Use kcov from official Ubuntu 20.04 repository (#25385)

* Ubuntu 20.04 provides kcov, so don't build from source

* Use two undocumented options for kcov v3.8

.codecov.yml

@@ -14,3 +14,21 @@ ignore:
   - share/spack/qa/.*
 
 comment: off
+
+# Inline codecov annotations make the code hard to read, and they add
+# annotations in files that seemingly have nothing to do with the PR.
+github_checks:
+    annotations: false
+
+# Attempt to fix "Missing base commit" messages in the codecov UI.
+# Because we do not run full tests on package PRs, package PRs' merge
+# commits on `develop` don't have coverage info.  It appears that
+# codecov will give you an error if the pseudo-base's coverage data
+# doesn't all apply properly to the real PR base.
+#
+# See here for docs:
+#   https://docs.codecov.com/docs/comparing-commits#pseudo-comparison
+# See here for another potential solution:
+#   https://community.codecov.com/t/2480/15
+codecov:
+  allow_coverage_offsets: true

.coveragerc

@@ -1,38 +0,0 @@
-# -*- conf -*-
-# .coveragerc to control coverage.py
-[run]
-parallel = True
-concurrency = multiprocessing
-branch = True
-source =
-     bin
-     lib
-omit =
-     lib/spack/spack/test/*
-     lib/spack/docs/*
-     lib/spack/external/*
-     share/spack/qa/*
-
-[report]
-# Regexes for lines to exclude from consideration
-exclude_lines =
-    # Have to re-enable the standard pragma
-    pragma: no cover
-
-    # Don't complain about missing debug-only code:
-    def __repr__
-    if self\.debug
-
-    # Don't complain if tests don't hit defensive assertion code:
-    raise AssertionError
-    raise NotImplementedError
-
-    # Don't complain if non-runnable code isn't run:
-    if 0:
-    if False:
-    if __name__ == .__main__.:
-
-ignore_errors = True
-
-[html]
-directory = htmlcov

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,42 +0,0 @@
----
-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 ..." -->
-
-### Steps to reproduce the issue
-
-```console
-$ spack <command1> <spec>
-$ spack <command2> <spec>
-...
-```
-
-### Error Message
-
-<!-- If Spack reported an error, provide the error message. If it did not report an error but the output appears incorrect, provide the incorrect output. If there was no error message and no output but the result is incorrect, describe how it does not match what you expect. -->
-```console
-$ spack --debug --stacktrace <command>
-```
-
-### Information on your system
-
-<!-- Please include the output of `spack debug report` -->
-
-<!-- If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well. -->
-
-### Additional information
-
-<!-- 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! -->

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,58 @@
+name: "\U0001F41E Bug report"
+description: Report a bug in the core of Spack (command not working as expected, etc.)
+labels: [bug, triage]
+body:
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to reproduce
+      description: |
+        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 ..."
+      placeholder: |
+        ```console
+        $ spack <command1> <spec>
+        $ spack <command2> <spec>
+        ...
+        ```
+    validations:
+      required: true
+  - type: textarea
+    id: error
+    attributes:
+      label: Error message
+      description: |
+        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.
+      placeholder: |
+        ```console
+        $ spack --debug --stacktrace <command>
+        ```
+  - type: textarea
+    id: information
+    attributes:
+      label: Information on your system
+      description: Please include the output of `spack debug report`
+    validations:
+      required: true
+  - type: markdown
+    attributes:
+      value: |
+        If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well.
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: General information
+      options:
+        - label: I have run `spack debug report` and reported the version of Spack/Python/Platform
+          required: true
+        - label: I have searched the issues of this repo and believe this is not a duplicate
+          required: true
+        - label: I have run the failing commands in debug mode and reported the output
+          required: true
+  - type: markdown
+    attributes:
+      value: |
+        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](https://slack.spack.io/) first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
+        
+        Other than that, thanks for taking the time to contribute to Spack!

.github/ISSUE_TEMPLATE/build_error.md

@@ -1,43 +0,0 @@
----
-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:
-
-1. Title the issue "Installation issue: <name-of-the-package>".
-2. Provide the information required below.
-
-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>
-...
-```
-
-### Information on your system
-
-<!-- Please include the output of `spack debug report` -->
-
-<!-- If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well. -->
-
-### Additional information
-
-<!-- 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]()
-
-<!-- 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. -->
-
-### General information
-
-<!-- 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/build_error.yml

@@ -0,0 +1,64 @@
+name: "\U0001F4A5 Build error"
+description: Some package in Spack didn't build correctly
+title: "Installation issue: "
+labels: [build-error]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        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.
+        
+        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!
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to reproduce the issue
+      description: |
+        Fill in the exact spec you are trying to build and the relevant part of the error message
+      placeholder: |
+        ```console
+        $ spack install <spec>
+        ...
+        ```
+    validations:
+      required: true
+  - type: textarea
+    id: information
+    attributes:
+      label: Information on your system
+      description: Please include the output of `spack debug report`
+    validations:
+      required: true
+  - type: markdown
+    attributes:
+      value: |
+        If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well.
+  - type: textarea
+    id: additional_information
+    attributes:
+      label: Additional information
+      description: |
+        Please upload the following files:
+        * **`spack-build-out.txt`**
+        * **`spack-build-env.txt`**
+        
+        They should be present in the stage directory of the failing build. Also upload any `config.log` or similar file if one exists.
+  - type: markdown
+    attributes:
+      value: |
+        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.
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: General information
+      options:
+        - label: I have run `spack debug report` and reported the version of Spack/Python/Platform
+          required: true
+        - label: I have run `spack maintainers <name-of-the-package>` and **@mentioned** any maintainers
+          required: true
+        - label: I have uploaded the build log and environment files
+          required: true
+        - label: I have searched the issues of this repo and believe this is not a duplicate
+          required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,33 +0,0 @@
----
-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.*-->
-
-### Rationale
-
-<!--*Is your feature request related to a problem? Please describe it!*-->
-
-### Description
-
-<!--*Describe the solution you'd like and the alternatives you have considered.*-->
-
-
-### Additional information
-<!--*Add any other context about the feature request here.*-->
-
-
-### 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!
--->

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,41 @@
+name: "\U0001F38A Feature request" 
+description: Suggest adding a feature that is not yet in Spack
+labels: [feature]
+body:
+  - type: textarea
+    id: summary
+    attributes:
+      label: Summary
+      description: Please add a concise summary of your suggestion here.
+    validations:
+      required: true
+  - type: textarea
+    id: rationale
+    attributes:
+      label: Rationale
+      description: Is your feature request related to a problem? Please describe it!
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: Describe the solution you'd like and the alternatives you have considered.
+  - type: textarea
+    id: additional_information
+    attributes:
+      label: Additional information
+      description: Add any other context about the feature request here.
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: General information
+      options:
+        - label: I have run `spack --version` and reported the version of Spack
+          required: true
+        - label: I have searched the issues of this repo and believe this is not a duplicate
+          required: true
+  - type: markdown
+    attributes:
+      value: |
+        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](https://slack.spack.io/) 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

@@ -1,6 +0,0 @@
-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

@@ -1,85 +0,0 @@
-#!/usr/bin/env python
-#
-# Copyright 2013-2021 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/bootstrap.yml

@@ -0,0 +1,160 @@
+name: Bootstrapping
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - releases/**
+    paths-ignore:
+      # Don't run if we only modified packages in the
+      # built-in repository or documentation
+      - 'var/spack/repos/builtin/**'
+      - '!var/spack/repos/builtin/packages/clingo-bootstrap/**'
+      - '!var/spack/repos/builtin/packages/python/**'
+      - 'lib/spack/docs/**'
+  schedule:
+    # nightly at 2:16 AM
+    - cron: '16 2 * * *'
+
+jobs:
+
+  fedora-sources:
+    runs-on: ubuntu-latest
+    container: "fedora:latest"
+    steps:
+      - name: Install dependencies
+        run: |
+          dnf install -y \
+              bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
+              make patch unzip which xz python3 python3-devel tree \
+              cmake bison bison-devel libstdc++-static
+      - uses: actions/checkout@v2
+      - name: Setup repo and non-root user
+        run: |
+          git --version
+          git fetch --unshallow
+          . .github/workflows/setup_git.sh
+          useradd spack-test
+          chown -R spack-test .
+      - name: Bootstrap clingo
+        shell: runuser -u spack-test -- bash {0}
+        run: |
+          source share/spack/setup-env.sh
+          spack bootstrap untrust github-actions
+          spack external find cmake bison
+          spack -d solve zlib
+          tree ~/.spack/bootstrap/store/
+
+  ubuntu-sources:
+    runs-on: ubuntu-latest
+    container: "ubuntu:latest"
+    steps:
+      - name: Install dependencies
+        env:
+          DEBIAN_FRONTEND: noninteractive
+        run: |
+          apt-get update -y && apt-get upgrade -y
+          apt-get install -y \
+              bzip2 curl file g++ gcc gfortran git gnupg2 gzip \
+              make patch unzip xz-utils python3 python3-dev tree \
+              cmake bison
+      - uses: actions/checkout@v2
+      - name: Setup repo and non-root user
+        run: |
+          git --version
+          git fetch --unshallow
+          . .github/workflows/setup_git.sh
+          useradd -m spack-test
+          chown -R spack-test .
+      - name: Bootstrap clingo
+        shell: runuser -u spack-test -- bash {0}
+        run: |
+          source share/spack/setup-env.sh
+          spack bootstrap untrust github-actions
+          spack external find cmake bison
+          spack -d solve zlib
+          tree ~/.spack/bootstrap/store/
+
+  opensuse-sources:
+    runs-on: ubuntu-latest
+    container: "opensuse/tumbleweed:latest"
+    steps:
+      - name: Install dependencies
+        run: |
+          zypper update -y
+          zypper install -y \
+              bzip2 curl file gcc-c++ gcc gcc-fortran tar git gpg2 gzip \
+              make patch unzip which xz python3 python3-devel tree \
+              cmake bison
+      - uses: actions/checkout@v2
+      - name: Setup repo and non-root user
+        run: |
+          git --version
+          git fetch --unshallow
+          . .github/workflows/setup_git.sh
+      - name: Bootstrap clingo
+        run: |
+          source share/spack/setup-env.sh
+          spack bootstrap untrust github-actions
+          spack external find cmake bison
+          spack -d solve zlib
+          tree ~/.spack/bootstrap/store/
+
+  macos-sources:
+    runs-on: macos-latest
+    steps:
+      - name: Install dependencies
+        run: |
+          brew install cmake bison@2.7 tree
+      - uses: actions/checkout@v2
+      - name: Bootstrap clingo
+        run: |
+          source share/spack/setup-env.sh
+          export PATH=/usr/local/opt/bison@2.7/bin:$PATH
+          spack bootstrap untrust github-actions
+          spack external find --not-buildable cmake bison
+          spack -d solve zlib
+          tree ~/.spack/bootstrap/store/
+
+  macos-clingo-binaries:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ['3.5', '3.6', '3.7', '3.8', '3.9']
+    steps:
+      - name: Install dependencies
+        run: |
+          brew install tree
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Bootstrap clingo
+        run: |
+          source share/spack/setup-env.sh
+          spack bootstrap untrust spack-install
+          spack -d solve zlib
+          tree ~/.spack/bootstrap/store/
+
+
+  ubuntu-clingo-binaries:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['2.7', '3.5', '3.6', '3.7', '3.8', '3.9']
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup repo and non-root user
+        run: |
+          git --version
+          git fetch --unshallow
+          . .github/workflows/setup_git.sh
+      - name: Bootstrap clingo
+        run: |
+          source share/spack/setup-env.sh
+          spack bootstrap untrust spack-install
+          spack -d solve zlib
+          tree ~/.spack/bootstrap/store/

.github/workflows/build-containers.yml

@@ -0,0 +1,72 @@
+name: Build & Deploy Docker Containers
+on:
+  # Build new Spack develop containers nightly.
+  schedule:
+    - cron: '34 0 * * *'
+  # Let's also build & tag Spack containers on releases.
+  release:
+    types: [published]
+
+jobs:
+  deploy-images:
+    runs-on: ubuntu-latest 
+    strategy:
+      # Even if one container fails to build we still want the others
+      # to continue their builds.
+      fail-fast: false
+      # A matrix of Dockerfile paths, associated tags, and which architectures
+      # they support.
+      matrix:
+        dockerfile: [[amazon-linux, amazonlinux-2.dockerfile, 'linux/amd64,linux/arm64'], 
+                     [centos7, centos-7.dockerfile, 'linux/amd64,linux/arm64'],
+                     [leap15, leap-15.dockerfile, 'linux/amd64,linux/arm64'],
+                     [ubuntu-xenial, ubuntu-1604.dockerfile, 'linux/amd64,linux/arm64'],
+                     [ubuntu-bionic, ubuntu-1804.dockerfile, 'linux/amd64,linux/arm64']]
+    name: Build ${{ matrix.dockerfile[0] }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set Container Tag Normal (Nightly)
+        run: |
+          container="ghcr.io/spack/${{ matrix.dockerfile[0]}}:latest"
+          echo "container=${container}" >> $GITHUB_ENV
+          echo "versioned=${container}" >> $GITHUB_ENV
+
+        # On a new release create a container with the same tag as the release.
+      - name: Set Container Tag on Release
+        if: github.event_name == 'release'
+        run: |
+          versioned="ghcr.io/spack/${{matrix.dockerfile[0]}}:${GITHUB_REF##*/}"
+          echo "versioned=${versioned}" >> $GITHUB_ENV
+
+      - name: Check ${{ matrix.dockerfile[1] }} Exists
+        run: |
+          printf "Preparing to build ${{ env.container }} from ${{ matrix.dockerfile[1] }}"
+          if [ ! -f "share/spack/docker/${{ matrix.dockerfile[1]}}" ]; then
+              printf "Dockerfile ${{ matrix.dockerfile[0]}} does not exist"
+              exit 1;
+          fi
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Build & Deploy ${{ matrix.dockerfile[1] }}
+        uses: docker/build-push-action@v2
+        with:
+          file: share/spack/docker/${{matrix.dockerfile[1]}}
+          platforms: ${{ matrix.dockerfile[2] }}
+          push: true
+          tags: |
+            ${{ env.container }}
+            ${{ env.versioned }}

.github/workflows/linux_build_tests.yaml

@@ -1,77 +0,0 @@
-name: linux builds
-
-on:
-  push:
-    branches:
-    - develop
-    - releases/**
-    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/**'
-      - '!var/spack/repos/builtin/packages/ruby-rake/**'
-      # Don't run if we only modified documentation
-      - 'lib/spack/docs/**'
-  pull_request:
-    branches:
-    - develop
-    - releases/**
-    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/**'
-      - '!var/spack/repos/builtin/packages/ruby-rake/**'
-      # Don't run if we only modified documentation
-      - 'lib/spack/docs/**'
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        package:
-        - lz4  # MakefilePackage
-        - mpich~fortran  # AutotoolsPackage
-        - 'tut%gcc@:10.99.99'  # WafPackage
-        - py-setuptools  # PythonPackage
-        - openjpeg  # CMakePackage
-        - r-rcpp  # RPackage
-        - ruby-rake  # RubyPackage
-    steps:
-    - uses: actions/checkout@v2
-    - uses: actions/cache@v2.1.6
-      with:
-        path: ~/.ccache
-        key: ccache-build-${{ matrix.package }}
-        restore-keys: |
-          ccache-build-${{ matrix.package }}
-    - uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - 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 ruby findutils openssl libssl-dev libpciaccess-dev
-        R --version
-        perl --version
-        ruby --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/unit_tests.yaml

