygments.token import Generic, Comment, Text
+
+class SpackStyle(DefaultStyle):
+    styles = DefaultStyle.styles.copy()
+    background_color       = "#f4f4f8"
+    styles[Generic.Output] = "#355"
+    styles[Generic.Prompt] = "bold #346ec9"
+
+import pkg_resources
+dist = pkg_resources.Distribution(__file__)
+sys.path.append('.')  # make 'conf' module findable
+ep = pkg_resources.EntryPoint.parse('spack = conf:SpackStyle', dist=dist)
+dist._ep_map = {'pygments.styles': {'plugin1': ep}}
+pkg_resources.working_set.add(dist)
+
+pygments_style = 'spack'
 
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
@@ -220,12 +223,12 @@ 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

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -13,7 +13,7 @@ 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
@@ -30,25 +30,34 @@ Default is ``$spack/opt/spack``.
 ``install_hash_length`` and ``install_path_scheme``
 ---------------------------------------------------
 
-The default Spack installation path can be very long and can create
-problems for scripts with hardcoded shebangs. There are two parameters
-to help with that. Firstly, the ``install_hash_length`` parameter can
-set the length of the hash in the installation path from 1 to 32. The
-default path uses the full 32 characters.
+The default Spack installation path can be very long and can create problems
+for scripts with hardcoded shebangs. Additionally, when using the Intel
+compiler, and if there is also a long list of dependencies, the compiler may
+segfault. If you see the following:
 
-Secondly, it is
-also possible to modify the entire installation scheme. By default
-Spack uses
-``${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}``
+     .. code-block:: console
+
+       : internal error: ** The compiler has encountered an unexpected problem.
+       ** Segmentation violation signal raised. **
+       Access violation or stack overflow. Please contact Intel Support for assistance.
+
+it may be because variables containing dependency specs may be too long. There
+are two parameters to help with long path names. 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}/{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.
@@ -75,7 +84,6 @@ 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.
 
@@ -85,40 +93,46 @@ 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 file system.  On most systems,
-building in a temporary file system 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.
+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``
@@ -180,16 +194,23 @@ 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``
@@ -215,3 +236,24 @@ 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

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -36,8 +36,8 @@ Here is an example ``config.yaml`` file:
      module_roots:
        lmod: $spack/share/spack/lmod
      build_stage:
-       - $tempdir
-       - /nfs/tmp2/$user
+       - $tempdir/$user/spack-stage
+       - ~/.spack/stage
 
 Each Spack configuration file is nested under a top-level section
 corresponding to its name. So, ``config.yaml`` starts with ``config:``,
@@ -244,8 +244,8 @@ your configurations look like this:
      module_roots:
        lmod: $spack/share/spack/lmod
      build_stage:
-       - $tempdir
-       - /nfs/tmp2/$user
+       - $tempdir/$user/spack-stage
+       - ~/.spack/stage
 
 
 .. code-block:: yaml
@@ -269,8 +269,8 @@ command:
      module_roots:
        lmod: $spack/share/spack/lmod
      build_stage:
-       - $tempdir
-       - /nfs/tmp2/$user
+       - $tempdir/$user/spack-stage
+       - ~/.spack/stage
 
 
 .. _config-overrides:
@@ -312,8 +312,8 @@ Let's revisit the ``config.yaml`` example one more time. The
    :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``
@@ -323,7 +323,7 @@ paths:
    :caption: ~/.spack/config.yaml
 
    build_stage:
-     - /lustre-scratch/$user
+     - /lustre-scratch/$user/spack
      - ~/mystage
 
 
@@ -341,10 +341,10 @@ get config`` shows the result:
      module_roots:
        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
@@ -356,7 +356,7 @@ user config looked like this:
    :caption: ~/.spack/config.yaml
 
    build_stage::
-     - /lustre-scratch/$user
+     - /lustre-scratch/$user/spack
      - ~/mystage
 
 
@@ -371,7 +371,7 @@ The merged configuration would look like this:
      module_roots:
        lmod: $spack/share/spack/lmod
      build_stage:
-       - /lustre-scratch/$user
+       - /lustre-scratch/$user/spack
        - ~/mystage
 
 
@@ -427,6 +427,33 @@ 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.
 
+.. _configuration_environment_variables:
+
+-------------------------
+Environment Modifications
+-------------------------
+
+Spack allows to prescribe custom environment modifications in a few places
+within its configuration files. Every time these modifications are allowed
+they are specified as a dictionary, like in the following example:
+
+.. code-block:: yaml
+
+   environment:
+     set:
+       LICENSE_FILE: '/path/to/license'
+     unset:
+     - CPATH
+     - LIBRARY_PATH
+     append_path:
+       PATH: '/new/bin/dir'
+
+The possible actions that are permitted are ``set``, ``unset``, ``append_path``,
+``prepend_path`` and finally ``remove_path``. They all require a dictionary
+of variable names mapped to the values used for the modification.
+The only exception is ``unset`` that requires just a list of variable names.
+No particular order is ensured on the execution of each of these modifications.
+
 ----------------------------
 Seeing Spack's Configuration
 ----------------------------
@@ -459,14 +486,13 @@ account all scopes. For example, to see the fully merged
      install_tree: $spack/opt/spack
      template_dirs:
      - $spack/templates
-     directory_layout: ${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}
+     directory_layout: {architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}
      module_roots:
        tcl: $spack/share/spack/modules
        lmod: $spack/share/spack/lmod
-       dotkit: $spack/share/spack/dotkit
      build_stage:
-     - $tempdir
-     - /nfs/tmp2/$user
+     - $tempdir/$user/spack-stage
+     - ~/.spack/stage
      - $spack/var/spack/stage
      source_cache: $spack/var/spack/cache
      misc_cache: ~/.spack/cache
@@ -510,14 +536,13 @@ down the problem:
    ./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: ${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}
+   /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:35      dotkit: $spack/share/spack/dotkit
    /home/myuser/spack/etc/spack/defaults/config.yaml:49    build_stage:
-   /home/myuser/spack/etc/spack/defaults/config.yaml:50    - $tempdir
-   /home/myuser/spack/etc/spack/defaults/config.yaml:51    - /nfs/tmp2/$user
+   /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

lib/spack/docs/containers.rst

@@ -0,0 +1,307 @@
+.. Copyright 2013-2020 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)
+
+.. _containers:
+
+================
+Container Images
+================
+
+Spack can be an ideal tool to setup images for containers since all the
+features discussed in :ref:`environments` can greatly help to manage
+the installation of software during the image build process. Nonetheless,
+building a production image from scratch still requires a lot of
+boilerplate to:
+
+- Get Spack working within the image, possibly running as root
+- Minimize the physical size of the software installed
+- Properly update the system software in the base image
+
+To facilitate users with these tedious tasks, Spack provides a command
+to automatically generate recipes for container images based on
+Environments:
+
+.. code-block:: console
+
+   $ ls
+   spack.yaml
+
+   $ spack containerize
+   # Build stage with Spack pre-installed and ready to be used
+   FROM spack/centos7:latest as builder
+
+   # What we want to install and how we want to install it
+   # is specified in a manifest file (spack.yaml)
+   RUN mkdir /opt/spack-environment \
+   &&  (echo "spack:" \
+   &&   echo "  specs:" \
+   &&   echo "  - gromacs+mpi" \
+   &&   echo "  - mpich" \
+   &&   echo "  concretization: together" \
+   &&   echo "  config:" \
+   &&   echo "    install_tree: /opt/software" \
+   &&   echo "  view: /opt/view") > /opt/spack-environment/spack.yaml
+
+   # Install the software, remove unecessary deps
+   RUN cd /opt/spack-environment && spack install && spack gc -y
+
+   # Strip all the binaries
+   RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
+       xargs file -i | \
+       grep 'charset=binary' | \
+       grep 'x-executable\|x-archive\|x-sharedlib' | \
+       awk -F: '{print $1}' | xargs strip -s
+
+   # Modifications to the environment that are necessary to run
+   RUN cd /opt/spack-environment && \
+       spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
+
+
+   # Bare OS image to run the installed executables
+   FROM centos:7
+
+   COPY --from=builder /opt/spack-environment /opt/spack-environment
+   COPY --from=builder /opt/software /opt/software
+   COPY --from=builder /opt/view /opt/view
+   COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
+
+   RUN yum update -y && yum install -y epel-release && yum update -y                                   \
+    && yum install -y libgomp \
+    && rm -rf /var/cache/yum  && yum clean all
+
+   RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ \[$(tput sgr0)\]"' >> ~/.bashrc
+
+
+   LABEL "app"="gromacs"
+   LABEL "mpi"="mpich"
+
+   ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
+
+
+The bits that make this automation possible are discussed in details
+below. All the images generated in this way will be based on
+multi-stage builds with:
+
+- A fat ``build`` stage containing common build tools and Spack itself
+- A minimal ``final`` stage containing only the software requested by the user
+
+-----------------
+Spack Base Images
+-----------------
+
+Docker images with Spack preinstalled and ready to be used are
+built on `Docker Hub <https://hub.docker.com/u/spack>`_
+at every push to ``develop`` or to a release branch. The OS that
+are currently supported are summarized in the table below:
+
+.. _containers-supported-os:
+
+.. list-table:: Supported operating systems
+   :header-rows: 1
+
+   * - Operating System
+     - Base Image
+     - Spack Image
+   * - Ubuntu 16.04
+     - ``ubuntu:16.04``
+     - ``spack/ubuntu-xenial``
+   * - Ubuntu 18.04
+     - ``ubuntu:16.04``
+     - ``spack/ubuntu-bionic``
+   * - CentOS 6
+     - ``centos:6``
+     - ``spack/centos6``
+   * - CentOS 7
+     - ``centos:7``
+     - ``spack/centos7``
+
+All the images are tagged with the corresponding release of Spack:
+
+.. image:: dockerhub_spack.png
+
+with the exception of the ``latest`` tag that points to the HEAD
+of the ``develop`` branch. These images are available for anyone
+to use and take care of all the repetitive tasks that are necessary
+to setup Spack within a container. All the container recipes generated
+automatically by Spack use them as base images for their ``build`` stage.
+
+
+-------------------------
+Environment Configuration
+-------------------------
+
+Any Spack Environment can be used for the automatic generation of container
+recipes. Sensible defaults are provided for things like the base image or the
+version of Spack used in the image. If a finer tuning is needed it can be
+obtained by adding the relevant metadata under the ``container`` attribute
+of environments:
+
+.. code-block:: yaml
+
+   spack:
+     specs:
+     - gromacs+mpi
+     - mpich
+
+     container:
+       # Select the format of the recipe e.g. docker,
+       # singularity or anything else that is currently supported
+       format: docker
+
+       # Select from a valid list of images
+       base:
+         image: "centos:7"
+         spack: develop
+
+       # Whether or not to strip binaries
+       strip: true
+
+       # Additional system packages that are needed at runtime
+       os_packages:
+       - libgomp
+
+       # Extra instructions
+       extra_instructions:
+         final: |
+   RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ \[$(tput sgr0)\]"' >> ~/.bashrc
+
+       # Labels for the image
+       labels:
+         app: "gromacs"
+         mpi: "mpich"
+
+The tables below describe the configuration options that are currently supported:
+
+.. list-table:: General configuration options for the ``container`` section of ``spack.yaml``
+   :header-rows: 1
+
+   * - Option Name
+     - Description
+     - Allowed Values
+     - Required
+   * - ``format``
+     - The format of the recipe
+     - ``docker`` or ``singularity``
+     - Yes
+   * - ``base:image``
+     - Base image for ``final`` stage
+     - See :ref:`containers-supported-os`
+     - Yes
+   * - ``base:spack``
+     - Version of Spack
+     - Valid tags for ``base:image``
+     - Yes
+   * - ``strip``
+     - Whether to strip binaries
+     - ``true`` (default) or ``false``
+     - No
+   * - ``os_packages``
+     - System packages to be installed
+     - Valid packages for the ``final`` OS
+     - No
+   * - ``extra_instructions:build``
+     - Extra instructions (e.g. `RUN`, `COPY`, etc.) at the end of the ``build`` stage
+     - Anything understood by the current ``format``
+     - No
+   * - ``extra_instructions:final``
+     - Extra instructions (e.g. `RUN`, `COPY`, etc.) at the end of the ``final`` stage
+     - Anything understood by the current ``format``
+     - No
+   * - ``labels``
+     - Labels to tag the image
+     - Pairs of key-value strings
+     - No
+
+.. list-table:: Configuration options specific to Singularity
+   :header-rows: 1
+
+   * - Option Name
+     - Description
+     - Allowed Values
+     - Required
+   * - ``singularity:runscript``
+     - Content of ``%runscript``
+     - Any valid script
+     - No
+   * - ``singularity:startscript``
+     - Content of ``%startscript``
+     - Any valid script
+     - No
+   * - ``singularity:test``
+     - Content of ``%test``
+     - Any valid script
+     - No
+   * - ``singularity:help``
+     - Description of the image
+     - Description string
+     - No
+
+Once the Environment is properly configured a recipe for a container
+image can be printed to standard output by issuing the following
+command from the directory where the ``spack.yaml`` resides:
+
+.. code-block:: console
+
+   $ spack containerize
+
+The example ``spack.yaml`` above would produce for instance the
+following ``Dockerfile``:
+
+.. code-block:: docker
+
+   # Build stage with Spack pre-installed and ready to be used
+   FROM spack/centos7:latest as builder
+
+   # What we want to install and how we want to install it
+   # is specified in a manifest file (spack.yaml)
+   RUN mkdir /opt/spack-environment \
+   &&  (echo "spack:" \
+   &&   echo "  specs:" \
+   &&   echo "  - gromacs+mpi" \
+   &&   echo "  - mpich" \
+   &&   echo "  concretization: together" \
+   &&   echo "  config:" \
+   &&   echo "    install_tree: /opt/software" \
+   &&   echo "  view: /opt/view") > /opt/spack-environment/spack.yaml
+
+   # Install the software, remove unecessary deps
+   RUN cd /opt/spack-environment && spack install && spack gc -y
+
+   # Strip all the binaries
+   RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
+       xargs file -i | \
+       grep 'charset=binary' | \
+       grep 'x-executable\|x-archive\|x-sharedlib' | \
+       awk -F: '{print $1}' | xargs strip -s
+
+   # Modifications to the environment that are necessary to run
+   RUN cd /opt/spack-environment && \
+       spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
+
+
+   # Bare OS image to run the installed executables
+   FROM centos:7
+
+   COPY --from=builder /opt/spack-environment /opt/spack-environment
+   COPY --from=builder /opt/software /opt/software
+   COPY --from=builder /opt/view /opt/view
+   COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
+
+   RUN yum update -y && yum install -y epel-release && yum update -y                                   \
+    && yum install -y libgomp \
+    && rm -rf /var/cache/yum  && yum clean all
+
+   RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ \[$(tput sgr0)\]"' >> ~/.bashrc
+
+
+   LABEL "app"="gromacs"
+   LABEL "mpi"="mpich"
+
+   ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
+
+.. note::
+   Spack can also produce Singularity definition files to build the image. The
+   minimum version of Singularity required to build a SIF (Singularity Image Format)
+   from them is ``3.5.3``.

lib/spack/docs/contribution_guide.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -64,6 +64,8 @@ If you take a look in ``$SPACK_ROOT/.travis.yml``, you'll notice that we test
 against Python 2.6, 2.7, and 3.4-3.7 on both macOS and Linux. We currently
 perform 3 types of tests:
 
+.. _cmd-spack-test:
+
 ^^^^^^^^^^
 Unit Tests
 ^^^^^^^^^^
@@ -86,40 +88,83 @@ To run *all* of the unit tests, use:
 
    $ spack test
 
-These tests may take several minutes to complete. If you know you are only
-modifying a single Spack feature, you can run a single unit test at a time:
+These tests may take several minutes to complete. If you know you are
+only modifying a single Spack feature, you can run subsets of tests at a
+time.  For example, this would run all the tests in
+``lib/spack/spack/test/architecture.py``:
 
 .. code-block:: console
 
-   $ spack test architecture
+   $ spack test architecture.py
 
-This allows you to develop iteratively: make a change, test that change, make
-another change, test that change, etc. To get a list of all available unit
-tests, run:
+And this would run the ``test_platform`` test from that file:
+
+.. code-block:: console
+
+   $ spack test architecture.py::test_platform
+
+This allows you to develop iteratively: make a change, test that change,
+make another change, test that change, etc.  We use `pytest
+<http://pytest.org/>`_ as our tests fromework, and these types of
+arguments are just passed to the ``pytest`` command underneath. See `the
+pytest docs
+<http://doc.pytest.org/en/latest/usage.html#specifying-tests-selecting-tests>`_
+for more details on test selection syntax.
+
+``spack test`` has a few special options that can help you understand
+what tests are available.  To get a list of all available unit test
+files, run:
 
 .. command-output:: spack test --list
+   :ellipsis: 5
 
-A more detailed list of available unit tests can be found by running
-``spack test --long-list``.
+To see a more detailed list of available unit tests, use ``spack test
+--list-long``:
 
-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:
+.. command-output:: spack test --list-long
+   :ellipsis: 10
+
+And to see the fully qualified names of all tests, use ``--list-names``:
+
+.. command-output:: spack test --list-names
+   :ellipsis: 5
+
+You can combine these with ``pytest`` arguments to restrict which tests
+you want to know about.  For example, to see just the tests in
+``architecture.py``:
+
+.. command-output:: spack test --list-long architecture.py
+
+You can also combine any of these options with a ``pytest`` keyword
+search.  For example, to see the names of all tests that have "spec"
+or "concretize" somewhere in their names:
+
+.. command-output:: spack test --list-names -k "spec and concretize"
+
+By default, ``pytest`` captures the output of all unit tests, and it will
+print any captured output for failed tests. Sometimes it's helpful to see
+your output interactively, while the tests run (e.g., if you add print
+statements to a unit tests).  To see the output *live*, use the ``-s``
+argument to ``pytest``:
 
 .. code-block:: console
 
-   $ spack test -s -k architecture
+   $ spack test -s architecture.py::test_platform
 
-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.
+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 add new unit tests for your feature, and consider
+strengthening existing tests.  You will likely be asked to do this if you
+submit a pull request to the Spack project on GitHub.  Check out the
+`pytest docs <http://pytest.org/>`_ and feel free to ask for guidance on
+how to write tests!
 
 .. note::
 
-   There is also a ``run-unit-tests`` script in ``share/spack/qa`` that
-   runs the unit tests. Afterwards, it reports back to Codecov with the
-   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``.
+   You may notice the ``share/spack/qa/run-unit-tests`` script in the
+   repository.  This script is designed for Travis CI.  It runs the unit
+   tests and reports coverage statistics back to Codecov. If you want to
+   run the unit tests yourself, we suggest you use ``spack test``.
 
 ^^^^^^^^^^^^
 Flake8 Tests
@@ -223,8 +268,7 @@ documentation. In order to prevent things like broken links and missing imports,
 we added documentation tests that build the documentation and fail if there
 are any warning or error messages.
 
-Building the documentation requires several dependencies, all of which can be
-installed with Spack:
+Building the documentation requires several dependencies:
 
 * sphinx
 * sphinxcontrib-programoutput
@@ -234,11 +278,18 @@ installed with Spack:
 * mercurial
 * subversion
 
+All of these can be installed with Spack, e.g.
+
+.. code-block:: console
+
+   $ spack install py-sphinx py-sphinxcontrib-programoutput py-sphinx-rtd-theme graphviz git mercurial subversion
+
 .. warning::
 
    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:
+   If you're using a ``python`` from Spack and you installed
+   ``py-sphinx`` and friends, you need to make them available to your
+   ``python``. The easiest way to do this is to run:
 
    .. code-block:: console
 
@@ -246,8 +297,10 @@ installed with Spack:
       $ spack activate py-sphinx-rtd-theme
       $ spack activate py-sphinxcontrib-programoutput
 
-   so that all of the dependencies are symlinked to a central location.
-   If you see an error message like:
+   so that all of the dependencies are symlinked into that Python's
+   tree.  Alternatively, you could arrange for their library
+   directories to be added to PYTHONPATH.  If you see an error message
+   like:
 
    .. code-block:: console
 

lib/spack/docs/developer_guide.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -363,12 +363,12 @@ Developer commands
 ``spack doc``
 ^^^^^^^^^^^^^
 
-.. _cmd-spack-test:
-
 ^^^^^^^^^^^^^^
 ``spack test``
 ^^^^^^^^^^^^^^
 
+See the :ref:`contributor guide section <cmd-spack-test>` on ``spack test``.
+
 .. _cmd-spack-python:
 
 ^^^^^^^^^^^^^^^^
@@ -488,7 +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

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/environments.rst

@@ -0,0 +1,826 @@
+.. Copyright 2013-2020 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``
+
+.. _environments-using:
+
+------------------
+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 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 +1,122 @@
+.. Copyright 2013-2020 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
+=================
+
+*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

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -60,14 +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
@@ -130,7 +130,7 @@ 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
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/libelf/package.py
    :lines: 6-
 
 Spack also provides wrapper functions around common commands like

lib/spack/docs/getting_started.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -16,10 +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 (3.4 - 3.7)
-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
@@ -70,7 +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>`.
 
