update changelog for 0.15.2

Fixes #17299

Cray Shasta systems appear to use an unmodified Sles or other Linux operating system on the backend (like Cray "Cluster" systems and unlike Cray "XC40" systems that use CNL).

This updates the CNL version detection to properly note that this is the underlying OS instead of CNL and delegate to LinuxDistro.

.codecov.yml

@@ -4,33 +4,12 @@ coverage:
   range: 60...90
   status:
     project:
-      default: true
-      llnl:
-        threshold: 0.5
-        paths:
-          - lib/spack/llnl
-      commands:
-        threshold: 0.5
-        paths:
-          - lib/spack/spack/cmd
-      build_systems:
-        threshold: 0.5
-        paths:
-          - lib/spack/spack/build_systems
-      modules:
-        threshold: 0.5
-        paths:
-          - lib/spack/spack/modules
-      core:
-        threshold: 0.5
-        paths:
-          - "!lib/spack/llnl"
-          - "!lib/spack/spack/cmd"
+      default: yes
 
 ignore:
   - lib/spack/spack/test/.*
-  - lib/spack/env/.*
   - lib/spack/docs/.*
   - lib/spack/external/.*
+  - share/spack/qa/.*
 
 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).
+# is added (because 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

@@ -1,14 +1,11 @@
 ---
-name: Bug report 
-about: Report a bug in the core of Spack (command not working as expected, etc.) 
-
+name: "\U0001F41E Bug report"
+about: Report a bug in the core of Spack (command not working as expected, etc.)
+labels: "bug,triage"
 ---
 
-
-*Explain, in a clear and concise way, the command you ran and the result you were trying to achieve.
-Example: "I ran Spack find to list all the installed packages and..."*
-
-
+<!-- Explain, in a clear and concise way, the command you ran and the result you were trying to achieve.
+Example: "I ran `spack find` to list all the installed packages and ..." -->
 
 ### Steps to reproduce the issue
 
@@ -20,30 +17,26 @@ $ spack <command2> <spec>
 
 ### Error Message
 
-If Spack reported an error, provide the error message. If it did not report an error
-but the output appears incorrect, provide the incorrect output. If there was no error
-message and no output but the result is incorrect, describe how it does not match
-what you expect. To provide more information you might re-run the commands with 
-the additional -sd flags:
+<!-- If Spack reported an error, provide the error message. If it did not report an error but the output appears incorrect, provide the incorrect output. If there was no error message and no output but the result is incorrect, describe how it does not match what you expect. -->
 ```console
-$ spack -sd <command1> <spec>
-$ spack -sd <command2> <spec>
-...
+$ spack --debug --stacktrace <command>
 ```
-that activate the full debug output. 
-
 
 ### Information on your system
 
-This includes:
+<!-- Please include the output of `spack debug report` -->
 
- 1. which platform you are using
- 2. any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.)
+<!-- If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well. -->
 
------
+### Additional information
 
-We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
+<!-- These boxes can be checked by replacing [ ] with [x] or by clicking them after submitting the issue. -->
+- [ ] I have run `spack debug report` and reported the version of Spack/Python/Platform
+- [ ] I have searched the issues of this repo and believe this is not a duplicate
+- [ ] I have run the failing commands in debug mode and reported the output
+
+<!-- We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
 
 If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
 
-Other than that, thanks for taking the time to contribute to Spack!
+Other than that, thanks for taking the time to contribute to Spack! -->

.github/ISSUE_TEMPLATE/build_error.md

@@ -1,78 +1,43 @@
 ---
-name: Build error 
-about: Some package in Spack didn't build correctly  
-
+name: "\U0001F4A5 Build error"
+about: Some package in Spack didn't build correctly
+title: "Installation issue: "
+labels: "build-error"
 ---
 
-*Thanks for taking the time to report this build failure. To proceed with the
-report please:*
+<!-- Thanks for taking the time to report this build failure. To proceed with the report please:
+
 1. Title the issue "Installation issue: <name-of-the-package>".
 2. Provide the information required below.
-3. Remove the template instructions before posting the issue.
 
-We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
-
-
----
+We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively! -->
 
 ### Steps to reproduce the issue
 
+<!-- Fill in the exact spec you are trying to build and the relevant part of the error message -->
 ```console
-$ spack install <spec> # Fill in the exact spec you are using
-... # and the relevant part of the error message
+$ spack install <spec>
+...
 ```
 
-### Platform and user environment
+### Information on your system
 
-Please report your OS here:
-```commandline
-$ uname -a 
-Linux nuvolari 4.15.0-29-generic #31-Ubuntu SMP Tue Jul 17 15:39:52 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
-$ lsb_release -d
-Description:	Ubuntu 18.04.1 LTS
-``` 
-and, if relevant, post or attach:
+<!-- Please include the output of `spack debug report` -->
 
-- `packages.yaml`
-- `compilers.yaml`
-
-to the issue
+<!-- If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well. -->
 
 ### Additional information
 
-Sometimes the issue benefits from additional details. In these cases there are
-a few things we can suggest doing. First of all, you can post the full output of:
-```console
-$ spack spec --install-status <spec>
-...
-```
-to show people whether Spack installed a faulty software or if it was not able to
-build it at all. 
+<!-- Please upload the following files. They should be present in the stage directory of the failing build. Also upload any config.log or similar file if one exists. -->
+* [spack-build-out.txt]()
+* [spack-build-env.txt]()
 
-If your build didn't make it past the configure stage, Spack as also commands to parse 
-logs and report error and warning messages:
-```console
-$ spack log-parse --show=errors,warnings <file-to-parse>
-```
-You might want to run this command on the `config.log` or any other similar file
-found in the stage directory: 
-```console
-$ spack location -s <spec>
-```
-In case in `config.log` there are other settings that you think might be the cause 
-of the build failure, you can consider attaching the file to this issue.
+<!-- Some packages have maintainers who have volunteered to debug build failures. Run `spack maintainers <name-of-the-package>` and @mention them here if they exist. -->
 
-Rebuilding the package with the following options:
-```console
-$ spack -d install -j 1 <spec>
-...
-```
-will provide additional debug information. After the failure you will find two files in the current directory:
+### General information
 
-1. `spack-cc-<spec>.in`, which contains details on the command given in input 
-    to Spack's compiler wrapper  
-1. `spack-cc-<spec>.out`, which contains the command used to compile / link the 
-    failed object after Spack's compiler wrapper did its processing 
-
-You can post or attach those files to provide maintainers with more information on what
-is causing the failure.
+<!-- These boxes can be checked by replacing [ ] with [x] or by clicking them after submitting the issue. -->
+- [ ] I have run `spack debug report` and reported the version of Spack/Python/Platform
+- [ ] I have run `spack maintainers <name-of-the-package>` and @mentioned any maintainers
+- [ ] I have uploaded the build log and environment files
+- [ ] I have searched the issues of this repo and believe this is not a duplicate

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,27 +1,33 @@
 ---
-name: Feature request 
+name: "\U0001F38A Feature request" 
 about: Suggest adding a feature that is not yet in Spack  
+labels: feature
 
 ---
 
-*Please add a concise summary of your suggestion here.*
+<!--*Please add a concise summary of your suggestion here.*-->
 
 ### Rationale
 
-*Is your feature request related to a problem? Please describe it!*
+<!--*Is your feature request related to a problem? Please describe it!*-->
 
 ### Description
 
-*Describe the solution you'd like and the alternatives you have considered.*
+<!--*Describe the solution you'd like and the alternatives you have considered.*-->
 