@@ -24,9 +24,9 @@ jobs:
         pip install --upgrade pip
         pip install --upgrade vermin
     - name: vermin (Spack's Core)
-      run: vermin --backport argparse --backport typing -t=2.6- -t=3.5- -v lib/spack/spack/ lib/spack/llnl/ bin/
+      run: vermin --backport argparse --violations --backport typing -t=2.6- -t=3.5- -vvv lib/spack/spack/ lib/spack/llnl/ bin/
     - name: vermin (Repositories)
-      run: vermin --backport argparse --backport typing -t=2.6- -t=3.5- -v var/spack/repos
+      run: vermin --backport argparse --violations --backport typing -t=2.6- -t=3.5- -vvv var/spack/repos
   # Run style checks on the files that have been changed
   style:
     runs-on: ubuntu-latest
@@ -39,7 +39,7 @@ jobs:
         python-version: 3.9
     - name: Install Python packages
       run: |
-        pip install --upgrade pip six setuptools flake8 mypy>=0.800 black
+        pip install --upgrade pip six setuptools types-six
     - name: Setup git configuration
       run: |
         # Need this for the git tests to succeed.
@@ -129,39 +129,34 @@ jobs:
       run: |
           sudo apt-get -y update
           # Needed for unit tests
-          sudo apt-get install -y coreutils gfortran graphviz gnupg2 mercurial
-          sudo apt-get install -y ninja-build patchelf
-          # Needed for kcov
-          sudo apt-get -y install cmake binutils-dev libcurl4-openssl-dev
-          sudo apt-get -y install zlib1g-dev libdw-dev libiberty-dev
+          sudo apt-get -y install \
+              coreutils cvs gfortran graphviz gnupg2 mercurial ninja-build \
+              patchelf cmake bison libbison-dev kcov
     - name: Install Python packages
       run: |
-          pip install --upgrade pip six setuptools codecov coverage
+          pip install --upgrade pip six setuptools codecov coverage[toml]
+          # ensure style checks are not skipped in unit tests for python >= 3.6
+          # note that true/false (i.e., 1/0) are opposite in conditions in python and bash
+          if python -c 'import sys; sys.exit(not sys.version_info >= (3, 6))'; then
+              pip install --upgrade flake8 isort>=4.3.5 mypy>=0.900 black
+          fi
     - name: Setup git configuration
       run: |
           # Need this for the git tests to succeed.
           git --version
           . .github/workflows/setup_git.sh
-    - name: Install kcov for bash script coverage
-      if: ${{ needs.changes.outputs.with_coverage == 'true' }}
-      env:
-          KCOV_VERSION: 34
-      run: |
-          KCOV_ROOT=$(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: Bootstrap clingo from sources
+    - name: Bootstrap clingo
       if: ${{ matrix.concretizer == 'clingo' }}
+      env:
+          SPACK_PYTHON: python
       run: |
           . share/spack/setup-env.sh
-          spack external find --not-buildable cmake bison
+          spack bootstrap untrust spack-install
           spack -v solve zlib
     - name: Run unit tests (full suite with coverage)
       if: ${{ needs.changes.outputs.with_coverage == 'true' }}
       env:
+          SPACK_PYTHON: python
           COVERAGE: true
           SPACK_TEST_SOLVER: ${{ matrix.concretizer }}
       run: |
@@ -171,11 +166,12 @@ jobs:
     - name: Run unit tests (reduced suite without coverage)
       if: ${{ needs.changes.outputs.with_coverage == 'false' }}
       env:
+          SPACK_PYTHON: python
           ONLY_PACKAGES: true
           SPACK_TEST_SOLVER: ${{ matrix.concretizer }}
       run: |
           share/spack/qa/run-unit-tests
-    - uses: codecov/codecov-action@v1
+    - uses: codecov/codecov-action@v2.0.2
       if: ${{ needs.changes.outputs.with_coverage == 'true' }}
       with:
         flags: unittests,linux,${{ matrix.concretizer }}
@@ -194,29 +190,15 @@ jobs:
       run: |
           sudo apt-get -y update
           # Needed for shell tests
-          sudo apt-get install -y coreutils csh zsh tcsh fish dash bash
-          # Needed for kcov
-          sudo apt-get -y install cmake binutils-dev libcurl4-openssl-dev
-          sudo apt-get -y install zlib1g-dev libdw-dev libiberty-dev
+          sudo apt-get install -y coreutils kcov csh zsh tcsh fish dash bash
     - name: Install Python packages
       run: |
-          pip install --upgrade pip six setuptools codecov coverage
+          pip install --upgrade pip six setuptools codecov coverage[toml]
     - name: Setup git configuration
       run: |
           # Need this for the git tests to succeed.
           git --version
           . .github/workflows/setup_git.sh
-    - name: Install kcov for bash script coverage
-      if: ${{ needs.changes.outputs.with_coverage == 'true' }}
-      env:
-          KCOV_VERSION: 38
-      run: |
-          KCOV_ROOT=$(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 shell tests (without coverage)
       if: ${{ needs.changes.outputs.with_coverage == 'false' }}
       run: |
@@ -227,7 +209,7 @@ jobs:
           COVERAGE: true
       run: |
           share/spack/qa/run-shell-tests
-    - uses: codecov/codecov-action@v1
+    - uses: codecov/codecov-action@v2.0.2
       if: ${{ needs.changes.outputs.with_coverage == 'true' }}
       with:
         flags: shelltests,linux
@@ -286,7 +268,7 @@ jobs:
       shell: runuser -u spack-test -- bash {0}
       run: |
           source share/spack/setup-env.sh
-          spack unit-test -k 'not svn and not hg' -x --verbose
+          spack unit-test -k 'not cvs and not svn and not hg' -x --verbose
   # Test for the clingo based solver (using clingo-cffi)
   clingo-cffi:
     needs: [ validate, style, documentation, changes ]
@@ -302,25 +284,12 @@ jobs:
       run: |
           sudo apt-get -y update
           # Needed for unit tests
-          sudo apt-get install -y coreutils gfortran graphviz gnupg2 mercurial
-          sudo apt-get install -y ninja-build patchelf
-          # Needed for kcov
-          sudo apt-get -y install cmake binutils-dev libcurl4-openssl-dev
-          sudo apt-get -y install zlib1g-dev libdw-dev libiberty-dev
-    - name: Install kcov for bash script coverage
-      if: ${{ needs.changes.outputs.with_coverage == 'true' }}
-      env:
-          KCOV_VERSION: 34
-      run: |
-          KCOV_ROOT=$(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
+          sudo apt-get -y install \
+              coreutils cvs gfortran graphviz gnupg2 mercurial ninja-build \
+              patchelf kcov
     - name: Install Python packages
       run: |
-          pip install --upgrade pip six setuptools codecov coverage clingo
+          pip install --upgrade pip six setuptools codecov coverage[toml] clingo
     - name: Setup git configuration
       run: |
           # Need this for the git tests to succeed.
@@ -342,7 +311,7 @@ jobs:
           SPACK_TEST_SOLVER: clingo
       run: |
           share/spack/qa/run-unit-tests
-    - uses: codecov/codecov-action@v1
+    - uses: codecov/codecov-action@v2.0.2
       if: ${{ needs.changes.outputs.with_coverage == 'true' }}
       with:
         flags: unittests,linux,clingo
@@ -363,8 +332,7 @@ jobs:
     - name: Install Python packages
       run: |
           pip install --upgrade pip six setuptools
-          pip install --upgrade codecov coverage
-          pip install --upgrade flake8 pep8-naming mypy
+          pip install --upgrade codecov coverage[toml]
     - name: Setup Homebrew packages
       run: |
         brew install dash fish gcc gnupg2 kcov
@@ -378,12 +346,15 @@ jobs:
           coverage run $(which spack) unit-test -x
           coverage combine
           coverage xml
+          # Delete the symlink going from ./lib/spack/docs/_spack_root back to
+          # the initial directory, since it causes ELOOP errors with codecov/actions@2
+          rm lib/spack/docs/_spack_root
         else
           echo "ONLY PACKAGE RECIPES CHANGED [skipping coverage]"
           $(which spack) unit-test -x -m "not maybeslow" -k "package_sanity"
         fi
-    - uses: codecov/codecov-action@v1
+    - uses: codecov/codecov-action@v2.0.2
       if: ${{ needs.changes.outputs.with_coverage == 'true' }}
       with:
-        file: ./coverage.xml
+        files: ./coverage.xml
         flags: unittests,macos

.gitignore

@@ -508,4 +508,4 @@ $RECYCLE.BIN/
 *.msp
 
 # Windows shortcuts
-*.lnk
+*.lnk

.mypy.ini

@@ -1,35 +0,0 @@
-[mypy]
-python_version = 3.7
-files=lib/spack/llnl/**/*.py,lib/spack/spack/**/*.py
-mypy_path=bin,lib/spack,lib/spack/external,var/spack/repos/builtin
-# This and a generated import file allows supporting packages
-namespace_packages=True
-# To avoid re-factoring all the externals, ignore errors and missing imports
-# globally, then turn back on in spack and spack submodules
-ignore_errors=True
-ignore_missing_imports=True
-
-[mypy-spack.*]
-ignore_errors=False
-ignore_missing_imports=False
-
-[mypy-packages.*]
-ignore_errors=False
-ignore_missing_imports=False
-
-[mypy-llnl.*]
-ignore_errors=False
-ignore_missing_imports=False
-
-[mypy-spack.test.packages]
-ignore_errors=True
-
-# ignore errors in fake import path for packages
-[mypy-spack.pkg.*]
-ignore_errors=True
-ignore_missing_imports=True
-
-# jinja has syntax in it that requires python3 and causes a parse error
-# skip importing it
-[mypy-jinja2]
-follow_imports=skip

README.md

@@ -1,7 +1,7 @@
 # <img src="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo.svg" width="64" valign="middle" alt="Spack"/> Spack
 
 [![Unit 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)
+[![Bootstrapping](https://github.com/spack/spack/actions/workflows/bootstrap.yml/badge.svg)](https://github.com/spack/spack/actions/workflows/bootstrap.yml)
 [![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)
 [![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)
@@ -36,6 +36,8 @@ Documentation
 [**Full documentation**](https://spack.readthedocs.io/) is available, or
 run `spack help` or `spack help --all`.
 
+For a cheat sheet on Spack syntax, run `spack help --spec`.
+
 Tutorial
 ----------------
 

bin/spack

@@ -28,6 +28,7 @@ exit 1
 from __future__ import print_function
 
 import os
+import os.path
 import sys
 
 min_python3 = (3, 5)
@@ -70,6 +71,28 @@ if "ruamel.yaml" in sys.modules:
 if "ruamel" in sys.modules:
     del sys.modules["ruamel"]
 
+# The following code is here to avoid failures when updating
+# the develop version, due to spurious argparse.pyc files remaining
+# in the libs/spack/external directory, see:
+# https://github.com/spack/spack/pull/25376
+# TODO: Remove in v0.18.0 or later
+try:
+    import argparse
+except ImportError:
+    argparse_pyc = os.path.join(spack_external_libs, 'argparse.pyc')
+    if not os.path.exists(argparse_pyc):
+        raise
+    try:
+        os.remove(argparse_pyc)
+        import argparse  # noqa
+    except Exception:
+        msg = ('The file\n\n\t{0}\n\nis corrupted and cannot be deleted by Spack. '
+               'Either delete it manually or ask some administrator to '
+               'delete it for you.')
+        print(msg.format(argparse_pyc))
+        sys.exit(1)
+
+
 import spack.main  # noqa
 
 # Once we've set up the system path, run the spack main method

etc/spack/defaults/bootstrap.yaml

@@ -0,0 +1,32 @@
+bootstrap:
+  # If set to false Spack will not bootstrap missing software,
+  # but will instead raise an error.
+  enable: true
+  # Root directory for bootstrapping work. The software bootstrapped
+  # by Spack is installed in a "store" subfolder of this root directory
+  root: ~/.spack/bootstrap
+  # Methods that can be used to bootstrap software. Each method may or
+  # may not be able to bootstrap all of the software that Spack needs,
+  # depending on its type.
+  sources:
+  - name: 'github-actions'
+    type: buildcache
+    description: |
+      Buildcache generated from a public workflow using Github Actions.
+      The sha256 checksum of binaries is checked before installation.
+    info:
+      url: https://mirror.spack.io/bootstrap/github-actions/v0.1
+      homepage: https://github.com/alalazo/spack-bootstrap-mirrors
+      releases: https://github.com/alalazo/spack-bootstrap-mirrors/releases
+  # This method is just Spack bootstrapping the software it needs from sources.
+  # It has been added here so that users can selectively disable bootstrapping
+  # from sources by "untrusting" it.
+  - name: spack-install
+    type: install
+    description: |
+      Specs built from sources by Spack. May take a long time.
+  trusted:
+    # By default we trust bootstrapping from sources and from binaries
+    # produced on Github via the workflow
+    github-actions: true
+    spack-install: true

etc/spack/defaults/config.yaml

@@ -134,6 +134,10 @@ config:
   # enabling locks.
   locks: true
 
+  # The default url fetch method to use. 
+  # If set to 'curl', Spack will require curl on the user's system
+  # If set to 'urllib', Spack will use python built-in libs to fetch
+  url_fetch_method: urllib
 
   # The maximum number of jobs to use for the build system (e.g. `make`), when
   # the -j flag is not given on the command line. Defaults to 16 when not set.

etc/spack/defaults/linux/modules.yaml

@@ -14,9 +14,8 @@
 #   ~/.spack/modules.yaml
 # -------------------------------------------------------------------------
 modules:
-  default:
-    prefix_inspections:
-      lib:
-        - LD_LIBRARY_PATH
-      lib64:
-        - LD_LIBRARY_PATH
+  prefix_inspections:
+    lib:
+      - LD_LIBRARY_PATH
+    lib64:
+      - LD_LIBRARY_PATH

etc/spack/defaults/packages.yaml

@@ -34,19 +34,22 @@ packages:
       java: [openjdk, jdk, ibm-java]
       jpeg: [libjpeg-turbo, libjpeg]
       lapack: [openblas, amdlibflame]
+      lua-lang: [lua, lua-luajit]
       mariadb-client: [mariadb-c-client, mariadb]
       mkl: [intel-mkl]
       mpe: [mpe2]
       mpi: [openmpi, mpich]
       mysql-client: [mysql, mariadb-c-client]
       opencl: [pocl]
+      onedal: [intel-oneapi-dal]
       osmesa: [mesa+osmesa, mesa18+osmesa]
+      pbs: [openpbs, torque]
       pil: [py-pillow]
       pkgconfig: [pkgconf, pkg-config]
       rpc: [libtirpc]
       scalapack: [netlib-scalapack, amdscalapack]
       sycl: [hipsycl]
-      szip: [libszip, libaec]
+      szip: [libaec, libszip]
       tbb: [intel-tbb]
       unwind: [libunwind]
       uuid: [util-linux-uuid, libuuid]

lib/spack/docs/Makefile

@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    = -W
+SPHINXOPTS    = -W --keep-going
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build

lib/spack/docs/basic_usage.rst

@@ -695,6 +695,136 @@ structured the way you want:
     }
 
 
+^^^^^^^^^^^^^^
+``spack diff``
+^^^^^^^^^^^^^^
+
+It's often the case that you have two versions of a spec that you need to
+disambiguate. Let's say that we've installed two variants of zlib, one with
+and one without the optimize variant:
+
+.. code-block:: console
+
+   $ spack install zlib
+   $ spack install zlib -optimize
+
+When we do ``spack find`` we see the two versions.
+
+.. code-block:: console
+
+    $ spack find zlib
+    ==> 2 installed packages
+    -- linux-ubuntu20.04-skylake / gcc@9.3.0 ------------------------
+    zlib@1.2.11  zlib@1.2.11
+
+
+Let's now say that we want to uninstall zlib. We run the command, and hit a problem
+real quickly since we have two!
+
+.. code-block:: console
+
+    $ spack uninstall zlib
+    ==> Error: zlib matches multiple packages:
+
+        -- linux-ubuntu20.04-skylake / gcc@9.3.0 ------------------------
+        efzjziy zlib@1.2.11  sl7m27m zlib@1.2.11
+
+    ==> Error: You can either:
+        a) use a more specific spec, or
+        b) specify the spec by its hash (e.g. `spack uninstall /hash`), or
+        c) use `spack uninstall --all` to uninstall ALL matching specs.
+
+Oh no! We can see from the above that we have two different versions of zlib installed,
+and the only difference between the two is the hash. This is a good use case for
+``spack diff``, which can easily show us the "diff" or set difference
+between properties for two packages. Let's try it out.
+Since the only difference we see in the ``spack find`` view is the hash, let's use
+``spack diff`` to look for more detail. We will provide the two hashes:
+
+.. code-block:: console
+
+    $ spack diff /efzjziy /sl7m27m
+    ==> Warning: This interface is subject to change.
+
+    --- zlib@1.2.11efzjziyc3dmb5h5u5azsthgbgog5mj7g
+    +++ zlib@1.2.11sl7m27mzkbejtkrajigj3a3m37ygv4u2
+    @@ variant_value @@
+    -  zlib optimize False
+    +  zlib optimize True
+
+
+The output is colored, and written in the style of a git diff. This means that you
+can copy and paste it into a GitHub markdown as a code block with language "diff"
+and it will render nicely! Here is an example:
+
+.. code-block:: md
+
+    ```diff
+    --- zlib@1.2.11/efzjziyc3dmb5h5u5azsthgbgog5mj7g
+    +++ zlib@1.2.11/sl7m27mzkbejtkrajigj3a3m37ygv4u2
+    @@ variant_value @@
+    -  zlib optimize False
+    +  zlib optimize True
+    ```
+
+Awesome! Now let's read the diff. It tells us that our first zlib was built with ``~optimize``
+(``False``) and the second was built with ``+optimize`` (``True``). You can't see it in the docs
+here, but the output above is also colored based on the content being an addition (+) or
+subtraction (-).
+
+This is a small example, but you will be able to see differences for any attributes on the
+installation spec. Running ``spack diff A B`` means we'll see which spec attributes are on
+``B`` but not on ``A`` (green) and which are on ``A`` but not on ``B`` (red). Here is another
+example with an additional difference type, ``version``:
+
+.. code-block:: console
+
+    $ spack diff python@2.7.8 python@3.8.11
+    ==> Warning: This interface is subject to change.
+
+    --- python@2.7.8/tsxdi6gl4lihp25qrm4d6nys3nypufbf
+    +++ python@3.8.11/yjtseru4nbpllbaxb46q7wfkyxbuvzxx
+    @@ variant_value @@
+    -  python patches a8c52415a8b03c0e5f28b5d52ae498f7a7e602007db2b9554df28cd5685839b8
+    +  python patches 0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87
+    @@ version @@
+    -  openssl 1.0.2u
+    +  openssl 1.1.1k
+    -  python 2.7.8
+    +  python 3.8.11
+
+Let's say that we were only interested in one kind of attribute above, ``version``.
+We can ask the command to only output this attribute.  To do this, you'd add
+the ``--attribute`` for attribute parameter, which defaults to all. Here is how you
+would filter to show just versions:
+
+.. code-block:: console
+
+    $ spack diff --attribute version python@2.7.8 python@3.8.11
+    ==> Warning: This interface is subject to change.
+
+    --- python@2.7.8/tsxdi6gl4lihp25qrm4d6nys3nypufbf
+    +++ python@3.8.11/yjtseru4nbpllbaxb46q7wfkyxbuvzxx
+    @@ version @@
+    -  openssl 1.0.2u
+    +  openssl 1.1.1k
+    -  python 2.7.8
+    +  python 3.8.11
+
+And you can add as many attributes as you'd like with multiple `--attribute` arguments
+(for lots of attributes, you can use ``-a`` for short). Finally, if you want to view the
+data as json (and possibly pipe into an output file) just add ``--json``:
+
+
+.. code-block:: console
+
+    $ spack diff --json python@2.7.8 python@3.8.11
+
+
+This data will be much longer because along with the differences for ``A`` vs. ``B`` and
+``B`` vs. ``A``, the JSON output also showsthe intersection.
+
+
 ------------------------
 Using installed packages
 ------------------------
@@ -1730,6 +1860,39 @@ This issue typically manifests with the error below:
 
 A nicer error message is TBD in future versions of Spack.
 