@@ -96,7 +97,7 @@ Check Installation
 With Spack installed, you should be able to run some basic Spack
 commands.  For example:
 
-.. command-output:: spack spec netcdf
+.. command-output:: spack spec netcdf-c
 
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -189,7 +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
@@ -201,7 +202,7 @@ 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
@@ -246,7 +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:
@@ -262,7 +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``:
@@ -468,18 +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
@@ -590,11 +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
 

lib/spack/docs/index.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -55,7 +55,7 @@ or refer to the full manual below.
    getting_started
    basic_usage
    workflows
-   tutorial
+   Tutorial: Spack 101 <https://spack-tutorial.readthedocs.io>
    known_issues
 
 .. toctree::
@@ -65,12 +65,17 @@ or refer to the full manual below.
    configuration
    config_yaml
    build_settings
+   environments
+   containers
    mirrors
    module_file_support
    repositories
    binary_caches
    command_index
    package_list
+   chain
+   extensions
+   pipelines
 
 .. toctree::
    :maxdepth: 2
@@ -81,6 +86,11 @@ or refer to the full manual below.
    build_systems
    developer_guide
    docker_for_developers
+
+.. toctree::
+   :maxdepth: 2
+   :caption: API Docs
+
    Spack API Docs <spack>
    LLNL API Docs <llnl>
 

lib/spack/docs/known_issues.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/mirrors.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/module_file_support.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -13,8 +13,8 @@ The use of module systems to manage user environment in a controlled way
 is a common practice at HPC centers that is often embraced also by individual
 programmers on their development machines. To support this common practice
 Spack integrates with `Environment Modules
-<http://modules.sourceforge.net/>`_ ,  `LMod
-<http://lmod.readthedocs.io/en/latest/>`_ and `Dotkit <https://computing.llnl.gov/?set=jobs&page=dotkit>`_ by
+<http://modules.sourceforge.net/>`_  and  `LMod
+<http://lmod.readthedocs.io/en/latest/>`_ by
 providing post-install hooks that generate module files and commands to manipulate them.
 
 .. note::
@@ -67,7 +67,7 @@ to load the ``cmake`` module:
    $ module load cmake-3.7.2-gcc-6.3.0-fowuuby
 
 Neither of these is particularly pretty, easy to remember, or
-easy to type. Luckily, Spack has its own interface for using modules and dotkits.
+easy to type. Luckily, Spack has its own interface for using modules.
 
 ^^^^^^^^^^^^^
 Shell support
@@ -108,20 +108,10 @@ that the startup time may be slightly increased because of that.
 ^^^^^^^^^^^^^^^^^^^^^^^
 
 Once you have shell support enabled you can use the same spec syntax
-you're used to:
+you're used to and you can use the same shortened names you use
+everywhere else in Spack.
 
-=========================  ==========================
-Modules                    Dotkit
-=========================  ==========================
-``spack load <spec>``      ``spack use <spec>``
-``spack unload <spec>``    ``spack unuse <spec>``
-=========================  ==========================
-
-And you can use the same shortened names you use everywhere else in
-Spack.
-
-For example, if you are using dotkit, this will add the ``mpich``
-package built with ``gcc`` to your path:
+For example this will add the ``mpich`` package built with ``gcc`` to your path:
 
 .. code-block:: console
 
@@ -129,45 +119,39 @@ package built with ``gcc`` to your path:
 
    # ... wait for install ...
 
-   $ spack use mpich %gcc@4.4.7     # dotkit
-   Prepending: mpich@3.0.4%gcc@4.4.7 (ok)
+   $ spack load mpich %gcc@4.4.7
    $ which mpicc
    ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc
 
-Or, similarly if you are using modules, you could type:
-
-.. code-block:: console
-
-   $ spack load mpich %gcc@4.4.7    # modules
-
 These commands will add appropriate directories to your ``PATH``,
 ``MANPATH``, ``CPATH``, and ``LD_LIBRARY_PATH``.  When you no longer
 want to use a package, you can type unload or unuse similarly:
 
 .. code-block:: console
 
-   $ spack unload mpich %gcc@4.4.7  # modules
-   $ spack unuse  mpich %gcc@4.4.7  # dotkit
+   $ spack unload mpich %gcc@4.4.7
 
 .. note::
 
-   These ``use``, ``unuse``, ``load``, and ``unload`` subcommands are
-   only available if you have enabled Spack's shell support *and* you
-   have dotkit or modules installed on your machine.
+   The ``load`` and ``unload`` subcommands are only available if you
+   have enabled Spack's shell support. These command DO NOT use the
+   underlying Spack-generated module files.
 
-^^^^^^^^^^^^^^^^^^^^^^
-Ambiguous module names
-^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^
+Ambiguous specs
+^^^^^^^^^^^^^^^
 
-If a spec used with load/unload or use/unuse is ambiguous (i.e. more
-than one installed package matches it), then Spack will warn you:
+If a spec used with load/unload or is ambiguous (i.e. more than one
+installed package matches it), then Spack will warn you:
 
 .. code-block:: console
 
    $ spack load libelf
-   ==> Error: Multiple matches for spec libelf.  Choose one:
-   libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64
-   libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64
+   ==> Error: libelf matches multiple packages.
+   Matching packages:
+     libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64
+     libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64
+   Use a more specific spec
 
 You can either type the ``spack load`` command again with a fully
 qualified argument, or you can add just enough extra constraints to
@@ -189,8 +173,15 @@ To identify just the one built with the Intel compiler.
 ``spack module tcl loads``
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-In some cases, it is desirable to load not just a module, but also all
-the modules it depends on.  This is not required for most modules
+In some cases, it is desirable to use a Spack-generated module, rather
+than relying on Spack's built-in user-environment modification
+capabilities. To translate a spec into a module name, use ``spack
+module tcl loads`` or ``spack module lmod loads`` depending on the
+module system desired.
+
+
+To load not just a module, but also all the modules it depends on, use
+the ``--dependencies`` option. This is not required for most modules
 because Spack builds binaries with RPATH support.  However, not all
 packages use RPATH to find their dependencies: this can be true in
 particular for Python extensions, which are currently *not* built with
@@ -215,8 +206,8 @@ Module Commands for Shell Scripts
 
 Although Spack is flexible, the ``module`` command is much faster.
 This could become an issue when emitting a series of ``spack load``
-commands inside a shell script.  By adding the ``--shell`` flag,
-``spack module tcl find`` may also be used to generate code that can be
+commands inside a shell script.  By adding the ``--dependencies`` flag,
+``spack module tcl loads`` may also be used to generate code that can be
 cut-and-pasted into a shell script.  For example:
 
 .. code-block:: console
@@ -292,8 +283,6 @@ that can be generated by Spack:
   +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
   |                             | **Hook name**      |  **Default root directory**   | **Default template file**                    | **Compatible tools** |
   +=============================+====================+===============================+==============================================+======================+
-  |  **Dotkit**                 | ``dotkit``         |  share/spack/dotkit           | share/spack/templates/modules/modulefile.dk  | DotKit               |
-  +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
   |  **TCL - Non-Hierarchical** | ``tcl``            |  share/spack/modules          | share/spack/templates/modules/modulefile.tcl | Env. Modules/LMod    |
   +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
   |  **Lua - Hierarchical**     | ``lmod``           |  share/spack/lmod             | share/spack/templates/modules/modulefile.lua | LMod                 |
@@ -323,8 +312,7 @@ content of the module files generated by Spack. The first one:
 
 .. code-block:: python
 
-   def setup_environment(self, spack_env, run_env):
-       """Set up the compile and runtime environments for a package."""
+   def setup_run_environment(self, env):
        pass
 
 can alter the content of the module file associated with the same package where it is overridden.
@@ -332,16 +320,15 @@ The second method:
 
 .. code-block:: python
 
-   def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-       """Set up the environment of packages that depend on this one"""
+   def setup_dependent_run_environment(self, env, dependent_spec):
        pass
 
 can instead inject run-time environment modifications in the module files of packages
 that depend on it. In both cases you need to fill ``run_env`` with the desired
 list of environment modifications.
 
-.. note::
- The ``r`` package and callback APIs
+.. admonition:: The ``r`` package and callback APIs
+
   An example in which it is crucial to override both methods
   is given by the ``r`` package. This package installs libraries and headers
   in non-standard locations and it is possible to prepend the appropriate directory
@@ -355,15 +342,15 @@ list of environment modifications.
 
   with the following snippet:
 
-  .. literalinclude:: ../../../var/spack/repos/builtin/packages/r/package.py
-     :pyobject: R.setup_environment
+  .. literalinclude:: _spack_root/var/spack/repos/builtin/packages/r/package.py
+     :pyobject: R.setup_run_environment
 
   The ``r`` package also knows which environment variable should be modified
   to make language extensions provided by other packages available, and modifies
   it appropriately in the override of the second method:
 
-  .. literalinclude:: ../../../var/spack/repos/builtin/packages/r/package.py
-     :pyobject: R.setup_dependent_environment
+  .. literalinclude:: _spack_root/var/spack/repos/builtin/packages/r/package.py
+     :pyobject: R.setup_dependent_run_environment
 
 .. _modules-yaml:
 
@@ -374,10 +361,10 @@ Write a configuration file
 The configuration files that control module generation behavior
 are named ``modules.yaml``. The default configuration:
 
-.. literalinclude:: ../../../etc/spack/defaults/modules.yaml
+.. literalinclude:: _spack_root/etc/spack/defaults/modules.yaml
    :language: yaml
 
-activates the hooks to generate ``tcl`` and ``dotkit`` module files and inspects
+activates the hooks to generate ``tcl`` module files and inspects
 the installation folder of each package for the presence of a set of subdirectories
 (``bin``, ``man``, ``share/man``, etc.). If any is found its full path is prepended
 to the environment variables listed below the folder name.
@@ -399,12 +386,9 @@ to the generator being customized:
    modules:
      enable:
        - tcl
-       - dotkit
        - lmod
      tcl:
        # contains environment modules specific customizations
-     dotkit:
-       # contains dotkit specific customizations
      lmod:
        # contains lmod specific customizations
 
@@ -535,17 +519,17 @@ most likely via the ``+blas`` variant specification.
 
        modules:
          tcl:
-           naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
+           naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
            all:
              conflict:
-               - '${PACKAGE}'
+               - '{name}'
                - 'intel/14.0.1'
 
      will create module files that will conflict with ``intel/14.0.1`` and with the
      base directory of the same module, effectively preventing the possibility to
      load two or more versions of the same software at the same time. The tokens
      that are available for use in this directive are the same understood by
-     the ``Spec.format`` method.
+     the :meth:`~spack.spec.Spec.format` method.
 
 
 .. note::
@@ -590,15 +574,17 @@ do so by using the environment blacklist:
 .. code-block:: yaml
 
    modules:
-     dotkit:
+     tcl:
        all:
          filter:
            # Exclude changes to any of these variables
            environment_blacklist: ['CPATH', 'LIBRARY_PATH']
 
-The configuration above will generate dotkit module files that will not contain
-modifications to either ``CPATH`` or ``LIBRARY_PATH`` and environment module
-files that instead will contain these modifications.
+The configuration above will generate module files that will not contain
+modifications to either ``CPATH`` or ``LIBRARY_PATH``.
+
+
+.. _autoloading-dependencies:
 
 """""""""""""""""""""
 Autoload dependencies
@@ -618,7 +604,21 @@ activated using ``spack activate``:
 The configuration file above will produce module files that will
 load their direct dependencies if the package installed depends on ``python``.
 The allowed values for the ``autoload`` statement are either ``none``,
-``direct`` or ``all``.
+``direct`` or ``all``.  The default is ``none``.
+
+.. tip::
+  Building external software
+     Setting ``autoload`` to ``direct`` for all packages can be useful
+     when building software outside of a Spack installation that depends on
+     artifacts in that installation.  E.g. (adjust ``lmod`` vs ``tcl``
+     as appropriate):
+
+  .. code-block:: yaml
+
+     modules:
+       lmod:
+         all:
+           autoload: 'direct'
 
 .. note::
   TCL prerequisites

lib/spack/docs/package_list.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/packaging_guide.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)
@@ -136,6 +136,10 @@ generates a boilerplate template for your package, and opens up the new
        homepage = "http://www.example.com"
        url      = "https://gmplib.org/download/gmp/gmp-6.1.2.tar.bz2"
 
+       # FIXME: Add a list of GitHub accounts to
+       # notify when the package is updated.
+       # maintainers = ['github_user1', 'github_user2']
+
        version('6.1.2', '8ddbb26dc3bd4e2302984debba1406a5')
        version('6.1.1', '4c175f86e11eb32d8bf9872ca3a8e11d')
        version('6.1.0', '86ee6e54ebfc4a90b643a65e402c4048')
@@ -184,6 +188,17 @@ The rest of the tasks you need to do are as follows:
    The ``homepage`` is displayed when users run ``spack info`` so
    that they can learn more about your package.
 
+#. Add a comma-separated list of maintainers.
+
+   The ``maintainers`` field is a list of GitHub accounts of people
+   who want to be notified any time the package is modified. When a
+   pull request is submitted that updates the package, these people
+   will be requested to review the PR. This is useful for developers
+   who maintain a Spack package for their own software, as well as
+   users who rely on a piece of software and want to ensure that the
+   package doesn't break. It also gives users a list of people to
+   contact for help when someone reports a build error with the package.
+
 #. Add ``depends_on()`` calls for the package's dependencies.
 
    ``depends_on`` tells Spack that other packages need to be built
@@ -410,6 +425,8 @@ For tarball downloads, Spack can currently support checksums using the
 MD5, SHA-1, SHA-224, SHA-256, SHA-384, and SHA-512 algorithms.  It
 determines the algorithm to use based on the hash length.
 
+.. _versions-and-fetching:
+
 ---------------------
 Versions and fetching
 ---------------------
@@ -460,7 +477,7 @@ https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.bz2
 In order to handle this, you can define a ``url_for_version()`` function
 like so:
 
-.. literalinclude:: ../../../var/spack/repos/builtin/packages/openmpi/package.py
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/openmpi/package.py
    :pyobject: Openmpi.url_for_version
 
 With the use of this ``url_for_version()``, Spack knows to download OpenMPI ``2.1.1``
@@ -536,14 +553,43 @@ version. This is useful for packages that have an easy to extrapolate URL, but
 keep changing their URL format every few releases. With this method, you only
 need to specify the ``url`` when the URL changes.
 
+"""""""""""""""""""""""
+Mirrors of the main URL
+"""""""""""""""""""""""
+
+Spack supports listing mirrors of the main URL in a package by defining
+the ``urls`` attribute:
+
+.. code-block:: python
+
+  class Foo(Package):
+
+    urls = [
+        'http://example.com/foo-1.0.tar.gz',
+        'http://mirror.com/foo-1.0.tar.gz'
+    ]
+
+instead of just a single ``url``. This attribute is a list of possible URLs that
+will be tried in order when fetching packages. Notice that either one of ``url``
+or ``urls`` can be present in a package, but not both at the same time.
+
+A well-known case of packages that can be fetched from multiple mirrors is that
+of GNU. For that, Spack goes a step further and defines a mixin class that
+takes care of all of the plumbing and requires packagers to just define a proper
+``gnu_mirror_path`` attribute:
+
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/autoconf/package.py
+   :lines: 9-18
+
 ^^^^^^^^^^^^^^^^^^^^^^^^
 Skipping the expand step
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 Spack normally expands archives (e.g. ``*.tar.gz`` and ``*.zip``) automatically
-after downloading them. If you want to skip this step (e.g., for
-self-extracting executables and other custom archive types), you can add
-``expand=False`` to a ``version`` directive.
+into a standard stage source directory (``self.stage.source_path``) after
+downloading them. If you want to skip this step (e.g., for self-extracting
+executables and other custom archive types), you can add ``expand=False`` to a
+``version`` directive.
 
 .. code-block:: python
 
@@ -573,7 +619,11 @@ Download caching
 Spack maintains a cache (described :ref:`here <caching>`) which saves files
 retrieved during package installations to avoid re-downloading in the case that
 a package is installed with a different specification (but the same version) or
-reinstalled on account of a change in the hashing scheme.
+reinstalled on account of a change in the hashing scheme. It may (rarely) be
+necessary to avoid caching for a particular version by adding ``no_cache=True``
+as an option to the ``version()`` directive. Example situations would be a
+"snapshot"-like Version Control System (VCS) tag, a VCS branch such as
+``v6-16-00-patches``, or a URL specifying a regularly updated snapshot tarball.
 
 ^^^^^^^^^^^^^^^^^^
 Version comparison
@@ -590,13 +640,15 @@ with `RPM <https://bugzilla.redhat.com/show_bug.cgi?id=50977>`_.
 
 Spack versions may also be arbitrary non-numeric strings; any string
 here will suffice; for example, ``@develop``, ``@master``, ``@local``.
-The following rules determine the sort order of numeric
-vs. non-numeric versions:
+Versions are compared as follows. First, a version string is split into
+multiple fields based on delimiters such as ``.``, ``-`` etc. Then
+matching fields are compared using the rules below:
 
-#. The non-numeric version ``@develop`` is considered greatest (newest).
+#. The following develop-like strings are greater (newer) than all
+   numbers and are ordered as ``develop > master > head > trunk``.
 
-#. Numeric versions are all less than ``@develop`` version, and are
-   sorted numerically.
+#. Numbers are all less than the chosen develop-like strings above,
+   and are sorted numerically.
 
 #. All other non-numeric versions are less than numeric versions, and
    are sorted alphabetically.
@@ -610,7 +662,7 @@ The logic behind this sort order is two-fold:
 
 #. The most-recent development version of a package will usually be
    newer than any released numeric versions.  This allows the
-   ``develop`` version to satisfy dependencies like ``depends_on(abc,
+   ``@develop`` version to satisfy dependencies like ``depends_on(abc,
    when="@x.y.z:")``
 
 ^^^^^^^^^^^^^^^^^
@@ -812,7 +864,8 @@ For some packages, source code is provided in a Version Control System
 (VCS) repository rather than in a tarball.  Spack can fetch packages
 from VCS repositories. Currently, Spack supports fetching with `Git
 <git-fetch_>`_, `Mercurial (hg) <hg-fetch_>`_, `Subversion (svn)
-<svn-fetch_>`_, and `Go <go-fetch_>`_.
+<svn-fetch_>`_, and `Go <go-fetch_>`_.  In all cases, the destination
+is the standard stage source path.
 
 To fetch a package from a source repository, Spack needs to know which
 VCS to use and where to download from. Much like with ``url``, package
@@ -876,9 +929,19 @@ Git fetching supports the following parameters to ``version``:
 * ``tag``: Name of a tag to fetch.
 * ``commit``: SHA hash (or prefix) of a commit to fetch.
 * ``submodules``: Also fetch submodules recursively when checking out this repository.
+* ``submodules_delete``: A list of submodules to forcibly delete from the repository
+  after fetching. Useful if a version in the repository has submodules that
+  have disappeared/are no longer accessible.
+* ``get_full_repo``: Ensure the full git history is checked out with all remote
+  branch information. Normally (``get_full_repo=False``, the default), the git
+  option ``--depth 1`` will be used if the version of git and the specified
+  transport protocol support it, and ``--single-branch`` will be used if the
+  version of git supports it.
 
 Only one of ``tag``, ``branch``, or ``commit`` can be used at a time.
 
+The destination directory for the clone is the standard stage source path.
+
 Default branch
   To fetch a repository's default branch:
 
@@ -979,6 +1042,7 @@ Mercurial
 
 Fetching with Mercurial works much like `Git <git-fetch>`_, but you
 use the ``hg`` parameter.
+The destination directory is still the standard stage source path.
 
 Default branch
   Add the ``hg`` attribute with no ``revision`` passed to ``version``:
@@ -1017,6 +1081,7 @@ Subversion
 ^^^^^^^^^^
 
 To fetch with subversion, use the ``svn`` and ``revision`` parameters.
+The destination directory will be the standard stage source path.
 