 
 ### Additional information
-*Add any other context about the feature request here.*
+<!--*Add any other context about the feature request here.*-->
 
 
------
+### General information
+
+- [ ] I have run `spack --version` and reported the version of Spack
+- [ ] I have searched the issues of this repo and believe this is not a duplicate
 
 
-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!
+<!--If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
+
+Other than that, thanks for taking the time to contribute to Spack!
+-->

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

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

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

@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+#
+# Copyright 2013-2020 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/install_spack.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env sh
+git clone https://github.com/spack/spack.git
+echo -e "config:\n  build_jobs: 2" > spack/etc/spack/config.yaml
+. spack/share/spack/setup-env.sh
+spack compilers

.github/workflows/linux_build_tests.yaml

@@ -0,0 +1,61 @@
+name: linux builds
+
+on:
+  push:
+    branches:
+    - master
+    - develop
+    - releases/**
+  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/**'
+      # Don't run if we only modified documentation
+      - 'lib/spack/docs/**'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        package: [lz4, mpich, tut, py-setuptools, openjpeg, r-rcpp]
+    steps:
+    - uses: actions/checkout@v2
+    - 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 update
+        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/linux_unit_tests.yaml

@@ -0,0 +1,62 @@
+name: linux tests
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+      - releases/**
+  pull_request:
+    branches:
+      - master
+      - develop
+jobs:
+  unittests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [2.7, 3.5, 3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install System packages
+      run: |
+          sudo apt-get -y update
+          sudo apt-get install -y coreutils gfortran graphviz gnupg2 mercurial ninja-build patchelf
+          # Needed for kcov
+          sudo apt-get -y install cmake binutils-dev libcurl4-openssl-dev zlib1g-dev libdw-dev libiberty-dev
+    - name: Install Python packages
+      run: |
+          pip install --upgrade pip six setuptools codecov coverage
+    - name: Setup git configuration
+      run: |
+          # Need this for the git tests to succeed.
+          git --version
+          git config --global user.email "spack@example.com"
+          git config --global user.name "Test User"
+          git fetch -u origin develop:develop
+    - name: Install kcov for bash script coverage
+      env:
+          KCOV_VERSION: 34
+      run: |
+          KCOV_ROOT=$(mktemp -d)
+          wget --output-document=${KCOV_ROOT}/${KCOV_VERSION}.tar.gz https://github.com/SimonKagstrom/kcov/archive/v${KCOV_VERSION}.tar.gz
+          tar -C ${KCOV_ROOT} -xzvf ${KCOV_ROOT}/${KCOV_VERSION}.tar.gz
+          mkdir -p ${KCOV_ROOT}/build
+          cd ${KCOV_ROOT}/build && cmake -Wno-dev ${KCOV_ROOT}/kcov-${KCOV_VERSION} && cd -
+          make -C ${KCOV_ROOT}/build && sudo  make -C ${KCOV_ROOT}/build install
+    - name: Run unit tests
+      env:
+          COVERAGE: true
+      run: |
+          share/spack/qa/run-unit-tests
+          coverage combine
+          coverage xml
+    - name: Upload to codecov.io
+      uses: codecov/codecov-action@v1
+      with:
+        flags: unittests,linux

.github/workflows/macos_python.yml

@@ -0,0 +1,58 @@
+# These are nightly package tests for macOS
+# focus areas:
+# - initial user experience
+# - scientific python stack
+name: macOS builds nightly
+
+on:
+  schedule:
+    # nightly at 1 AM
+    - cron: '0 1 * * *'
+
+# GitHub Action Limits
+# https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions
+
+jobs:
+  install_gcc:
+    name: gcc with clang
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: spack install
+      run: |
+        . .github/workflows/install_spack.sh
+        spack install -v gcc
+
+  install_jupyter_clang:
+    name: jupyter
+    runs-on: macos-latest
+    timeout-minutes: 700
+    steps:
+    - uses: actions/checkout@v2
+    - name: spack install
+      run: |
+        . .github/workflows/install_spack.sh
+        spack install -v py-jupyter %clang
+
+  install_scipy_clang:
+    name: scipy, mpl, pd
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: spack install
+      run: |
+        . .github/workflows/install_spack.sh
+        spack install -v py-scipy %clang
+        spack install -v py-matplotlib %clang
+        spack install -v py-pandas %clang
+
+  install_mpi4py_clang:
+    name: mpi4py, petsc4py
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: spack install
+      run: |
+        . .github/workflows/install_spack.sh
+        spack install -v py-mpi4py %clang
+        spack install -v py-petsc4py %clang

.github/workflows/macos_unit_tests.yaml

@@ -0,0 +1,49 @@
+name: macos tests
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+      - releases/**
+  pull_request:
+    branches:
+      - master
+      - develop
+jobs:
+  build:
+
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: [3.7]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Python packages
+      run: |
+          pip install --upgrade pip six setuptools
+          pip install --upgrade codecov coverage
+          pip install --upgrade flake8 pep8-naming
+    - name: Setup Homebrew packages
+      run: |
+        brew update
+        brew upgrade
+        brew install gcc gnupg2 dash kcov
+    - name: Run unit tests
+      run: |
+        git --version
+        git fetch -u origin develop:develop
+        . share/spack/setup-env.sh
+        coverage run $(which spack) test
+        coverage combine
+        coverage xml
+    - name: Upload to codecov.io
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml
+        flags: unittests,macos

.github/workflows/minimum_python_versions.yaml

@@ -0,0 +1,31 @@
+name: python version check
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+      - releases/**
+  pull_request:
+    branches:
+      - master
+      - develop
+jobs:
+  validate:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - 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

@@ -4,6 +4,7 @@
 /var/spack/environments
 /var/spack/repos/*/index.yaml
 /var/spack/repos/*/lock
+__pycache__/
 *.pyc
 /opt
 *~
@@ -20,9 +21,20 @@
 *.swp
 /htmlcov
 .coverage
-#*
+\#*
 .#*
+.cache
 lib/spack/spack/test/.cache
 /bin/spackc
 *.in.log
 *.out.log
+*.orig
+
+# Eclipse files
+.project
+.cproject
+.pydevproject
+
+# VSCode files
+.vscode
+.devcontainer

.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

@@ -12,161 +12,90 @@ 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: bionic
 
 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: 'unit tests + documentation'
       python: '2.6'
-      sudo: required
+      dist: trusty
       os: linux
       language: python
-      env: TEST_SUITE=unit
-    - python: '2.7'
-      sudo: required
+      addons:
+        apt:
+          # Everything but patchelf, that is not available for trusty
+          packages:
+            - ccache
+            - gfortran
+            - graphviz
+            - gnupg2
+            - kcov
+            - mercurial
+            - ninja-build
+            - realpath
+            - zsh
+            - fish
+      env: [ TEST_SUITE=unit, COVERAGE=true ]
+    - python: '3.8'
       os: linux
       language: python
-      env: TEST_SUITE=unit
-    - python: '3.4'
-      sudo: required
-      os: linux
-      language: python
-      env: TEST_SUITE=unit
-    - 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
+      env: [ TEST_SUITE=shell, COVERAGE=true, KCOV_VERSION=38 ]
+    - 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'
 
 stages:
   - 'style checks'
   - 'unit tests + documentation'
-  - 'build tests'
-  - name: 'docker build'
-    if: type = push AND branch IN (develop, master)
 