+---------------
+Troubleshooting
+---------------
+
+The ``spack audit`` command:
+
+.. command-output:: spack audit -h
+
+can be used to detect a number of configuration issues. This command detects
+configuration settings which might not be strictly wrong but are not likely
+to be useful outside of special cases.
+
+It can also be used to detect dependency issues with packages - for example
+cases where a package constrains a dependency with a variant that doesn't
+exist (in this case Spack could report the problem ahead of time but
+automatically performing the check would slow down most runs of Spack).
+
+A detailed list of the checks currently implemented for each subcommand can be
+printed with:
+
+.. command-output:: spack -v audit list
+
+Depending on the use case, users might run the appropriate subcommands to obtain
+diagnostics. Issues, if found, are reported to stdout:
+
+.. code-block:: console
+
+   % spack audit packages lammps
+   PKG-DIRECTIVES: 1 issue found
+   1. lammps: wrong variant in "conflicts" directive
+       the variant 'adios' does not exist
+       in /home/spack/spack/var/spack/repos/builtin/packages/lammps/package.py
+
 
 ------------
 Getting Help

lib/spack/docs/binary_caches.rst

@@ -31,9 +31,25 @@ Build caches are created via:
 
 .. code-block:: console
 
-   $ spack buildcache create spec
+    $ spack buildcache create <spec>
 
 
+If you wanted to create a build cache in a local directory, you would provide
+the ``-d`` argument to target that directory, again also specifying the spec.
+Here is an example creating a local directory, "spack-cache" and creating
+build cache files for the "ninja" spec:
+
+.. code-block:: console
+
+    $ mkdir -p ./spack-cache
+    $ spack buildcache create -d ./spack-cache ninja
+    ==> Buildcache files will be output to file:///home/spackuser/spack/spack-cache/build_cache
+    gpgconf: socketdir is '/run/user/1000/gnupg'
+    gpg: using "E6DF6A8BD43208E4D6F392F23777740B7DBD643D" as default secret key for signing
+
+Note that the targeted spec must already be installed. Once you have a build cache,
+you can add it as a mirror, discussed next.
+
 ---------------------------------------
 Finding or installing build cache files
 ---------------------------------------
@@ -43,19 +59,98 @@ with:
 
 .. code-block:: console
 
-   $ spack mirror add <name> <url>
+    $ spack mirror add <name> <url>
+
+
+Note that the url can be a web url _or_ a local filesystem location. In the previous
+example, you might add the directory "spack-cache" and call it ``mymirror``:
 
-Build caches are found via:
 
 .. code-block:: console
 
-   $ spack buildcache list
+    $ spack mirror add mymirror ./spack-cache
 
-Build caches are installed via:
+
+You can see that the mirror is added with ``spack mirror list`` as follows:
 
 .. code-block:: console
 
-   $ spack buildcache install
+
+    $ spack mirror list
+    mymirror           file:///home/spackuser/spack/spack-cache
+    spack-public       https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/
+
+
+At this point, you've create a buildcache, but spack hasn't indexed it, so if
+you run ``spack buildcache list`` you won't see any results. You need to index
+this new build cache as follows:
+
+.. code-block:: console
+
+    $ spack buildcache update-index -d spack-cache/
+
+Now you can use list:
+
+.. code-block:: console
+
+    $  spack buildcache list
+    ==> 1 cached build.
+    -- linux-ubuntu20.04-skylake / gcc@9.3.0 ------------------------
+    ninja@1.10.2
+
+
+Great! So now let's say you have a different spack installation, or perhaps just
+a different environment for the same one, and you want to install a package from
+that build cache. Let's first uninstall the actual library "ninja" to see if we can
+re-install it from the cache.
+
+.. code-block:: console
+
+    $ spack uninstall ninja
+
+
+And now reinstall from the buildcache
+
+.. code-block:: console
+
+    $ spack buildcache install ninja
+    ==> buildcache spec(s) matching ninja 
+    ==> Fetching file:///home/spackuser/spack/spack-cache/build_cache/linux-ubuntu20.04-skylake/gcc-9.3.0/ninja-1.10.2/linux-ubuntu20.04-skylake-gcc-9.3.0-ninja-1.10.2-i4e5luour7jxdpc3bkiykd4imke3mkym.spack
+    ####################################################################################################################################### 100.0%
+    ==> Installing buildcache for spec ninja@1.10.2%gcc@9.3.0 arch=linux-ubuntu20.04-skylake
+    gpgconf: socketdir is '/run/user/1000/gnupg'
+    gpg: Signature made Tue 23 Mar 2021 10:16:29 PM MDT
+    gpg:                using RSA key E6DF6A8BD43208E4D6F392F23777740B7DBD643D
+    gpg: Good signature from "spackuser (GPG created for Spack) <spackuser@noreply.users.github.com>" [ultimate]
+
+
+It worked! You've just completed a full example of creating a build cache with
+a spec of interest, adding it as a mirror, updating it's index, listing the contents,
+and finally, installing from it.
+
+
+Note that the above command is intended to install a particular package to a
+build cache you have created, and not to install a package from a build cache.
+For the latter, once a mirror is added, by default when you do ``spack install`` the ``--use-cache``
+flag is set, and you will install a package from a build cache if it is available.
+If you want to always use the cache, you can do:
+
+.. code-block:: console
+
+   $ spack install --cache-only <package>
+
+For example, to combine all of the commands above to add the E4S build cache
+and then install from it exclusively, you would do:
+
+.. code-block:: console
+
+    $ spack mirror add E4S https://cache.e4s.io
+    $ spack buildcache keys --install --trust
+    $ spack install --cache-only <package>
+
+We use ``--install`` and ``--trust`` to say that we are installing keys to our
+keyring, and trusting all downloaded keys.
+
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 List of popular build caches

lib/spack/docs/build_systems/cmakepackage.rst

@@ -130,8 +130,8 @@ Adding flags to cmake
 To add additional flags to the ``cmake`` call, simply override the
 ``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:
+and without the :meth:`~spack.build_systems.cmake.CMakePackage.define` and
+:meth:`~spack.build_systems.cmake.CMakePackage.define_from_variant` helper functions:
 
 .. code-block:: python
 

lib/spack/docs/conf.py

@@ -17,10 +17,10 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
 import re
 import subprocess
+import sys
 from glob import glob
 
 from sphinx.ext.apidoc import main as sphinx_apidoc
@@ -82,6 +82,8 @@
 # Disable duplicate cross-reference warnings.
 #
 from sphinx.domains.python import PythonDomain
+
+
 class PatchedPythonDomain(PythonDomain):
     def resolve_xref(self, env, fromdocname, builder, typ, target, node, contnode):
         if 'refspecific' in node:
@@ -95,15 +97,19 @@ def setup(sphinx):
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-needs_sphinx = '1.8'
+needs_sphinx = '3.4'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.graphviz',
-              'sphinx.ext.napoleon',
-              'sphinx.ext.todo',
-              'sphinxcontrib.programoutput']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.graphviz',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.todo',
+    'sphinx.ext.viewcode',
+    'sphinxcontrib.programoutput',
+]
 
 # Set default graphviz options
 graphviz_dot_args = [
@@ -136,6 +142,7 @@ def setup(sphinx):
 #
 # 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
@@ -161,6 +168,19 @@ def setup(sphinx):
 # directories to ignore when looking for source files.
 exclude_patterns = ['_build', '_spack_root', '.spack-env']
 
+nitpicky = True
+nitpick_ignore = [
+    # Python classes that intersphinx is unable to resolve
+    ('py:class', 'argparse.HelpFormatter'),
+    ('py:class', 'contextlib.contextmanager'),
+    ('py:class', 'module'),
+    ('py:class', '_io.BufferedReader'),
+    ('py:class', 'unittest.case.TestCase'),
+    ('py:class', '_frozen_importlib_external.SourceFileLoader'),
+    # Spack classes that are private and we don't want to expose
+    ('py:class', 'spack.provider_index._IndexBase'),
+]
+
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None
 
@@ -179,7 +199,8 @@ def setup(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
+from pygments.token import Comment, Generic, Text
+
 
 class SpackStyle(DefaultStyle):
     styles = DefaultStyle.styles.copy()
@@ -188,6 +209,7 @@ class SpackStyle(DefaultStyle):
     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)
@@ -353,3 +375,11 @@ class SpackStyle(DefaultStyle):
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
 #texinfo_show_urls = 'footnote'
+
+
+# -- Extension configuration -------------------------------------------------
+
+# sphinx.ext.intersphinx
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+}

lib/spack/docs/developer_guide.rst

@@ -108,9 +108,9 @@ with a high level view of Spack's directory structure:
 
             spack/                <- spack module; contains Python code
                analyzers/         <- modules to run analysis on installed packages
-               build_systems/     <- modules for different build systems 
+               build_systems/     <- modules for different build systems
                cmd/               <- each file in here is a spack subcommand
-               compilers/         <- compiler description files          
+               compilers/         <- compiler description files
                container/         <- module for spack containerize
                hooks/             <- hook modules to run at different points
                modules/           <- modules for lmod, tcl, etc.
@@ -151,24 +151,22 @@ Package-related modules
 ^^^^^^^^^^^^^^^^^^^^^^^
 
 :mod:`spack.package`
-  Contains the :class:`Package <spack.package.Package>` class, which
+  Contains the :class:`~spack.package.Package` class, which
   is the superclass for all packages in Spack.  Methods on ``Package``
   implement all phases of the :ref:`package lifecycle
   <package-lifecycle>` and manage the build process.
 
-:mod:`spack.packages`
-  Contains all of the packages in Spack and methods for managing them.
-  Functions like :func:`packages.get <spack.packages.get>` and
-  :func:`class_name_for_package_name
-  <packages.class_name_for_package_name>` handle mapping package module
-  names to class names and dynamically instantiating packages by name
-  from module files.
+:mod:`spack.util.naming`
+  Contains functions for mapping between Spack package names,
+  Python module names, and Python class names. Functions like
+  :func:`~spack.util.naming.mod_to_class` handle mapping package
+  module names to class names.
 
-:mod:`spack.relations`
-  *Relations* are relationships between packages, like
-  :func:`depends_on <spack.relations.depends_on>` and :func:`provides
-  <spack.relations.provides>`.  See :ref:`dependencies` and
-  :ref:`virtual-dependencies`.
+:mod:`spack.directives`
+  *Directives* are functions that can be called inside a package definition
+  to modify the package, like :func:`~spack.directives.depends_on`
+  and :func:`~spack.directives.provides`.  See :ref:`dependencies`
+  and :ref:`virtual-dependencies`.
 
 :mod:`spack.multimethod`
   Implementation of the :func:`@when <spack.multimethod.when>`
@@ -180,31 +178,27 @@ Spec-related modules
 ^^^^^^^^^^^^^^^^^^^^
 
 :mod:`spack.spec`
-  Contains :class:`Spec <spack.spec.Spec>` and :class:`SpecParser
-  <spack.spec.SpecParser>`. Also implements most of the logic for
-  normalization and concretization of specs.
+  Contains :class:`~spack.spec.Spec` and :class:`~spack.spec.SpecParser`.
+  Also implements most of the logic for normalization and concretization
+  of specs.
 
 :mod:`spack.parse`
   Contains some base classes for implementing simple recursive descent
-  parsers: :class:`Parser <spack.parse.Parser>` and :class:`Lexer
-  <spack.parse.Lexer>`.  Used by :class:`SpecParser
-  <spack.spec.SpecParser>`.
+  parsers: :class:`~spack.parse.Parser` and :class:`~spack.parse.Lexer`.
+  Used by :class:`~spack.spec.SpecParser`.
 
 :mod:`spack.concretize`
-  Contains :class:`DefaultConcretizer
-  <spack.concretize.DefaultConcretizer>` implementation, which allows
-  site administrators to change Spack's :ref:`concretization-policies`.
+  Contains :class:`~spack.concretize.Concretizer` implementation,
+  which allows site administrators to change Spack's :ref:`concretization-policies`.
 
 :mod:`spack.version`
-  Implements a simple :class:`Version <spack.version.Version>` class
-  with simple comparison semantics.  Also implements
-  :class:`VersionRange <spack.version.VersionRange>` and
-  :class:`VersionList <spack.version.VersionList>`.  All three are
-  comparable with each other and offer union and intersection
-  operations.  Spack uses these classes to compare versions and to
-  manage version constraints on specs.  Comparison semantics are
-  similar to the ``LooseVersion`` class in ``distutils`` and to the
-  way RPM compares version strings.
+  Implements a simple :class:`~spack.version.Version` class with simple
+  comparison semantics.  Also implements :class:`~spack.version.VersionRange`
+  and :class:`~spack.version.VersionList`. All three are comparable with each
+  other and offer union and intersection operations. Spack uses these classes
+  to compare versions and to manage version constraints on specs. Comparison
+  semantics are similar to the ``LooseVersion`` class in ``distutils`` and to
+  the way RPM compares version strings.
 
 :mod:`spack.compilers`
   Submodules contains descriptors for all valid compilers in Spack.
@@ -232,7 +226,7 @@ Build environment
 :mod:`spack.stage`
   Handles creating temporary directories for builds.
 
-:mod:`spack.compilation`
+:mod:`spack.build_environment`
   This contains utility functions used by the compiler wrapper script,
   ``cc``.
 
@@ -257,22 +251,19 @@ Unit tests
   Implements Spack's test suite.  Add a module and put its name in
   the test suite in ``__init__.py`` to add more unit tests.
 
-:mod:`spack.test.mock_packages`
-  This is a fake package hierarchy used to mock up packages for
-  Spack's test suite.
-
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Research and Monitoring Modules
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 :mod:`spack.monitor`
-  Contains :class:`SpackMonitor <spack.monitor.SpackMonitor>`. This is accessed
-  from the ``spack install`` and ``spack analyze`` commands to send build
-  and package metadada up to a `Spack Monitor <https://github.com/spack/spack-monitor>`_ server. 
+  Contains :class:`~spack.monitor.SpackMonitorClient`. This is accessed from
+  the ``spack install`` and ``spack analyze`` commands to send build and
+  package metadata up to a `Spack Monitor
+  <https://github.com/spack/spack-monitor>`_ server.
 
 
 :mod:`spack.analyzers`
-  A module folder with a :class:`AnalyzerBase <spack.analyzers.analyzer_base.AnalyzerBase>`
+  A module folder with a :class:`~spack.analyzers.analyzer_base.AnalyzerBase`
   that provides base functions to run, save, and (optionally) upload analysis
   results to a `Spack Monitor <https://github.com/spack/spack-monitor>`_ server.
 
@@ -286,7 +277,7 @@ Other Modules
   tarball URLs.
 
 :mod:`spack.error`
-  :class:`SpackError <spack.error.SpackError>`, the base class for
+  :class:`~spack.error.SpackError`, the base class for
   Spack's exception hierarchy.
 
 :mod:`llnl.util.tty`
@@ -335,8 +326,8 @@ Writing analyzers
 To write an analyzer, you should add a new python file to the
 analyzers module directory at ``lib/spack/spack/analyzers`` .
 Your analyzer should be a subclass of the :class:`AnalyzerBase <spack.analyzers.analyzer_base.AnalyzerBase>`. For example, if you want
-to add an analyzer class ``Myanalyzer`` you woul write to 
-``spack/analyzers/myanalyzer.py`` and import and 
+to add an analyzer class ``Myanalyzer`` you would write to
+``spack/analyzers/myanalyzer.py`` and import and
 use the base as follows:
 
 .. code-block:: python
@@ -347,7 +338,7 @@ use the base as follows:
 
 
 Note that the class name is your module file name, all lowercase
-except for the first capital letter. You can  look at other analyzers in 
+except for the first capital letter. You can  look at other analyzers in
 that analyzer directory for examples. The guide here will tell you about the basic functions needed.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -356,13 +347,13 @@ Analyzer Output Directory
 
 By default, when you run ``spack analyze run`` an analyzer output directory will
 be created in your spack user directory in your ``$HOME``. The reason we output here
-is because the install directory might not always be writable. 
+is because the install directory might not always be writable.
 