 Fetching the head
   Simply add an ``svn`` parameter to the package:
@@ -1061,7 +1126,9 @@ Go
 Go isn't a VCS, it is a programming language with a builtin command,
 `go get <https://golang.org/cmd/go/#hdr-Download_and_install_packages_and_dependencies>`_,
 that fetches packages and their dependencies automatically.
-It can clone a Git repository, or download from another source location.
+The destination directory will be the standard stage source path.
+
+This strategy can clone a Git repository, or download from another source location.
 For example:
 
 .. code-block:: python
@@ -1077,6 +1144,174 @@ Go cannot be used to fetch a particular commit or branch, it always
 downloads the head of the repository. This download method is untrusted,
 and is not recommended. Use another fetch strategy whenever possible.
 
+--------
+Variants
+--------
+
+Many software packages can be configured to enable optional
+features, which often come at the expense of additional dependencies or
+longer build-times. To be flexible enough and support a wide variety of
+use cases, Spack permits to expose to the end-user the ability to choose
+which features should be activated in a package at the time it is installed.
+The mechanism to be employed is the :py:func:`spack.directives.variant` directive.
+
+^^^^^^^^^^^^^^^^
+Boolean variants
+^^^^^^^^^^^^^^^^
+
+In their simplest form variants are boolean options specified at the package
+level:
+
+  .. code-block:: python
+
+    class Hdf5(AutotoolsPackage):
+        ...
+        variant(
+            'shared', default=True, description='Builds a shared version of the library'
+        )
+
+with a default value and a description of their meaning / use in the package.
+*Variants can be tested in any context where a spec constraint is expected.*
+In the example above the ``shared`` variant is tied to the build of shared dynamic
+libraries. To pass the right option at configure time we can branch depending on
+its value:
+
+  .. code-block:: python
+
+    def configure_args(self):
+        ...
+        if '+shared' in self.spec:
+            extra_args.append('--enable-shared')
+        else:
+            extra_args.append('--disable-shared')
+            extra_args.append('--enable-static-exec')
+
+As explained in :ref:`basic-variants` the constraint ``+shared`` means
+that the boolean variant is set to ``True``, while ``~shared`` means it is set
+to ``False``.
+Another common example is the optional activation of an extra dependency
+which requires to use the variant in the ``when`` argument of
+:py:func:`spack.directives.depends_on`:
+
+  ..  code-block:: python
+
+    class Hdf5(AutotoolsPackage):
+        ...
+        variant('szip', default=False, description='Enable szip support')
+        depends_on('szip', when='+szip')
+
+as shown in the snippet above where ``szip`` is modeled to be an optional
+dependency of ``hdf5``.
+
+^^^^^^^^^^^^^^^^^^^^^
+Multi-valued variants
+^^^^^^^^^^^^^^^^^^^^^
+
+If need be, Spack can go beyond Boolean variants and permit an arbitrary
+number of allowed values. This might be useful when modeling
+options that are tightly related to each other.
+The values in this case are passed to the :py:func:`spack.directives.variant`
+directive as a tuple:
+
+  .. code-block:: python
+
+    class Blis(Package):
+        ...
+        variant(
+            'threads', default='none', description='Multithreading support',
+            values=('pthreads', 'openmp', 'none'), multi=False
+        )
+
+In the example above the argument ``multi`` is set to ``False`` to indicate
+that only one among all the variant values can be active at any time. This
+constraint is enforced by the parser and an error is emitted if a user
+specifies two or more values at the same time:
+
+  .. code-block:: console
+
+    $ spack spec blis threads=openmp,pthreads
+    Input spec
+    --------------------------------
+    blis threads=openmp,pthreads
+
+    Concretized
+    --------------------------------
+    ==> Error: multiple values are not allowed for variant "threads"
+
+Another useful note is that *Python's* ``None`` *is not allowed as a default value*
+and therefore it should not be used to denote that no feature was selected.
+Users should instead select another value, like ``'none'``, and handle it explicitly
+within the package recipe if need be:
+
+  .. code-block:: python
+
+      if self.spec.variants['threads'].value == 'none':
+         options.append('--no-threads')
+
+In cases where multiple values can be selected at the same time ``multi`` should
+be set to ``True``:
+
+  .. code-block:: python
+
+    class Gcc(AutotoolsPackage):
+        ...
+        variant(
+            'languages', default='c,c++,fortran',
+            values=('ada', 'brig', 'c', 'c++', 'fortran',
+                    'go', 'java', 'jit', 'lto', 'objc', 'obj-c++'),
+            multi=True,
+            description='Compilers and runtime libraries to build'
+        )
+
+Within a package recipe a multi-valued variant is tested using a ``key=value`` syntax:
+
+  .. code-block:: python
+
+    if 'languages=jit' in spec:
+        options.append('--enable-host-shared')
+
+"""""""""""""""""""""""""""""""""""""""""""
+Complex validation logic for variant values
+"""""""""""""""""""""""""""""""""""""""""""
+To cover complex use cases, the :py:func:`spack.directives.variant` directive
+could accept as the ``values`` argument a full-fledged object which has
+``default`` and other arguments of the directive embedded as attributes.
+
+An example, already implemented in Spack's core, is :py:class:`spack.variant.DisjointSetsOfValues`.
+This class is used to implement a few convenience functions, like
+:py:func:`spack.variant.any_combination_of`:
+
+  ..  code-block:: python
+
+    class Adios(AutotoolsPackage):
+        ...
+        variant(
+            'staging',
+            values=any_combination_of('flexpath', 'dataspaces'),
+            description='Enable dataspaces and/or flexpath staging transports'
+        )
+
+that allows any combination of the specified values, and also allows the
+user to specify ``'none'`` (as a string) to choose none of them.
+The objects returned by these functions can be modified at will by chaining
+method calls to change the default value, customize the error message or
+other similar operations:
+
+  .. code-block:: python
+
+    class Mvapich2(AutotoolsPackage):
+        ...
+        variant(
+            'process_managers',
+            description='List of the process managers to activate',
+            values=disjoint_sets(
+                ('auto',), ('slurm',), ('hydra', 'gforker', 'remshell')
+            ).prohibit_empty_set().with_error(
+                "'slurm' or 'auto' cannot be activated along with "
+                "other process managers"
+            ).with_default('auto').with_non_feature_values('auto'),
+        )
+
 ------------------------------------
 Resources (expanding extra tarballs)
 ------------------------------------
@@ -1275,8 +1510,8 @@ that the same package with different patches applied will have different
 hash identifiers.  To ensure that the hashing scheme is consistent, you
 must use a ``sha256`` checksum for the patch.  Patches will be fetched
 from their URLs, checked, and applied to your source code.  You can use
-the ``spack sha256`` command to generate a checksum for a patch file or
-URL.
+the GNU utils ``sha256sum`` or the macOS ``shasum -a 256`` commands to
+generate a checksum for a patch file.
 
 Spack can also handle compressed patches.  If you use these, Spack needs
 a little more help.  Specifically, it needs *two* checksums: the
@@ -1395,7 +1630,7 @@ handles ``RPATH``:
 
 .. _pyside-patch:
 
-.. literalinclude:: ../../../var/spack/repos/builtin/packages/py-pyside/package.py
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/py-pyside/package.py
    :pyobject: PyPyside.patch
    :linenos:
 
@@ -1422,6 +1657,73 @@ with all packages in Spack, a patched dependency library can coexist with
 other versions of that library.  See the `section on depends_on
 <dependency_dependency_patching_>`_ for more details.
 
+.. _patch_inspecting_patches:
+
+^^^^^^^^^^^^^^^^^^^
+Inspecting patches
+^^^^^^^^^^^^^^^^^^^
+
+If you want to better understand the patches that Spack applies to your
+packages, you can do that using ``spack spec``, ``spack find``, and other
+query commands.  Let's look at ``m4``.  If you run ``spack spec m4``, you
+can see the patches that would be applied to ``m4``::
+
+  $ spack spec m4
+  Input spec
+  --------------------------------
+  m4
+
+  Concretized
+  --------------------------------
+  m4@1.4.18%clang@9.0.0-apple patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=darwin-highsierra-x86_64
+      ^libsigsegv@2.11%clang@9.0.0-apple arch=darwin-highsierra-x86_64
+
+You can also see patches that have been applied to installed packages
+with ``spack find -v``::
+
+  $ spack find -v m4
+  ==> 1 installed package
+  -- darwin-highsierra-x86_64 / clang@9.0.0-apple -----------------
+  m4@1.4.18 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv
+
+.. _cmd-spack-resource:
+
+In both cases above, you can see that the patches' sha256 hashes are
+stored on the spec as a variant.  As mentioned above, this means that you
+can have multiple, differently-patched versions of a package installed at
+once.
+
+You can look up a patch by its sha256 hash (or a short version of it)
+using the ``spack resource show`` command::
+
+  $ spack resource show 3877ab54
+  3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00
+      path:       /home/spackuser/src/spack/var/spack/repos/builtin/packages/m4/gnulib-pgi.patch
+      applies to: builtin.m4
+
+``spack resource show`` looks up downloadable resources from package
+files by hash and prints out information about them.  Above, we see that
+the ``3877ab54`` patch applies to the ``m4`` package.  The output also
+tells us where to find the patch.
+
+Things get more interesting if you want to know about dependency
+patches. For example, when ``dealii`` is built with ``boost@1.68.0``, it
+has to patch boost to work correctly.  If you didn't know this, you might
+wonder where the extra boost patches are coming from::
+
+  $ spack spec dealii ^boost@1.68.0 ^hdf5+fortran | grep '\^boost'
+      ^boost@1.68.0
+          ^boost@1.68.0%clang@9.0.0-apple+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199,b37164268f34f7133cbc9a4066ae98fda08adf51e1172223f6a969909216870f ~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=darwin-highsierra-x86_64
+  $ spack resource show b37164268
+  b37164268f34f7133cbc9a4066ae98fda08adf51e1172223f6a969909216870f
+      path:       /home/spackuser/src/spack/var/spack/repos/builtin/packages/dealii/boost_1.68.0.patch
+      applies to: builtin.boost
+      patched by: builtin.dealii
+
+Here you can see that the patch is applied to ``boost`` by ``dealii``,
+and that it lives in ``dealii``'s directory in Spack's ``builtin``
+package repository.
+
 .. _handling_rpaths:
 
 ---------------
@@ -1476,12 +1778,11 @@ RPATHs in Spack are handled in one of three ways:
 Parallel builds
 ---------------
 
-By default, Spack will invoke ``make()`` with a ``-j <njobs>``
-argument, so that builds run in parallel.  It figures out how many
-jobs to run by determining how many cores are on the host machine.
-Specifically, it uses the number of CPUs reported by Python's
-`multiprocessing.cpu_count()
-<http://docs.python.org/library/multiprocessing.html#multiprocessing.cpu_count>`_.
+By default, Spack will invoke ``make()``, or any other similar tool,
+with a ``-j <njobs>`` argument, so that builds run in parallel.
+The parallelism is determined by the value of the ``build_jobs`` entry
+in ``config.yaml`` (see :ref:`here <build-jobs>` for more details on
+how this value is computed).
 
 If a package does not build properly in parallel, you can override
 this setting by adding ``parallel = False`` to your package.  For
@@ -1652,6 +1953,8 @@ issues with 1.64.0, 1.65.0, and 1.66.0, you can say:
    depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:')
 
 
+.. _dependency-types:
+
 ^^^^^^^^^^^^^^^^
 Dependency types
 ^^^^^^^^^^^^^^^^
@@ -1689,6 +1992,28 @@ inject the dependency's ``prefix/lib`` directory, but the package needs to
 be in ``PATH`` and ``PYTHONPATH`` during the build process and later when
 a user wants to run the package.
 
+^^^^^^^^^^^^^^^^^^^^^^^^
+Conditional dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+You may have a package that only requires a dependency under certain
+conditions. For example, you may have a package that has optional MPI support,
+- MPI is only a dependency when you want to enable MPI support for the
+package. In that case, you could say something like:
+
+.. code-block:: python
+
+   variant('mpi', default=False)
+   depends_on('mpi', when='+mpi')
+
+``when`` can include constraints on the variant, version, compiler, etc. and
+the :mod:`syntax<spack.spec>` is the same as for Specs written on the command
+line.
+
+If a dependency/feature of a package isn't typically used, you can save time
+by making it conditional (since Spack will not build the dependency unless it
+is required for the Spec).
+
 .. _dependency_dependency_patching:
 
 ^^^^^^^^^^^^^^^^^^^
@@ -1777,55 +2102,58 @@ appear in the package file (or in this case, in the list).
 
 .. _setup-dependent-environment:
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-``setup_dependent_environment()``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Influence how dependents are built or run
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Spack provides a mechanism for dependencies to provide variables that
-can be used in their dependents' build.  Any package can declare a
-``setup_dependent_environment()`` function, and this function will be
-called before the ``install()`` method of any dependent packages.
-This allows dependencies to set up environment variables and other
-properties to be used by dependents.
+Spack provides a mechanism for dependencies to influence the
+environment of their dependents by overriding  the
+:meth:`setup_dependent_run_environment <spack.package.PackageBase.setup_dependent_run_environment>`
+or the
+:meth:`setup_dependent_build_environment <spack.package.PackageBase.setup_dependent_build_environment>`
+methods.
+The Qt package, for instance, uses this call:
 
-The function declaration should look like this:
-
-.. literalinclude:: ../../../var/spack/repos/builtin/packages/qt/package.py
-   :pyobject: Qt.setup_dependent_environment
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/qt/package.py
+   :pyobject: Qt.setup_dependent_build_environment
    :linenos:
 
-Here, the Qt package sets the ``QTDIR`` environment variable so that
-packages that depend on a particular Qt installation will find it.
+to set the ``QTDIR`` environment variable so that packages
+that depend on a particular Qt installation will find it.
+Another good example of how a dependency can influence
+the build environment of dependents is the Python package:
 
-The arguments to this function are:
-
-* **spack_env**: List of environment modifications to be applied when
-  the dependent package is built within Spack.
-* **run_env**: List of environment modifications to be applied when
-  the dependent package is run outside of Spack. These are added to the
-  resulting module file.
-* **dependent_spec**: The spec of the dependent package about to be
-  built. This allows the extendee (self) to query the dependent's state.
-  Note that *this* package's spec is available as ``self.spec``.
-
-A good example of using these is in the Python package:
-
-.. literalinclude:: ../../../var/spack/repos/builtin/packages/python/package.py
-   :pyobject: Python.setup_dependent_environment
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py
+   :pyobject: Python.setup_dependent_build_environment
    :linenos:
 
-The first thing that happens here is that the ``python`` command is
-inserted into module scope of the dependent.  This allows most python
-packages to have a very simple install method, like this:
+In the method above it is ensured that any package that depends on Python
+will have the ``PYTHONPATH``, ``PYTHONHOME`` and ``PATH`` environment
+variables set appropriately before starting the installation. To make things
+even simpler the ``python setup.py`` command is also inserted into the module
+scope of dependents by overriding a third method called
+:meth:`setup_dependent_package <spack.package.PackageBase.setup_dependent_package>`
+:
+
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py
+   :pyobject: Python.setup_dependent_package
+   :linenos:
+
+This allows most python packages to have a very simple install procedure,
+like the following:
 
 .. code-block:: python
 
    def install(self, spec, prefix):
-       python('setup.py', 'install', '--prefix={0}'.format(prefix))
+       setup_py('install', '--prefix={0}'.format(prefix))
+
+Finally the Python package takes also care of the modifications to ``PYTHONPATH``
+to allow dependencies to run correctly:
+
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py
+    :pyobject: Python.setup_dependent_run_environment
+    :linenos:
 
-Python's ``setup_dependent_environment`` method also sets up some
-other variables, creates a directory, and sets up the ``PYTHONPATH``
-so that dependent packages can find their dependencies at build time.
 
 .. _packaging_conflicts:
 
@@ -1972,7 +2300,7 @@ same way that Python does.
 
 Let's look at Python's activate function:
 
-.. literalinclude:: ../../../var/spack/repos/builtin/packages/python/package.py
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py
    :pyobject: Python.activate
    :linenos:
 
@@ -1984,7 +2312,7 @@ Python's setuptools.
 
 Deactivate behaves similarly to activate, but it unlinks files:
 
-.. literalinclude:: ../../../var/spack/repos/builtin/packages/python/package.py
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py
    :pyobject: Python.deactivate
    :linenos:
 
@@ -2426,7 +2754,7 @@ docs at :py:mod:`~.spack.build_systems`, or using the ``spack info`` command:
 
 Typically, phases have default implementations that fit most of the common cases:
 
-.. literalinclude:: ../../../lib/spack/spack/build_systems/autotools.py
+.. literalinclude:: _spack_root/lib/spack/spack/build_systems/autotools.py
     :pyobject: AutotoolsPackage.configure
     :linenos:
 
@@ -2434,7 +2762,7 @@ It is thus just sufficient for a packager to override a few
 build system specific helper methods or attributes to provide, for instance,
 configure arguments:
 
-.. literalinclude::  ../../../var/spack/repos/builtin/packages/m4/package.py
+.. literalinclude::  _spack_root/var/spack/repos/builtin/packages/m4/package.py
     :pyobject: M4.configure_args
     :linenos:
 
@@ -2609,7 +2937,7 @@ Shell command functions
 
 Recall the install method from ``libelf``:
 
-.. literalinclude::  ../../../var/spack/repos/builtin/packages/libelf/package.py
+.. literalinclude::  _spack_root/var/spack/repos/builtin/packages/libelf/package.py
    :pyobject: Libelf.install
    :linenos:
 
@@ -2692,8 +3020,7 @@ as arguments.
 
 Here are the definitions of the three built-in flag handlers:
 
-   def build_system_flags(self, name, flags):
-       return (None, None, flags)
+.. code-block:: python
 
    def inject_flags(pkg, name, flags):
        return (flags, None, None)
@@ -2961,6 +3288,137 @@ the two functions is that ``satisfies()`` tests whether spec
 constraints overlap at all, while ``in`` tests whether a spec or any
 of its dependencies satisfy the provided spec.
 
+^^^^^^^^^^^^^^^^^^^^^^^
+Architecture specifiers
+^^^^^^^^^^^^^^^^^^^^^^^
+
+As mentioned in :ref:`support-for-microarchitectures` each node in a concretized spec
+object has an architecture attribute which is a triplet of ``platform``, ``os`` and ``target``.
+Each of these three items can be queried to take decisions when configuring, building or
+installing a package.
+
+""""""""""""""""""""""""""""""""""""""""""""""
+Querying the platform and the operating system
+""""""""""""""""""""""""""""""""""""""""""""""
+
+Sometimes the actions to be taken to install a package might differ depending on the
+platform we are installing for. If that is the case we can use conditionals:
+
+.. code-block:: python
+
+   if spec.platform == 'darwin':
+       # Actions that are specific to Darwin
+       args.append('--darwin-specific-flag')
+
+and branch based on the current spec platform. If we need to make a package directive
+conditional on the platform we can instead employ the usual spec syntax and pass the
+corresponding constraint to the appropriate argument of that directive:
+
+.. code-block:: python
+
+   class Libnl(AutotoolsPackage):
+
+       conflicts('platform=darwin', msg='libnl requires FreeBSD or Linux')
+
+Similar considerations are also valid for the ``os`` part of a spec's architecture.
+For instance:
+
+.. code-block:: python
+
+   class Glib(AutotoolsPackage)
+
+       patch('old-kernels.patch', when='os=centos6')
+
+will apply the patch only when the operating system is Centos 6.
+
+.. note::
+
+   Even though experienced Python programmers might recognize that there are other ways
+   to retrieve information on the platform:
+
+   .. code-block:: python
+
+      if sys.platform == 'darwin':
+          # Actions that are specific to Darwin
+          args.append('--darwin-specific-flag')
+
+   querying the spec architecture's platform should be considered the preferred. The key difference
+   is that a query on ``sys.platform``, or anything similar, is always bound to the host on which the
+   interpreter running Spack is located and as such it won't work correctly in environments where
+   cross-compilation is required.
+
+"""""""""""""""""""""""""""""""""""""
+Querying the target microarchitecture
+"""""""""""""""""""""""""""""""""""""
+
+The third item of the architecture tuple is the ``target`` which abstracts the information on the
+CPU microarchitecture. A list of all the targets known to Spack can be obtained via the
+command line:
+
+.. command-output:: spack arch --known-targets
+
+Within directives each of the names above can be used to match a particular target:
+
+.. code-block:: python
+
+   class Julia(Package):
+       # This patch is only applied on icelake microarchitectures
+       patch("icelake.patch", when="target=icelake")
+
+It's also possible to select all the architectures belonging to the same family
+using an open range:
+
+.. code-block:: python
+
+   class Julia(Package):
+       # This patch is applied on all x86_64 microarchitectures.
+       # The trailing colon that denotes an open range of targets
+       patch("generic_x86_64.patch", when="target=x86_64:")
+
+in a way that resembles what was shown in :ref:`versions-and-fetching` for versions.
+Where ``target`` objects really shine though is when they are used in methods
+called at configure, build or install time. In that case we can test targets
+for supported features, for instance:
+
+.. code-block:: python
+
+   if 'avx512' in spec.target:
+       args.append('--with-avx512')
+
+The snippet above will append the ``--with-avx512`` item to a list of arguments only if the corresponding
+feature is supported by the current target. Sometimes we need to take different actions based
+on the architecture family and not on the specific microarchitecture. In those cases
+we can check the ``family`` attribute:
+
+.. code-block:: python
+
+   if spec.target.family == 'ppc64le':
+       args.append('--enable-power')
+
+Possible values for the ``family`` attribute are displayed by ``spack arch --known-targets``
+under the "Generic architectures (families)" header.
+Finally it's possible to perform actions based on whether the current microarchitecture
+is compatible with a known one:
+
+.. code-block:: python
+
+   if spec.target > 'haswell':
+       args.append('--needs-at-least-haswell')
+
+The snippet above will add an item to a list of configure options only if the current
+architecture is a superset of ``haswell`` or, said otherwise, only if the current
+architecture is a later microarchitecture still compatible with ``haswell``.
+
+.. admonition:: Using Spack on unknown microarchitectures
+
+   If Spack is used on an unknown microarchitecture it will try to perform a best match
+   of the features it detects and will select the closest microarchitecture it has
+   information for. In case nothing matches, it will create on the fly a new generic
+   architecture. This is done to allow users to still be able to use Spack
+   for their work. The software built won't be probably as optimized as it could but just
+   as you need a newer compiler to build for newer architectures, you may need newer
+   versions of Spack for new architectures to be correctly labeled.
+
 ^^^^^^^^^^^^^^^^^^^^^^
 Accessing Dependencies
 ^^^^^^^^^^^^^^^^^^^^^^
@@ -3269,7 +3727,7 @@ the one passed to install, only the MPI implementations all set some
 additional properties on it to help you out.  E.g., in mvapich2, you'll
 find this:
 
-.. literalinclude:: ../../../var/spack/repos/builtin/packages/mvapich2/package.py
+.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/mvapich2/package.py
    :pyobject: Mvapich2.setup_dependent_package
 
 That code allows the mvapich2 package to associate an ``mpicc`` property
@@ -3604,7 +4062,6 @@ variant names are:
   Name    Default   Description
   ======= ======== ========================
   shared   True     Build shared libraries
-  static   True     Build static libraries
   mpi      True     Use MPI
   python   False    Build Python extension
   ======= ======== ========================
@@ -3612,6 +4069,12 @@ variant names are:
 If specified in this table, the corresponding default should be used
 when declaring a variant.
 