 
 #=============================================================================
 # Environment
 #=============================================================================
-# Use new Travis infrastructure (Docker can't sudo yet)
-sudo: false
 
 # Docs need graphviz to build
 addons:
+  # for Linux builds, we use APT
   apt:
     packages:
+      - ccache
+      - coreutils
       - gfortran
-      - mercurial
       - graphviz
       - gnupg2
-      - cmake
+      - mercurial
       - ninja-build
-      - r-base
-      - r-base-core
-      - r-base-dev
-      - perl
-      - perl-base
+      - patchelf
+      - zsh
+      - fish
+    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 [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-        brew update;
-        export HOMEBREW_NO_AUTO_UPDATE=1;
-        rm /usr/local/include/c++ ;
-        brew ls --versions python@2 > /dev/null || brew install python@2;
-        brew ls --versions gcc      > /dev/null || brew install gcc;
-        brew ls --versions gnupg2   > /dev/null || brew install gnupg2;
-        pip2 install --upgrade pip;
-        pip2 install virtualenv;
-        virtualenv venv;
-        source venv/bin/activate;
+  - ccache -M 2G && ccache -z
+  # Install kcov manually, since it's not packaged for bionic beaver
+  - if [[ "$KCOV_VERSION" ]]; then
+        sudo apt-get -y install cmake binutils-dev libcurl4-openssl-dev zlib1g-dev libdw-dev libiberty-dev;
+        KCOV_ROOT=$(mktemp -d);
+        wget --output-document=${KCOV_ROOT}/${KCOV_VERSION}.tar.gz https://github.com/SimonKagstrom/kcov/archive/v${KCOV_VERSION}.tar.gz;
+        tar -C ${KCOV_ROOT} -xzvf ${KCOV_ROOT}/${KCOV_VERSION}.tar.gz;
+        mkdir -p ${KCOV_ROOT}/build;
+        cd ${KCOV_ROOT}/build && cmake -Wno-dev ${KCOV_ROOT}/kcov-${KCOV_VERSION} && cd - ;
+        make -C ${KCOV_ROOT}/build && sudo  make -C ${KCOV_ROOT}/build install;
     fi
 
 # Install various dependencies
@@ -174,7 +103,7 @@ 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
@@ -187,49 +116,37 @@ 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
+            ;;
+        shell)
+            codecov --env PYTHON_VERSION
+            --required
+            --flags "${TEST_SUITE}${TRAVIS_OS_NAME}";
+    esac
 
 #=============================================================================
 # Notifications
 #=============================================================================
 notifications:
   email:
-    recipients: tgamblin@llnl.gov
+    recipients:
+    - tgamblin@llnl.gov
+    - massimiliano.culpo@gmail.com
     on_success: change
     on_failure: always

CHANGELOG.md

@@ -0,0 +1,580 @@
+# v0.15.2 (2020-07-23)
+
+This minor release includes two new features:
+
+* Spack install verbosity is decreased, and more debug levels are added (#17546)
+* The $spack/share/spack/keys directory contains public keys that may be optionally trusted for public binary mirrors (#17684)
+
+This release also includes several important fixes:
+
+* MPICC and related variables are now cleand in the build environment (#17450)
+* LLVM flang only builds CUDA offload components when +cuda (#17466)
+* CI pipelines no longer upload user environments that can contain secrets to the internet (#17545)
+* CI pipelines add bootstrapped compilers to the compiler config (#17536)
+* `spack buildcache list` does not exit on first failure and lists later mirrors (#17565)
+* Apple's "gcc" executable that is an apple-clang compiler does not generate a gcc compiler config (#17589)
+* Mixed compiler toolchains are merged more naturally across different compiler suffixes (#17590)
+* Cray Shasta platforms detect the OS properly (#17467)
+* Additional more minor fixes.
+
+# v0.15.1 (2020-07-10)
+
+This minor release includes several important fixes:
+
+* Fix shell support on Cray (#17386)
+* Fix use of externals installed with other Spack instances (#16954)
+* Fix gcc+binutils build (#9024)
+* Fixes for usage of intel-mpi (#17378 and #17382)
+* Fixes to Autotools config.guess detection (#17333 and #17356)
+* Update `spack install` message to prompt user when an environment is not
+  explicitly activated (#17454)
+
+This release also adds a mirror for all sources that are
+fetched in Spack (#17077). It is expected to be useful when the
+official website for a Spack package is unavailable.
+
+# v0.15.0 (2020-06-28)
+
+`v0.15.0` is a major feature release.
+
+## Major Features in this release
+
+1. **Cray support** Spack will now work properly on Cray "Cluster"
+systems (non XC systems) and after a `module purge` command on Cray
+systems. See #12989
+
+2. **Virtual package configuration** Virtual packages are allowed in
+packages.yaml configuration. This allows users to specify a virtual
+package as non-buildable without needing to specify for each
+implementation. See #14934
+
+3. **New config subcommands** This release adds `spack config add` and
+`spack config remove` commands to add to and remove from yaml
+configuration files from the CLI. See #13920
+
+4. **Environment activation** Anonymous environments are **no longer**
+automatically activated in the current working directory. To activate
+an environment from a `spack.yaml` file in the current directory, use
+the `spack env activate .` command. This removes a concern that users
+were too easily polluting their anonymous environments with accidental
+installations. See #17258
+
+5. **Apple clang compiler** The clang compiler and the apple-clang
+compiler are now separate compilers in Spack. This allows Spack to
+improve support for the apple-clang compiler. See #17110
+
+6. **Finding external packages** Spack packages can now support an API
+for finding external installations. This allows the `spack external
+find` command to automatically add installations of those packages to
+the user's configuration. See #15158
+
+
+## Additional new features of note
+
+* support for using Spack with the fish shell (#9279)
+* `spack load --first` option to load first match (instead of prompting user) (#15622)
+* support the Cray cce compiler both new and classic versions (#17256, #12989)
+* `spack dev-build` command:
+  * supports stopping before a specified phase (#14699)
+  * supports automatically launching a shell in the build environment (#14887)
+* `spack install --fail-fast` allows builds to fail at the first error (rather than best-effort) (#15295)
+* environments: SpecList references can be dereferenced as compiler or dependency constraints (#15245)
+* `spack view` command: new support for a copy/relocate view type (#16480)
+* ci pipelines: see documentation for several improvements
+* `spack mirror -a` command now supports excluding packages (#14154)
+* `spack buildcache create` is now environment-aware (#16580)
+* module generation: more flexible format for specifying naming schemes (#16629)
+* lmod module generation: packages can be configured as core specs for lmod hierarchy (#16517)
+
+## Deprecations and Removals
+
+The following commands were deprecated in v0.13.0, and have now been removed:
+
+* `spack configure`
+* `spack build`
+* `spack diy`
+
+The following commands were deprecated in v0.14.0, and will be removed in the next major release:
+
+* `spack bootstrap`
+
+## Bugfixes
+
+Some of the most notable bugfixes in this release include:
+
+* Spack environments can now contain the string `-h` (#15429)
+* The `spack install` gracefully handles being backgrounded (#15723, #14682)
+* Spack uses `-isystem` instead of `-I` in cases that the underlying build system does as well (#16077)
+* Spack no longer prints any specs that cannot be safely copied into a Spack command (#16462)
+* Incomplete Spack environments containing python no longer cause problems (#16473)
+* Several improvements to binary package relocation
+
+## Package Improvements
+
+The Spack project is constantly engaged in routine maintenance,
+bugfixes, and improvements for the package ecosystem. Of particular
+note in this release are the following:
+
+* Spack now contains 4339 packages. There are 430 newly supported packages in v0.15.0
+* GCC now builds properly on ARM architectures (#17280)
+* Python: patched to support compiling mixed C/C++ python modules through distutils (#16856)
+* improvements to pytorch and py-tensorflow packages
+* improvements to major MPI implementations: mvapich2, mpich, openmpi, and others
+
+## Spack Project Management:
+
+* Much of the Spack CI infrastructure has moved from Travis to GitHub Actions (#16610, #14220, #16345)
+* All merges to the `develop` branch run E4S CI pipeline (#16338)
+* New `spack debug report` command makes reporting bugs easier (#15834)
+
+# v0.14.2 (2020-04-15)
+
+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 (2020-03-20)
+
+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 integrated 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 already added patches (#13908)
+* avoid re-fetching already 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 +1,10 @@
 # <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)
+[![MacOS Tests](https://github.com/spack/spack/workflows/macos%20tests/badge.svg)](https://github.com/spack/spack/actions)
+[![Linux Tests](https://github.com/spack/spack/workflows/linux%20tests/badge.svg)](https://github.com/spack/spack/actions)
+[![Linux Builds](https://github.com/spack/spack/workflows/linux%20builds/badge.svg)](https://github.com/spack/spack/actions)
+[![macOS Builds (nightly)](https://github.com/spack/spack/workflows/macOS%20builds%20nightly/badge.svg?branch=develop)](https://github.com/spack/spack/actions?query=workflow%3A%22macOS+builds+nightly%22)
+[![Build Status](https://travis-ci.com/spack/spack.svg?branch=develop)](https://travis-ci.com/spack/spack)
 [![codecov](https://codecov.io/gh/spack/spack/branch/develop/graph/badge.svg)](https://codecov.io/gh/spack/spack)
 [![Read the Docs](https://readthedocs.org/projects/spack/badge/?version=latest)](https://spack.readthedocs.io)
 [![Slack](https://spackpm.herokuapp.com/badge.svg)](https://spackpm.herokuapp.com)
@@ -26,55 +30,43 @@ 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 +84,13 @@ 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 +121,6 @@ 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-811652