 .. code-block:: console
 
     ~/.spack/
       analyzers
-      
+
 Result files will be written here, organized in subfolders in the same structure
 as the package, with each analyzer owning it's own subfolder. for example:
 
@@ -380,11 +371,11 @@ as the package, with each analyzer owning it's own subfolder. for example:
                 │   └── spack-analyzer-install-files.json
                 └── libabigail
                     └── lib
-                        └── spack-analyzer-libabigail-libz.so.1.2.11.xml 
+                        └── spack-analyzer-libabigail-libz.so.1.2.11.xml
 
 
 Notice that for the libabigail analyzer, since results are generated per object,
-we honor the object's folder in case there are equivalently named files in 
+we honor the object's folder in case there are equivalently named files in
 different folders. The result files are typically written as json so they can be easily read and  uploaded in a future interaction with a monitor.
 
 
@@ -426,7 +417,7 @@ and then return the object with a key as the analyzer name. The result data
 should be a list of objects, each with a name, ``analyzer_name``, ``install_file``,
 and one of ``value`` or ``binary_value``. The install file should be for a relative
 path, and not the absolute path. For example, let's say we extract a metric called
-``metric`` for ``bin/wget`` using our analyzer ``thebest-analyzer``. 
+``metric`` for ``bin/wget`` using our analyzer ``thebest-analyzer``.
 We might have data that looks like this:
 
 .. code-block:: python
@@ -482,7 +473,7 @@ Saving Analyzer Results
 The analyzer will have ``save_result`` called, with the result object generated
 to save it to the filesystem, and if the user has added the ``--monitor`` flag
 to upload it to a monitor server. If your result follows an accepted result
-format and you don't need to parse it further, you don't need to add this 
+format and you don't need to parse it further, you don't need to add this
 function to your class. However, if your result data is large or otherwise
 needs additional parsing, you can define it. If you define the function, it
 is useful to know about the ``output_dir`` property, which you can join
@@ -548,7 +539,7 @@ each one (separately) to the monitor:
 
 Notice that this function, if you define it, requires a result object (generated by
 ``run()``, a monitor (if you want to send), and a boolean ``overwrite`` to be used
-to check if a result exists first, and not write to it if the result exists and 
+to check if a result exists first, and not write to it if the result exists and
 overwrite is False. Also notice that since we already saved these files to the analyzer metadata folder, we return early if a monitor isn't defined, because this function serves to send  results to the monitor. If you haven't saved anything to the analyzer metadata folder
 yet, you might want to do that here. You should also use ``tty.info`` to give
 the user a message of "Writing result to $DIRNAME."
@@ -616,7 +607,7 @@ types of hooks in the ``__init__.py``, and then python files in that folder
 can use hook functions. The files are automatically parsed, so if you write
 a new file for some integration (e.g., ``lib/spack/spack/hooks/myintegration.py``
 you can then write hook functions in that file that will be automatically detected,
-and run whenever your hook is called. This section will cover the basic kind 
+and run whenever your hook is called. This section will cover the basic kind
 of hooks, and how to write them.
 
 ^^^^^^^^^^^^^^
@@ -624,7 +615,7 @@ Types of Hooks
 ^^^^^^^^^^^^^^
 
 The following hooks are currently implemented to make it easy for you,
-the developer, to add hooks at different stages of a spack install or similar. 
+the developer, to add hooks at different stages of a spack install or similar.
 If there is a hook that you would like and is missing, you can propose to add a new one.
 
 """""""""""""""""""""
@@ -632,9 +623,9 @@ If there is a hook that you would like and is missing, you can propose to add a
 """""""""""""""""""""
 
 A ``pre_install`` hook is run within an install subprocess, directly before
-the install starts. It expects a single argument of a spec, and is run in 
+the install starts. It expects a single argument of a spec, and is run in
 a multiprocessing subprocess. Note that if you see ``pre_install`` functions associated with packages these are not hooks
-as we have defined them here, but rather callback functions associated with 
+as we have defined them here, but rather callback functions associated with
 a package install.
 
 
@@ -657,7 +648,7 @@ here.
 This hook is run at the beginning of ``lib/spack/spack/installer.py``,
 in the install function of a ``PackageInstaller``,
 and importantly is not part of a build process, but before it. This is when
-we have just newly grabbed the task, and are preparing to install. If you 
+we have just newly grabbed the task, and are preparing to install. If you
 write a hook of this type, you should provide the spec to it.
 
 .. code-block:: python
@@ -666,7 +657,7 @@ write a hook of this type, you should provide the spec to it.
         """On start of an install, we want to...
         """
         print('on_install_start')
-    
+
 
 """"""""""""""""""""""""""""
 ``on_install_success(spec)``
@@ -744,8 +735,8 @@ to trigger after anything is written to a logger. You would add it as follows:
     post_install = HookRunner('post_install')
 
     # hooks related to logging
-    post_log_write = HookRunner('post_log_write') # <- here is my new hook! 
-    
+    post_log_write = HookRunner('post_log_write') # <- here is my new hook!
+
 
 You then need to decide what arguments my hook would expect. Since this is
 related to logging, let's say that you want a message and level. That means
@@ -775,7 +766,7 @@ In this example, we use it outside of a logger that is already defined:
 
 This is not to say that this would be the best way to implement an integration
 with the logger (you'd probably want to write a custom logger, or you could
-have the hook defined within the logger) but serves as an example of writing a hook. 
+have the hook defined within the logger) but serves as an example of writing a hook.
 
 ----------
 Unit tests
@@ -785,6 +776,38 @@ Unit tests
 Unit testing
 ------------
 
+---------------------
+Developer environment
+---------------------
+
+.. warning::
+
+    This is an experimental feature. It is expected to change and you should
+    not use it in a production environment.
+
+
+When installing a package, we currently have support to export environment
+variables to specify adding debug flags to the build. By default, a package
+install will build without any debug flag. However, if you want to add them,
+you can export:
+
+.. code-block:: console
+
+   export SPACK_ADD_DEBUG_FLAGS=true
+   spack install zlib
+
+
+If you want to add custom flags, you should export an additional variable:
+
+.. code-block:: console
+
+   export SPACK_ADD_DEBUG_FLAGS=true
+   export SPACK_DEBUG_FLAGS="-g"
+   spack install zlib
+
+These environment variables will eventually be integrated into spack so
+they are set from the command line.
+
 ------------------
 Developer commands
 ------------------
@@ -795,6 +818,29 @@ Developer commands
 ``spack doc``
 ^^^^^^^^^^^^^
 
+.. _cmd-spack-style:
+
+^^^^^^^^^^^^^^^
+``spack style``
+^^^^^^^^^^^^^^^
+
+spack style exists to help the developer user to check imports and style with
+mypy, flake8, isort, and (soon) black. To run all style checks, simply do:
+
+.. code-block:: console
+
+    $ spack style
+
+To run automatic fixes for isort you can do:
+
+.. code-block:: console
+
+    $ spack style --fix
+
+You do not need any of these Python packages installed on your system for
+the checks to work! Spack will bootstrap install them from packages for
+your use.
+
 ^^^^^^^^^^^^^^^^^^^
 ``spack unit-test``
 ^^^^^^^^^^^^^^^^^^^
@@ -873,7 +919,7 @@ just like you would with the normal ``python`` command.
 ^^^^^^^^^^^^^^^
 
 Spack blame is a way to quickly see contributors to packages or files
-in the spack repository. You should provide a target package name or 
+in the spack repository. You should provide a target package name or
 file name to the command. Here is an example asking to see contributions
 for the package "python":
 
@@ -883,8 +929,8 @@ for the package "python":
     LAST_COMMIT  LINES  %      AUTHOR            EMAIL
     2 weeks ago  3      0.3    Mickey Mouse   <cheddar@gmouse.org>
     a month ago  927    99.7   Minnie Mouse   <swiss@mouse.org>
-                                        
-    2 weeks ago  930    100.0  
+
+    2 weeks ago  930    100.0
 
 
 By default, you will get a table view (shown above) sorted by date of contribution,
@@ -1255,7 +1301,7 @@ Publishing a release on GitHub
 
 #. Create the release in GitHub.
 
-   * Go to 
+   * Go to
      `github.com/spack/spack/releases <https://github.com/spack/spack/releases>`_
      and click ``Draft a new release``.
 

lib/spack/docs/environments.rst

@@ -363,7 +363,7 @@ to ``spack install`` on the command line, ``--no-add`` is the default,
 while for dependency specs on the other hand, it is optional.  In other
 words, if there is an unambiguous match in the active concrete environment
 for a root spec provided to ``spack install`` on the command line, spack
-does not require you to specify the ``--no-add` option to prevent the spec
+does not require you to specify the ``--no-add`` option to prevent the spec
 from being added again.  At the same time, a spec that already exists in the
 environment, but only as a dependency, will be added to the environment as a
 root spec without the ``--no-add`` option.
@@ -732,13 +732,17 @@ 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
+optionally the projections for the view, ``select`` and
+``exclude`` lists for the view and link information via ``link`` and
+``link_type``. 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.
+All the dependencies of each root spec in the environment will be linked
+in the view due to the command ``link: all`` and the files in the view will
+be symlinks to the spack install directories.
 
 .. code-block:: yaml
 
@@ -751,11 +755,16 @@ excludes those built with the PGI compiler at version 18.5.
          exclude: ['%pgi@18.5']
          projections:
            all: {name}/{version}-{compiler.name}
+         link: all
+         link_type: symlink
 
 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 (``{}``).
+default projection is the default view projection (``{}``). The ``link``
+defaults to ``all`` but can also be ``roots`` when only the root specs
+in the environment are desired in the view. The ``link_type`` defaults
+to ``symlink`` but can also take the value of ``hardlink`` or ``copy``.
 
 Any number of views may be defined under the ``view`` heading in a
 Spack Environment.

lib/spack/docs/getting_started.rst

@@ -9,21 +9,16 @@
 Getting Started
 ===============
 
--------------
-Prerequisites
--------------
+--------------------
+System Prerequisites
+--------------------
 
-Spack has the following minimum requirements, which must be installed
-before Spack is run:
+Spack has the following minimum system requirements, which are assumed to
+be present on the machine where Spack is run:
 
-#. Python 2 (2.6 or 2.7) or 3 (3.5 - 3.9) to run Spack
-#. A C/C++ compiler for building
-#. The ``make`` executable for building
-#. The ``tar``, ``gzip``, ``unzip``, ``bzip2``, ``xz`` and optionally ``zstd``
-   executables for extracting source code
-#. The ``patch`` command to apply patches
-#. The ``git`` and ``curl`` commands for fetching
-#. If using the ``gpg`` subcommand, ``gnupg2`` is required
+.. csv-table:: System prerequisites for Spack
+   :file: tables/system_prerequisites.csv
+   :header-rows: 1
 
 These requirements can be easily installed on most modern Linux systems;
 on macOS, XCode is required.  Spack is designed to run on HPC
@@ -70,7 +65,13 @@ Sourcing these files will put the ``spack`` command in your ``PATH``, set
 up your ``MODULEPATH`` to use Spack's packages, and add other useful
 shell integration for :ref:`certain commands <packaging-shell-support>`,
 :ref:`environments <environments>`, and :ref:`modules <modules>`. For
-``bash``, it also sets up tab completion.
+``bash`` and ``zsh``, it also sets up tab completion.
+
+In order to know which directory to add to your ``MODULEPATH``, these scripts
+query the ``spack`` command. On shared filesystems, this can be a bit slow,
+especially if you log in frequently. If you don't use modules, or want to set
+``MODULEPATH`` manually instead, you can set the ``SPACK_SKIP_MODULES``
+environment variable to skip this step and speed up sourcing the file.
 
 If you do not want to use Spack's shell support, you can always just run
 the ``spack`` command directly from ``spack/bin/spack``.
@@ -83,6 +84,151 @@ sourcing time, ensuring future invocations of the ``spack`` command will
 continue to use the same consistent python version regardless of changes in
 the environment.
 
+^^^^^^^^^^^^^^^^^^^^
+Bootstrapping clingo
+^^^^^^^^^^^^^^^^^^^^
+
+Spack supports using ``clingo`` as an external solver to compute which software
+needs to be installed. The default configuration allows Spack to install
+``clingo`` from a public buildcache, created by a Github Action workflow. In this
+case the bootstrapping procedure is transparent to the user, except for a
+slightly long waiting time on the first concretization of a spec:
+
+.. code-block:: console
+
+   $ spack find -b
+   ==> Showing internal bootstrap store at "/home/spack/.spack/bootstrap/store"
+   ==> 0 installed packages
+
+   $ time spack solve zlib
+   ==> Best of 2 considered solutions.
+   ==> Optimization Criteria:
+     Priority  Criterion                                 Value
+     1         deprecated versions used                      0
+     2         version weight                                0
+     3         number of non-default variants (roots)        0
+     4         multi-valued variants                         0
+     5         preferred providers for roots                 0
+     6         number of non-default variants (non-roots)    0
+     7         preferred providers (non-roots)               0
+     8         compiler mismatches                           0
+     9         version badness                               0
+     10        count of non-root multi-valued variants       0
+     11        non-preferred compilers                       0
+     12        target mismatches                             0
+     13        non-preferred targets                         0
+
+   zlib@1.2.11%gcc@11.1.0+optimize+pic+shared arch=linux-ubuntu18.04-broadwell
+
+   real	0m30,618s
+   user	0m27,278s
+   sys	0m1,549s
+
+After this command you'll see that ``clingo`` has been installed for Spack's own use:
+
+.. code-block:: console
+
+   $ spack find -b
+   ==> Showing internal bootstrap store at "/home/spack/.spack/bootstrap/store"
+   ==> 2 installed packages
+   -- linux-rhel5-x86_64 / gcc@9.3.0 -------------------------------
+   clingo-bootstrap@spack  python@3.6
+
+Subsequent calls to the concretizer will then be much faster:
+
+.. code-block:: console
+
+   $ time spack solve zlib
+   [ ... ]
+   real	0m1,222s
+   user	0m1,146s
+   sys	0m0,059s
+
+If for security or for other reasons you don't want to or can't install precompiled
+binaries, Spack can fall-back to bootstrap ``clingo`` from source files. To forbid
+Spack from retrieving binaries from the bootstrapping buildcache, the following
+command must be given:
+
+.. code-block:: console
+
+   $ spack bootstrap untrust github-actions
+   ==> "github-actions" is now untrusted and will not be used for bootstrapping
+
+since an "untrusted" way of bootstrapping software will not be considered
+by Spack. You can verify the new settings are effective with:
+
+.. code-block:: console
+
+   $ spack bootstrap list
+   Name: github-actions UNTRUSTED
+
+     Type: buildcache
+
+     Info:
+       url: https://mirror.spack.io/bootstrap/github-actions/v0.1
+       homepage: https://github.com/alalazo/spack-bootstrap-mirrors
+       releases: https://github.com/alalazo/spack-bootstrap-mirrors/releases
+
+     Description:
+       Buildcache generated from a public workflow using Github Actions.
+       The sha256 checksum of binaries is checked before installation.
+
+
+   Name: spack-install TRUSTED
+
+     Type: install
+
+     Description:
+       Specs built from sources by Spack. May take a long time.
+
+When bootstrapping from sources, Spack requires a compiler with support
+for C++14 (GCC on ``linux``, Apple Clang on ``darwin``) and static C++
+standard libraries on ``linux``. Spack will build the required software
+on the first request to concretize a spec:
+
+.. code-block:: console
+
+   $ spack solve zlib
+   [+] /usr (external bison-3.0.4-wu5pgjchxzemk5ya2l3ddqug2d7jv6eb)
+   [+] /usr (external cmake-3.19.4-a4kmcfzxxy45mzku4ipmj5kdiiz5a57b)
+   [+] /usr (external python-3.6.9-x4fou4iqqlh5ydwddx3pvfcwznfrqztv)
+   ==> Installing re2c-1.2.1-e3x6nxtk3ahgd63ykgy44mpuva6jhtdt
+   [ ... ]
+   ==> Optimization: [0, 0, 0, 0, 0, 1, 0, 0, 0]
+   zlib@1.2.11%gcc@10.1.0+optimize+pic+shared arch=linux-ubuntu18.04-broadwell
+
+.. tip::
+
+   If you want to speed-up bootstrapping ``clingo`` from sources, you may try to
+   search for ``cmake`` and ``bison`` on your system:
+
+   .. code-block:: console
+
+      $ spack external find cmake bison
+      ==> The following specs have been detected on this system and added to /home/spack/.spack/packages.yaml
+      bison@3.0.4  cmake@3.19.4
+
+"""""""""""""""""""
+The Bootstrap Store
+"""""""""""""""""""
+
+All the tools Spack needs for its own functioning are installed in a separate store, which lives
+under the ``${HOME}/.spack`` directory. The software installed there can be queried with:
+
+.. code-block:: console
+
+   $ spack find --bootstrap
+   ==> Showing internal bootstrap store at "/home/spack/.spack/bootstrap/store"
+   ==> 3 installed packages
+   -- linux-ubuntu18.04-x86_64 / gcc@10.1.0 ------------------------
+   clingo-bootstrap@spack  python@3.6.9  re2c@1.2.1
+
+In case it's needed the bootstrap store can also be cleaned with:
+
+.. code-block:: console
+
+   $ spack clean -b
+   ==> Removing software in "/home/spack/.spack/bootstrap/store"
 
 ^^^^^^^^^^^^^^^^^^
 Check Installation
@@ -111,53 +257,6 @@ environment*, especially for ``PATH``.  Only software that comes with
 the system, or that you know you wish to use with Spack, should be
 included.  This procedure will avoid many strange build errors.
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Optional: Bootstrapping clingo
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Spack supports using clingo as an external solver to compute which software
-needs to be installed. If you have a default compiler supporting C++14 Spack
-can automatically bootstrap this tool from sources the first time it is
-needed:
-
-.. code-block:: console
-
-   $ spack solve zlib
-   [+] /usr (external bison-3.0.4-wu5pgjchxzemk5ya2l3ddqug2d7jv6eb)
-   [+] /usr (external cmake-3.19.4-a4kmcfzxxy45mzku4ipmj5kdiiz5a57b)
-   [+] /usr (external python-3.6.9-x4fou4iqqlh5ydwddx3pvfcwznfrqztv)
-   ==> Installing re2c-1.2.1-e3x6nxtk3ahgd63ykgy44mpuva6jhtdt
-   [ ... ]
-   ==> Optimization: [0, 0, 0, 0, 0, 1, 0, 0, 0]
-   zlib@1.2.11%gcc@10.1.0+optimize+pic+shared arch=linux-ubuntu18.04-broadwell
-
-If you want to speed-up bootstrapping, you may try to search for ``cmake`` and ``bison``
-on your system:
-
-.. code-block:: console
-
-   $ spack external find cmake bison
-   ==> The following specs have been detected on this system and added to /home/spack/.spack/packages.yaml
-   bison@3.0.4  cmake@3.19.4
-
-All the tools Spack needs for its own functioning are installed in a separate store, which lives
-under the ``${HOME}/.spack`` directory. The software installed there can be queried with:
-
-.. code-block:: console
-
-   $ spack find --bootstrap
-   ==> Showing internal bootstrap store at "/home/spack/.spack/bootstrap/store"
-   ==> 3 installed packages
-   -- linux-ubuntu18.04-x86_64 / gcc@10.1.0 ------------------------
-   clingo-bootstrap@spack  python@3.6.9  re2c@1.2.1
-
-In case it's needed the bootstrap store can also be cleaned with:
-
-.. code-block:: console
-
-   $ spack clean -b
-   ==> Removing software in "/home/spack/.spack/bootstrap/store"
-
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 Optional: Alternate Prefix
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -771,7 +870,7 @@ an OpenMPI installed in /opt/local, one would use:
             buildable: False
 
 In general, Spack is easier to use and more reliable if it builds all of
-its own dependencies.  However, there are two packages for which one
+its own dependencies.  However, there are several packages for which one
 commonly needs to use system versions:
 
 ^^^
@@ -1166,7 +1265,7 @@ the key that we just created:
           60D2685DAB647AD4DB54125961E09BB6F2A0ADCB
     uid           [ultimate] dinosaur (GPG created for Spack) <dinosaur@thedinosaurthings.com>
 
-    
+
 Note that the name "dinosaur" can be seen under the uid, which is the unique
 id. We might need this reference if we want to export or otherwise reference the key.
 