+The semantics of the `shared` variant are important. When a package is
+built `~shared`, the package guarantees that no shared libraries are
+built. When a package is built `+shared`, the package guarantees that
+shared libraries are built, but it makes no guarantee about whether
+static libraries are built.
+
 ^^^^^^^^^^^^^
 Version Lists
 ^^^^^^^^^^^^^
@@ -3658,7 +4121,8 @@ The first step of ``spack install``.  Takes a spec and determines the
 correct download URL to use for the requested package version, then
 downloads the archive, checks it against an MD5 checksum, and stores
 it in a staging directory if the check was successful.  The staging
-directory will be located under ``$SPACK_HOME/var/spack``.
+directory will be located under the first writable directory in the
+``build_stage`` configuration setting.
 
 When run after the archive has already been downloaded, ``spack
 fetch`` is idempotent and will not download the archive again.
@@ -3781,32 +4245,36 @@ Spack provides the ``spack graph`` command for graphing dependencies.
 The command by default generates an ASCII rendering of a spec's
 dependency graph.  For example:
 
-.. command-output:: spack graph mpileaks
+.. command-output:: spack graph hdf5
 
 At the top is the root package in the DAG, with dependency edges emerging
 from it.  On a color terminal, the edges are colored by which dependency
 they lead to.
 
-.. command-output:: spack graph --deptype=all mpileaks
+.. command-output:: spack graph --deptype=link hdf5
 
 The ``deptype`` argument tells Spack what types of dependencies to graph.
 By default it includes link and run dependencies but not build
-dependencies.  Supplying ``--deptype=all`` will show the build
-dependencies as well.  This is equivalent to
-``--deptype=build,link,run``.  Options for ``deptype`` include:
+dependencies.  Supplying ``--deptype=link`` will show only link
+dependencies.  The default is ``--deptype=all``, which is equivalent to
+``--deptype=build,link,run,test``.  Options for ``deptype`` include:
 
-* Any combination of ``build``, ``link``, and ``run`` separated by
-  commas.
-* ``all`` or ``alldeps`` for all types of dependencies.
+* Any combination of ``build``, ``link``, ``run``, and ``test`` separated
+  by commas.
+* ``all`` for all types of dependencies.
 
 You can also use ``spack graph`` to generate graphs in the widely used
-`Dot <http://www.graphviz.org/doc/info/lang.html>`_ format.  For
-example:
+`Dot <http://www.graphviz.org/doc/info/lang.html>`_ format.  For example:
 
-.. command-output:: spack graph --dot mpileaks
+.. command-output:: spack graph --dot hdf5
 
 This graph can be provided as input to other graphing tools, such as
-those in `Graphviz <http://www.graphviz.org>`_.
+those in `Graphviz <http://www.graphviz.org>`_.  If you have graphviz
+installed, you can write straight to PDF like this:
+
+.. code-block:: console
+
+   $ spack graph --dot hdf5 | dot -Tpdf > hdf5.pdf
 
 .. _packaging-shell-support:
 
@@ -3986,7 +4454,7 @@ translate variant flags into CMake definitions.  For example:
 
 .. code-block:: python
 
-   def configure_args(self):
+   def cmake_args(self):
        spec = self.spec
        return [
            '-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'),
@@ -4033,3 +4501,8 @@ Autotools-based packages would be easy (and should be done by a
 developer who actively uses Autotools).  Packages that use
 non-standard build systems can gain ``setup`` functionality by
 subclassing ``StagedPackage`` directly.
+
+.. Emacs local variables
+   Local Variables:
+   fill-column: 79
+   End:

lib/spack/docs/pipelines.rst

@@ -0,0 +1,439 @@
+.. 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)
+
+.. _pipelines:
+
+=========
+Pipelines
+=========
+
+Spack provides commands that support generating and running automated build
+pipelines designed for Gitlab CI.  At the highest level it works like this:
+provide a spack environment describing the set of packages you care about,
+and include within that environment file a description of how those packages
+should be mapped to Gitlab runners.  Spack can then generate a ``.gitlab-ci.yml``
+file containing job descriptions for all your packages that can be run by a
+properly configured Gitlab CI instance.  When run, the generated pipeline will
+build and deploy binaries, and it can optionally report to a CDash instance
+regarding the health of the builds as they evolve over time.
+
+------------------------------
+Getting started with pipelines
+------------------------------
+
+It is fairly straightforward to get started with automated build pipelines.  At
+a minimum, you'll need to set up a Gitlab instance (more about Gitlab CI
+`here <https://about.gitlab.com/product/continuous-integration/>`_) and configure
+at least one `runner <https://docs.gitlab.com/runner/>`_.  Then the basic steps
+for setting up a build pipeline are as follows:
+
+#. Create a repository on your gitlab instance
+#. Add a ``spack.yaml`` at the root containing your pipeline environment (see
+   below for details)
+#. Add a ``.gitlab-ci.yml`` at the root containing a single job, similar to
+   this one:
+
+   .. code-block:: yaml
+
+      pipeline-job:
+        tags:
+          - <custom-tag>
+          ...
+        script:
+          - spack ci start
+
+#. Add any secrets required by the CI process to environment variables using the
+   CI web ui
+#. Push a commit containing the ``spack.yaml`` and ``.gitlab-ci.yml`` mentioned above
+   to the gitlab repository
+
+The ``<custom-tag>``, above, is used to pick one of your configured runners,
+while the use of the ``spack ci start`` command implies that runner has an
+appropriate version of spack installed and configured for use.  Of course, there
+are myriad ways to customize the process.  You can configure CDash reporting
+on the progress of your builds, set up S3 buckets to mirror binaries built by
+the pipeline, clone a custom spack repository/ref for use by the pipeline, and
+more.
+
+While it is possible to set up pipelines on gitlab.com, the builds there are
+limited to 60 minutes and generic hardware.  It is also possible to
+`hook up <https://about.gitlab.com/blog/2018/04/24/getting-started-gitlab-ci-gcp>`_
+Gitlab to Google Kubernetes Engine (`GKE <https://cloud.google.com/kubernetes-engine/>`_)
+or Amazon Elastic Kubernetes Service (`EKS <https://aws.amazon.com/eks>`_), though those
+topics are outside the scope of this document.
+
+-----------------------------------
+Spack commands supporting pipelines
+-----------------------------------
+
+Spack provides a command `ci` with sub-commands for doing various things related
+to automated build pipelines.  All of the ``spack ci ...`` commands must be run
+from within a environment, as each one makes use of the environment for different
+purposes.  Additionally, some options to the commands (or conditions present in
+the spack environment file) may require particular environment variables to be
+set in order to function properly.  Examples of these are typically secrets
+needed for pipeline operation that should not be visible in a spack environment
+file.  These environment variables are described in more detail
+:ref:`ci_environment_variables`.
+
+.. _cmd_spack_ci:
+
+^^^^^^^^^^^^^^^^^^
+``spack ci``
+^^^^^^^^^^^^^^^^^^
+
+Super-command for functionality related to generating pipelines and executing
+pipeline jobs.
+
+.. _cmd_spack_ci_start:
+
+^^^^^^^^^^^^^^^^^^
+``spack ci start``
+^^^^^^^^^^^^^^^^^^
+
+Currently this command is a short-cut to first run ``spack ci generate``, followed
+by ``spack ci pushyaml``.
+
+.. _cmd_spack_ci_generate:
+
+^^^^^^^^^^^^^^^^^^^^^
+``spack ci generate``
+^^^^^^^^^^^^^^^^^^^^^
+
+Concretizes the specs in the active environment, stages them (as described in
+:ref:`staging_algorithm`), and writes the resulting ``.gitlab-ci.yml`` to disk.
+
+.. _cmd_spack_ci_pushyaml:
+
+^^^^^^^^^^^^^^^^^^^^^
+``spack ci pushyaml``
+^^^^^^^^^^^^^^^^^^^^^
+
+Generates a commit containing the generated ``.gitlab-ci.yml`` and pushes it to a
+``DOWNSTREAM_CI_REPO``, which is frequently the same repository.  The branch
+created has the same name as the current branch being tested, but has ``multi-ci-``
+prepended to the branch name.  Once Gitlab CI has full support for dynamically
+defined workloads, this command will be deprecated.
+
+.. _cmd_spack_ci_rebuild:
+
+^^^^^^^^^^^^^^^^^^^^
+``spack ci rebuild``
+^^^^^^^^^^^^^^^^^^^^
+
+This sub-command is responsible for ensuring a single spec from the release
+environment is up to date on the remote mirror configured in the environment,
+and as such, corresponds to a single job in the ``.gitlab-ci.yml`` file.
+
+------------------------------------
+A pipeline-enabled spack environment
+------------------------------------
+
+Here's an example of a spack environment file that has been enhanced with
+sections desribing a build pipeline:
+
+.. code-block:: yaml
+
+   spack:
+     definitions:
+     - pkgs:
+       - readline@7.0
+     - compilers:
+       - '%gcc@5.5.0'
+     - oses:
+       - os=ubuntu18.04
+       - os=centos7
+     specs:
+     - matrix:
+       - [$pkgs]
+       - [$compilers]
+       - [$oses]
+     mirrors:
+       cloud_gitlab: https://mirror.spack.io
+     gitlab-ci:
+       mappings:
+         - match:
+             - os=ubuntu18.04
+           runner-attributes:
+             tags:
+               - spack-k8s
+             image: spack/spack_builder_ubuntu_18.04
+         - match:
+             - os=centos7
+           runner-attributes:
+             tags:
+               - spack-k8s
+             image: spack/spack_builder_centos_7
+     cdash:
+       build-group: Release Testing
+       url: https://cdash.spack.io
+       project: Spack
+       site: Spack AWS Gitlab Instance
+
+Hopefully, the ``definitions``, ``specs``, ``mirrors``, etc. sections are already
+familiar, as they are part of spack :ref:`environments`.  So let's take a more
+in-depth look some of the pipeline-related sections in that environment file
+that might not be as familiar.
+
+The ``gitlab-ci`` section is used to configure how the pipeline workload should be
+generated, mainly how the jobs for building specs should be assigned to the
+configured runners on your instance.  Each entry within the list of ``mappings``
+corresponds to a known gitlab runner, where the ``match`` section is used
+in assigning a release spec to one of the runners, and the ``runner-attributes``
+section is used to configure the spec/job for that particular runner.
+
+There are other pipeline options you can configure within the ``gitlab-ci`` section
+as well.  The ``bootstrap`` section allows you to specify lists of specs from
+your ``definitions`` that should be staged ahead of the environment's ``specs`` (this
+section is described in more detail below).  The ``enable-artifacts-buildcache`` key
+takes a boolean and determines whether the pipeline uses artifacts to store and
+pass along the buildcaches from one stage to the next (the default if you don't
+provide this option is ``False``).  The ``enable-debug-messages`` key takes a boolean
+and allows you to choose whether the pipeline build jobs are run as ``spack -d ci rebuild``
+or just ``spack ci rebuild`` (the default is not to enable debug messages).  The
+``final-stage-rebuild-index`` section controls whether an extra job is added to the
+end of your pipeline (in a stage by itself) which will regenerate the mirror's
+buildcache index.  Under normal operation, each pipeline job that rebuilds a package
+will re-generate the mirror's buildcache index after the buildcache entry for that
+job has been created and pushed to the mirror.  Since jobs in the same stage can run in
+parallel, there is the possibility that at the end of some stage, the index may not
+reflect all the binaries in the buildcache.  Adding the ``final-stage-rebuild-index``
+section ensures that at the end of the pipeline, the index will be in sync with the
+binaries on the mirror.  If the mirror lives in an S3 bucket, this job will need to
+run on a machine with the Python ``boto3`` module installed, and consequently the
+``final-stage-rebuild-index`` needs to specify a list of ``tags`` to pick a runner
+satisfying that condition.  It can also take an ``image`` key so Docker executor type
+runners can pick the right image for the index regeneration job.
+
+The optional ``cdash`` section provides information that will be used by the
+``spack ci generate`` command (invoked by ``spack ci start``) for reporting
+to CDash.  All the jobs generated from this environment will belong to a
+"build group" within CDash that can be tracked over time.  As the release
+progresses, this build group may have jobs added or removed. The url, project,
+and site are used to specify the CDash instance to which build results should
+be reported.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Assignment of specs to runners
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``mappings`` section corresponds to a list of runners, and during assignment
+of specs to runners, the list is traversed in order looking for matches, the
+first runner that matches a release spec is assigned to build that spec.  The
+``match`` section within each runner mapping section is a list of specs, and
+if any of those specs match the release spec (the ``spec.satisfies()`` method
+is used), then that runner is considered a match.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Configuration of specs/jobs for a runner
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Once a runner has been chosen to build a release spec, the ``runner-attributes``
+section provides information determining details of the job in the context of
+the runner.  The ``runner-attributes`` section must have a ``tags`` key, which
+is a list containing at least one tag used to select the runner from among the
+runners known to the gitlab instance.  For Docker executor type runners, the
+``image`` key is used to specify the Docker image used to build the release spec
+(and could also appear as a dictionary with a ``name`` specifying the image name,
+as well as an ``entrypoint`` to override whatever the default for that image is).
+For other types of runners the ``variables`` key will be useful to pass any
+information on to the runner that it needs to do its work (e.g. scheduler
+parameters, etc.).
+
+.. _staging_algorithm:
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Summary of ``.gitlab-ci.yml`` generation algorithm
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+All specs yielded by the matrix (or all the specs in the environment) have their
+dependencies computed, and the entire resulting set of specs are staged together
+before being run through the ``gitlab-ci/mappings`` entries, where each staged
+spec is assigned a runner.  "Staging" is the name we have given to the process
+of figuring out in what order the specs should be built, taking into consideration
+Gitlab CI rules about jobs/stages.  In the staging process the goal is to maximize
+the number of jobs in any stage of the pipeline, while ensuring that the jobs in
+any stage only depend on jobs in previous stages (since those jobs are guaranteed
+to have completed already).  As a runner is determined for a job, the information
+in the ``runner-attributes`` is used to populate various parts of the job
+description that will be used by Gitlab CI. Once all the jobs have been assigned
+a runner, the ``.gitlab-ci.yml`` is written to disk.
+
+The short example provided above would result in the ``readline``, ``ncurses``,
+and ``pkgconf`` packages getting staged and built on the runner chosen by the
+``spack-k8s`` tag.  In this example, we assume the runner is a Docker executor
+type runner, and thus certain jobs will be run in the ``centos7`` container,
+and others in the ``ubuntu-18.04`` container.  The resulting ``.gitlab-ci.yml``
+will contain 6 jobs in three stages.  Once the jobs have been generated, the
+presence of a ``SPACK_CDASH_AUTH_TOKEN`` environment variable during the
+``spack ci generate`` command would result in all of the jobs being put in a
+build group on CDash called "Release Testing" (that group will be created if
+it didn't already exist).
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Optional compiler bootstrapping
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Spack pipelines also have support for bootstrapping compilers on systems that
+may not already have the desired compilers installed. The idea here is that
+you can specify a list of things to bootstrap in your ``definitions``, and
+spack will guarantee those will be installed in a phase of the pipeline before
+your release specs, so that you can rely on those packages being available in
+the binary mirror when you need them later on in the pipeline.  At the moment
+the only viable use-case for bootstrapping is to install compilers.
+
+Here's an example of what bootstrapping some compilers might look like:
+
+.. code-block:: yaml
+
+   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
+     - 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'
+     gitlab-ci:
+       bootstrap:
+         - name: compiler-pkgs
+           compiler-agnostic: true
+       mappings:
+         # mappings similar to the example higher up in this description
+         ...
+
+In the example above, we have added a list to the ``definitions`` called
+``compiler-pkgs`` (you can add any number of these), which lists compiler packages
+we want to be staged ahead of the full matrix of release specs (which consists
+only of readline in our example).  Then within the ``gitlab-ci`` section, we
+have added a ``bootstrap`` section, which can contain a list of items, each
+referring to a list in the ``definitions`` section.  These items can either
+be a dictionary or a string.  If you supply a dictionary, it must have a name
+key whose value must match one of the lists in definitions and it can have a
+``compiler-agnostic`` key whose value is a boolean.  If you supply a string,
+then it needs to match one of the lists provided in ``definitions``.  You can
+think of the bootstrap list as an ordered list of pipeline "phases" that will
+be staged before your actual release specs.  While this introduces another
+layer of bottleneck in the pipeline (all jobs in all stages of one phase must
+complete before any jobs in the next phase can begin), it also means you are
+guaranteed your bootstrapped compilers will be available when you need them.
+
+The ``compiler-agnostic`` key can be provided with each item in the
+bootstrap list. It tells the ``spack ci generate`` command that any jobs staged
+from that particular list should have the compiler removed from the spec, so
+that any compiler available on the runner where the job is run can be used to
+build the package.
+
+When including a bootstrapping phase as in the example above, the result is that
+the bootstrapped compiler packages will be pushed to the binary mirror (and the
+local artifacts mirror) before the actual release specs are built. In this case,
+the jobs corresponding to subsequent release specs are configured to
+``install_missing_compilers``, so that if spack is asked to install a package
+with a compiler it doesn't know about, it can be quickly installed from the
+binary mirror first.
+
+Since bootstrapping compilers is optional, those items can be left out of the
+environment/stack file, and in that case no bootstrapping will be done (only the
+specs will be staged for building) and the runners will be expected to already
+have all needed compilers installed and configured for spack to use.
+
+-------------------------------------
+Using a custom spack in your pipeline
+-------------------------------------
+
+If your runners will not have a version of spack ready to invoke, or if for some
+other reason you want to use a custom version of spack to run your pipelines,
+this can be accomplished fairly simply.  First, create CI environment variables
+containing the url and branch/tag you want to clone (calling them, for example,
+``SPACK_REPO`` and ``SPACK_REF``), use them to clone spack in your pre-ci
+``before_script``, and finally pass those same values along to the workload
+generation process via the ``spack-repo`` and ``spack-ref`` cli args.  Here's
+an example:
+
+.. code-block:: yaml
+
+   pipeline-job:
+     tags:
+       - <some-other-tag>
+   before_script:
+     - git clone ${SPACK_REPO} --branch ${SPACK_REF}
+     - . ./spack/share/spack/setup-env.sh
+   script:
+     - spack ci start --spack-repo ${SPACK_REPO} --spack-ref ${SPACK_REF} <...args>
+   after_script:
+     - rm -rf ./spack
+
+If the ``spack ci start`` command receives those extra command line arguments,
+then it adds similar ``before_script`` and ``after_script`` sections for each of
+the ``spack ci rebuild`` jobs it generates (cloning and sourcing a custom
+spack in the ``before_script`` and removing it again in the ``after_script``).
+This gives you control over the version of spack used when the rebuild jobs
+are actually run on the gitlab runner.
+
+.. _ci_environment_variables:
+
+--------------------------------------------------
+Environment variables affecting pipeline operation
+--------------------------------------------------
+
+Certain secrets and some other information should be provided to the pipeline
+infrastructure via environment variables, usually for reasons of security, but
+in some cases to support other pipeline use cases such as PR testing.  The
+environment variables used by the pipeline infrastructure are described here.
+
+^^^^^^^^^^^^^^^^^
+AWS_ACCESS_KEY_ID
+^^^^^^^^^^^^^^^^^
+
+Needed when binary mirror is an S3 bucket.
+
+^^^^^^^^^^^^^^^^^^^^^
+AWS_SECRET_ACCESS_KEY
+^^^^^^^^^^^^^^^^^^^^^
+
+Needed when binary mirror is an S3 bucket.
+
+^^^^^^^^^^^^^^^
+S3_ENDPOINT_URL
+^^^^^^^^^^^^^^^
+
+Needed when binary mirror is an S3 bucket that is *not* on AWS.
+
+^^^^^^^^^^^^^^^^^
+CDASH_AUTH_TOKEN
+^^^^^^^^^^^^^^^^^
+
+Needed in order to report build groups to CDash.
+
+^^^^^^^^^^^^^^^^^
+SPACK_SIGNING_KEY
+^^^^^^^^^^^^^^^^^
+
+Needed to sign/verify binary packages from the remote binary mirror.
+
+^^^^^^^^^^^^^^^^^^
+DOWNSTREAM_CI_REPO
+^^^^^^^^^^^^^^^^^^
+
+Needed until Gitlab CI supports dynamic job generation.  Can contain connection
+credentials, and could be the same repository or a different one.

lib/spack/docs/repositories.rst

@@ -1,4 +1,4 @@
-.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+.. Copyright 2013-2020 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)

lib/spack/docs/requirements.txt

@@ -1,6 +1,7 @@
 # These dependencies should be installed using pip in order
 # to build the documentation.
 