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)
@@ -22,4 +22,4 @@
 #
 # This is compatible across platforms.
 #
-/usr/bin/env spack python "$@"
+exec /usr/bin/env spack python "$@"

etc/spack/defaults/config.yaml

@@ -32,24 +32,37 @@ config:
   module_roots:
     tcl:    $spack/share/spack/modules
     lmod:   $spack/share/spack/lmod
-    dotkit: $spack/share/spack/dotkit
 
 
   # Temporary locations Spack can try to use for builds.
   #
-  # Spack will use the first one it finds that exists and is writable.
-  # You can use $tempdir to refer to the system default temp directory
-  # (as returned by tempfile.gettempdir()).
+  # Recommended options are given below.
   #
-  # A value of $spack/var/spack/stage indicates that Spack should run
-  # builds directly inside its install directory without staging them in
-  # temporary space.
+  # Builds can be faster in temporary directories on some (e.g., HPC) systems.
+  # Specifying `$tempdir` will ensure use of the default temporary directory
+  # (i.e., ``$TMP` or ``$TMPDIR``).
   #
-  # The build stage can be purged with `spack 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
@@ -62,11 +75,31 @@ config:
   misc_cache: ~/.spack/cache
 
 
+  # Timeout in seconds used for downloading sources etc. This only applies
+  # to the connection phase and can be increased for slow connections or
+  # servers. 0 means no timeout.
+  connect_timeout: 10
+
+
   # If this is false, tools like curl that use SSL will not verify
   # certifiates. (e.g., curl will use use the -k option)
   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 +127,12 @@ 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 +143,7 @@ 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 +152,12 @@ 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'
+
+  # Set to 'false' to allow installation on filesystems that doesn't allow setgid bit
+  # manipulation by unprivileged user (e.g. AFS)
+  allow_sgid: true

etc/spack/defaults/darwin/modules.yaml

@@ -16,8 +16,6 @@
 modules:
   prefix_inspections:
     lib:
-      - DYLD_LIBRARY_PATH
       - DYLD_FALLBACK_LIBRARY_PATH
     lib64:
-      - DYLD_LIBRARY_PATH
       - DYLD_FALLBACK_LIBRARY_PATH

etc/spack/defaults/darwin/packages.yaml

@@ -15,7 +15,11 @@
 # -------------------------------------------------------------------------
 packages:
   all:
-    compiler: [clang, gcc, intel]
+    compiler:
+    - apple-clang
+    - clang
+    - gcc
+    - intel
     providers:
       elf: [libelf]
       unwind: [apple-libunwind]

etc/spack/defaults/mirrors.yaml

@@ -0,0 +1,2 @@
+mirrors:
+  spack-public: https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/

etc/spack/defaults/modules.yaml

@@ -16,7 +16,6 @@
 modules:
   enable:
     - tcl
-    - dotkit
   prefix_inspections:
     bin:
       - PATH
@@ -31,11 +30,17 @@ modules:
     lib64:
       - LIBRARY_PATH
     include:
-      - CPATH
+      - C_INCLUDE_PATH
+      - CPLUS_INCLUDE_PATH
+      # The INCLUDE env variable specifies paths to look for
+      # .mod file for Intel Fortran compilers
+      - INCLUDE
     lib/pkgconfig:
       - 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 +23,30 @@ 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]
+      iconv: [libiconv]
       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]
+      rpc: [libtirpc]
       scalapack: [netlib-scalapack]
+      sycl: [hipsycl]
       szip: [libszip, libaec]
       tbb: [intel-tbb]
       unwind: [libunwind]
+      sycl: [hipsycl]
     permissions:
       read: world
       write: user

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)
@@ -25,6 +25,14 @@ It is recommended that the following be put in your ``.bashrc`` file:
 
     alias less='less -R'
 
+If you do not see colorized output when using ``less -R`` it is because color
+is being disabled in the piped output. In this case, tell spack to force
+colorized output.
+
+.. code-block:: console
+
+    $ spack --color always | less -R 
+
 --------------------------
 Listing available packages
 --------------------------
@@ -39,12 +47,15 @@ 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 thousands 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 +240,50 @@ 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 package database
+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 +329,86 @@ 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 +466,19 @@ 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 +531,8 @@ 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 +542,10 @@ 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 +573,109 @@ 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": "apple-clang",
+       "version": "10.0.0"
+      },
+      "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:
 
 --------------------
@@ -612,7 +862,7 @@ Variants are named options associated with a particular package. They are
 optional, as each package must provide default values for each variant it
 makes available. Variants can be specified using
 a flexible parameter syntax ``name=<value>``. For example,
-``spack install libelf debug=True`` will install libelf build with debug
+``spack install libelf debug=True`` will install libelf built with debug
 flags. The names of particular variants available for a package depend on
 what was provided by the package author. ``spack info <package>`` will
 provide information on what build variants are available.
@@ -673,10 +923,10 @@ 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"``.
+by a space. The command ``spack install libelf 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 +937,13 @@ 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 +960,130 @@ 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:
 
@@ -753,7 +1091,7 @@ used on Cray machines, see :ref:`cray-support`
 Virtual dependencies
 --------------------
 
-The dependence graph for ``mpileaks`` we saw above wasn't *quite*
+The dependency graph for ``mpileaks`` we saw above wasn't *quite*
 accurate.  ``mpileaks`` uses MPI, which is an interface that has many
 different implementations.  Above, we showed ``mpileaks`` and
 ``callpath`` depending on ``mpich``, which is one *particular*
@@ -896,6 +1234,8 @@ add a version specifier to the spec:
 Notice that the package versions that provide insufficient MPI
 versions are now filtered out.
 