@@ -1205,7 +1304,7 @@ If you want to include the private key, then just add `--secret`:
 
     $ spack gpg export --secret dinosaur.priv dinosaur
 
-This will write the private key to the file `dinosaur.priv`. 
+This will write the private key to the file `dinosaur.priv`.
 
 .. warning::
 

lib/spack/docs/monitoring.rst

@@ -103,6 +103,140 @@ more tags to your build, you can do:
     $ spack install --monitor --monitor-tags pizza,pasta hdf5
 
 
+----------------------------
+Monitoring with Containerize
+----------------------------
+
+The same argument group is available to add to a containerize command. 
+
+^^^^^^
+Docker
+^^^^^^
+
+To add monitoring to a Docker container recipe generation using the defaults,
+and assuming a monitor server running on localhost, you would
+start with a spack.yaml in your present working directory:
+
+.. code-block:: yaml
+
+   spack:
+     specs:
+       - samtools
+
+And then do:
+
+.. code-block:: console
+
+    # preview first
+    spack containerize --monitor
+    
+    # and then write to a Dockerfile
+    spack containerize --monitor > Dockerfile
+    
+    
+The install command will be edited to include commands for enabling monitoring.
+However, getting secrets into the container for your monitor server is something
+that should be done carefully. Specifically you should:
+
+ - Never try to define secrets as ENV, ARG, or using ``--build-arg``
+ - Do not try to get the secret into the container via a "temporary" file that you remove (it in fact will still exist in a layer)
+
+Instead, it's recommended to use buildkit `as explained here <https://pythonspeed.com/articles/docker-build-secrets/>`_.
+You'll need to again export environment variables for your spack monitor server:
+
+.. code-block:: console
+
+    $ export SPACKMON_TOKEN=50445263afd8f67e59bd79bff597836ee6c05438
+    $ export SPACKMON_USER=spacky
+
+And then use buildkit along with your build and identifying the name of the secret:
+
+.. code-block:: console
+
+    $ DOCKER_BUILDKIT=1 docker build --secret id=st,env=SPACKMON_TOKEN --secret id=su,env=SPACKMON_USER -t spack/container . 
+    
+The secrets are expected to come from your environment, and then will be temporarily mounted and available
+at ``/run/secrets/<name>``. If you forget to supply them (and authentication is required) the build
+will fail. If you need to build on your host (and interact with a spack monitor at localhost) you'll
+need to tell Docker to use the host network:
+
+.. code-block:: console
+
+    $ DOCKER_BUILDKIT=1 docker build --network="host" --secret id=st,env=SPACKMON_TOKEN --secret id=su,env=SPACKMON_USER -t spack/container . 
+    
+
+^^^^^^^^^^^
+Singularity
+^^^^^^^^^^^
+
+To add monitoring to a Singularity container build, the spack.yaml needs to
+be modified slightly to specify wanting a different format:
+
+
+.. code-block:: yaml
+
+   spack:
+     specs:
+       - samtools
+     container:
+       format: singularity
+       
+       
+Again, generate the recipe:
+
+
+.. code-block:: console
+
+    # preview first
+    $ spack containerize --monitor
+    
+    # then write to a Singularity recipe
+    $ spack containerize --monitor > Singularity
+
+
+Singularity doesn't have a direct way to define secrets at build time, so we have
+to do a bit of a manual command to add a file, source secrets in it, and remove it.
+Since Singularity doesn't have layers like Docker, deleting a file will truly
+remove it from the container and history. So let's say we have this file,
+``secrets.sh``:
+
+.. code-block:: console
+
+    # secrets.sh
+    export SPACKMON_USER=spack
+    export SPACKMON_TOKEN=50445263afd8f67e59bd79bff597836ee6c05438
+
+
+We would then generate the Singularity recipe, and add a files section,
+a source of that file at the start of ``%post``, and **importantly**
+a removal of the final at the end of that same section.
+
+.. code-block::
+
+    Bootstrap: docker
+    From: spack/ubuntu-bionic:latest
+    Stage: build
+
+    %files
+      secrets.sh /opt/secrets.sh 
+
+    %post
+      . /opt/secrets.sh
+
+      # spack install commands are here
+      ...
+      
+      # Don't forget to remove here!
+      rm /opt/secrets.sh
+
+
+You can then build the container as your normally would.
+
+.. code-block:: console
+
+    $ sudo singularity build container.sif Singularity 
+
+
 ------------------
 Monitoring Offline
 ------------------
@@ -117,4 +251,15 @@ flag.
     $ spack install --monitor --monitor-save-local hdf5 
 
 This will save results in a subfolder, "monitor" in your designated spack
-reports folder, which defaults to ``$HOME/.spack/reports/monitor``.
+reports folder, which defaults to ``$HOME/.spack/reports/monitor``. When
+you are ready to upload them to a spack monitor server:
+
+
+.. code-block:: console
+
+    $ spack monitor upload ~/.spack/reports/monitor 
+
+
+You can choose the root directory of results as shown above, or a specific
+subdirectory. The command accepts other arguments to specify configuration
+for the monitor.

lib/spack/docs/packaging_guide.rst

@@ -920,12 +920,13 @@ For some packages, source code is provided in a Version Control System
 (VCS) repository rather than in a tarball.  Spack can fetch packages
 from VCS repositories. Currently, Spack supports fetching with `Git
 <git-fetch_>`_, `Mercurial (hg) <hg-fetch_>`_, `Subversion (svn)
-<svn-fetch_>`_, and `Go <go-fetch_>`_.  In all cases, the destination
+<svn-fetch_>`_, `CVS (cvs) <cvs-fetch_>`_, and `Go <go-fetch_>`_.
+In all cases, the destination
 is the standard stage source path.
 
 To fetch a package from a source repository, Spack needs to know which
 VCS to use and where to download from. Much like with ``url``, package
-authors can specify a class-level ``git``, ``hg``, ``svn``, or ``go``
+authors can specify a class-level ``git``, ``hg``, ``svn``, ``cvs``, or ``go``
 attribute containing the correct download location.
 
 Many packages developed with Git have both a Git repository as well as
@@ -1173,6 +1174,55 @@ you can check out a branch or tag by changing the URL. If you want to
 package multiple branches, simply add a ``svn`` argument to each
 version directive.
 
+.. _cvs-fetch:
+
+^^^
+CVS
+^^^
+
+CVS (Concurrent Versions System) is an old centralized version control
+system. It is a predecessor of Subversion.
+
+To fetch with CVS, use the ``cvs``, branch, and ``date`` parameters.
+The destination directory will be the standard stage source path.
+
+Fetching the head
+  Simply add a ``cvs`` parameter to the package:
+
+  .. code-block:: python
+
+     class Example(Package):
+
+         cvs = ":pserver:outreach.scidac.gov/cvsroot%module=modulename"
+
+         version('1.1.2.4')
+
+  CVS repository locations are described using an older syntax that
+  is different from today's ubiquitous URL syntax. ``:pserver:``
+  denotes the transport method. CVS servers can host multiple
+  repositories (called "modules") at the same location, and one needs
+  to specify both the server location and the module name to access.
+  Spack combines both into one string using the ``%module=modulename``
+  suffix shown above.
+
+  This download method is untrusted.
+
+Fetching a date
+  Versions in CVS are commonly specified by date. To fetch a
+  particular branch or date, add a ``branch`` and/or ``date`` argument
+  to the version directive:
+
+  .. code-block:: python
+
+     version('2021.4.22', branch='branchname', date='2021-04-22')
+
+  Unfortunately, CVS does not identify repository-wide commits via a
+  revision or hash like Subversion, Git, or Mercurial do. This makes
+  it impossible to specify an exact commit to check out.
+
+CVS has more features, but since CVS is rarely used these days, Spack
+does not support all of them.
+
 .. _go-fetch:
 
 ^^
@@ -1207,7 +1257,7 @@ Variants
 Many software packages can be configured to enable optional
 features, which often come at the expense of additional dependencies or
 longer build times. To be flexible enough and support a wide variety of
-use cases, Spack permits to expose to the end-user the ability to choose
+use cases, Spack allows you to expose to the end-user the ability to choose
 which features should be activated in a package at the time it is installed.
 The mechanism to be employed is the :py:func:`spack.directives.variant` directive.
 
@@ -2725,6 +2775,57 @@ packages be built with MVAPICH and GCC.
 
 See the :ref:`concretization-preferences` section for more details.
 
+
+.. _group_when_spec:
+
+----------------------------
+Common ``when=`` constraints
+----------------------------
+
+In case a package needs many directives to share the whole ``when=``
+argument, or just part of it, Spack allows you to group the common part
+under a context manager:
+
+.. code-block:: python
+
+   class Gcc(AutotoolsPackage):
+
+       with when('+nvptx'):
+           depends_on('cuda')
+           conflicts('@:6', msg='NVPTX only supported in gcc 7 and above')
+           conflicts('languages=ada')
+           conflicts('languages=brig')
+           conflicts('languages=go')
+
+The snippet above is equivalent to the more verbose:
+
+.. code-block:: python
+
+   class Gcc(AutotoolsPackage):
+
+       depends_on('cuda', when='+nvptx')
+       conflicts('@:6', when='+nvptx', msg='NVPTX only supported in gcc 7 and above')
+       conflicts('languages=ada', when='+nvptx')
+       conflicts('languages=brig', when='+nvptx')
+       conflicts('languages=go', when='+nvptx')
+
+Constraints stemming from the context are added to what is explicitly present in the
+``when=`` argument of a directive, so:
+
+.. code-block:: python
+
+   with when('+elpa'):
+       depends_on('elpa+openmp', when='+openmp')
+
+is equivalent to:
+
+.. code-block:: python
+
+   depends_on('elpa+openmp', when='+openmp+elpa')
+
+Constraints from nested context managers are also added together, but they are rarely
+needed or recommended.
+
 .. _install-method:
 
 ------------------
@@ -2783,52 +2884,52 @@ The package base class, usually specialized for a given build system, determines
 actual set of entities available for overriding.
 The classes that are currently provided by Spack are:
 
-    +-------------------------------+----------------------------------+
-    |        **Base Class**         |           **Purpose**            |
-    +===============================+==================================+
-    | :py:class:`.Package`          | General base class not           |
-    |                               | specialized for any build system |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.MakefilePackage`  | Specialized class for packages   |
-    |                               | built invoking                   |
-    |                               | hand-written Makefiles           |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.AutotoolsPackage` | Specialized class for packages   |
-    |                               | built using GNU Autotools        |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.CMakePackage`     | Specialized class for packages   |
-    |                               | built using CMake                |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.CudaPackage`      | A helper class for packages that |
-    |                               | use CUDA                         |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.QMakePackage`     | Specialized class for packages   |
-    |                               | build using QMake                |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.ROCmPackage`      | A helper class for packages that |
-    |                               | use ROCm                         |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.SConsPackage`     | Specialized class for packages   |
-    |                               | built using SCons                |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.WafPackage`       | Specialized class for packages   |
-    |                               | built using Waf                  |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.RPackage`         | Specialized class for            |
-    |                               | :py:class:`.R` extensions        |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.OctavePackage`    | Specialized class for            |
-    |                               | :py:class:`.Octave` packages     |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.PythonPackage`    | Specialized class for            |
-    |                               | :py:class:`.Python` extensions   |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.PerlPackage`      | Specialized class for            |
-    |                               | :py:class:`.Perl` extensions     |
-    +-------------------------------+----------------------------------+
-    | :py:class:`.IntelPackage`     | Specialized class for licensed   |
-    |                               | Intel software                   |
-    +-------------------------------+----------------------------------+
++-------------------------=--------------------------------+----------------------------------+
+|     **Base Class**                                       |           **Purpose**            |
++==========================================================+==================================+
+| :class:`~spack.package.Package`                          | General base class not           |
+|                                                          | specialized for any build system |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.makefile.MakefilePackage`   | Specialized class for packages   |
+|                                                          | built invoking                   |
+|                                                          | hand-written Makefiles           |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.autotools.AutotoolsPackage` | Specialized class for packages   |
+|                                                          | built using GNU Autotools        |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.cmake.CMakePackage`         | Specialized class for packages   |
+|                                                          | built using CMake                |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.cuda.CudaPackage`           | A helper class for packages that |
+|                                                          | use CUDA                         |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.qmake.QMakePackage`         | Specialized class for packages   |
+|                                                          | built using QMake                |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.rocm.ROCmPackage`           | A helper class for packages that |
+|                                                          | use ROCm                         |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.scons.SConsPackage`         | Specialized class for packages   |
+|                                                          | built using SCons                |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.waf.WafPackage`             | Specialized class for packages   |
+|                                                          | built using Waf                  |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.r.RPackage`                 | Specialized class for            |
+|                                                          | R extensions                     |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.octave.OctavePackage`       | Specialized class for            |
+|                                                          | Octave packages                  |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.python.PythonPackage`       | Specialized class for            |
+|                                                          | Python extensions                |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.perl.PerlPackage`           | Specialized class for            |
+|                                                          | Perl extensions                  |
++----------------------------------------------------------+----------------------------------+
+| :class:`~spack.build_systems.intel.IntelPackage`         | Specialized class for licensed   |
+|                                                          | Intel software                   |
++----------------------------------------------------------+----------------------------------+
 
 
 .. note::
@@ -2838,7 +2939,7 @@ The classes that are currently provided by Spack are:
         rare cases where manual intervention is needed we need to stress that a
         package base class depends on the *build system* being used, not the language of the package.
         For example, a Python extension installed with CMake would ``extends('python')`` and
-        subclass from :py:class:`.CMakePackage`.
+        subclass from :class:`~spack.build_systems.cmake.CMakePackage`.
 
 ^^^^^^^^^^^^^^^^^^^^^
 Installation pipeline
@@ -3978,7 +4079,7 @@ prefix **before** ``make install``. Builds like this can falsely report
 success when an error occurs before the installation is complete. Simple
 sanity checks can be used to identify files and or directories that are
 required of a successful installation. Spack checks for the presence of
-the files and directories after ``install()`` runs. 
+the files and directories after ``install()`` runs.
 
 If any of the listed files or directories are missing, then the build will
 fail and the install prefix will be removed. If they all exist, then Spack
@@ -4092,7 +4193,7 @@ need to use two decorators for each phase test method:
 The first decorator tells Spack when in the installation process to
 run your test method installation process; namely *after* the provided
 installation phase. The second decorator tells Spack to only run the
-checks when the ``--test`` option is provided on the command line. 
+checks when the ``--test`` option is provided on the command line.
 
 .. note::
 
@@ -4166,17 +4267,17 @@ tests can be performed days, even weeks, after the software is installed.
 
 Stand-alone tests are checks that should run relatively quickly -- as
 in on the order of at most a few minutes -- and ideally execute all
-aspects of the installed software, or at least key functionality. 
+aspects of the installed software, or at least key functionality.
 