-sphinx==1.7.0
+sphinx
 sphinxcontrib-programoutput
 sphinx-rtd-theme
+python-levenshtein

lib/spack/docs/spack.yaml

@@ -0,0 +1,19 @@
+# Copyright 2013-2020 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)
+
+#
+# These are requirements for building the documentation.  You can run
+# these commands in this directory to install Sphinx and its plugins,
+# then build the docs:
+#
+#     spack install
+#     spack env activate .
+#     make
+#
+spack:
+  specs:
+  - py-sphinx
+  - py-sphinxcontrib-programoutput
+  - py-sphinx-rtd-theme

lib/spack/docs/tutorial.rst

@@ -1,60 +0,0 @@
-.. Copyright 2013-2018 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)
-
-.. _spack-101:
-
-=============================
-Tutorial: Spack 101
-=============================
-
-This is a full-day introduction to Spack with lectures and live demos.  It
-was presented as a tutorial at `Supercomputing 2018
-<http://sc18.supercomputing.org>`_.  You can use these materials to teach
-a course on Spack at your own site, or you can just skip ahead and read
-the live demo scripts to see how Spack is used in practice.
-
-.. _sc16-slides:
-
-.. rubric:: Slides
-
-.. figure:: tutorial/sc16-tutorial-slide-preview.png
-   :target: http://spack.io/slides/Spack-SC18-Tutorial.pdf
-   :height: 72px
-   :align: left
-   :alt: Slide Preview
-
-`Download Slides <http://spack.io/slides/Spack-SC18-Tutorial.pdf>`_.
-
-**Full citation:** Todd Gamblin, Gregory Becker, Massimiliano Culpo, Matt
-Legendre, Mario Melara, Peter Scheibel, and Adam Stewart.
-`Managing HPC Software Complexity with Spack
-<https://sc18.supercomputing.org/presentation/?id=tut165&sess=sess252>`_.
-Tutorial presented at Supercomputing 2018. November 12, 2018, Dallas, TX, USA.
-
-.. _sc16-live-demos:
-
-.. rubric:: Live Demos
-
-These scripts will take you step-by-step through basic Spack tasks.  They
-correspond to sections in the slides above.
-
-  1. :ref:`basics-tutorial`
-  2. :ref:`configs-tutorial`
-  3. :ref:`packaging-tutorial`
-  4. :ref:`environments-tutorial`
-  5. :ref:`modules-tutorial`
-  6. :ref:`build-systems-tutorial`
-  7. :ref:`advanced-packaging-tutorial`
-
-Full contents:
-
-.. toctree::
-   tutorial_basics
-   tutorial_configuration
-   tutorial_packaging
-   tutorial_environments
-   tutorial_modules
-   tutorial_buildsystems
-   tutorial_advanced_packaging

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

@@ -1,39 +0,0 @@
-# Copyright 2013-2018 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 is a template package file for Spack.  We've put "FIXME"
-# next to all the things you'll want to change. Once you've handled
-# them, you can save this file and test your package like this:
-#
-#     spack install mpileaks
-#
-# You can edit this file again by typing:
-#
-#     spack edit mpileaks
-#
-# See the Spack documentation for more information on packaging.
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
-from spack import *
-
-
-class Mpileaks(Package):
-    """FIXME: Put a proper description of your package here."""
-
-    # FIXME: Add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    # FIXME: Add dependencies if required.
-    # depends_on('foo')
-
-    def install(self, spec, prefix):
-        # FIXME: Unknown build system
-        make()
-        make('install')

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

@@ -1,23 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Mpileaks(Package):
-    """Tool to detect and report MPI objects like MPI_Requests and
-    MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"  # NOQA
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    # FIXME: Add dependencies if required.
-    # depends_on('foo')
-
-    def install(self, spec, prefix):
-        # FIXME: Unknown build system
-        make()
-        make('install')

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

@@ -1,25 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Mpileaks(Package):
-    """Tool to detect and report MPI objects like MPI_Requests and
-    MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    depends_on('mpi')
-    depends_on('adept-utils')
-    depends_on('callpath')
-
-    def install(self, spec, prefix):
-        # FIXME: Unknown build system
-        make()
-        make('install')

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

@@ -1,25 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Mpileaks(Package):
-    """Tool to detect and report MPI objects like MPI_Requests and
-    MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    depends_on('mpi')
-    depends_on('adept-utils')
-    depends_on('callpath')
-
-    def install(self, spec, prefix):
-        configure()
-        make()
-        make('install')

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

@@ -1,27 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Mpileaks(Package):
-    """Tool to detect and report MPI objects like MPI_Requests and
-    MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    depends_on('mpi')
-    depends_on('adept-utils')
-    depends_on('callpath')
-
-    def install(self, spec, prefix):
-        configure('--with-adept-utils=%s' % self.spec['adept-utils'].prefix,
-                  '--with-callpath=%s' % self.spec['callpath'].prefix,
-                  '--prefix=%s' % self.spec.prefix)
-        make()
-        make('install')

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

@@ -1,34 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Mpileaks(Package):
-    """Tool to detect and report MPI objects like MPI_Requests and
-    MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    variant('stackstart', values=int, default=0, description='Specify the number of stack frames to truncate.')
-
-    depends_on('mpi')
-    depends_on('adept-utils')
-    depends_on('callpath')
-
-    def install(self, spec, prefix):
-        stackstart = int(self.spec.variants['stackstart'].value)
-        confargs = ['--with-adept-utils=%s' % self.spec['adept-utils'].prefix,
-                    '--with-callpath=%s' % self.spec['callpath'].prefix,
-                    '--prefix=%s' % self.spec.prefix]
-        if stackstart:
-            confargs.extend(['--with-stack-start-c=%s' % stackstart,
-                             '--with-stack-start-fortran=%s' % stackstart])
-        configure(*confargs)
-        make()
-        make('install')

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

@@ -1,27 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Mpileaks(AutotoolsPackage):
-    """Tool to detect and report leaked MPI objects like MPI_Requests and
-       MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    depends_on("mpi")
-    depends_on("adept-utils")
-    depends_on("callpath")
-
-    def install(self, spec, prefix):
-        configure("--prefix=" + prefix,
-                  "--with-adept-utils=" + spec['adept-utils'].prefix,
-                  "--with-callpath=" + spec['callpath'].prefix)
-        make()
-        make("install")

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

@@ -1,32 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Mpileaks(AutotoolsPackage):
-    """Tool to detect and report leaked MPI objects like MPI_Requests and
-       MPI_Datatypes."""
-
-    homepage = "https://github.com/hpc/mpileaks"
-    url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
-    version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
-    variant("stackstart", values=int, default=0,
-            description="Specify the number of stack frames to truncate")
-
-    depends_on("mpi")
-    depends_on("adept-utils")
-    depends_on("callpath")
-
-    def configure_args(self):
-        stackstart = int(self.spec.variants['stackstart'].value)
-        args = ["--with-adept-utils=" + spec['adept-utils'].prefix,
-                "--with-callpath=" + spec['callpath'].prefix]
-        if stackstart:
-            args.extend(['--with-stack-start-c=%s' % stackstart,
-                         '--with-stack-start-fortran=%s' % stackstart])
-        return args

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

@@ -1,41 +0,0 @@
-# Copyright 2013-2018 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 is a template package file for Spack.  We've put "FIXME"
-# next to all the things you'll want to change. Once you've handled
-# them, you can save this file and test your package like this:
-#
-#     spack install callpath
-#
-# You can edit this file again by typing:
-#
-#     spack edit callpath
-#
-# See the Spack documentation for more information on packaging.
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
-from spack import *
-
-
-class Callpath(CMakePackage):
-    """FIXME: Put a proper description of your package here."""
-
-    # FIXME: Add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
-    url      = "https://github.com/llnl/callpath/archive/v1.0.1.tar.gz"
-
-    version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a')
-
-    # FIXME: Add dependencies if required.
-    # depends_on('foo')
-
-    def cmake_args(self):
-        # FIXME: Add arguments other than
-        # FIXME: CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE
-        # FIXME: If not needed delete this function
-        args = []
-        return args

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

@@ -1,23 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Callpath(CMakePackage):
-    """Library for representing callpaths consistently in
-       distributed-memory performance tools."""
-
-    homepage = "https://github.com/llnl/callpath"
-    url      = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz"
-
-    version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a')
-
-    depends_on("elf", type="link")
-    depends_on("libdwarf")
-    depends_on("dyninst")
-    depends_on("adept-utils")
-    depends_on("mpi")
-    depends_on("cmake@2.8:", type="build")

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

@@ -1,33 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Callpath(CMakePackage):
-    """Library for representing callpaths consistently in
-       distributed-memory performance tools."""
-
-    homepage = "https://github.com/llnl/callpath"
-    url      = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz"
-
-    version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a')
-
-    depends_on("elf", type="link")
-    depends_on("libdwarf")
-    depends_on("dyninst")
-    depends_on("adept-utils")
-    depends_on("mpi")
-    depends_on("cmake@2.8:", type="build")
-
-    def cmake_args(self):
-        args = ["-DCALLPATH_WALKER=dyninst"]
-
-        if self.spec.satisfies("^dyninst@9.3.0:"):
-            std.flag = self.compiler.cxx_flag
-            args.append("-DCMAKE_CXX_FLAGS='{0}' -fpermissive'".format(
-                std_flag))
-
-        return args

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

@@ -1,26 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Bowtie(MakefilePackage):
-    """FIXME: Put a proper description of your package here."""
-
-    # FIXME: Add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
-    url      = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
-    version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
-    # FIXME: Add dependencies if required.
-    # depends_on('foo')
-
-    def edit(self, spec, prefix):
-        # FIXME: Edit the Makefile if necessary
-        # FIXME: If not needed delete this function
-        # makefile = FileFilter('Makefile')
-        # makefile.filter('CC = .*', 'CC = cc')
-        return

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

@@ -1,27 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Bowtie(MakefilePackage):
-    """Bowtie is an ultrafast, memory efficient short read aligner
-    for short DNA sequences (reads) from next-gen sequencers."""
-
-    homepage = "https://sourceforge.net/projects/bowtie-bio/"
-    url      = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
-    version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
-    variant("tbb", default=False, description="Use Intel thread building block")
-
-    depends_on("tbb", when="+tbb")
-
-    def edit(self, spec, prefix):
-        # FIXME: Edit the Makefile if necessary
-        # FIXME: If not needed delete this function
-        # makefile = FileFilter('Makefile')
-        # makefile.filter('CC = .*', 'CC = cc')
-        return

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

@@ -1,25 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Bowtie(MakefilePackage):
-    """Bowtie is an ultrafast, memory efficient short read aligner
-    for short DNA sequences (reads) from next-gen sequencers."""
-
-    homepage = "https://sourceforge.net/projects/bowtie-bio/"
-    url      = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
-    version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
-    variant("tbb", default=False, description="Use Intel thread building block")
-
-    depends_on("tbb", when="+tbb")
-
-    def edit(self, spec, prefix):
-        makefile = FileFilter("Makefile")
-        makefile.filter('CC= .*', 'CC = ' + env['CC'])
-        makefile.filter('CXX = .*', 'CXX = ' + env['CXX'])

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

@@ -1,36 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class Bowtie(MakefilePackage):
-    """Bowtie is an ultrafast, memory efficient short read aligner
-    for short DNA sequences (reads) from next-gen sequencers."""
-
-    homepage = "https://sourceforge.net/projects/bowtie-bio/"
-    url      = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
-    version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
-    variant("tbb", default=False, description="Use Intel thread building block")
-
-    depends_on("tbb", when="+tbb")
-
-    def edit(self, spec, prefix):
-        makefile = FileFilter("Makefile")
-        makefile.filter('CC= .*', 'CC = ' + env['CC'])
-        makefile.filter('CXX = .*', 'CXX = ' + env['CXX'])
-
-    @property
-    def build_targets(self):
-        if "+tbb" in spec:
-            return []
-        else:
-            return ["NO_TBB=1"]
-
-    @property
-    def install_targets(self):
-        return ['prefix={0}'.format(self.prefix), 'install']

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

@@ -1,41 +0,0 @@
-# Copyright 2013-2018 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 is a template package file for Spack.  We've put "FIXME"
-# next to all the things you'll want to change. Once you've handled
-# them, you can save this file and test your package like this:
-#
-#     spack install py-pandas
-#
-# You can edit this file again by typing:
-#
-#     spack edit py-pandas
-#
-# See the Spack documentation for more information on packaging.
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
-from spack import *
-
-
-class PyPandas(PythonPackage):
-    """FIXME: Put a proper description of your package here."""
-
-    # FIXME: Add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
-    url      = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz"
-
-    version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3')
-
-    # FIXME: Add dependencies if required.
-    # depends_on('py-setuptools', type='build')
-    # depends_on('py-foo',        type=('build', 'run'))
-
-    def build_args(self, spec, prefix):
-        # FIXME: Add arguments other than --prefix
-        # FIXME: If not needed delete this function
-        args = []
-        return args

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

@@ -1,32 +0,0 @@
-# Copyright 2013-2018 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)
-
-from spack import *
-
-
-class PyPandas(PythonPackage):
-    """pandas is a Python package providing fast, flexible, and expressive
-       data structures designed to make working with relational or
-       labeled data both easy and intuitive. It aims to be the
-       fundamental high-level building block for doing practical, real
-       world data analysis in Python. Additionally, it has the broader
-       goal of becoming the most powerful and flexible open source data
-       analysis / manipulation tool available in any language.
-    """
-    homepage = "http://pandas.pydata.org/"
-    url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz"
-
-    version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3')
-    version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
-    version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
-    version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
-
-    depends_on('py-dateutil', type=('build', 'run'))
-    depends_on('py-numpy', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
-    depends_on('py-cython', type='build')
-    depends_on('py-pytz', type=('build', 'run'))
-    depends_on('py-numexpr', type=('build', 'run'))
-    depends_on('py-bottleneck', type=('build', 'run'))