+.. _extensions:
+
 ---------------------------
 Extensions & Python support
 ---------------------------
@@ -903,8 +1243,7 @@ Extensions & Python support
 Spack's installation model assumes that each package will live in its
 own install prefix.  However, certain packages are typically installed
 *within* the directory hierarchy of other packages.  For example,
-modules in interpreted languages like `Python
-<https://www.python.org>`_ are typically installed in the
+`Python <https://www.python.org>`_ packages are typically installed in the
 ``$prefix/lib/python-2.7/site-packages`` directory.
 
 Spack has support for this type of installation as well.  In Spack,
@@ -980,33 +1319,41 @@ 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.
@@ -1072,12 +1419,12 @@ packages listed as activated:
    py-nose@1.3.4  py-numpy@1.9.1  py-setuptools@11.3.1
 
 Now, when a user runs python, ``numpy`` will be available for import
-*without* the user having to explicitly loaded.  ``python@2.7.8`` now
+*without* the user having to explicitly load it.  ``python@2.7.8`` now
 acts like a system Python installation with ``numpy`` installed inside
 of it.
 
 Spack accomplishes this by symbolically linking the *entire* prefix of
-the ``py-numpy`` into the prefix of the ``python`` package.  To the
+the ``py-numpy`` package into the prefix of the ``python`` package.  To the
 python interpreter, it looks like ``numpy`` is installed in the
 ``site-packages`` directory.
 

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)
@@ -57,6 +57,12 @@ Build caches are installed via:
 
    $ spack buildcache install
 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+List of popular build caches
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+* `Extreme-scale Scientific Software Stack (E4S) <https://e4s-project.github.io/>`_: `build cache <https://oaciss.uoregon.edu/e4s/inventory.html>`_
+
 
 ----------
 Relocation

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
@@ -114,6 +124,78 @@ The ``buildable`` does not need to be paired with external packages.
 It could also be used alone to forbid packages that may be
 buggy or otherwise undesirable.
 
+Virtual packages in Spack can also be specified as not buildable, and
+external implementations can be provided. In the example above,
+OpenMPI is configured as not buildable, but Spack will often prefer
+other MPI implementations over the externally available OpenMPI. Spack
+can be configured with every MPI provider not buildable individually,
+but more conveniently:
+
+.. code-block:: yaml
+
+   packages:
+     mpi:
+       buildable: False
+     openmpi:
+       paths:
+         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
+
+Implementations can also be listed immediately under the virtual they provide:
+
+.. code-block:: yaml
+
+   packages:
+     mpi:
+       buildable: False
+         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
+         mpich@3.3 %clang@9.0.0 arch=linux-debian7-x86_64: /opt/mpich-3.3-intel
+
+Spack can then use any of the listed external implementations of MPI
+to satisfy a dependency, and will choose depending on the compiler and
+architecture.
+
+.. _cmd-spack-external-find:
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Automatically Find External Packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can run the :ref:`spack external find <spack-external-find>` command
+to search for system-provided packages and add them to ``packages.yaml``.
+After running this command your ``packages.yaml`` may include new entries:
+
+.. code-block:: yaml
+
+   packages:
+     cmake:
+       paths:
+         cmake@3.17.2: /usr
+
+Generally this is useful for detecting a small set of commonly-used packages;
+for now this is generally limited to finding build-only dependencies.
+Specific limitations include:
+
+* Packages are not discoverable by default: For a package to be
+  discoverable with ``spack external find``, it needs to add special
+  logic. See :ref:`here <make-package-findable>` for more details.
+* The current implementation only collects and examines executable files,
+  so it is typically only useful for build/run dependencies (in some cases
+  if a library package also provides an executable, it may be possible to
+  extract a meaningful Spec by running the executable - for example the
+  compiler wrappers in MPI implementations).
+* The logic does not search through module files, it can only detect
+  packages with executables defined in ``PATH``; you can help Spack locate
+  externals which use module files by loading any associated modules for
+  packages that you want Spack to know about before running
+  ``spack external find``.
+* Spack does not overwrite existing entries in the package configuration:
+  If there is an external defined for a spec at any configuration scope,
+  then Spack will not add a new external entry (``spack config blame packages``
+  can help locate all external entries).
 
 .. _concretization-preferences:
 
@@ -138,7 +220,8 @@ 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 +235,11 @@ 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)
@@ -233,7 +233,124 @@ You may have noticed that most of the Autotools flags are of the form
 ``--without-baz``. Since these flags are so common, Spack provides a
 couple of helper functions to make your life easier.
 
-TODO: document ``with_or_without`` and ``enable_or_disable``.
+"""""""""""""""""
+enable_or_disable
+"""""""""""""""""
+
+Autotools flags for simple boolean variants can be automatically
+generated by calling the ``enable_or_disable`` method. This is
+typically used to enable or disable some feature within the package.
+
+.. code-block:: python
+
+   variant(
+       'memchecker',
+       default=False,
+       description='Memchecker support for debugging [degrades performance]'
+   )
+   config_args.extend(self.enable_or_disable('memchecker'))
+
+In this example, specifying the variant ``+memchecker`` will generate
+the following configuration options:
+
+.. code-block:: console
+
+   --enable-memchecker
+
+"""""""""""""""
+with_or_without
+"""""""""""""""
+
+Autotools flags for more complex variants, including boolean variants
+and multi-valued variants, can be automatically generated by calling
+the ``with_or_without`` method.
+
+.. code-block:: python
+
+   variant(
+       'schedulers',
+       values=disjoint_sets(
+           ('auto',), ('alps', 'lsf', 'tm', 'slurm', 'sge', 'loadleveler')
+       ).with_non_feature_values('auto', 'none'),
+       description="List of schedulers for which support is enabled; "
+       "'auto' lets openmpi determine",
+   )
+   if 'schedulers=auto' not in spec:
+       config_args.extend(self.with_or_without('schedulers'))
+
+In this example, specifying the variant ``schedulers=slurm,sge`` will
+generate the following configuration options:
+
+.. code-block:: console
+
+   --with-slurm --with-sge
+
+``enable_or_disable`` is actually functionally equivalent with
+``with_or_without``, and accepts the same arguments and variant types;
+but idiomatic autotools packages often follow these naming
+conventions.
+
+""""""""""""""""
+activation_value
+""""""""""""""""
+
+Autotools parameters that require an option can still be automatically
+generated, using the ``activation_value`` argument to
+``with_or_without`` (or, rarely, ``enable_or_disable``).
+
+.. code-block:: python
+
+   variant(
+      'fabrics',
+       values=disjoint_sets(
+           ('auto',), ('psm', 'psm2', 'verbs', 'mxm', 'ucx', 'libfabric')
+       ).with_non_feature_values('auto', 'none'),
+       description="List of fabrics that are enabled; "
+       "'auto' lets openmpi determine",
+   )
+   if 'fabrics=auto' not in spec:
+       config_args.extend(self.with_or_without('fabrics',
+           activation_value='prefix'))
+
+``activation_value`` accepts a callable that generates the configure
+parameter value given the variant value; but the special value
+``prefix`` tells Spack to automatically use the dependenency's
+installation prefix, which is the most common use for such
+parameters. In this example, specifying the variant
+``fabrics=libfabric`` will generate the following configuration
+options:
+
+.. code-block:: console
+
+   --with-libfabric=</path/to/libfabric>
+
+""""""""""""""""""""
+activation overrides
+""""""""""""""""""""
+
+Finally, the behavior of either ``with_or_without`` or
+``enable_or_disable`` can be overridden for specific variant
+values. This is most useful for multi-values variants where some of
+the variant values require atypical behavior.
+
+.. code-block:: python
+
+   def with_or_without_verbs(self, activated):
+       # Up through version 1.6, this option was named --with-openib.
+       # In version 1.7, it was renamed to be --with-verbs.
+       opt = 'verbs' if self.spec.satisfies('@1.7:') else 'openib'
+       if not activated:
+           return '--without-{0}'.format(opt)
+       return '--with-{0}={1}'.format(opt, self.spec['rdma-core'].prefix)
+
+Defining ``with_or_without_verbs`` overrides the behavior of a
+``fabrics=verbs`` variant, changing the configure-time option to
+``--with-openib`` for older versions of the package and specifying an
+alternative dependency name:
+
+.. code-block::
+
+   --with-openib=</path/to/rdma-core>
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Configure script in a sub-directory