 .. note::
 
     Execution speed is important because these tests are intended
     to quickly assess whether the installed software works on the
     system.
-    
+
     Failing stand-alone tests indicate that there is no reason to
     proceed with more resource-intensive tests.
-    
+
     Passing stand-alone (or smoke) tests can lead to more thorough
     testing, such as extensive unit or regression tests, or tests
     that run at scale. Spack support for more thorough testing is
@@ -4206,7 +4307,7 @@ file such that:
      test_stage: /path/to/stage
 
 The package can access this path **during test processing** using
-`self.test_suite.stage`. 
+`self.test_suite.stage`.
 
 .. note::
 
@@ -4287,7 +4388,7 @@ can be implemented as shown below.
        @run_after('install')
        def copy_test_sources(self):
            srcs = ['tests',
-                   join_path('examples', 'foo.c'), 
+                   join_path('examples', 'foo.c'),
                    join_path('examples', 'bar.c')]
            self.cache_extra_test_sources(srcs)
 
@@ -4345,7 +4446,7 @@ Examples include:
 - expected test output
 
 These extra files should be added to the ``test`` subdirectory of the
-package in the Spack repository. 
+package in the Spack repository.
 
 Spack will **automatically copy** the contents of that directory to the
 test staging directory for stand-alone testing. The ``test`` method can
@@ -4370,7 +4471,7 @@ The signature for ``get_escaped_text_output`` is:
 
 where ``filename`` is the path to the file containing the expected output.
 
-The ``filename`` for a :ref:`custom file <cache_custom_files>` can be 
+The ``filename`` for a :ref:`custom file <cache_custom_files>` can be
 accessed and used as illustrated by a simplified version of an ``sqlite``
 package check:
 
@@ -4490,10 +4591,10 @@ where each argument has the following meaning:
 
   Options are a list of strings to be passed to the executable when
   it runs.
-  
+
   The default is ``[]``, which means no options are provided to the
   executable.
- 
+
 * ``expected`` is an optional list of expected output strings.
 
   Spack requires every string in ``expected`` to be a regex matching
@@ -4504,31 +4605,31 @@ where each argument has the following meaning:
 
   The expected output can be :ref:`read from a file
   <expected_test_output_from_file>`.
-  
+
   The default is ``expected=[]``, so Spack will not check the output.
- 
+
 * ``status`` is the optional expected return code(s).
 
   A list of return codes corresponding to successful execution can
   be provided (e.g., ``status=[0,3,7]``). Support for non-zero return
   codes allows for basic **expected failure** tests as well as different
   return codes across versions of the software.
-  
+
   The default is ``status=[0]``, which corresponds to **successful**
   execution in the sense that the executable does not exit with a
   failure code or raise an exception.
- 
+
 * ``installed`` is used to require ``exe`` to be within the package
   prefix.
-  
+
   If ``True``, then the path for ``exe`` is required to be within the
   package prefix; otherwise, the path is not constrained.
-  
+
   The default is ``False``, so the fully qualified path for ``exe``
   does **not** need to be within the installation directory.
- 
+
 * ``purpose`` is an optional heading describing the the test part.
- 
+
   Output from the test is written to a test log file so this argument
   serves as a searchable heading in text logs to highlight the start
   of the test part. Having a description can be helpful when debugging
@@ -4543,10 +4644,10 @@ where each argument has the following meaning:
 
   The default is ``False``, which means the test executable must be
   present for any installable version of the software.
- 
+
 * ``work_dir`` is the path to the directory from which the executable
   will run.
-  
+
   The default of ``None`` corresponds to the current directory (``'.'``).
 
 """""""""""""""""""""""""""""""""""""""""
@@ -4653,7 +4754,7 @@ where only the outputs for the first of each set are shown:
    Copyright (C) 2018 Free Software Foundation, Inc.
    This is free software; see the source for copying conditions.  There is NO
    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-   
+
    PASSED
    ...
    ==> [2021-04-26-17:35:20.493921] test: checking mpirun output
@@ -4814,7 +4915,7 @@ This is already part of the boilerplate for packages created with
 Filtering functions
 ^^^^^^^^^^^^^^^^^^^
 
-:py:func:`filter_file(regex, repl, *filenames, **kwargs) <spack.filter_file>`
+:py:func:`filter_file(regex, repl, *filenames, **kwargs) <llnl.util.filesystem.filter_file>`
   Works like ``sed`` but with Python regular expression syntax.  Takes
   a regular expression, a replacement, and a set of files.  ``repl``
   can be a raw string or a callable function.  If it is a raw string,
@@ -4852,7 +4953,7 @@ Filtering functions
         filter_file('CXX="c++"', 'CXX="%s"' % self.compiler.cxx,
                     prefix.bin.mpicxx)
 
-:py:func:`change_sed_delimiter(old_delim, new_delim, *filenames) <spack.change_sed_delim>`
+:py:func:`change_sed_delimiter(old_delim, new_delim, *filenames) <llnl.util.filesystem.change_sed_delimiter>`
     Some packages, like TAU, have a build system that can't install
     into directories with, e.g. '@' in the name, because they use
     hard-coded ``sed`` commands in their build.
@@ -4874,14 +4975,14 @@ Filtering functions
 File functions
 ^^^^^^^^^^^^^^
 
-:py:func:`ancestor(dir, n=1) <spack.ancestor>`
+:py:func:`ancestor(dir, n=1) <llnl.util.filesystem.ancestor>`
   Get the n\ :sup:`th` ancestor of the directory ``dir``.
 
-:py:func:`can_access(path) <spack.can_access>`
+:py:func:`can_access(path) <llnl.util.filesystem.can_access>`
   True if we can read and write to the file at ``path``.  Same as
   native python ``os.access(file_name, os.R_OK|os.W_OK)``.
 
-:py:func:`install(src, dest) <spack.install>`
+:py:func:`install(src, dest) <llnl.util.filesystem.install>`
   Install a file to a particular location.  For example, install a
   header into the ``include`` directory under the install ``prefix``:
 
@@ -4889,14 +4990,14 @@ File functions
 
      install('my-header.h', prefix.include)
 
-:py:func:`join_path(*paths) <spack.join_path>`
+:py:func:`join_path(*paths) <llnl.util.filesystem.join_path>`
   An alias for ``os.path.join``. This joins paths using the OS path separator.
 
-:py:func:`mkdirp(*paths) <spack.mkdirp>`
+:py:func:`mkdirp(*paths) <llnl.util.filesystem.mkdirp>`
   Create each of the directories in ``paths``, creating any parent
   directories if they do not exist.
 
-:py:func:`working_dir(dirname, kwargs) <spack.working_dir>`
+:py:func:`working_dir(dirname, kwargs) <llnl.util.filesystem.working_dir>`
   This is a Python `Context Manager
   <https://docs.python.org/2/library/contextlib.html>`_ that makes it
   easier to work with subdirectories in builds.  You use this with the
@@ -4938,7 +5039,7 @@ File functions
      The ``create=True`` keyword argument causes the command to create
      the directory if it does not exist.
 
-:py:func:`touch(path) <spack.touch>`
+:py:func:`touch(path) <llnl.util.filesystem.touch>`
   Create an empty file at ``path``.
 
 .. _make-package-findable:

lib/spack/docs/pipelines.rst

@@ -169,11 +169,28 @@ have disabled it (using ``rebuild-index: False``) because the index would only b
 generated in the artifacts mirror anyway, and consequently would not be available
 during subesequent pipeline runs.
 
+.. note::
+   With the addition of reproducible builds (#22887) a previously working
+   pipeline will require some changes:
+
+   * In the build jobs (``runner-attributes``), the environment location changed.
+     This will typically show as a ``KeyError`` in the failing job. Be sure to
+     point to ``${SPACK_CONCRETE_ENV_DIR}``.
+
+   * When using ``include`` in your environment, be sure to make the included
+     files available in the build jobs. This means adding those files to the
+     artifact directory. Those files will also be missing in the reproducibility
+     artifact.
+
+   * Because the location of the environment changed, including files with
+     relative path may have to be adapted to work both in the project context
+     (generation job) and in the concrete env dir context (build job).
+
 -----------------------------------
 Spack commands supporting pipelines
 -----------------------------------
 
-Spack provides a command ``ci`` command with a few sub-commands supporting spack
+Spack provides a ``ci`` command with a few sub-commands supporting spack
 ci pipelines.  These commands are covered in more detail in this section.
 
 .. _cmd-spack-ci:

lib/spack/docs/requirements.txt

@@ -1,7 +1,7 @@
 # These dependencies should be installed using pip in order
 # to build the documentation.
 
-sphinx
+sphinx>=3.4,!=4.1.2
 sphinxcontrib-programoutput
 sphinx-rtd-theme
 python-levenshtein

lib/spack/docs/spack.yaml

@@ -8,12 +8,20 @@
 # these commands in this directory to install Sphinx and its plugins,
 # then build the docs:
 #
-#     spack install
 #     spack env activate .
+#     spack install
 #     make
 #
 spack:
   specs:
-  - py-sphinx
+  # Sphinx
+  - "py-sphinx@3.4:4.1.1,4.1.3:"
   - py-sphinxcontrib-programoutput
   - py-sphinx-rtd-theme
+  # VCS
+  - git
+  - mercurial
+  - subversion
+  # Plotting
+  - graphviz
+  concretization: together

lib/spack/docs/tables/system_prerequisites.csv

@@ -0,0 +1,17 @@
+Name, Supported Versions, Notes, Requirement Reason
+Python, 2.6/2.7/3.5-3.9, , Interpreter for Spack
+C/C++ Compilers, , , Building software
+make, , , Build software
+patch, , , Build software
+bash, , , Compiler wrappers
+tar, , , Extract/create archives
+gzip, , , Compress/Decompress archives
+unzip, , , Compress/Decompress archives
+bzip, , , Compress/Decompress archives
+xz, , , Compress/Decompress archives
+zstd, , Optional, Compress/Decompress archives
+file, , , Create/Use Buildcaches
+gnupg2, , , Sign/Verify Buildcaches
+git, , , Manage Software Repositories
+svn, , Optional, Manage Software Repositories
+hg, , Optional, Manage Software Repositories

lib/spack/docs/workflows.rst

@@ -543,7 +543,8 @@ specified from the command line using the ``--projection-file`` option
 to the ``spack view`` command.
 
 The projections configuration file is a mapping of partial specs to
-spec format strings, as shown in the example below.
+spec format strings, defined by the :meth:`~spack.spec.Spec.format`
+function, as shown in the example below.
 
 .. code-block:: yaml
 

lib/spack/env/cc

@@ -40,6 +40,14 @@ parameters=(
     SPACK_SYSTEM_DIRS
 )
 
+# Optional parameters that aren't required to be set
+
+# Boolean (true/false/custom) if we want to add debug flags
+# SPACK_ADD_DEBUG_FLAGS
+
+# If a custom flag is requested, it will be defined
+# SPACK_DEBUG_FLAGS
+
 # The compiler input variables are checked for sanity later:
 #   SPACK_CC, SPACK_CXX, SPACK_F77, SPACK_FC
 # The default compiler flags are passed from these variables:
@@ -87,6 +95,25 @@ for param in "${parameters[@]}"; do
     fi
 done
 
+# Check if optional parameters are defined
+# If we aren't asking for debug flags, don't add them
+if [[ -z ${SPACK_ADD_DEBUG_FLAGS+x} ]]; then
+    SPACK_ADD_DEBUG_FLAGS="false"
+fi
+
+# SPACK_ADD_DEBUG_FLAGS must be true/false/custom
+is_valid="false"
+for param in "true" "false" "custom"; do
+  if [ "$param" == "$SPACK_ADD_DEBUG_FLAGS" ];  then
+      is_valid="true"
+  fi
+done
+
+# Exit with error if we are given an incorrect value
+if [ "$is_valid" == "false" ]; then
+    die "SPACK_ADD_DEBUG_FLAGS, if defined, must be one of 'true' 'false' or 'custom'"
+fi
+
 # Figure out the type of compiler, the language, and the mode so that
 # the compiler script knows what to do.
 #
@@ -106,30 +133,35 @@ comp="CC"
 case "$command" in
     cpp)
         mode=cpp
+        debug_flags="-g"
         ;;
     cc|c89|c99|gcc|clang|armclang|icc|icx|pgcc|nvc|xlc|xlc_r|fcc)
         command="$SPACK_CC"
         language="C"
         comp="CC"
         lang_flags=C
+        debug_flags="-g"
         ;;
     c++|CC|g++|clang++|armclang++|icpc|icpx|pgc++|nvc++|xlc++|xlc++_r|FCC)
         command="$SPACK_CXX"
         language="C++"
         comp="CXX"
         lang_flags=CXX
+        debug_flags="-g"
         ;;
     ftn|f90|fc|f95|gfortran|flang|armflang|ifort|ifx|pgfortran|nvfortran|xlf90|xlf90_r|nagfor|frt)
         command="$SPACK_FC"
         language="Fortran 90"
         comp="FC"
         lang_flags=F
+        debug_flags="-g"
         ;;
     f77|xlf|xlf_r|pgf77)
         command="$SPACK_F77"
         language="Fortran 77"
         comp="F77"
         lang_flags=F
+        debug_flags="-g"
         ;;
     ld)
         mode=ld
@@ -415,6 +447,16 @@ done
 #
 flags=()
 
+# Add debug flags
+if [ "${SPACK_ADD_DEBUG_FLAGS}" == "true" ]; then
+    flags=("${flags[@]}" "${debug_flags}")
+
+# If a custom flag is requested, derive from environment
+elif [ "$SPACK_ADD_DEBUG_FLAGS" == "custom" ]; then
+    IFS=' ' read -ra SPACK_DEBUG_FLAGS <<< "$SPACK_DEBUG_FLAGS"
+    flags=("${flags[@]}" "${SPACK_DEBUG_FLAGS[@]}")
+fi
+
 # Fortran flags come before CPPFLAGS
 case "$mode" in
     cc|ccld)

lib/spack/external/__init__.py

@@ -11,7 +11,7 @@
 
 * Homepage: https://pypi.python.org/pypi/archspec
 * Usage: Labeling, comparison and detection of microarchitectures
-* Version: 0.1.2 (commit 130607c373fd88cd3c43da94c0d3afd3a44084b0)
+* Version: 0.1.2 (commit 4dbf253daf37e4a008e4beb6489f347b4a35aed4)
 
 argparse
 --------

lib/spack/external/archspec/json/cpu/microarchitectures.json

@@ -1725,6 +1725,12 @@
             "versions": ":",
             "flags": "-march=armv8-a -mtune=generic"
           }
+        ],
+        "arm": [
+          {
+            "versions": ":",
+            "flags": "-march=armv8-a -mtune=generic"
+          }
         ]
       }
     },
@@ -1828,6 +1834,12 @@
             "versions": "5:",
             "flags": "-march=armv8.2-a+crc+crypto+fp16+sve"
           }
+        ],
+        "arm": [
+          {
+            "versions": "20:",
+            "flags": "-march=armv8.2-a+crc+crypto+fp16+sve"
+          }
         ]
       }
     },
@@ -1930,6 +1942,12 @@
                   "versions": "5:",
                   "flags" : "-march=armv8.2-a+fp16+rcpc+dotprod+crypto"
               }
+          ],
+          "arm" : [
+              {
+                  "versions": "20:",
+                  "flags" : "-march=armv8.2-a+fp16+rcpc+dotprod+crypto"
+              }
           ]
       }
     },

lib/spack/llnl/util/argparsewriter.py

@@ -5,9 +5,9 @@
 
 from __future__ import print_function
 
-import re
 import argparse
 import errno
+import re
 import sys
 
 from six import StringIO
@@ -326,7 +326,7 @@ def end_function(self, prog=None):
         """Returns the syntax needed to end a function definition.
 