lib/spack/docs/tutorial_advanced_packaging.rst

@@ -1,505 +0,0 @@
-.. Copyright 2013-2018 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)
-
-.. _advanced-packaging-tutorial:
-
-============================
-Advanced Topics in Packaging
-============================
-
-Spack tries to automatically configure packages with information from
-dependencies such that all you need to do is to list the dependencies
-(i.e., with the ``depends_on`` directive) and the build system (for example
-by deriving from :code:`CmakePackage`).
-
-However, there are many special cases. Often you need to retrieve details
-about dependencies to set package-specific configuration options, or to
-define package-specific environment variables used by the package's build
-system. This tutorial covers how to retrieve build information from
-dependencies, and how you can automatically provide important information to
-dependents in your package.
-
-----------------------
-Setup for the tutorial
-----------------------
-
-.. note::
-
-  If you are not using the tutorial docker image, it is recommended that you
-  do this section of the tutorial in a fresh clone of Spack
-
-The tutorial uses custom package definitions with missing sections that
-will be filled in during the tutorial. These package definitions are stored
-in a separate package repository, which can be enabled with:
-
-.. code-block:: console
-
-  $ spack repo add --scope=site var/spack/repos/tutorial
-
-This section of the tutorial may also require a newer version of gcc, which
-you can add with:
-
-.. code-block:: console
-
-  $ spack install gcc@7.2.0
-  $ spack compiler add --scope=site path/to/spack-installed-gcc/bin
-
-If you are using the tutorial docker image, all dependency packages
-will have been installed. Otherwise, to install these packages you can use
-the following commands:
-
-.. code-block:: console
-
-  $ spack install openblas
-  $ spack install netlib-lapack
-  $ spack install mpich
-
-Now, you are ready to set your preferred ``EDITOR`` and continue with
-the rest of the tutorial.
-
-.. note::
-
-  Several of these packages depend on an MPI implementation. You can use
-  OpenMPI if you install it from scratch, but this is slow (>10 min.).
-  A binary cache of MPICH may be provided, in which case you can force
-  the package to use it and install quickly. All tutorial examples with
-  packages that depend on MPICH include the spec syntax for building with it
-
-.. _adv_pkg_tutorial_start:
-
----------------------------------------
-Modifying a package's build environment
----------------------------------------
-
-Spack sets up several environment variables like ``PATH`` by default to aid in
-building a package, but many packages make use of environment variables which
-convey specific information about their dependencies (e.g., ``MPICC``).
-This section covers how to update your Spack packages so that package-specific
-environment variables are defined at build-time.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Set environment variables in dependent packages at build-time
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Dependencies can set environment variables that are required when their
-dependents build. For example, when a package depends on a python extension
-like py-numpy, Spack's ``python`` package will add it to ``PYTHONPATH``
-so it is available at build time; this is required because the default setup
-that spack does is not sufficient for python to import modules.
-
-To provide environment setup for a dependent, a package can implement the
-:py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
-function. This function takes as a parameter a :py:class:`EnvironmentModifications <spack.util.environment.EnvironmentModifications>`
-object which includes convenience methods to update the environment. For
-example, an MPI implementation can set ``MPICC`` for packages that depend on it:
-
-.. code-block:: python
-
-  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-      spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
-
-In this case packages that depend on ``mpi`` will have ``MPICC`` defined in
-their environment when they build. This section is focused on modifying the
-build-time environment represented by ``spack_env``, but it's worth noting that
-modifications to ``run_env`` are included in Spack's automatically-generated
-module files.
-
-We can practice by editing the ``mpich`` package to set the ``MPICC``
-environment variable in the build-time environment of dependent packages.
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit mpich
-
-Once you're finished, the method should look like this:
-
-.. code-block:: python
-
-  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-      spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
-      spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
-      spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
-      spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
-
-      spack_env.set('MPICH_CC', spack_cc)
-      spack_env.set('MPICH_CXX', spack_cxx)
-      spack_env.set('MPICH_F77', spack_f77)
-      spack_env.set('MPICH_F90', spack_fc)
-      spack_env.set('MPICH_FC', spack_fc)
-
-At this point we can, for instance, install ``netlib-scalapack`` with
-``mpich``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich
-  ...
-  ==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
-  ==> No patches needed for netlib-scalapack
-  ==> Building netlib-scalapack [CMakePackage]
-  ==> Executing phase: 'cmake'
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed netlib-scalapack
-    Fetch: 0.01s.  Build: 3m 59.86s.  Total: 3m 59.87s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
-
-
-and double check the environment logs to verify that every variable was
-set to the correct value.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Set environment variables in your own package
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Packages can modify their own build-time environment by implementing the
-:py:func:`setup_environment <spack.package.PackageBase.setup_environment>` function.
-For ``qt`` this looks like:
-
-.. code-block:: python
-
-    def setup_environment(self, spack_env, run_env):
-        spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
-        run_env.set('QTDIR', self.prefix)
-
-When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment.
-
-To contrast with ``qt``'s :py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
-function:
-
-.. code-block:: python
-
-    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        spack_env.set('QTDIR', self.prefix)
-
-Let's see how it works by completing the ``elpa`` package:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit elpa
-
-In the end your method should look like:
-
-.. code-block:: python
-
-  def setup_environment(self, spack_env, run_env):
-      spec = self.spec
-
-      spack_env.set('CC', spec['mpi'].mpicc)
-      spack_env.set('FC', spec['mpi'].mpifc)
-      spack_env.set('CXX', spec['mpi'].mpicxx)
-      spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
-
-      spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags)
-      spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags)
-
-At this point it's possible to proceed with the installation of ``elpa ^mpich``
-
-------------------------------
-Retrieving library information
-------------------------------
-
-Although Spack attempts to help packages locate their dependency libraries
-automatically (e.g. by setting ``PKG_CONFIG_PATH`` and ``CMAKE_PREFIX_PATH``),
-a package may have unique configuration options that are required to locate
-libraries. When a package needs information about dependency libraries, the
-general approach in Spack is to query the dependencies for the locations of
-their libraries and set configuration options accordingly. By default most
-Spack packages know how to automatically locate their libraries. This section
-covers how to retrieve library information from dependencies and how to locate
-libraries when the default logic doesn't work.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Accessing dependency libraries
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-If you need to access the libraries of a dependency, you can do so
-via the ``libs`` property of the spec, for example in the ``arpack-ng``
-package:
-
-.. code-block:: python
-
-    def install(self, spec, prefix):
-        lapack_libs = spec['lapack'].libs.joined(';')
-        blas_libs = spec['blas'].libs.joined(';')
-
-        cmake(*[
-            '-DLAPACK_LIBRARIES={0}'.format(lapack_libs),
-            '-DBLAS_LIBRARIES={0}'.format(blas_libs)
-        ], '.')
-
-Note that ``arpack-ng`` is querying virtual dependencies, which Spack
-automatically resolves to the installed implementation (e.g. ``openblas``
-for ``blas``).
-
-We've started work on a package for ``armadillo``. You should open it,
-read through the comment that starts with ``# TUTORIAL:`` and complete
-the ``cmake_args`` section:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit armadillo
-
-If you followed the instructions in the package, when you are finished your
-``cmake_args`` method should look like:
-
-.. code-block:: python
-
-  def cmake_args(self):
-        spec = self.spec
-
-        return [
-            # ARPACK support
-            '-DARPACK_LIBRARY={0}'.format(spec['arpack-ng'].libs.joined(";")),
-            # BLAS support
-            '-DBLAS_LIBRARY={0}'.format(spec['blas'].libs.joined(";")),
-            # LAPACK support
-            '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].libs.joined(";")),
-            # SuperLU support
-            '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
-            '-DSuperLU_LIBRARY={0}'.format(spec['superlu'].libs.joined(";")),
-            # HDF5 support
-            '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
-        ]
-
-As you can see, getting the list of libraries that your dependencies provide
-is as easy as accessing the their ``libs`` attribute. Furthermore, the interface
-remains the same whether you are querying regular or virtual dependencies.
-
-At this point you can complete the installation of ``armadillo`` using ``openblas``
-as a LAPACK provider (``armadillo ^openblas ^mpich``):
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install armadillo ^openblas ^mpich
-  ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
-  ...
-  ==> superlu is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-5.2.1-q2mbtw2wo4kpzis2e2n227ip2fquxrno
-  ==> Installing armadillo
-  ==> Using cached archive: /usr/local/var/spack/cache/armadillo/armadillo-8.100.1.tar.xz
-  ==> Staging archive: /usr/local/var/spack/stage/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4/armadillo-8.100.1.tar.xz
-  ==> Created stage in /usr/local/var/spack/stage/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4
-  ==> Applied patch undef_linux.patch
-  ==> Building armadillo [CMakePackage]
-  ==> Executing phase: 'cmake'
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed armadillo
-    Fetch: 0.01s.  Build: 3.96s.  Total: 3.98s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4
-
-Hopefully the installation went fine and the code we added expanded to the right list
-of semicolon separated libraries (you are encouraged to open ``armadillo``'s
-build logs to double check).
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Providing libraries to dependents
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Spack provides a default implementation for ``libs`` which often works
-out of the box. A user can write a package definition without having to
-implement a ``libs`` property and dependents can retrieve its libraries
-as shown in the above section. However, the default implementation assumes that
-libraries follow the naming scheme ``lib<package name>.so`` (or e.g.
-``lib<package name>.a`` for static libraries). Packages which don't
-follow this naming scheme must implement this function themselves, e.g.
-``opencv``:
-
-.. code-block:: python
-
-    @property
-    def libs(self):
-        shared = "+shared" in self.spec
-        return find_libraries(
-            "libopencv_*", root=self.prefix, shared=shared, recurse=True
-        )
-
-This issue is common for packages which implement an interface (i.e.
-virtual package providers in Spack). If we try to build another version of
-``armadillo`` tied to ``netlib-lapack`` (``armadillo ^netlib-lapack ^mpich``)
-we'll notice that this time the installation won't complete:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install  armadillo ^netlib-lapack ^mpich
-  ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
-  ...
-  ==> openmpi is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f
-  ==> Installing arpack-ng
-  ==> Using cached archive: /usr/local/var/spack/cache/arpack-ng/arpack-ng-3.5.0.tar.gz
-  ==> Already staged arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un in /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un
-  ==> No patches needed for arpack-ng
-  ==> Building arpack-ng [Package]
-  ==> Executing phase: 'install'
-  ==> Error: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z
-  RuntimeError: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z
-
-  /usr/local/var/spack/repos/builtin/packages/arpack-ng/package.py:105, in install:
-       5             options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
-       6
-       7             # Make sure we use Spack's blas/lapack:
-    >> 8             lapack_libs = spec['lapack'].libs.joined(';')
-       9             blas_libs = spec['blas'].libs.joined(';')
-       10
-       11            options.extend([
-
-  See build log for details:
-    /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un/arpack-ng-3.5.0/spack-build.out
-
-Unlike ``openblas`` which provides a library named ``libopenblas.so``,
-``netlib-lapack`` provides ``liblapack.so``, so it needs to implement
-customized library search logic. Let's edit it:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit netlib-lapack
-
-and follow the instructions in the ``# TUTORIAL:`` comment as before.
-What we need to implement is:
-
-.. code-block:: python
-
-  @property
-  def lapack_libs(self):
-      shared = True if '+shared' in self.spec else False
-      return find_libraries(
-          'liblapack', root=self.prefix, shared=shared, recursive=True
-      )
-
-i.e., a property that returns the correct list of libraries for the LAPACK interface.
-
-We use the name ``lapack_libs`` rather than ``libs`` because
-``netlib-lapack`` can also provide ``blas``, and when it does it is provided
-as a separate library file. Using this name ensures that when
-dependents ask for ``lapack`` libraries, ``netlib-lapack`` will retrieve only
-the libraries associated with the ``lapack`` interface. Now we can finally
-install ``armadillo ^netlib-lapack ^mpich``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install  armadillo ^netlib-lapack ^mpich
-  ...
-
-  ==> Building armadillo [CMakePackage]
-  ==> Executing phase: 'cmake'
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed armadillo
-    Fetch: 0.01s.  Build: 3.75s.  Total: 3.76s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-sxmpu5an4dshnhickh6ykchyfda7jpyn
-
-Since each implementation of a virtual package is responsible for locating the
-libraries associated with the interfaces it provides, dependents do not need
-to include special-case logic for different implementations and for example
-need only ask for :code:`spec['blas'].libs`.
-
-----------------------
-Other Packaging Topics
-----------------------
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Attach attributes to other packages
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Build tools usually also provide a set of executables that can be used
-when another package is being installed. Spack gives you the opportunity
-to monkey-patch dependent modules and attach attributes to them. This
-helps make the packager experience as similar as possible to what would
-have been the manual installation of the same package.
-
-An example here is the ``automake`` package, which overrides
-:py:func:`setup_dependent_package <spack.package.PackageBase.setup_dependent_package>`:
-
-.. code-block:: python
-
-  def setup_dependent_package(self, module, dependent_spec):
-      # Automake is very likely to be a build dependency,
-      # so we add the tools it provides to the dependent module
-      executables = ['aclocal', 'automake']
-      for name in executables:
-          setattr(module, name, self._make_executable(name))
-
-so that every other package that depends on it can use directly ``aclocal``
-and ``automake`` with the usual function call syntax of :py:class:`Executable <spack.util.executable.Executable>`:
-
-.. code-block:: python
-
-  aclocal('--force')
-
-^^^^^^^^^^^^^^^^^^^^^^^
-Extra query parameters
-^^^^^^^^^^^^^^^^^^^^^^^
-
-An advanced feature of the Spec's build-interface protocol is the support
-for extra parameters after the subscript key. In fact, any of the keys used in the query
-can be followed by a comma-separated list of extra parameters which can be
-inspected by the package receiving the request to fine-tune a response.
-
-Let's look at an example and try to install ``netcdf ^mpich``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install netcdf ^mpich
-  ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
-  ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
-  ...
-  ==> Error: AttributeError: 'list' object has no attribute 'search_flags'
-  AttributeError: AttributeError: 'list' object has no attribute 'search_flags'
-
-  /usr/local/var/spack/repos/builtin/packages/netcdf/package.py:207, in configure_args:
-       50            # used instead.
-       51            hdf5_hl = self.spec['hdf5:hl']
-       52            CPPFLAGS.append(hdf5_hl.headers.cpp_flags)
-    >> 53            LDFLAGS.append(hdf5_hl.libs.search_flags)
-       54
-       55            if '+parallel-netcdf' in self.spec:
-       56                config_args.append('--enable-pnetcdf')
-
-  See build log for details:
-    /usr/local/var/spack/stage/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj/netcdf-4.4.1.1/spack-build.out
-
-We can see from the error that ``netcdf`` needs to know how to link the *high-level interface*
-of ``hdf5``, and thus passes the extra parameter ``hl`` after the request to retrieve it.
-Clearly the implementation in the ``hdf5`` package is not complete, and we need to fix it:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit hdf5
-
-If you followed the instructions correctly, the code added to the
-``lib`` property should be similar to:
-
-.. code-block:: python
-  :emphasize-lines: 1
-
-  query_parameters = self.spec.last_query.extra_parameters
-  key = tuple(sorted(query_parameters))
-  libraries = query2libraries[key]
-  shared = '+shared' in self.spec
-  return find_libraries(
-      libraries, root=self.prefix, shared=shared, recurse=True
-  )
-
-where we highlighted the line retrieving the extra parameters. Now we can successfully
-complete the installation of ``netcdf ^mpich``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install netcdf ^mpich
-  ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
-  ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
-  ...
-  ==> Installing netcdf
-  ==> Using cached archive: /usr/local/var/spack/cache/netcdf/netcdf-4.4.1.1.tar.gz
-  ==> Already staged netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj in /usr/local/var/spack/stage/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj
-  ==> Already patched netcdf
-  ==> Building netcdf [AutotoolsPackage]
-  ==> Executing phase: 'autoreconf'
-  ==> Executing phase: 'configure'
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed netcdf
-    Fetch: 0.01s.  Build: 24.61s.  Total: 24.62s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj