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)
@@ -128,17 +128,20 @@ Adding flags to cmake
 ^^^^^^^^^^^^^^^^^^^^^
 
 To add additional flags to the ``cmake`` call, simply override the
-``cmake_args`` function:
+``cmake_args`` function. The following example defines values for the flags
+``WHATEVER``, ``ENABLE_BROKEN_FEATURE``, ``DETECT_HDF5``, and ``THREADS`` with
+and without the :py:meth:`~.CMakePackage.define` and
+:py:meth:`~.CMakePackage.define_from_variant` helper functions:
 
 .. code-block:: python
 
    def cmake_args(self):
-       args = []
-
-       if '+hdf5' in self.spec:
-           args.append('-DDETECT_HDF5=ON')
-       else:
-           args.append('-DDETECT_HDF5=OFF')
+       args = [
+           '-DWHATEVER:STRING=somevalue',
+           self.define('ENABLE_BROKEN_FEATURE', False),
+           self.define_from_variant('DETECT_HDF5', 'hdf5'),
+           self.define_from_variant('THREADS'), # True if +threads
+       ]
 
        return args
 

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)
@@ -37,7 +37,7 @@ In order to use it, just add another base class to your package, for example:
             if '+cuda' in spec:
                 options.append('-DWITH_CUDA=ON')
                 cuda_arch = spec.variants['cuda_arch'].value
-                if cuda_arch is not None:
+                if cuda_arch != 'none':
                     options.append('-DCUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch[0]))
             else:
                 options.append('-DWITH_CUDA=OFF')

lib/spack/docs/build_systems/custompackage.rst

@@ -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:...
        ...
@@ -553,7 +553,7 @@ follow `the next section <intel-install-libs_>`_ instead.
                f77:      stub
                fc:       stub
 
-      Replace ``18.0.3`` with the version that you determined in the preceeding
+      Replace ``18.0.3`` with the version that you determined in the preceding
       step. The contents under ``paths:`` do not matter yet.
 
    You are right to ask: "Why on earth is that necessary?" [fn8]_.
@@ -696,7 +696,7 @@ follow `the next section <intel-install-libs_>`_ instead.
              - /home/$user/spack-stage
 
         Do not duplicate the ``config:`` line if it already is present.
-        Adapt the location, which here is the same as in the preceeding example.
+        Adapt the location, which here is the same as in the preceding example.
 
    3. Retry installing the large package.
 
@@ -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>`.
 
@@ -965,14 +965,14 @@ a *virtual* ``mkl`` package is declared in Spack.
 
   Likewise, in a
   :ref:`MakefilePackage <makefilepackage>`
-  or similiar package that does not use AutoTools you may need to provide include
+  or similar package that does not use AutoTools you may need to provide include
   and link options for use on command lines or in environment variables.
   For example, to generate an option string of the form ``-I<dir>``, use:
 
   .. 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
@@ -1055,6 +1055,6 @@ Footnotes
    2. Set the hash length in ``install-path-scheme``, also in ``config.yaml``
       (:ref:`q.v. <config-yaml>`).
    3. You will want to set the *same* hash length for
-      :ref:`tcl module files <modules-naming-scheme>`
-      if you have Spack produce them for you, under ``naming_scheme`` in
-      ``modules.yaml``.  Other module dialects cannot be altered in this manner.
+      :ref:`module files <modules-projections>`
+      if you have Spack produce them for you, under ``projections`` in
+      ``modules.yaml``.

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 +1,135 @@
+.. 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. All of these dependencies are automatically
+added via the base class
+
+.. code-block:: python
+
+   extends('python')
+
+   depends_on('qt', type='build')
+
+   depends_on('py-sip', type='build')
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+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)
@@ -47,8 +47,9 @@ Each phase provides a ``<phase>`` function that runs:
 
 where ``<jobs>`` is the number of parallel jobs to build with. Each phase
 also has a ``<phase_args>`` function that can pass arguments to this call.
-All of these functions are empty except for the ``configure_args``
-function, which passes ``--prefix=/path/to/installation/prefix``.
+All of these functions are empty. The ``configure`` phase
+automatically adds  ``--prefix=/path/to/installation/prefix``, so you
+don't need to add that in the ``configure_args``.
 
 ^^^^^^^
 Testing

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 unnecessary 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:18.04``
+     - ``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 unnecessary 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
 
@@ -332,8 +385,8 @@ coverage. This helps us tell what percentage of lines of code in Spack are
 covered by unit tests. Although code covered by unit tests can still contain
 bugs, it is much less error prone than code that is not covered by unit tests.
 
-Codecov provides `browser extensions <https://github.com/codecov/browser-extension>`_
-for Google Chrome, Firefox, and Opera. These extensions integrate with GitHub
+Codecov provides `browser extensions <https://github.com/codecov/sourcegraph-codecov>`_
+for Google Chrome and Firefox. These extensions integrate with GitHub
 and allow you to see coverage line-by-line when viewing the Spack repository.
 If you are new to Spack, a great way to get started is to write unit tests to
 increase coverage!

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 +1,855 @@
+.. 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-view`` 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
+
+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 env 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: arch.satisfies('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``. A Spack spec satisfying the default Spack
+   architecture on the system. This supports querying via the ``satisfies``
+   method, as shown above.
+
+#. ``arch_str``. The architecture 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).
+
+""""""""""""""""""""""""
+SpecLists as Constraints
+""""""""""""""""""""""""
+
+Dependencies and compilers in Spack can be both packages in an
+environment and constraints on other packages. References to SpecLists
+allow a shorthand to treat packages in a list as either a compiler or
+a dependency using the ``$%`` or ``$^`` syntax respectively.
+
+For example, the following environment has three root packages:
+``gcc@8.1.0``, ``mvapich2@2.3.1 %gcc@8.1.0``, and ``hdf5+mpi
+%gcc@8.1.0 ^mvapich2@2.3.1``.
+
+.. code-block:: yaml
+
+   spack:
+     definitions:
+     - compilers: [gcc@8.1.0]
+     - mpis: [mvapich2@2.3.1]
+     - packages: [hdf5+mpi]
+
+     specs:
+     - $compilers
+     - matrix:
+       - [$mpis]
+       - [$%compilers]
+     - matrix:
+       - [$packages]
+       - [$^mpis]
+       - [$%compilers]
+
+This allows for a much-needed reduction in redundancy between packages
+and constraints.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+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
@@ -70,10 +71,6 @@ 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
-installed and available, the ``spack`` command can also load and unload
-:ref:`modules <modules>`.
-
 ^^^^^^^^^^^^^^^^^
 Clean Environment
 ^^^^^^^^^^^^^^^^^
@@ -96,7 +93,7 @@ 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 +186,7 @@ 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 +198,7 @@ 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 +243,7 @@ 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 +259,7 @@ 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 +465,21 @@ 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: apple-clang@11.0.0
+
 
    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 +590,12 @@ 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
 
@@ -846,7 +847,7 @@ from websites and from git.
 