         Parameters:
-            prog (str, optional): the command name
+            prog (str or None): the command name
 
         Returns:
             str: the function definition ending

lib/spack/llnl/util/filesystem.py

@@ -4,9 +4,9 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import collections
 import errno
-import hashlib
 import glob
 import grp
+import hashlib
 import itertools
 import numbers
 import os
@@ -19,10 +19,11 @@
 from contextlib import contextmanager
 
 import six
+
 from llnl.util import tty
 from llnl.util.lang import dedupe, memoized
-from spack.util.executable import Executable
 
+from spack.util.executable import Executable
 
 if sys.version_info >= (3, 3):
     from collections.abc import Sequence  # novm
@@ -443,7 +444,7 @@ def copy_tree(src, dest, symlinks=True, ignore=None, _permissions=False):
         src (str): the directory to copy
         dest (str): the destination directory
         symlinks (bool): whether or not to preserve symlinks
-        ignore (function): function indicating which files to ignore
+        ignore (typing.Callable): function indicating which files to ignore
         _permissions (bool): for internal use only
 
     Raises:
@@ -517,7 +518,7 @@ def install_tree(src, dest, symlinks=True, ignore=None):
         src (str): the directory to install
         dest (str): the destination directory
         symlinks (bool): whether or not to preserve symlinks
-        ignore (function): function indicating which files to ignore
+        ignore (typing.Callable): function indicating which files to ignore
 
     Raises:
         IOError: if *src* does not match any files or directories
@@ -556,12 +557,12 @@ def mkdirp(*paths, **kwargs):
         paths (str): paths to create with mkdirp
 
     Keyword Aguments:
-        mode (permission bits or None, optional): optional permissions to set
+        mode (permission bits or None): optional permissions to set
             on the created directory -- use OS default if not provided
-        group (group name or None, optional): optional group for permissions of
+        group (group name or None): optional group for permissions of
             final created directory -- use OS default if not provided. Only
             used if world write permissions are not set
-        default_perms ('parents' or 'args', optional): The default permissions
+        default_perms (str or None): one of 'parents' or 'args'. The default permissions
             that are set for directories that are not themselves an argument
             for mkdirp. 'parents' means intermediate directories get the
             permissions of their direct parent directory, 'args' means
@@ -865,7 +866,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
     Keyword Arguments:
         order (str): Whether to do pre- or post-order traversal. Accepted
             values are 'pre' and 'post'
-        ignore (function): function indicating which files to ignore
+        ignore (typing.Callable): function indicating which files to ignore
         follow_nonexisting (bool): Whether to descend into directories in
             ``src`` that do not exit in ``dest``. Default is True
         follow_links (bool): Whether to descend into symlinks in ``src``
@@ -1101,23 +1102,23 @@ def find(root, files, recursive=True):
 
     Accepts any glob characters accepted by fnmatch:
 
-    =======  ====================================
-    Pattern  Meaning
-    =======  ====================================
-    *        matches everything
-    ?        matches any single character
-    [seq]    matches any character in ``seq``
-    [!seq]   matches any character not in ``seq``
-    =======  ====================================
+    ==========  ====================================
+    Pattern     Meaning
+    ==========  ====================================
+    ``*``       matches everything
+    ``?``       matches any single character
+    ``[seq]``   matches any character in ``seq``
+    ``[!seq]``  matches any character not in ``seq``
+    ==========  ====================================
 
     Parameters:
         root (str): The root directory to start searching from
         files (str or Sequence): Library name(s) to search for
-        recurse (bool, optional): if False search only root folder,
+        recursive (bool): if False search only root folder,
             if True descends top-down from the root. Defaults to True.
 
     Returns:
-        list of strings: The files that have been found
+        list: The files that have been found
     """
     if isinstance(files, six.string_types):
         files = [files]
@@ -1199,7 +1200,7 @@ def directories(self):
         ['/dir1', '/dir2']
 
         Returns:
-            list of strings: A list of directories
+            list: A list of directories
         """
         return list(dedupe(
             os.path.dirname(x) for x in self.files if os.path.dirname(x)
@@ -1217,7 +1218,7 @@ def basenames(self):
         ['a.h', 'b.h']
 
         Returns:
-            list of strings: A list of base-names
+            list: A list of base-names
         """
         return list(dedupe(os.path.basename(x) for x in self.files))
 
@@ -1304,7 +1305,7 @@ def headers(self):
         """Stable de-duplication of the headers.
 
         Returns:
-            list of strings: A list of header files
+            list: A list of header files
         """
         return self.files
 
@@ -1317,7 +1318,7 @@ def names(self):
         ['a', 'b']
 
         Returns:
-            list of strings: A list of files without extensions
+            list: A list of files without extensions
         """
         names = []
 
@@ -1408,9 +1409,9 @@ def find_headers(headers, root, recursive=False):
     =======  ====================================
 
     Parameters:
-        headers (str or list of str): Header name(s) to search for
+        headers (str or list): Header name(s) to search for
         root (str): The root directory to start searching from
-        recursive (bool, optional): if False search only root folder,
+        recursive (bool): if False search only root folder,
             if True descends top-down from the root. Defaults to False.
 
     Returns:
@@ -1446,7 +1447,7 @@ def find_all_headers(root):
     in the directory passed as argument.
 
     Args:
-        root (path): directory where to look recursively for header files
+        root (str): directory where to look recursively for header files
 
     Returns:
         List of all headers found in ``root`` and subdirectories.
@@ -1466,7 +1467,7 @@ def libraries(self):
         """Stable de-duplication of library files.
 
         Returns:
-            list of strings: A list of library files
+            list: A list of library files
         """
         return self.files
 
@@ -1479,7 +1480,7 @@ def names(self):
         ['a', 'b']
 
         Returns:
-            list of strings: A list of library names
+            list: A list of library names
         """
         names = []
 
@@ -1564,8 +1565,8 @@ def find_system_libraries(libraries, shared=True):
     =======  ====================================
 
     Parameters:
-        libraries (str or list of str): Library name(s) to search for
-        shared (bool, optional): if True searches for shared libraries,
+        libraries (str or list): Library name(s) to search for
+        shared (bool): if True searches for shared libraries,
             otherwise for static. Defaults to True.
 
     Returns:
@@ -1615,11 +1616,11 @@ def find_libraries(libraries, root, shared=True, recursive=False):
     =======  ====================================
 
     Parameters:
-        libraries (str or list of str): Library name(s) to search for
+        libraries (str or list): Library name(s) to search for
         root (str): The root directory to start searching from
-        shared (bool, optional): if True searches for shared libraries,
+        shared (bool): if True searches for shared libraries,
             otherwise for static. Defaults to True.
-        recursive (bool, optional): if False search only root folder,
+        recursive (bool): if False search only root folder,
             if True descends top-down from the root. Defaults to False.
 
     Returns:

lib/spack/llnl/util/lang.py

@@ -5,14 +5,15 @@
 
 from __future__ import division
 
+import functools
+import inspect
 import multiprocessing
 import os
 import re
-import functools
-import inspect
-from datetime import datetime, timedelta
-from six import string_types
 import sys
+from datetime import datetime, timedelta
+
+from six import string_types
 
 if sys.version_info < (3, 0):
     from itertools import izip_longest  # novm
@@ -257,6 +258,47 @@ def new_dec(*args, **kwargs):
     return new_dec
 
 
+def key_ordering(cls):
+    """Decorates a class with extra methods that implement rich comparison
+       operations and ``__hash__``.  The decorator assumes that the class
+       implements a function called ``_cmp_key()``.  The rich comparison
+       operations will compare objects using this key, and the ``__hash__``
+       function will return the hash of this key.
+
+       If a class already has ``__eq__``, ``__ne__``, ``__lt__``, ``__le__``,
+       ``__gt__``, or ``__ge__`` defined, this decorator will overwrite them.
+
+       Raises:
+           TypeError: If the class does not have a ``_cmp_key`` method
+    """
+    def setter(name, value):
+        value.__name__ = name
+        setattr(cls, name, value)
+
+    if not has_method(cls, '_cmp_key'):
+        raise TypeError("'%s' doesn't define _cmp_key()." % cls.__name__)
+
+    setter('__eq__',
+           lambda s, o:
+           (s is o) or (o is not None and s._cmp_key() == o._cmp_key()))
+    setter('__lt__',
+           lambda s, o: o is not None and s._cmp_key() < o._cmp_key())
+    setter('__le__',
+           lambda s, o: o is not None and s._cmp_key() <= o._cmp_key())
+
+    setter('__ne__',
+           lambda s, o:
+           (s is not o) and (o is None or s._cmp_key() != o._cmp_key()))
+    setter('__gt__',
+           lambda s, o: o is None or s._cmp_key() > o._cmp_key())
+    setter('__ge__',
+           lambda s, o: o is None or s._cmp_key() >= o._cmp_key())
+
+    setter('__hash__', lambda self: hash(self._cmp_key()))
+
+    return cls
+
+
 #: sentinel for testing that iterators are done in lazy_lexicographic_ordering
 done = object()
 
@@ -572,8 +614,8 @@ def pretty_date(time, now=None):
     """Convert a datetime or timestamp to a pretty, relative date.
 
     Args:
-        time (datetime or int): date to print prettily
-        now (datetime): dateimte for 'now', i.e. the date the pretty date
+        time (datetime.datetime or int): date to print prettily
+        now (datetime.datetime): datetime for 'now', i.e. the date the pretty date
             is relative to (default is datetime.now())
 
     Returns:
@@ -647,7 +689,7 @@ def pretty_string_to_date(date_str, now=None):
             or be a *pretty date* (like ``yesterday`` or ``two months ago``)
 
     Returns:
-        (datetime): datetime object corresponding to ``date_str``
+        (datetime.datetime): datetime object corresponding to ``date_str``
     """
 
     pattern = {}

lib/spack/llnl/util/link_tree.py

@@ -7,12 +7,12 @@
 
 from __future__ import print_function
 
+import filecmp
 import os
 import shutil
-import filecmp
 
-from llnl.util.filesystem import traverse_tree, mkdirp, touch
 import llnl.util.tty as tty
+from llnl.util.filesystem import mkdirp, touch, traverse_tree
 
 __all__ = ['LinkTree']
 

lib/spack/llnl/util/lock.py

@@ -3,20 +3,30 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os
-import fcntl
 import errno
-import time
+import fcntl
+import os
 import socket
+import time
 from datetime import datetime
 
 import llnl.util.tty as tty
+
 import spack.util.string
 
-
-__all__ = ['Lock', 'LockTransaction', 'WriteTransaction', 'ReadTransaction',
-           'LockError', 'LockTimeoutError',
-           'LockPermissionError', 'LockROFileError', 'CantCreateLockError']
+__all__ = [
+    'Lock',
+    'LockDowngradeError',
+    'LockUpgradeError',
+    'LockTransaction',
+    'WriteTransaction',
+    'ReadTransaction',
+    'LockError',
+    'LockTimeoutError',
+    'LockPermissionError',
+    'LockROFileError',
+    'CantCreateLockError'
+]
 
 #: Mapping of supported locks to description
 lock_type = {fcntl.LOCK_SH: 'read', fcntl.LOCK_EX: 'write'}
@@ -401,7 +411,7 @@ def release_read(self, release_fn=None):
         """Releases a read lock.
 
         Arguments:
-            release_fn (callable): function to call *before* the last recursive
+            release_fn (typing.Callable): function to call *before* the last recursive
                 lock (read or write) is released.
 
         If the last recursive lock will be released, then this will call
@@ -437,7 +447,7 @@ def release_write(self, release_fn=None):
         """Releases a write lock.
 
         Arguments:
-            release_fn (callable): function to call before the last recursive
+            release_fn (typing.Callable): function to call before the last recursive
                 write is released.
 
         If the last recursive *write* lock will be released, then this
@@ -533,10 +543,10 @@ class LockTransaction(object):
     Arguments:
         lock (Lock): underlying lock for this transaction to be accquired on
             enter and released on exit
-        acquire (callable or contextmanager): function to be called after lock
-            is acquired, or contextmanager to enter after acquire and leave
+        acquire (typing.Callable or contextlib.contextmanager): function to be called
+            after lock is acquired, or contextmanager to enter after acquire and leave
             before release.
-        release (callable): function to be called before release. If
+        release (typing.Callable): function to be called before release. If
             ``acquire`` is a contextmanager, this will be called *after*
             exiting the nexted context and before the lock is released.
         timeout (float): number of seconds to set for the timeout when

lib/spack/llnl/util/tty/__init__.py

@@ -5,6 +5,7 @@
 
 from __future__ import unicode_literals
 
+import contextlib
 import fcntl
 import os
 import struct
@@ -12,12 +13,13 @@
 import termios
 import textwrap
 import traceback
-import six
 from datetime import datetime
+
+import six
 from six import StringIO
 from six.moves import input
 
-from llnl.util.tty.color import cprint, cwrite, cescape, clen
+from llnl.util.tty.color import cescape, clen, cprint, cwrite
 
 # Globals
 _debug = 0
@@ -27,6 +29,7 @@
 _msg_enabled = True
 _warn_enabled = True
 _error_enabled = True
+_output_filter = lambda s: s
 indent = "  "
 
 
@@ -89,6 +92,18 @@ def error_enabled():
     return _error_enabled
 
 
+@contextlib.contextmanager
+def output_filter(filter_fn):
+    """Context manager that applies a filter to all output."""
+    global _output_filter
+    saved_filter = _output_filter
+    try:
+        _output_filter = filter_fn
+        yield
+    finally:
+        _output_filter = saved_filter
+
+
 class SuppressOutput:
     """Class for disabling output in a scope using 'with' keyword"""
 
@@ -165,13 +180,23 @@ def msg(message, *args, **kwargs):
     if _stacktrace:
         st_text = process_stacktrace(2)
     if newline:
-        cprint("@*b{%s==>} %s%s" % (
-            st_text, get_timestamp(), cescape(message)))
+        cprint(
+            "@*b{%s==>} %s%s" % (
+                st_text,
+                get_timestamp(),
+                cescape(_output_filter(message))
+            )
+        )
     else:
-        cwrite("@*b{%s==>} %s%s" % (
-            st_text, get_timestamp(), cescape(message)))
+        cwrite(
+            "@*b{%s==>} %s%s" % (
+                st_text,
+                get_timestamp(),
+                cescape(_output_filter(message))
+            )
+        )
     for arg in args:
-        print(indent + six.text_type(arg))
+        print(indent + _output_filter(six.text_type(arg)))
 
 
 def info(message, *args, **kwargs):
@@ -187,18 +212,29 @@ def info(message, *args, **kwargs):
     st_text = ""
     if _stacktrace:
         st_text = process_stacktrace(st_countback)
-    cprint("@%s{%s==>} %s%s" % (
-        format, st_text, get_timestamp(), cescape(six.text_type(message))
-    ), stream=stream)
+    cprint(
+        "@%s{%s==>} %s%s" % (
+            format,
+            st_text,
+            get_timestamp(),
+            cescape(_output_filter(six.text_type(message)))
+        ),
+        stream=stream
+    )
     for arg in args:
         if wrap:
             lines = textwrap.wrap(
-                six.text_type(arg), initial_indent=indent,
-                subsequent_indent=indent, break_long_words=break_long_words)
+                _output_filter(six.text_type(arg)),
+                initial_indent=indent,
+                subsequent_indent=indent,
+                break_long_words=break_long_words
+            )
             for line in lines:
                 stream.write(line + '\n')
         else:
-            stream.write(indent + six.text_type(arg) + '\n')
+            stream.write(
+                indent + _output_filter(six.text_type(arg)) + '\n'
+            )
 
 
 def verbose(message, *args, **kwargs):

lib/spack/llnl/util/tty/colify.py

@@ -10,10 +10,11 @@
 
 import os
 import sys
+
 from six import StringIO, text_type
 
 from llnl.util.tty import terminal_size
-from llnl.util.tty.color import clen, cextra
+from llnl.util.tty.color import cextra, clen
 
 
 class ColumnConfig:
@@ -108,19 +109,17 @@ def colify(elts, **options):
     using ``str()``.
 
     Keyword Arguments:
-        output (stream): A file object to write to. Default is ``sys.stdout``
-        indent (int):    Optionally indent all columns by some number of spaces
-        padding (int):   Spaces between columns. Default is 2
-        width (int):     Width of the output. Default is 80 if tty not detected
-        cols (int):      Force number of columns. Default is to size to
-                         terminal, or single-column if no tty
-        tty (bool):      Whether to attempt to write to a tty. Default is to
-                         autodetect a tty. Set to False to force single-column
-                         output
-        method (str):    Method to use to fit columns. Options are variable or
-                         uniform. Variable-width columns are tighter, uniform
-                         columns are all the same width and fit less data on
-                         the screen
+        output (typing.IO): A file object to write to. Default is ``sys.stdout``
+        indent (int): Optionally indent all columns by some number of spaces
+        padding (int): Spaces between columns. Default is 2
+        width (int): Width of the output. Default is 80 if tty not detected
+        cols (int): Force number of columns. Default is to size to terminal, or
+            single-column if no tty
+        tty (bool): Whether to attempt to write to a tty. Default is to autodetect a
+            tty. Set to False to force single-column output
+        method (str): Method to use to fit columns. Options are variable or uniform.
+            Variable-width columns are tighter, uniform columns are all the same width
+            and fit less data on the screen
     """
     # Get keyword arguments or set defaults
     cols         = options.pop("cols", 0)

lib/spack/llnl/util/tty/color.py

@@ -60,9 +60,9 @@
 To output an @, use '@@'.  To output a } inside braces, use '}}'.
 """
 from __future__ import unicode_literals
+
 import re
 import sys
-
 from contextlib import contextmanager
 
 import six

lib/spack/llnl/util/tty/log.py

@@ -13,15 +13,14 @@
 import os
 import re
 import select
+import signal
 import sys
 import traceback
-import signal
 from contextlib import contextmanager
-from six import string_types
-from six import StringIO
-
-from typing import Optional  # novm
 from types import ModuleType  # novm
+from typing import Optional  # novm
+
+from six import StringIO, string_types
 
 import llnl.util.tty as tty
 
@@ -437,7 +436,7 @@ class log_output(object):
     """
 
     def __init__(self, file_like=None, echo=False, debug=0, buffer=False,
-                 env=None):
+                 env=None, filter_fn=None):
         """Create a new output log context manager.
 