lib/spack/docs/tutorial_buildsystems.rst

@@ -1,807 +0,0 @@
-.. Copyright 2013-2018 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-tutorial:
-
-==============================
-Spack Package Build Systems
-==============================
-
-You may begin to notice after writing a couple of package template files a
-pattern emerge for some packages. For example, you may find yourself writing
-an :code:`install()` method that invokes: :code:`configure`, :code:`cmake`,
-:code:`make`, :code:`make install`. You may also find yourself writing
-:code:`"prefix=" + prefix` as an argument to :code:`configure` or :code:`cmake`.
-Rather than having you repeat these lines for all packages, Spack has
-classes that can take care of these patterns. In addition,
-these package files allow for finer grained control of these build systems.
-In this section, we will describe each build system and give examples on
-how these can be manipulated to install a package.
-
------------------------
-Package Class Hierarchy
------------------------
-
-.. graphviz::
-
-    digraph G {
-
-        node [
-            shape = "record"
-        ]
-        edge [
-            arrowhead = "empty"
-        ]
-
-        PackageBase -> Package [dir=back]
-        PackageBase -> MakefilePackage [dir=back]
-        PackageBase -> AutotoolsPackage [dir=back]
-        PackageBase -> CMakePackage [dir=back]
-        PackageBase -> PythonPackage [dir=back]
-    }
-
-The above diagram gives a high level view of the class hierarchy and how each
-package relates. Each subclass inherits from the :code:`PackageBaseClass`
-super class. The bulk of the work is done in this super class which includes
-fetching, extracting to a staging directory and installing. Each subclass
-then adds additional build-system-specific functionality. In the following
-sections, we will go over examples of how to utilize each subclass and to see
-how powerful these abstractions are when packaging.
-
------------------
-Package
------------------
-
-We've already seen examples of a :code:`Package` class in our walkthrough for writing
-package files, so we won't be spending much time with them here. Briefly,
-the Package class allows for abitrary control over the build process, whereas
-subclasses rely on certain patterns (e.g. :code:`configure` :code:`make`
-:code:`make install`) to be useful. :code:`Package` classes are particularly useful
-for packages that have a non-conventional way of being built since the packager
-can utilize some of Spack's helper functions to customize the building and
-installing of a package.
-
--------------------
-Autotools
--------------------
-
-As we have seen earlier, packages using :code:`Autotools` use :code:`configure`,
-:code:`make` and :code:`make install` commands to execute the build and
-install process. In our :code:`Package` class, your typical build incantation will
-consist of the following:
-
-.. code-block:: python
-
-    def install(self, spec, prefix):
-        configure("--prefix=" + prefix)
-        make()
-        make("install")
-
-You'll see that this looks similar to what we wrote in our packaging tutorial.
-
-The :code:`Autotools` subclass aims to simplify writing package files and provides
-convenience methods to manipulate each of the different phases for a :code:`Autotools`
-build system.
-
-:code:`Autotools` packages consist of four phases:
-
-1. :code:`autoreconf()`
-2. :code:`configure()`
-3. :code:`build()`
-4. :code:`install()`
-
-
-Each of these phases have sensible defaults. Let's take a quick look at some
-the internals of the :code:`Autotools` class:
-
-.. code-block:: console
-
-    $ spack edit --build-system autotools
-
-
-This will open the :code:`AutotoolsPackage` file in your text editor.
-
-.. note::
-    The examples showing code for these classes is abridged to avoid having
-    long examples. We only show what is relevant to the packager.
-
-
-.. literalinclude:: ../../../lib/spack/spack/build_systems/autotools.py
-    :language: python
-    :emphasize-lines: 33,36,54
-    :lines: 30-76,240-248
-    :linenos:
-
-
-Important to note are the highlighted lines. These properties allow the
-packager to set what build targets and install targets they want for their
-package. If, for example, we wanted to add as our build target :code:`foo`
-then we can append to our :code:`build_targets` property:
-
-.. code-block:: python
-
-    build_targets = ["foo"]
-
-Which is similiar to invoking make in our Package
-
-.. code-block:: python
-
-     make("foo")
-
-This is useful if we have packages that ignore environment variables and need
-a command-line argument.
-
-Another thing to take note of is in the :code:`configure()` method.
-Here we see that the :code:`prefix` argument is already included since it is a
-common pattern amongst packages using :code:`Autotools`. We then only have to
-override :code:`configure_args()`, which will then return it's output to
-to :code:`configure()`. Then, :code:`configure()` will append the common
-arguments
-
-Packagers also have the option to run :code:`autoreconf` in case a package
-needs to update the build system and generate a new :code:`configure`. Though,
-for the most part this will be unnecessary.
-
-Let's look at the :code:`mpileaks` package.py file that we worked on earlier:
-
-.. code-block:: console
-
-    $ spack edit mpileaks
-
-Notice that mpileaks is a :code:`Package` class but uses the :code:`Autotools`
-build system. Although this package is acceptable let's make this into an
-:code:`AutotoolsPackage` class and simplify it further.
-
-.. literalinclude:: tutorial/examples/Autotools/0.package.py
-   :language: python
-   :emphasize-lines: 9
-   :linenos:
-
-We first inherit from the :code:`AutotoolsPackage` class.
-
-
-Although we could keep the :code:`install()` method, most of it can be handled
-by the :code:`AutotoolsPackage` base class. In fact, the only thing that needs
-to be overridden is :code:`configure_args()`.
-
-.. literalinclude:: tutorial/examples/Autotools/1.package.py
-   :language: python
-   :emphasize-lines: 25,26,27,28,29,30,31,32
-   :linenos:
-
-Since Spack takes care of setting the prefix for us we can exclude that as
-an argument to :code:`configure`. Our packages look simpler, and the packager
-does not need to worry about whether they have properly included :code:`configure`
-and :code:`make`.
-
-This version of the :code:`mpileaks` package installs the same as the previous,
-but the :code:`AutotoolsPackage` class lets us do it with a cleaner looking
-package file.
-
------------------
-Makefile
------------------
-
-Packages that utilize :code:`Make` or a :code:`Makefile` usually require you
-to edit a :code:`Makefile` to set up platform and compiler specific variables.
-These packages are handled by the :code:`Makefile` subclass which provides
-convenience methods to help write these types of packages.
-
-A :code:`MakefilePackage` class has three phases that can be overridden. These include:
-
-    1. :code:`edit()`
-    2. :code:`build()`
-    3. :code:`install()`
-
-Packagers then have the ability to control how a :code:`Makefile` is edited, and
-what targets to include for the build phase or install phase.
-
-Let's also take a look inside the :code:`MakefilePackage` class:
-
-.. code-block:: console
-
-    $ spack edit --build-system makefile
-
-Take note of the following:
-
-
-.. literalinclude:: ../../../lib/spack/spack/build_systems/makefile.py
-   :language: python
-   :lines: 14,43-61,70-88
-   :emphasize-lines: 21,27,34
-   :linenos:
-
-Similar to :code:`Autotools`, :code:`MakefilePackage` class has properties
-that can be set by the packager. We can also override the different
-methods highlighted.
-
-
-Let's try to recreate the Bowtie_ package:
-
-.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
-
-
-.. code-block:: console
-
-    $ spack create -f https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip
-    ==> This looks like a URL for bowtie
-    ==> Found 1 version of bowtie:
-
-    1.2.1.1  https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip
-
-    ==> How many would you like to checksum? (default is 1, q to abort) 1
-    ==> Downloading...
-    ==> Fetching https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip
-    ######################################################################## 100.0%
-    ==> Checksummed 1 version of bowtie
-    ==> This package looks like it uses the makefile build system
-    ==> Created template for bowtie package
-    ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/bowtie/package.py
-
-Once the fetching is completed, Spack will open up your text editor in the
-usual fashion and create a template of a :code:`MakefilePackage` package.py.
-
-.. literalinclude:: tutorial/examples/Makefile/0.package.py
-   :language: python
-   :linenos:
-
-Spack was successfully able to detect that :code:`Bowtie` uses :code:`Make`.
-Let's add in the rest of our details for our package:
-
-.. literalinclude:: tutorial/examples/Makefile/1.package.py
-   :language: python
-   :emphasize-lines: 10,11,13,14,18,20
-   :linenos:
-
-As we mentioned earlier, most packages using a :code:`Makefile` have hard-coded
-variables that must be edited. These variables are fine if you happen to not
-care about setup or types of compilers used but Spack is designed to work with
-any compiler. The :code:`MakefilePackage` subclass makes it easy to edit
-these :code:`Makefiles` by having an :code:`edit()` method that
-can be overridden.
-
-Let's take a look at the default :code:`Makefile` that :code:`Bowtie` provides.
-If we look inside, we see that :code:`CC` and :code:`CXX` point to our GNU
-compiler:
-
-.. code-block:: console
-
-    $ spack stage bowtie
-
-.. note::
-    As usual make sure you have shell support activated with spack:
-        :code:`source /path/to/spack_root/spack/share/spack/setup-env.sh`
-
-.. code-block:: console
-
-    $ spack cd -s bowtie
-    $ cd bowtie-1.2
-    $ vim Makefile
-
-
-.. code-block:: make
-
-    CPP = g++ -w
-    CXX = $(CPP)
-    CC = gcc
-    LIBS = $(LDFLAGS) -lz
-    HEADERS = $(wildcard *.h)
-
-To fix this, we need to use the :code:`edit()` method to write our custom
-:code:`Makefile`.
-
-.. literalinclude:: tutorial/examples/Makefile/2.package.py
-   :language: python
-   :emphasize-lines: 23,24,25
-   :linenos:
-
-Here we use a :code:`FileFilter` object to edit our :code:`Makefile`. It takes
-in a regular expression and then replaces :code:`CC` and :code:`CXX` to whatever
-Spack sets :code:`CC` and :code:`CXX` environment variables to. This allows us to
-build :code:`Bowtie` with whatever compiler we specify through Spack's
-:code:`spec` syntax.
-
-Let's change the build and install phases of our package:
-
-.. literalinclude:: tutorial/examples/Makefile/3.package.py
-   :language: python
-   :emphasize-lines: 28,29,30,31,32,35,36
-   :linenos:
-
-Here demonstrate another strategy that we can use to manipulate our package
-We can provide command-line arguments to :code:`make()`. Since :code:`Bowtie`
-can use :code:`tbb` we can either add :code:`NO_TBB=1` as a argument to prevent
-:code:`tbb` support or we can just invoke :code:`make` with no arguments.
-
-:code:`Bowtie` requires our :code:`install_target` to provide a path to
-the install directory. We can do this by providing :code:`prefix=` as a command
-line argument to :code:`make()`.
-
-Let's look at a couple of other examples and go through them:
-
-.. code-block:: console
-
-    $ spack edit esmf
-
-Some packages allow environment variables to be set and will honor them.
-Packages that use :code:`?=` for assignment in their :code:`Makefile`
-can be set using environment variables. In our :code:`esmf` example we
-set two environment variables in our :code:`edit()` method:
-
-.. code-block:: python
-
-    def edit(self, spec, prefix):
-        for var in os.environ:
-            if var.startswith('ESMF_'):
-                os.environ.pop(var)
-
-        # More code ...
-
-        if self.compiler.name == 'gcc':
-            os.environ['ESMF_COMPILER'] = 'gfortran'
-        elif self.compiler.name == 'intel':
-            os.environ['ESMF_COMPILER'] = 'intel'
-        elif self.compiler.name == 'clang':
-            os.environ['ESMF_COMPILER'] = 'gfortranclang'
-        elif self.compiler.name == 'nag':
-            os.environ['ESMF_COMPILER'] = 'nag'
-        elif self.compiler.name == 'pgi':
-            os.environ['ESMF_COMPILER'] = 'pgi'
-        else:
-            msg  = "The compiler you are building with, "
-            msg += "'{0}', is not supported by ESMF."
-            raise InstallError(msg.format(self.compiler.name))
-
-As you may have noticed, we didn't really write anything to the :code:`Makefile`
-but rather we set environment variables that will override variables set in
-the :code:`Makefile`.
-
-Some packages include a configuration file that sets certain compiler variables,
-platform specific variables, and the location of dependencies or libraries.
-If the file is simple and only requires a couple of changes, we can overwrite
-those entries with our :code:`FileFilter` object. If the configuration involves
-complex changes, we can write a new configuration file from scratch.
-
-Let's look at an example of this in the :code:`elk` package:
-
-.. code-block:: console
-
-    $ spack edit elk
-
-.. code-block:: python
-
-        def edit(self, spec, prefix):
-            # Dictionary of configuration options
-            config = {
-                'MAKE': 'make',
-                'AR':   'ar'
-            }
-
-            # Compiler-specific flags
-            flags = ''
-            if self.compiler.name == 'intel':
-                flags = '-O3 -ip -unroll -no-prec-div'
-            elif self.compiler.name == 'gcc':
-                flags = '-O3 -ffast-math -funroll-loops'
-            elif self.compiler.name == 'pgi':
-                flags = '-O3 -lpthread'
-            elif self.compiler.name == 'g95':
-                flags = '-O3 -fno-second-underscore'
-            elif self.compiler.name == 'nag':
-                flags = '-O4 -kind=byte -dusty -dcfuns'
-            elif self.compiler.name == 'xl':
-                flags = '-O3'
-            config['F90_OPTS'] = flags
-            config['F77_OPTS'] = flags
-
-            # BLAS/LAPACK support
-            # Note: BLAS/LAPACK must be compiled with OpenMP support
-            # if the +openmp variant is chosen
-            blas = 'blas.a'
-            lapack = 'lapack.a'
-            if '+blas' in spec:
-                blas = spec['blas'].libs.joined()
-            if '+lapack' in spec:
-                lapack = spec['lapack'].libs.joined()
-            # lapack must come before blas
-            config['LIB_LPK'] = ' '.join([lapack, blas])
-
-            # FFT support
-            if '+fft' in spec:
-                config['LIB_FFT'] = join_path(spec['fftw'].prefix.lib,
-                                            'libfftw3.so')
-                config['SRC_FFT'] = 'zfftifc_fftw.f90'
-            else:
-                config['LIB_FFT'] = 'fftlib.a'
-                config['SRC_FFT'] = 'zfftifc.f90'
-
-            # MPI support
-            if '+mpi' in spec:
-                config['F90'] = spec['mpi'].mpifc
-                config['F77'] = spec['mpi'].mpif77
-            else:
-                config['F90'] = spack_fc
-                config['F77'] = spack_f77
-                config['SRC_MPI'] = 'mpi_stub.f90'
-
-            # OpenMP support
-            if '+openmp' in spec:
-                config['F90_OPTS'] += ' ' + self.compiler.openmp_flag
-                config['F77_OPTS'] += ' ' + self.compiler.openmp_flag
-            else:
-                config['SRC_OMP'] = 'omp_stub.f90'
-
-            # Libxc support
-            if '+libxc' in spec:
-                config['LIB_libxc'] = ' '.join([
-                    join_path(spec['libxc'].prefix.lib, 'libxcf90.so'),
-                    join_path(spec['libxc'].prefix.lib, 'libxc.so')
-                ])
-                config['SRC_libxc'] = ' '.join([
-                    'libxc_funcs.f90',
-                    'libxc.f90',
-                    'libxcifc.f90'
-                ])
-            else:
-                config['SRC_libxc'] = 'libxcifc_stub.f90'
-
-            # Write configuration options to include file
-            with open('make.inc', 'w') as inc:
-                for key in config:
-                    inc.write('{0} = {1}\n'.format(key, config[key]))
-
-:code:`config` is just a dictionary that we can add key-value pairs to. By the
-end of the :code:`edit()` method we write the contents of our dictionary to
-:code:`make.inc`.
-
----------------
-CMake
----------------
-
-CMake_ is another common build system that has been gaining popularity. It works
-in a similar manner to :code:`Autotools` but with differences in variable names,
-the number of configuration options available, and the handling of shared libraries.
-Typical build incantations look like this:
-
-.. _CMake: https://cmake.org
-
-.. code-block:: python
-
-    def install(self, spec, prefix):
-        cmake("-DCMAKE_INSTALL_PREFIX:PATH=/path/to/install_dir ..")
-        make()
-        make("install")
-
-As you can see from the example above, it's very similar to invoking
-:code:`configure` and :code:`make` in an :code:`Autotools` build system. However,
-the variable names and options differ. Most options in CMake are prefixed
-with a :code:`'-D'` flag to indicate a configuration setting.
-
-In the :code:`CMakePackage` class we can override the following phases:
-
-1. :code:`cmake()`
-2. :code:`build()`
-3. :code:`install()`
-
-The :code:`CMakePackage` class also provides sensible defaults so we only need to
-override :code:`cmake_args()`.
-
-Let's look at these defaults in the :code:`CMakePackage` class in the :code:`_std_args()` method:
-
-.. code-block:: console
-
-    $ spack edit --build-system cmake
-
-.. literalinclude:: ../../../lib/spack/spack/build_systems/cmake.py
-   :language: python
-   :lines: 102-147
-   :emphasize-lines: 10,18,24,36,37,38,44
-   :linenos:
-
-Some :code:`CMake` packages use different generators. Spack is able to support
-Unix-Makefile_ generators as well as Ninja_ generators.
-
-.. _Unix-Makefile: https://cmake.org/cmake/help/v3.4/generator/Unix%20Makefiles.html
-.. _Ninja: https://cmake.org/cmake/help/v3.4/generator/Ninja.html
-
-If no generator is specified Spack will default to :code:`Unix Makefiles`.
-
-Next we setup the build type. In :code:`CMake` you can specify the build type
-that you want. Options include:
-
-1. :code:`empty`
-2. :code:`Debug`
-3. :code:`Release`
-4. :code:`RelWithDebInfo`
-5. :code:`MinSizeRel`
-
-With these options you can specify whether you want your executable to have
-the debug version only, release version or the release with debug information.
-Release executables tend to be more optimized than Debug. In Spack, we set
-the default as RelWithDebInfo unless otherwise specified through a variant.
-
-Spack then automatically sets up the :code:`-DCMAKE_INSTALL_PREFIX` path,
-appends the build type (:code:`RelWithDebInfo` default), and then specifies a verbose
-:code:`Makefile`.
-
-Next we add the :code:`rpaths` to :code:`-DCMAKE_INSTALL_RPATH:STRING`.
-
-
-Finally we add to :code:`-DCMAKE_PREFIX_PATH:STRING` the locations of all our
-dependencies so that :code:`CMake` can find them.
-
-In the end our :code:`cmake` line will look like this (example is :code:`xrootd`):
-
-.. code-block:: console
-
-    $ cmake $HOME/spack/var/spack/stage/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/xrootd-4.6.0 -G Unix Makefiles -DCMAKE_INSTALL_PREFIX:PATH=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_FIND_FRAMEWORK:STRING=LAST -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE -DCMAKE_INSTALL_RPATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib:$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib64 -DCMAKE_PREFIX_PATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/cmake-3.9.4-hally3vnbzydiwl3skxcxcbzsscaasx5
-
-We can see now how :code:`CMake` takes care of a lot of the boilerplate code
-that would have to be otherwise typed in.
-
-Let's try to recreate callpath_:
-
-.. _callpath: https://github.com/LLNL/callpath.git
-
-.. code-block:: console
-
-    $ spack create -f https://github.com/llnl/callpath/archive/v1.0.3.tar.gz
-    ==> This looks like a URL for callpath
-    ==> Found 4 versions of callpath:
-
-    1.0.3  https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz
-    1.0.2  https://github.com/LLNL/callpath/archive/v1.0.2.tar.gz
-    1.0.1  https://github.com/LLNL/callpath/archive/v1.0.1.tar.gz
-    1.0    https://github.com/LLNL/callpath/archive/v1.0.tar.gz
-
-    ==> How many would you like to checksum? (default is 1, q to abort) 1
-    ==> Downloading...
-    ==> Fetching https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz
-    ######################################################################## 100.0%
-    ==> Checksummed 1 version of callpath
-    ==> This package looks like it uses the cmake build system
-    ==> Created template for callpath package
-    ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/callpath/package.py
-
-
-which then produces the following template:
-
-.. literalinclude:: tutorial/examples/Cmake/0.package.py
-   :language: python
-   :linenos:
-
-Again we fill in the details:
-
-.. literalinclude:: tutorial/examples/Cmake/1.package.py
-   :language: python
-   :linenos:
-   :emphasize-lines: 9,13,14,18,19,20,21,22,23
-
-As mentioned earlier, Spack will use sensible defaults to prevent repeated code
-and to make writing :code:`CMake` package files simpler.
-
-In callpath, we want to add options to :code:`CALLPATH_WALKER` as well as add
-compiler flags. We add the following options like so:
-
-.. literalinclude:: tutorial/examples/Cmake/2.package.py
-   :language: python
-   :linenos:
-   :emphasize-lines: 26,30,31
-
-Now we can control our build options using :code:`cmake_args()`. If defaults are
-sufficient enough for the package, we can leave this method out.
-
-:code:`CMakePackage` classes allow for control of other features in the
-build system. For example, you can specify the path to the "out of source"
-build directory and also point to the root of the :code:`CMakeLists.txt` file if it
-is placed in a non-standard location.
-
-A good example of a package that has its :code:`CMakeLists.txt` file located at a
-different location is found in :code:`spades`.
-
-.. code-block:: console
-
-    $ spack edit spades
-
-.. code-block:: python
-
-    root_cmakelists_dir = "src"
-
-Here :code:`root_cmakelists_dir` will tell Spack where to find the location
-of :code:`CMakeLists.txt`. In this example, it is located a directory level below in
-the :code:`src` directory.
-
-Some :code:`CMake` packages also require the :code:`install` phase to be
-overridden. For example, let's take a look at :code:`sniffles`.
-
-.. code-block:: console
-
-    $ spack edit sniffles
-
-In the :code:`install()` method, we have to manually install our targets
-so we override the :code:`install()` method to do it for us:
-
-.. code-block:: python
-
-    # the build process doesn't actually install anything, do it by hand
-    def install(self, spec, prefix):
-        mkdir(prefix.bin)
-        src = "bin/sniffles-core-{0}".format(spec.version.dotted)
-        binaries = ['sniffles', 'sniffles-debug']
-        for b in binaries:
-            install(join_path(src, b), join_path(prefix.bin, b))
-
-
---------------
-PythonPackage
---------------
-
-Python extensions and modules are built differently from source than most
-applications. Python uses a :code:`setup.py` script to install Python modules.
-The script consists of a call to :code:`setup()` which provides the information
-required to build a module to Distutils. If you're familiar with pip or
-easy_install, setup.py does the same thing.
-
-These modules are usually installed using the following line:
-
-.. code-block:: console
-
-    $ python setup.py install
-
-There are also a list of commands and phases that you can call. To see the full
-list you can run:
-
-.. code-block:: console
-
-    $ python setup.py --help-commands
-    Standard commands:
-        build             build everything needed to install
-        build_py          "build" pure Python modules (copy to build directory)
-        build_ext         build C/C++ extensions (compile/link to build directory)
-        build_clib        build C/C++ libraries used by Python extensions
-        build_scripts     "build" scripts (copy and fixup #! line)
-        clean             (no description available)
-        install           install everything from build directory
-        install_lib       install all Python modules (extensions and pure Python)
-        install_headers   install C/C++ header files
-        install_scripts   install scripts (Python or otherwise)
-        install_data      install data files
-        sdist             create a source distribution (tarball, zip file, etc.)
-        register          register the distribution with the Python package index
-        bdist             create a built (binary) distribution
-        bdist_dumb        create a "dumb" built distribution
-        bdist_rpm         create an RPM distribution
-        bdist_wininst     create an executable installer for MS Windows
-        upload            upload binary package to PyPI
-        check             perform some checks on the package
-
-
-We can write package files for Python packages using the :code:`Package` class,
-but the class brings with it a lot of methods that are useless for Python packages.
-Instead, Spack has a :code:`PythonPackage` subclass that allows packagers
-of Python modules to be able to invoke :code:`setup.py` and use :code:`Distutils`,
-which is much more familiar to a typical python user.
-
-To see the defaults that Spack has for each a methods, we will take a look
-at the :code:`PythonPackage` class:
-
-.. code-block:: console
-
-    $ spack edit --build-system python
-
-We see the following:
-
-
-.. literalinclude:: ../../../lib/spack/spack/build_systems/python.py
-   :language: python
-   :lines: 19,146-357
-   :linenos:
-
-Each of these methods have sensible defaults or they can be overridden.
-
-We will write a package file for Pandas_:
-
-.. _pandas: https://pandas.pydata.org
-
-.. code-block:: console
-
-    $ spack create -f https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz
-    ==> This looks like a URL for pandas
-    ==> Warning: Spack was unable to fetch url list due to a certificate verification problem. You can try running spack -k, which will not check SSL certificates. Use this at your own risk.
-    ==> Found 1 version of pandas:
-
-    0.19.0  https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz
-
-    ==> How many would you like to checksum? (default is 1, q to abort) 1
-    ==> Downloading...
-    ==> Fetching https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz
-    ######################################################################## 100.0%
-    ==> Checksummed 1 version of pandas
-    ==> This package looks like it uses the python build system
-    ==> Changing package name from pandas to py-pandas
-    ==> Created template for py-pandas package
-    ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/py-pandas/package.py
-
-And we are left with the following template:
-
-.. literalinclude:: tutorial/examples/PyPackage/0.package.py
-   :language: python
-   :linenos:
-
-As you can see this is not any different than any package template that we have
-written. We have the choice of providing build options or using the sensible
-defaults
-
-Luckily for us, there is no need to provide build args.
-
-Next we need to find the dependencies of a package. Dependencies are usually
-listed in :code:`setup.py`. You can find the dependencies by searching for
-:code:`install_requires` keyword in that file. Here it is for :code:`Pandas`:
-
-.. code-block:: python
-
-    # ... code
-    if sys.version_info[0] >= 3:
-
-    setuptools_kwargs = {
-                         'zip_safe': False,
-                         'install_requires': ['python-dateutil >= 2',
-                                              'pytz >= 2011k',
-                                              'numpy >= %s' % min_numpy_ver],
-                         'setup_requires': ['numpy >= %s' % min_numpy_ver],
-                         }
-    if not _have_setuptools:
-        sys.exit("need setuptools/distribute for Py3k"
-                 "\n$ pip install distribute")
-
-    # ... more code
-
-You can find a more comprehensive list at the Pandas documentation_.
-
-.. _documentation: https://pandas.pydata.org/pandas-docs/stable/install.html
-
-
-By reading the documentation and :code:`setup.py` we found that :code:`Pandas`
-depends on :code:`python-dateutil`, :code:`pytz`, and :code:`numpy`, :code:`numexpr`,
-and finally :code:`bottleneck`.
-
-Here is the completed :code:`Pandas` script:
-
-.. literalinclude:: tutorial/examples/PyPackage/1.package.py
-   :language: python
-   :linenos:
-
-It is quite important to declare all the dependencies of a Python package.
-Spack can "activate" Python packages to prevent the user from having to
-load each dependency module explictly. If a dependency is missed, Spack will
-be unable to properly activate the package and it will cause an issue. To
-learn more about extensions go to :ref:`cmd-spack-extensions`.
-
-From this example, you can see that building Python modules is made easy
-through the :code:`PythonPackage` class.
-
--------------------
-Other Build Systems
--------------------
-
-Although we won't get in depth with any of the other build systems that Spack
-supports, it is worth mentioning that Spack does provide subclasses
-for the following build systems:
-
-1. :code:`IntelPackage`
-2. :code:`SconsPackage`
-3. :code:`WafPackage`
-4. :code:`RPackage`
-5. :code:`PerlPackage`
-6. :code:`QMakePackage`
-
-
-Each of these classes have their own abstractions to help assist in writing
-package files. For whatever doesn't fit nicely into the other build-systems,
-you can use the :code:`Package` class.
-
-Hopefully by now you can see how we aim to make packaging simple and
-robust through these classes. If you want to learn more about these build
-systems, check out :ref:`installation_procedure` in the Packaging Guide.