 .. warning::
 
-   This workaround should be used ONLY as a last resort!  Wihout SSL
+   This workaround should be used ONLY as a last resort!  Without SSL
    certificate verification, spack and git will download from sites you
    wouldn't normally trust.  The code you download and run may then be
    compromised!  While this is not a major issue for archives that will
@@ -895,9 +896,8 @@ Core Spack Utilities
 ^^^^^^^^^^^^^^^^^^^^
 
 Core Spack uses the following packages, mainly to download and unpack
-source code, and to load generated environment modules: ``curl``,
-``env``, ``git``, ``go``, ``hg``, ``svn``, ``tar``, ``unzip``,
-``patch``, ``environment-modules``.
+source code: ``curl``, ``env``, ``git``, ``go``, ``hg``, ``svn``,
+``tar``, ``unzip``, ``patch``
 
 As long as the user's environment is set up to successfully run these
 programs from outside of Spack, they should work inside of Spack as
@@ -905,10 +905,6 @@ well.  They can generally be activated as in the ``curl`` example above;
 or some systems might already have an appropriate hand-built
 environment module that may be loaded.  Either way works.
 
-If you find that you are missing some of these programs, ``spack`` can
-build some of them for you with ``spack bootstrap``. Currently supported
-programs are ``environment-modules``.
-
 A few notes on specific programs in this list:
 
 """"""""""""""""""""""""""
@@ -936,45 +932,6 @@ other programs will also not work, because they also rely on OpenSSL.
 Once ``curl`` has been installed, you can similarly install the others.
 
 
-.. _InstallEnvironmentModules:
-
-"""""""""""""""""""
-Environment Modules
-"""""""""""""""""""
-
-In order to use Spack's generated module files, you must have
-installed ``environment-modules`` or ``lmod``. The simplest way
-to get the latest version of either of these tools is installing
-it as part of Spack's bootstrap procedure:
-
-.. code-block:: console
-
-   $ spack bootstrap
-
-.. warning::
-   At the moment ``spack bootstrap`` is only able to install ``environment-modules``.
-   Extending its capabilities to prefer ``lmod`` where possible is in the roadmap,
-   and likely to happen before the next release.
-
-Alternatively, on many Linux distributions, you can install a pre-built binary
-from the vendor's repository. On Fedora/RHEL/CentOS, for example, this can be
-done with the command:
-
-.. code-block:: console
-
-   $ yum install environment-modules
-
-Once you have the tool installed and available in your path, you can source
-Spack's setup file:
-
-.. code-block:: console
-
-   $ source share/spack/setup-env.sh
-
-This activates :ref:`shell support <shell-support>` and makes commands like
-``spack load`` available for use.
-
-
 ^^^^^^^^^^^^^^^^^
 Package Utilities
 ^^^^^^^^^^^^^^^^^

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)
@@ -13,26 +13,20 @@ 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::
-
-   If your machine does not already have a module system installed,
-   we advise you to use either Environment Modules or LMod. See :ref:`InstallEnvironmentModules`
-   for more details.
-
 .. _shell-support:
 
 ----------------------------
 Using module files via Spack
 ----------------------------
 
-If you have installed a supported module system either manually or through
-``spack bootstrap``, you should be able to run either ``module avail`` or
-``use -l spack`` to see what module files have been installed.  Here is
-sample output of those programs, showing lots of installed packages:
+If you have installed a supported module system you should be able to
+run either ``module avail`` or ``use -l spack`` to see what module
+files have been installed.  Here is sample output of those programs,
+showing lots of installed packages:
 
 .. code-block:: console
 
@@ -67,7 +61,7 @@ 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
@@ -93,9 +87,7 @@ Note that in the latter case it is necessary to explicitly set ``SPACK_ROOT``
 before sourcing the setup file (you will get a meaningful error message
 if you don't).
 
-When ``bash`` and ``ksh`` users update their environment with ``setup-env.sh``, it will check for spack-installed environment modules and add the ``module`` command to their environment; This only occurs if the module command is not already available. You can install ``environment-modules`` with ``spack bootstrap`` as described in :ref:`InstallEnvironmentModules`.
-
-Finally, if you want to have Spack's shell support available on the command line at
+If you want to have Spack's shell support available on the command line at
 any login you can put this source line in one of the files that are sourced
 at startup (like ``.profile``, ``.bashrc`` or ``.cshrc``). Be aware though
 that the startup time may be slightly increased because of that.
@@ -108,20 +100,10 @@ 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 +111,39 @@ 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
@@ -181,16 +157,21 @@ used ``gcc``.  You could therefore just type:
 
 To identify just the one built with the Intel compiler.
 
-.. _extensions:
-
 .. _cmd-spack-module-loads:
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 ``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 +196,8 @@ 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 +273,6 @@ 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 +302,7 @@ 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 +310,15 @@ 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 +332,15 @@ 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 +351,10 @@ 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 +376,9 @@ 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
 
@@ -485,14 +459,14 @@ is compiled with ``gcc@4.4.7``, with the only exception of any ``gcc``
 or any ``llvm`` installation.
 
 
-.. _modules-naming-scheme:
+.. _modules-projections:
 
-"""""""""""""""""""""""""""
-Customize the naming scheme
-"""""""""""""""""""""""""""
+"""""""""""""""""""""""""""""""
+Customize the naming of modules
+"""""""""""""""""""""""""""""""
 
 The names of environment modules generated by spack are not always easy to
-fully comprehend due to the long hash in the name. There are two module
+fully comprehend due to the long hash in the name. There are three module
 configuration options to help with that. The first is a global setting to
 adjust the hash length. It can be set anywhere from 0 to 32 and has a default
 length of 7. This is the representation of the hash in the module file name and
@@ -526,26 +500,52 @@ version of python a set of python extensions is associated with. Likewise, the
 ``openblas`` string is attached to any program that has openblas in the spec,
 most likely via the ``+blas`` variant specification.
 
+The most heavyweight solution to module naming is to change the entire
+naming convention for module files. This uses the projections format
+covered in :ref:`adding_projections_to_views`.
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      projections:
+        all: '{name}/{version}-{compiler.name}-{compiler.version}-module'
+        ^mpi: '{name}/{version}-{^mpi.name}-{^mpi.version}-{compiler.name}-{compiler.version}-module'
+
+will create module files that are nested in directories by package
+name, contain the version and compiler name and version, and have the
+word ``module`` before the hash for all specs that do not depend on
+mpi, and will have the same information plus the MPI implementation
+name and version for all packages that depend on mpi.
+
+When specifying module names by projection for Lmod modules, we
+recommend NOT including names of dependencies (e.g., MPI, compilers)
+that are already in the LMod hierarchy.
+
+
+
 .. note::
-   TCL module files
-     A modification that is specific to ``tcl`` module files is the possibility
-     to change the naming scheme of modules.
+   TCL modules
+     TCL modules also allow for explicit conflicts between modulefiles.
 