lib/spack/docs/tutorial_configuration.rst

@@ -1,935 +0,0 @@
-.. Copyright 2013-2018 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)
-
-.. _configs-tutorial:
-
-======================
-Configuration Tutorial
-======================
-
-This tutorial will guide you through various configuration options
-that allow you to customize Spack's behavior with respect to
-software installation. We will first cover the configuration file
-hierarchy. Then, we will cover configuration options for compilers,
-focusing on how they can be used to extend Spack's compiler auto-detection.
-Next, we will cover the packages configuration file, focusing on
-how it can be used to override default build options as well as
-specify external package installations to use. Finally, we will
-briefly touch on the config configuration file, which manages more
-high-level Spack configuration options.
-
-For all of these features we will demonstrate how we build up a full
-configuration file. For some we will then demonstrate how the
-configuration affects the install command, and for others we will use
-the ``spack spec`` command to demonstrate how the configuration
-changes have affected Spack's concretization algorithm. The provided
-output is all from a server running Ubuntu version 16.04.
-
-.. _configs-tutorial-scopes:
-
---------------------
-Configuration Scopes
---------------------
-
-Depending on your use case, you may want to provide configuration
-settings common to everyone on your team, or you may want to set
-default behaviors specific to a single user account. Spack provides
-six configuration *scopes* to handle this customization. These scopes,
-in order of decreasing priority, are:
-
-============   ===================================================
-Scope          Directory
-============   ===================================================
-Command-line   N/A
-Custom         Custom directory, specified with ``--config-scope``
-User           ``~/.spack/``
-Site           ``$SPACK_ROOT/etc/spack/``
-System         ``/etc/spack/``
-Defaults       ``$SPACK_ROOT/etc/spack/defaults/``
-============   ===================================================
-
-Spack's default configuration settings reside in
-``$SPACK_ROOT/etc/spack/defaults``. These are useful for reference,
-but should never be directly edited. To override these settings,
-create new configuration files in any of the higher-priority
-configuration scopes.
-
-A particular cluster may have multiple Spack installations associated
-with different projects. To provide settings common to all Spack
-installations, put your configuration files in ``/etc/spack``.
-To provide settings specific to a particular Spack installation,
-you can use the ``$SPACK_ROOT/etc/spack`` directory.
-
-For settings specific to a particular user, you will want to add
-configuration files to the ``~/.spack`` directory. When Spack first
-checked for compilers on your system, you may have noticed that it
-placed your compiler configuration in this directory.
-
-Configuration settings can also be placed in a custom location,
-which is then specified on the command line via ``--config-scope``.
-An example use case is managing two sets of configurations, one for
-development and another for production preferences.
-
-Settings specified on the command line have precedence over all
-other configuration scopes.
-
-^^^^^^^^^^^^^^^^^^^^^^^^
-Platform-specific Scopes
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Some facilities manage multiple platforms from a single shared
-file system. In order to handle this, each of the configuration
-scopes listed above has two *sub-scopes*: platform-specific and
-platform-independent. For example, compiler settings can be stored
-in ``compilers.yaml`` configuration files in the following locations:
-
-#. ``~/.spack/<platform>/compilers.yaml``
-#. ``~/.spack/compilers.yaml``
-#. ``$SPACK_ROOT/etc/spack/<platform>/compilers.yaml``
-#. ``$SPACK_ROOT/etc/spack/compilers.yaml``
-#. ``/etc/spack/<platform>/compilers.yaml``
-#. ``/etc/spack/compilers.yaml``
-#. ``$SPACK_ROOT/etc/defaults/<platform>/compilers.yaml``
-#. ``$SPACK_ROOT/etc/defaults/compilers.yaml``
-
-These files are listed in decreasing order of precedence, so files in
-``~/.spack/<platform>`` will override settings in ``~/.spack``.
-
------------
-YAML Format
------------
-
-Spack configurations are YAML dictionaries. Every configuration file
-begins with a top-level dictionary that tells Spack which
-configuration set it modifies. When Spack checks it's configuration,
-the configuration scopes are updated as dictionaries in increasing
-order of precedence, allowing higher precedence files to override
-lower. YAML dictionaries use a colon ":" to specify key-value
-pairs. Spack extends YAML syntax slightly to allow a double-colon
-"::" to specify a key-value pair. When a double-colon is used to
-specify a key-value pair, instead of adding that section Spack
-replaces what was in that section with the new value. For example, a
-user compilers configuration file as follows:
-
-.. code-block:: yaml
-
-   compilers::
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags: {}
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/gcc
-         cxx: /usr/bin/g++
-         f77: /usr/bin/gfortran
-         fc: /usr/bin/gfortran
-       spec: gcc@5.4.0
-       target: x86_64
-
-
-ensures that no other compilers are used, as the user configuration
-scope is the last scope searched and the ``compilers::`` line replaces
-all previous configuration files information. If the same
-configuration file had a single colon instead of the double colon, it
-would add the GCC version 5.4.0 compiler to whatever other compilers
-were listed in other configuration files.
-
-.. _configs-tutorial-compilers:
-
-----------------------
-Compiler Configuration
-----------------------
-
-For most tasks, we can use Spack with the compilers auto-detected the
-first time Spack runs on a system. As discussed in the basic
-installation tutorial, we can also tell Spack where compilers are
-located using the ``spack compiler add`` command. However, in some
-circumstances we want even more fine-grained control over the
-compilers available. This section will teach you how to exercise that
-control using the compilers configuration file.
-
-We will start by opening the compilers configuration file
-
-.. code-block:: console
-
-   $ spack config edit compilers
-
-
-.. code-block:: yaml
-
-   compilers:
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags: {}
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/clang-3.7
-         cxx: /usr/bin/clang++-3.7
-         f77: null
-         fc: null
-       spec: clang@3.7.1-2ubuntu2
-       target: x86_64
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags: {}
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/clang
-         cxx: /usr/bin/clang++
-         f77: null
-         fc: null
-       spec: clang@3.8.0-2ubuntu4
-       target: x86_64
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags: {}
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/gcc-4.7
-         cxx: /usr/bin/g++-4.7
-         f77: /usr/bin/gfortran-4.7
-         fc: /usr/bin/gfortran-4.7
-       spec: gcc@4.7
-       target: x86_64
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags: {}
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/gcc
-         cxx: /usr/bin/g++
-         f77: /usr/bin/gfortran
-         fc: /usr/bin/gfortran
-       spec: gcc@5.4.0
-       target: x86_64
-
-
-This specifies two versions of the GCC compiler and two versions of the
-Clang compiler with no Flang compiler. Now suppose we have a code that
-we want to compile with the Clang compiler for C/C++ code, but with
-gfortran for Fortran components. We can do this by adding another entry
-to the ``compilers.yaml`` file.
-
-.. code-block:: yaml
-
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags: {}
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/clang
-         cxx: /usr/bin/clang++
-         f77: /usr/bin/gfortran
-         fc: /usr/bin/gfortran
-       spec: clang@3.8.0-gfortran
-       target: x86_64
-
-
-Let's talk about the sections of this compiler entry that we've changed.
-The biggest change we've made is to the ``paths`` section. This lists
-the paths to the compilers to use for each language/specification.
-In this case, we point to the clang compiler for C/C++ and the gfortran
-compiler for both specifications of Fortran. We've also changed the
-``spec`` entry for this compiler. The ``spec`` entry is effectively the
-name of the compiler for Spack. It consists of a name and a version
-number, separated by the ``@`` sigil. The name must be one of the supported
-compiler names in Spack (gcc, intel, pgi, xl, xl_r, clang, nag, cce, arm).
-The version number can be an arbitrary string of alphanumeric characters,
-as well as ``-``, ``.``, and ``_``. The ``target`` and ``operating_system``
-sections we leave unchanged. These sections specify when Spack can use
-different compilers, and are primarily useful for configuration files that
-will be used across multiple systems.
-
-We can verify that our new compiler works by invoking it now:
-
-.. code-block:: console
-
-   $ spack install --no-cache zlib %clang@3.8.0-gfortran
-   ...
-
-
-This new compiler also works on Fortran codes:
-
-.. code-block:: console
-
-   $ spack install --no-cache cfitsio %clang@3.8.0-gfortran -bzip2
-   ...
-
-
-^^^^^^^^^^^^^^
-Compiler Flags
-^^^^^^^^^^^^^^
-
-Some compilers may require specific compiler flags to work properly in
-a particular computing environment. Spack provides configuration
-options for setting compiler flags every time a specific compiler is
-invoked. These flags become part of the package spec and therefore of
-the build provenance. As on the command line, the flags are set
-through the implicit build variables ``cflags``, ``cxxflags``, ``cppflags``,
-``fflags``, ``ldflags``, and ``ldlibs``.
-
-Let's open our compilers configuration file again and add a compiler flag.
-
-.. code-block:: yaml
-
-   - compiler:
-       environment: {}
-       extra_rpaths: []
-       flags:
-         cppflags: -g
-       modules: []
-       operating_system: ubuntu16.04
-       paths:
-         cc: /usr/bin/clang
-         cxx: /usr/bin/clang++
-         f77: /usr/bin/gfortran
-         fc: /usr/bin/gfortran
-       spec: clang@3.8.0-gfortran
-       target: x86_64
-
-
-We can test this out using the ``spack spec`` command to show how the
-spec is concretized.
-
-.. code-block:: console
-
-   $ spack spec cfitsio %clang@3.8.0-gfortran
-   Input spec
-   --------------------------------
-   cfitsio%clang@3.8.0-gfortran
-
-   Normalized
-   --------------------------------
-   cfitsio%clang@3.8.0-gfortran
-
-   Concretized
-   --------------------------------
-   cfitsio@3.410%clang@3.8.0-gfortran cppflags="-g" +bzip2+shared arch=linux-ubuntu16.04-x86_64
-       ^bzip2@1.0.6%clang@3.8.0-gfortran cppflags="-g" +shared arch=linux-ubuntu16.04-x86_64
-
-
-We can see that ``cppflags="-g"`` has been added to every node in the DAG.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Advanced Compiler Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-There are three fields of the compiler configuration entry that we
-have not yet talked about.
-
-The ``modules`` field of the compiler is used primarily on Cray systems,
-but can be useful on any system that has compilers that are only
-useful when a particular module is loaded. Any modules in the
-``modules`` field of the compiler configuration will be loaded as part
-of the build environment for packages using that compiler.
-
-The ``extra_rpaths`` field of the compiler configuration is used for
-compilers that do not rpath all of their dependencies by
-default. Since compilers are often installed externally to Spack,
-Spack is unable to manage compiler dependencies and enforce
-rpath usage. This can lead to packages not finding link dependencies
-imposed by the compiler properly. For compilers that impose link
-dependencies on the resulting executables that are not rpath'ed into
-the executable automatically, the ``extra_rpaths`` field of the compiler
-configuration tells Spack which dependencies to rpath into every
-executable created by that compiler. The executables will then be able
-to find the link dependencies imposed by the compiler. As an example,
-this field can be set by
-
-.. code-block:: yaml
-
-   - compiler:
-     ...
-     extra_rpaths:
-      - /apps/intel/ComposerXE2017/compilers_and_libraries_2017.5.239/linux/compiler/lib/intel64_lin
-     ...
-
-
-The ``environment`` field of the compiler configuration is used for
-compilers that require environment variables to be set during build
-time. For example, if your Intel compiler suite requires the
-``INTEL_LICENSE_FILE`` environment variable to point to the proper
-license server, you can set this in ``compilers.yaml`` as follows:
-
-.. code-block:: yaml
-
-  - compiler:
-      environment:
-        set:
-          INTEL_LICENSE_FILE: 1713@license4
-      ...
-
-
-In addition to ``set``, ``environment`` also supports ``unset``,
-``prepend-path``, and ``append-path``.
-
-.. _configs-tutorial-package-prefs:
-
--------------------------------
-Configuring Package Preferences
--------------------------------
-
-Package preferences in Spack are managed through the ``packages.yaml``
-configuration file. First, we will look at the default
-``packages.yaml`` file.
-
-.. code-block:: console
-
-   $ spack config --scope defaults edit packages
-
-
-.. literalinclude:: ../../../etc/spack/defaults/packages.yaml
-   :language: yaml
-
-
-This sets the default preferences for compilers and for providers of
-virtual packages. To illustrate how this works, suppose we want to
-change the preferences to prefer the Clang compiler and to prefer
-MPICH over OpenMPI. Currently, we prefer GCC and OpenMPI.
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
-           ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
-               ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                   ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                       ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
-                           ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                   ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                   ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-               ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
-                   ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                   ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
-               ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
-                   ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                       ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
-                           ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                               ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                                   ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
-                   ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-
-
-Now we will open the packages configuration file and update our
-preferences.
-
-.. code-block:: console
-
-  $ spack config edit packages
-
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-
-
-Because of the configuration scoping we discussed earlier, this
-overrides the default settings just for these two items.
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
-           ^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
-               ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
-                       ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
-                       ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                           ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                               ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
-                                   ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-               ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-               ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-               ^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
-
-
-^^^^^^^^^^^^^^^^^^^
-Variant Preferences
-^^^^^^^^^^^^^^^^^^^
-
-The packages configuration file can also set variant preferences for
-package variants. For example, let's change our preferences to build all
-packages without shared libraries. We will accomplish this by turning
-off the ``shared`` variant on all packages that have one.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-
-
-We can check the effect of this command with ``spack spec hdf5`` again.
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
-           ^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
-               ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
-                       ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64
-                       ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                           ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                               ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
-                                   ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-               ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-               ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-               ^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-So far we have only made global changes to the package preferences. As
-we've seen throughout this tutorial, hdf5 builds with MPI enabled by
-default in Spack. If we were working on a project that would routinely
-need serial hdf5, that might get annoying quickly, having to type
-``hdf5~mpi`` all the time. Instead, we'll update our preferences for
-hdf5.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     hdf5:
-       variants: ~mpi
-
-
-Now hdf5 will concretize without an MPI dependency by default.
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-In general, every attribute that we can set for all packages we can
-set separately for an individual package.
-
-^^^^^^^^^^^^^^^^^
-External Packages
-^^^^^^^^^^^^^^^^^
-
-The packages configuration file also controls when Spack will build
-against an externally installed package. On these systems we have a
-pre-installed zlib.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     hdf5:
-       variants: ~mpi
-     zlib:
-       paths:
-         zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
-
-
-Here, we've told Spack that zlib 1.2.8 is installed on our system.
-We've also told it the installation prefix where zlib can be found.
-We don't know exactly which variants it was built with, but that's
-okay.
-
-.. code-block:: console
-
-   $ spack spec hdf5
-   Input spec
-   --------------------------------
-   hdf5
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-You'll notice that Spack is now using the external zlib installation,
-but the compiler used to build zlib is now overriding our compiler
-preference of clang. If we explicitly specify clang:
-
-.. code-block:: console
-
-   $ spack spec hdf5 %clang
-   Input spec
-   --------------------------------
-   hdf5%clang
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-Spack concretizes to both hdf5 and zlib being built with clang.
-This has a side-effect of rebuilding zlib. If we want to force
-Spack to use the system zlib, we have two choices. We can either
-specify it on the command line, or we can tell Spack that it's
-not allowed to build its own zlib. We'll go with the latter.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     hdf5:
-       variants: ~mpi
-     zlib:
-       paths:
-         zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-
-
-Now Spack will be forced to choose the external zlib.
-
-.. code-block:: console
-
-   $ spack spec hdf5 %clang
-   Input spec
-   --------------------------------
-   hdf5%clang
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-This gets slightly more complicated with virtual dependencies. Suppose
-we don't want to build our own MPI, but we now want a parallel version
-of hdf5? Well, fortunately we have mpich installed on these systems.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     hdf5:
-       variants: ~mpi
-     zlib:
-       paths:
-         zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-     mpich:
-       paths:
-         mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-
-
-If we concretize ``hdf5+mpi`` with this configuration file, we will just
-build with an alternate MPI implementation.
-
-.. code-block:: console
-
-   $ spack spec hdf5 %clang +mpi
-   Input spec
-   --------------------------------
-   hdf5%clang+mpi
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^openmpi@3.1.3%clang@3.8.0-2ubuntu4~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
-           ^hwloc@1.11.9%clang@3.8.0-2ubuntu4~cairo~cuda+libxml2+pci~shared arch=linux-ubuntu16.04-x86_64
-               ^libpciaccess@0.13.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                       ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
-                           ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^util-macros@1.19.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-               ^libxml2@2.9.8%clang@3.8.0-2ubuntu4~python arch=linux-ubuntu16.04-x86_64
-                   ^xz@5.2.4%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-               ^numactl@2.0.11%clang@3.8.0-2ubuntu4 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
-                   ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                       ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64
-                           ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                               ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                                   ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
-                   ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-
-
-We have only expressed a preference for mpich over other MPI
-implementations, and Spack will happily build with one we haven't
-forbid it from building. We could resolve this by requesting
-``hdf5%clang+mpi^mpich`` explicitly, or we can configure Spack not to
-use any other MPI implementation. Since we're focused on
-configurations here and the former can get tedious, we'll need to
-modify our ``packages.yaml`` file again.
-
-While we're at it, we can configure hdf5 to build with MPI by default
-again.
-
-.. code-block:: yaml
-
-   packages:
-     all:
-       compiler: [clang, gcc, intel, pgi, xl, nag]
-       providers:
-         mpi: [mpich, openmpi]
-       variants: ~shared
-     zlib:
-       paths:
-         zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-     mpich:
-       paths:
-         mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr
-       buildable: False
-     openmpi:
-       buildable: False
-     mvapich2:
-       buildable: False
-     intel-mpi:
-       buildable: False
-     intel-parallel-studio:
-       buildable: False
-     spectrum-mpi:
-       buildable: False
-     mpilander:
-       buildable: False
-     charm:
-       buildable: False
-     charmpp:
-       buildable: False
-
-
-Now that we have configured Spack not to build any of the possible
-providers for MPI we can try again.
-
-.. code-block:: console
-
-   $ spack spec hdf5 %clang
-   Input spec
-   --------------------------------
-   hdf5%clang
-
-   Concretized
-   --------------------------------
-   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-By configuring most of our package preferences in ``packages.yaml``,
-we can cut down on the amount of work we need to do when specifying
-a spec on the command line. In addition to compiler and variant
-preferences, we can specify version preferences as well. Anything
-that you can specify on the command line can be specified in
-``packages.yaml`` with the exact same spec syntax.
-
-^^^^^^^^^^^^^^^^^^^^^^^^
-Installation Permissions
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-The ``packages.yaml`` file also controls the default permissions
-to use when installing a package. You'll notice that by default,
-the installation prefix will be world readable but only user writable.
-
-Let's say we need to install ``converge``, a licensed software package.
-Since a specific research group, ``fluid_dynamics``, pays for this
-license, we want to ensure that only members of this group can access
-the software. We can do this like so:
-
-.. code-block:: yaml
-
-   packages:
-     converge:
-       permissions:
-         read: group
-         group: fluid_dynamics
-
-
-Now, only members of the ``fluid_dynamics`` group can use any
-``converge`` installations.
-
-.. warning::
-
-   Make sure to delete or move the ``packages.yaml`` you have been
-   editing up to this point. Otherwise, it will change the hashes
-   of your packages, leading to differences in the output of later
-   tutorial sections.
-
-
------------------
-High-level Config
------------------
-
-In addition to compiler and package settings, Spack allows customization
-of several high-level settings. These settings are stored in the generic
-``config.yaml`` configuration file. You can see the default settings by
-running:
-
-.. code-block:: console
-
-   $ spack config --scope defaults edit config
-
-
-.. literalinclude:: ../../../etc/spack/defaults/config.yaml
-   :language: yaml
-
-
-As you can see, many of the directories Spack uses can be customized.
-For example, you can tell Spack to install packages to a prefix
-outside of the ``$SPACK_ROOT`` hierarchy. Module files can be
-written to a central location if you are using multiple Spack
-instances. If you have a fast scratch file system, you can run builds
-from this file system with the following ``config.yaml``:
-
-.. code-block:: yaml
-
-   config:
-     build_stage:
-       - /scratch/$user
-
-
-On systems with compilers that absolutely *require* environment variables
-like ``LD_LIBRARY_PATH``, it is possible to prevent Spack from cleaning
-the build environment with the ``dirty`` setting:
-
-.. code-block:: yaml
-
-   config:
-     dirty: true
-
-
-However, this is strongly discouraged, as it can pull unwanted libraries
-into the build.
-
-One last setting that may be of interest to many users is the ability
-to customize the parallelism of Spack builds. By default, Spack
-installs all packages in parallel with the number of jobs equal to the
-number of cores on the node. For example, on a node with 16 cores,
-this will look like:
-
-.. code-block:: console
-
-   $ spack install --no-cache --verbose zlib
-   ==> Installing zlib
-   ==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
-   ==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
-   ==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-   ==> No patches needed for zlib
-   ==> Building zlib [Package]
-   ==> Executing phase: 'install'
-   ==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
-   ...
-   ==> 'make' '-j16'
-   ...
-   ==> 'make' '-j16' 'install'
-   ...
-   ==> Successfully installed zlib
-     Fetch: 0.00s.  Build: 1.03s.  Total: 1.03s.
-   [+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-
-
-As you can see, we are building with all 16 cores on the node. If you are
-on a shared login node, this can slow down the system for other users. If
-you have a strict ulimit or restriction on the number of available licenses,
-you may not be able to build at all with this many cores. On nodes with 64+
-cores, you may not see a significant speedup of the build anyway. To limit
-the number of cores our build uses, set ``build_jobs`` like so:
-
-.. code-block:: yaml
-
-   config:
-     build_jobs: 4
-
-
-If we uninstall and reinstall zlib, we see that it now uses only 4 cores:
-
-.. code-block:: console
-
-   $ spack install --no-cache --verbose zlib
-   ==> Installing zlib
-   ==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
-   ==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
-   ==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-   ==> No patches needed for zlib
-   ==> Building zlib [Package]
-   ==> Executing phase: 'install'
-   ==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
-   ...
-   ==> 'make' '-j4'
-   ...
-   ==> 'make' '-j4' 'install'
-   ...
-   ==> Successfully installed zlib
-     Fetch: 0.00s.  Build: 1.03s.  Total: 1.03s.
-   [+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-
-
-Obviously, if you want to build everything in serial for whatever reason,
-you would set ``build_jobs`` to 1.
-
---------
-Examples
---------
-
-For examples of how other sites configure Spack, see
-https://github.com/spack/spack-configs. If you use Spack at your site
-and want to share your config files, feel free to submit a pull request!