      .. code-block:: yaml
 
-       modules:
-         tcl:
-           naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
-           all:
-             conflict:
-               - '${PACKAGE}'
-               - 'intel/14.0.1'
+        modules:
+          enable:
+            - tcl
+          tcl:
+            projections:
+              all: '{name}/{version}-{compiler.name}-{compiler.version}'
+            all:
+              conflict:
+                - '{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::
@@ -564,6 +564,8 @@ most likely via the ``+blas`` variant specification.
          lmod:
            core_compilers:
              - 'gcc@4.8'
+           core_specs:
+             - 'python'
            hierarchy:
              - 'mpi'
              - 'lapack'
@@ -573,6 +575,15 @@ most likely via the ``+blas`` variant specification.
      implementations of ``mpi`` and ``lapack``, and let LMod switch safely from one to the
      other.
 
+     All packages built with a compiler in ``core_compilers`` and all
+     packages that satisfy a spec in ``core_specs`` will be put in the
+     ``Core`` hierarchy of the lua modules.
+
+.. warning::
+  Consistency of Core packages
+   The user is responsible for maintining consistency among core packages, as ``core_specs``
+   bypasses the hierarchy that allows LMod to safely switch between coherent software stacks.
+
 .. warning::
   Deep hierarchies and ``lmod spider``
    For hierarchies that are deeper than three layers ``lmod spider`` may have some issues.
@@ -590,15 +601,17 @@ 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 +631,21 @@ 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/pipelines.rst

@@ -0,0 +1,445 @@
+.. 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 two jobs (one to generate
+   the pipeline dynamically, and one to run the generated jobs), similar to
+   this one:
+
+   .. code-block:: yaml
+
+      stages: [generate, build]
+
+      generate-pipeline:
+        stage: generate
+        tags:
+          - <custom-tag>
+        script:
+          - spack env activate .
+          - spack ci generate
+            --output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"
+        artifacts:
+          paths:
+            - "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"
+
+      build-jobs:
+        stage: build
+        trigger:
+          include:
+            - artifact: "jobs_scratch_dir/pipeline.yml"
+              job: generate-pipeline
+          strategy: depend
+
+
+#. 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 to
+run the pipeline generation phase (this is implemented in the ``spack ci generate``
+command, which assumes the runner has an appropriate version of spack installed
+and configured for use).  Of course, there are many 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's pipelines are now making use of the
+`trigger <https://docs.gitlab.com/12.9/ee/ci/yaml/README.html#trigger>` syntax to run
+dynamically generated
+`child pipelines <https://docs.gitlab.com/12.9/ee/ci/parent_child_pipelines.html>`.
+Note that the use of dynamic child pipelines requires running Gitlab version
+``>= 12.9``.
+
+-----------------------------------
+Spack commands supporting pipelines
+-----------------------------------
+
+Spack provides a command ``ci`` with two sub-commands: ``spack ci generate`` generates
+a pipeline (a .gitlab-ci.yml file) from a spack environment, and ``spack ci rebuild``
+checks a spec against a remote mirror and possibly rebuilds it from source and updates
+the binary mirror with the latest built package.  Both ``spack ci ...`` commands must
+be run from within the same 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-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-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 describing 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-kube
+             image: spack/ubuntu-bionic
+         - match:
+             - os=centos7
+           runner-attributes:
+             tags:
+               - spack-kube
+             image: spack/centos7
+     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
+the ``generate-pipeline`` job from the top of this document, updated to clone
+a custom spack and make sure the generated rebuild jobs will clone it too:
+
+.. code-block:: yaml
+
+   generate-pipeline:
+     tags:
+       - <some-other-tag>
+   before_script:
+     - git clone ${SPACK_REPO} --branch ${SPACK_REF}
+     - . ./spack/share/spack/setup-env.sh
+   script:
+     - spack env activate .
+     - spack ci generate
+       --spack-repo ${SPACK_REPO} --spack-ref ${SPACK_REF}
+       --output-file "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"
+   after_script:
+     - rm -rf ./spack
+   artifacts:
+     paths:
+       - "${CI_PROJECT_DIR}/jobs_scratch_dir/pipeline.yml"
+
+
+If the ``spack ci generate`` 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.

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)
@@ -280,16 +280,16 @@ you install it, you can use ``spack spec -N``:
 
    Concretized
    --------------------------------
-   builtin.hdf5@1.10.0-patch1%clang@7.0.2-apple+cxx~debug+fortran+mpi+shared~szip~threadsafe arch=darwin-elcapitan-x86_64
-       ^builtin.openmpi@2.0.1%clang@7.0.2-apple~mxm~pmi~psm~psm2~slurm~sqlite3~thread_multiple~tm~verbs+vt arch=darwin-elcapitan-x86_64
-           ^builtin.hwloc@1.11.4%clang@7.0.2-apple arch=darwin-elcapitan-x86_64
-               ^builtin.libpciaccess@0.13.4%clang@7.0.2-apple arch=darwin-elcapitan-x86_64
-                   ^builtin.libtool@2.4.6%clang@7.0.2-apple arch=darwin-elcapitan-x86_64
-                       ^builtin.m4@1.4.17%clang@7.0.2-apple+sigsegv arch=darwin-elcapitan-x86_64
-                           ^builtin.libsigsegv@2.10%clang@7.0.2-apple arch=darwin-elcapitan-x86_64
-                   ^builtin.pkg-config@0.29.1%clang@7.0.2-apple+internal_glib arch=darwin-elcapitan-x86_64
-                   ^builtin.util-macros@1.19.0%clang@7.0.2-apple arch=darwin-elcapitan-x86_64
-       ^builtin.zlib@1.2.8%clang@7.0.2-apple+pic arch=darwin-elcapitan-x86_64
+   builtin.hdf5@1.10.0-patch1%apple-clang@7.0.2+cxx~debug+fortran+mpi+shared~szip~threadsafe arch=darwin-elcapitan-x86_64
+       ^builtin.openmpi@2.0.1%apple-clang@7.0.2~mxm~pmi~psm~psm2~slurm~sqlite3~thread_multiple~tm~verbs+vt arch=darwin-elcapitan-x86_64
+           ^builtin.hwloc@1.11.4%apple-clang@7.0.2 arch=darwin-elcapitan-x86_64
+               ^builtin.libpciaccess@0.13.4%apple-clang@7.0.2 arch=darwin-elcapitan-x86_64
+                   ^builtin.libtool@2.4.6%apple-clang@7.0.2 arch=darwin-elcapitan-x86_64
+                       ^builtin.m4@1.4.17%apple-clang@7.0.2+sigsegv arch=darwin-elcapitan-x86_64
+                           ^builtin.libsigsegv@2.10%apple-clang@7.0.2 arch=darwin-elcapitan-x86_64
+                   ^builtin.pkg-config@0.29.1%apple-clang@7.0.2+internal_glib arch=darwin-elcapitan-x86_64
+                   ^builtin.util-macros@1.19.0%apple-clang@7.0.2 arch=darwin-elcapitan-x86_64
+       ^builtin.zlib@1.2.8%apple-clang@7.0.2+pic arch=darwin-elcapitan-x86_64
 
 .. warning::
 

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