         Args:
@@ -447,6 +446,8 @@ def __init__(self, file_like=None, echo=False, debug=0, buffer=False,
             debug (int): positive to enable tty debug mode during logging
             buffer (bool): pass buffer=True to skip unbuffering output; note
                 this doesn't set up any *new* buffering
+            filter_fn (callable, optional): Callable[str] -> str to filter each
+                line of output
 
         log_output can take either a file object or a filename. If a
         filename is passed, the file will be opened and closed entirely
@@ -466,6 +467,7 @@ def __init__(self, file_like=None, echo=False, debug=0, buffer=False,
         self.debug = debug
         self.buffer = buffer
         self.env = env  # the environment to use for _writer_daemon
+        self.filter_fn = filter_fn
 
         self._active = False  # used to prevent re-entry
 
@@ -531,20 +533,22 @@ def __enter__(self):
         # Sets a daemon that writes to file what it reads from a pipe
         try:
             # need to pass this b/c multiprocessing closes stdin in child.
+            input_multiprocess_fd = None
             try:
-                input_multiprocess_fd = MultiProcessFd(
-                    os.dup(sys.stdin.fileno())
-                )
+                if sys.stdin.isatty():
+                    input_multiprocess_fd = MultiProcessFd(
+                        os.dup(sys.stdin.fileno())
+                    )
             except BaseException:
                 # just don't forward input if this fails
-                input_multiprocess_fd = None
+                pass
 
             with replace_environment(self.env):
                 self.process = multiprocessing.Process(
                     target=_writer_daemon,
                     args=(
                         input_multiprocess_fd, read_multiprocess_fd, write_fd,
-                        self.echo, self.log_file, child_pipe
+                        self.echo, self.log_file, child_pipe, self.filter_fn
                     )
                 )
                 self.process.daemon = True  # must set before start()
@@ -668,7 +672,7 @@ def force_echo(self):
 
 
 def _writer_daemon(stdin_multiprocess_fd, read_multiprocess_fd, write_fd, echo,
-                   log_file_wrapper, control_pipe):
+                   log_file_wrapper, control_pipe, filter_fn):
     """Daemon used by ``log_output`` to write to a log file and to ``stdout``.
 
     The daemon receives output from the parent process and writes it both
@@ -713,6 +717,7 @@ def _writer_daemon(stdin_multiprocess_fd, read_multiprocess_fd, write_fd, echo,
         log_file_wrapper (FileWrapper): file to log all output
         control_pipe (Pipe): multiprocessing pipe on which to send control
             information to the parent
+        filter_fn (callable, optional): function to filter each line of output
 
     """
     # If this process was forked, then it will inherit file descriptors from
@@ -785,7 +790,10 @@ def _writer_daemon(stdin_multiprocess_fd, read_multiprocess_fd, write_fd, echo,
 
                             # Echo to stdout if requested or forced.
                             if echo or force_echo:
-                                sys.stdout.write(clean_line)
+                                output_line = clean_line
+                                if filter_fn:
+                                    output_line = filter_fn(clean_line)
+                                sys.stdout.write(output_line)
 
                             # Stripped output to log file.
                             log_file.write(_strip(clean_line))

lib/spack/llnl/util/tty/pty.py

@@ -14,10 +14,10 @@
 """
 from __future__ import print_function
 
-import os
-import signal
 import multiprocessing
+import os
 import re
+import signal
 import sys
 import termios
 import time

lib/spack/spack/__init__.py

@@ -3,9 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-
 #: major, minor, patch version for Spack, in a tuple
-spack_version_info = (0, 16, 1)
+spack_version_info = (0, 16, 2)
 
 #: String containing Spack version joined with .'s
 spack_version = '.'.join(str(v) for v in spack_version_info)

lib/spack/spack/abi.py

@@ -8,9 +8,9 @@
 from llnl.util.lang import memoized
 
 import spack.spec
+from spack.compilers.clang import Clang
 from spack.spec import CompilerSpec
 from spack.util.executable import Executable, ProcessError
-from spack.compilers.clang import Clang
 
 
 class ABI(object):

lib/spack/spack/analyzers/__init__.py

@@ -10,11 +10,10 @@
 
 from __future__ import absolute_import
 
-import spack.util.classes
-import spack.paths
-
 import llnl.util.tty as tty
 
+import spack.paths
+import spack.util.classes
 
 mod_path = spack.paths.analyzers_path
 analyzers = spack.util.classes.list_classes("spack.analyzers", mod_path)

lib/spack/spack/analyzers/analyzer_base.py

@@ -7,14 +7,15 @@
 and (optionally) interact with a Spack Monitor
 """
 
-import spack.monitor
-import spack.hooks
-import llnl.util.tty as tty
-import spack.util.path
-import spack.config
-
 import os
 
+import llnl.util.tty as tty
+
+import spack.config
+import spack.hooks
+import spack.monitor
+import spack.util.path
+
 
 def get_analyzer_dir(spec, analyzer_dir=None):
     """

lib/spack/spack/analyzers/config_args.py

@@ -8,11 +8,12 @@
 directory."""
 
 
-import spack.monitor
-from .analyzer_base import AnalyzerBase
-
 import os
 
+import spack.monitor
+
+from .analyzer_base import AnalyzerBase
+
 
 class ConfigArgs(AnalyzerBase):
 

lib/spack/spack/analyzers/environment_variables.py

@@ -8,11 +8,11 @@
 an index of key, value pairs for environment variables."""
 
 
-from .analyzer_base import AnalyzerBase
+import os
+
 from spack.util.environment import EnvironmentModifications
 
-
-import os
+from .analyzer_base import AnalyzerBase
 
 
 class EnvironmentVariables(AnalyzerBase):

lib/spack/spack/analyzers/install_files.py

@@ -8,11 +8,12 @@
 analyzer folder for further processing."""
 
 
-import spack.monitor
-from .analyzer_base import AnalyzerBase
-
 import os
 
+import spack.monitor
+
+from .analyzer_base import AnalyzerBase
+
 
 class InstallFiles(AnalyzerBase):
 

lib/spack/spack/analyzers/libabigail.py

@@ -4,20 +4,20 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
-import spack
-import spack.error
-import spack.bootstrap
-import spack.hooks
-import spack.monitor
-import spack.binary_distribution
-import spack.package
-import spack.repo
+import os
 
 import llnl.util.tty as tty
 
-from .analyzer_base import AnalyzerBase
+import spack
+import spack.binary_distribution
+import spack.bootstrap
+import spack.error
+import spack.hooks
+import spack.monitor
+import spack.package
+import spack.repo
 
-import os
+from .analyzer_base import AnalyzerBase
 
 
 class Libabigail(AnalyzerBase):

lib/spack/spack/architecture.py

@@ -60,20 +60,21 @@
 import functools
 import warnings
 
-import archspec.cpu
 import six
 
-import llnl.util.tty as tty
+import archspec.cpu
+
 import llnl.util.lang as lang
+import llnl.util.tty as tty
 
 import spack.compiler
 import spack.compilers
 import spack.config
-import spack.paths
 import spack.error as serr
+import spack.paths
+import spack.util.classes
 import spack.util.executable
 import spack.version
-import spack.util.classes
 from spack.util.spack_yaml import syaml_dict
 
 
@@ -192,8 +193,8 @@ def optimization_flags(self, compiler):
         the compiler passed as argument.
 
         Args:
-            compiler (CompilerSpec or Compiler): object that contains both the
-                name and the version of the compiler we want to use
+            compiler (spack.spec.CompilerSpec or spack.compiler.Compiler): object that
+                contains both the name and the version of the compiler we want to use
         """
         # Mixed toolchains are not supported yet
         import spack.compilers
@@ -592,17 +593,20 @@ def use_platform(new_platform):
     assert isinstance(new_platform, Platform), msg.format(new_platform)
 
     original_platform_fn, original_all_platforms_fn = platform, all_platforms
-    platform = _PickleableCallable(new_platform)
-    all_platforms = _PickleableCallable([type(new_platform)])
 
-    # Clear configuration and compiler caches
-    spack.config.config.clear_caches()
-    spack.compilers._cache_config_files = []
+    try:
+        platform = _PickleableCallable(new_platform)
+        all_platforms = _PickleableCallable([type(new_platform)])
 
-    yield new_platform
+        # Clear configuration and compiler caches
+        spack.config.config.clear_caches()
+        spack.compilers._cache_config_files = []
 
-    platform, all_platforms = original_platform_fn, original_all_platforms_fn
+        yield new_platform
 
-    # Clear configuration and compiler caches
-    spack.config.config.clear_caches()
-    spack.compilers._cache_config_files = []
+    finally:
+        platform, all_platforms = original_platform_fn, original_all_platforms_fn
+
+        # Clear configuration and compiler caches
+        spack.config.config.clear_caches()
+        spack.compilers._cache_config_files = []

lib/spack/spack/audit.py

@@ -0,0 +1,395 @@
+# Copyright 2013-2021 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)
+"""Classes and functions to register audit checks for various parts of
+Spack and run them on-demand.
+
+To register a new class of sanity checks (e.g. sanity checks for
+compilers.yaml), the first action required is to create a new AuditClass
+object:
+
+.. code-block:: python
+
+   audit_cfgcmp = AuditClass(
+       tag='CFG-COMPILER',
+       description='Sanity checks on compilers.yaml',
+       kwargs=()
+   )
+
+This object is to be used as a decorator to register functions
+that will perform each a single check:
+
+.. code-block:: python
+
+   @audit_cfgcmp
+   def _search_duplicate_compilers(error_cls):
+       pass
+
+These functions need to take as argument the keywords declared when
+creating the decorator object plus an ``error_cls`` argument at the
+end, acting as a factory to create Error objects. It should return a
+(possibly empty) list of errors.
+
+Calls to each of these functions are triggered by the ``run`` method of
+the decorator object, that will forward the keyword arguments passed
+as input.
+"""
+import collections
+import itertools
+
+try:
+    from collections.abc import Sequence  # novm
+except ImportError:
+    from collections import Sequence
+
+#: Map an audit tag to a list of callables implementing checks
+CALLBACKS = {}
+
+#: Map a group of checks to the list of related audit tags
+GROUPS = collections.defaultdict(list)
+
+
+class Error(object):
+    """Information on an error reported in a test."""
+    def __init__(self, summary, details):
+        self.summary = summary
+        self.details = tuple(details)
+
+    def __str__(self):
+        return self.summary + '\n' + '\n'.join([
+            '    ' + detail for detail in self.details
+        ])
+
+    def __eq__(self, other):
+        if self.summary != other.summary or self.details != other.details:
+            return False
+        return True
+
+    def __hash__(self):
+        value = (self.summary, self.details)
+        return hash(value)
+
+
+class AuditClass(Sequence):
+    def __init__(self, group, tag, description, kwargs):
+        """Return an object that acts as a decorator to register functions
+        associated with a specific class of sanity checks.
+
+        Args:
+            group (str): group in which this check is to be inserted
+            tag (str): tag uniquely identifying the class of sanity checks
+            description (str): description of the sanity checks performed
+                by this tag
+            kwargs (tuple of str): keyword arguments that each registered
+                function needs to accept
+        """
+        if tag in CALLBACKS:
+            msg = 'audit class "{0}" already registered'
+            raise ValueError(msg.format(tag))
+
+        self.group = group
+        self.tag = tag
+        self.description = description
+        self.kwargs = kwargs
+        self.callbacks = []
+
+        # Init the list of hooks
+        CALLBACKS[self.tag] = self
+
+        # Update the list of tags in the group
+        GROUPS[self.group].append(self.tag)
+
+    def __call__(self, func):
+        self.callbacks.append(func)
+
+    def __getitem__(self, item):
+        return self.callbacks[item]
+
+    def __len__(self):
+        return len(self.callbacks)
+
+    def run(self, **kwargs):
+        msg = 'please pass "{0}" as keyword arguments'
+        msg = msg.format(', '.join(self.kwargs))
+        assert set(self.kwargs) == set(kwargs), msg
+
+        errors = []
+        kwargs['error_cls'] = Error
+        for fn in self.callbacks:
+            errors.extend(fn(**kwargs))
+
+        return errors
+
+
+def run_group(group, **kwargs):
+    """Run the checks that are part of the group passed as argument.
+
+    Args:
+        group (str): group of checks to be run
+        **kwargs: keyword arguments forwarded to the checks
+
+    Returns:
+        List of (tag, errors) that failed.
+    """
+    reports = []
+    for check in GROUPS[group]:
+        errors = run_check(check, **kwargs)
+        reports.append((check, errors))
+    return reports
+
+
+def run_check(tag, **kwargs):
+    """Run the checks associated with a single tag.
+
+    Args:
+        tag (str): tag of the check
+        **kwargs: keyword arguments forwarded to the checks
+
+    Returns:
+        Errors occurred during the checks
+    """
+    return CALLBACKS[tag].run(**kwargs)
+
+
+# TODO: For the generic check to be useful for end users,
+# TODO: we need to implement hooks like described in
+# TODO: https://github.com/spack/spack/pull/23053/files#r630265011
+#: Generic checks relying on global state
+generic = AuditClass(
+    group='generic',
+    tag='GENERIC',
+    description='Generic checks relying on global variables',
+    kwargs=()
+)
+
+
+#: Sanity checks on compilers.yaml
+config_compiler = AuditClass(
+    group='configs',
+    tag='CFG-COMPILER',
+    description='Sanity checks on compilers.yaml',
+    kwargs=()
+)
+
+
+@config_compiler
+def _search_duplicate_compilers(error_cls):
+    """Report compilers with the same spec and two different definitions"""
+    import spack.config
+    errors = []
+
+    compilers = list(sorted(
+        spack.config.get('compilers'), key=lambda x: x['compiler']['spec']
+    ))
+    for spec, group in itertools.groupby(
+            compilers, key=lambda x: x['compiler']['spec']
+    ):
+        group = list(group)
+        if len(group) == 1:
+            continue
+
+        error_msg = 'Compiler defined multiple times: {0}'
+        try:
+            details = [str(x._start_mark).strip() for x in group]
+        except Exception:
+            details = []
+        errors.append(error_cls(
+            summary=error_msg.format(spec), details=details
+        ))
+
+    return errors
+
+
+#: Sanity checks on packages.yaml
+config_packages = AuditClass(
+    group='configs',
+    tag='CFG-PACKAGES',
+    description='Sanity checks on packages.yaml',
+    kwargs=()
+)
+
+
+@config_packages
+def _search_duplicate_specs_in_externals(error_cls):
+    """Search for duplicate specs declared as externals"""
+    import spack.config
+
+    errors, externals = [], collections.defaultdict(list)
+    packages_yaml = spack.config.get('packages')
+
+    for name, pkg_config in packages_yaml.items():
+        # No externals can be declared under all
+        if name == 'all' or 'externals' not in pkg_config:
+            continue
+
+        current_externals = pkg_config['externals']
+        for entry in current_externals:
+            # Ask for the string representation of the spec to normalize
+            # aspects of the spec that may be represented in multiple ways
+            # e.g. +foo or foo=true
+            key = str(spack.spec.Spec(entry['spec']))
+            externals[key].append(entry)
+
+    for spec, entries in sorted(externals.items()):
+        # If there's a single external for a spec we are fine
+        if len(entries) < 2:
+            continue
+
+        # Otherwise wwe need to report an error
+        error_msg = 'Multiple externals share the same spec: {0}'.format(spec)
+        try:
+            lines = [str(x._start_mark).strip() for x in entries]
+            details = [
+                'Please remove all but one of the following entries:'
+            ] + lines + [
+                'as they might result in non-deterministic hashes'
+            ]
+        except TypeError:
+            details = []
+
+        errors.append(error_cls(summary=error_msg, details=details))
+
+    return errors
+
+
+#: Sanity checks on package directives
+package_directives = AuditClass(
+    group='packages',
+    tag='PKG-DIRECTIVES',
+    description='Sanity checks on specs used in directives',
+    kwargs=('pkgs',)
+)
+
+
+@package_directives
+def _unknown_variants_in_directives(pkgs, error_cls):
+    """Report unknown or wrong variants in directives for this package"""
+    import llnl.util.lang
+
+    import spack.repo
+    import spack.spec
+
+    errors = []
+    for pkg_name in pkgs:
+        pkg = spack.repo.get(pkg_name)
+
+        # Check "conflicts" directive
+        for conflict, triggers in pkg.conflicts.items():
+            for trigger, _ in triggers:
+                vrn = spack.spec.Spec(conflict)
+                try:
+                    vrn.constrain(trigger)
+                except Exception as e:
+                    msg = 'Generic error in conflict for package "{0}": '
+                    errors.append(error_cls(msg.format(pkg.name), [str(e)]))
+                    continue
+                errors.extend(_analyze_variants_in_directive(
+                    pkg, vrn, directive='conflicts', error_cls=error_cls
+                ))
+
+        # Check "depends_on" directive
+        for _, triggers in pkg.dependencies.items():
+            triggers = list(triggers)
+            for trigger in list(triggers):
+                vrn = spack.spec.Spec(trigger)
+                errors.extend(_analyze_variants_in_directive(
+                    pkg, vrn, directive='depends_on', error_cls=error_cls
+                ))
+
+        # Check "patch" directive
+        for _, triggers in pkg.provided.items():
+            triggers = [spack.spec.Spec(x) for x in triggers]
+            for vrn in triggers:
+                errors.extend(_analyze_variants_in_directive(
+                    pkg, vrn, directive='patch', error_cls=error_cls
+                ))
+
+        # Check "resource" directive
+        for vrn in pkg.resources:
+            errors.extend(_analyze_variants_in_directive(
+                pkg, vrn, directive='resource', error_cls=error_cls
+            ))
+
+    return llnl.util.lang.dedupe(errors)
+
+
+@package_directives
+def _unknown_variants_in_dependencies(pkgs, error_cls):
+    """Report unknown dependencies and wrong variants for dependencies"""
+    import spack.repo
+    import spack.spec
+
+    errors = []
+    for pkg_name in pkgs:
+        pkg = spack.repo.get(pkg_name)
+        filename = spack.repo.path.filename_for_package_name(pkg_name)
+        for dependency_name, dependency_data in pkg.dependencies.items():
+            # No need to analyze virtual packages
+            if spack.repo.path.is_virtual(dependency_name):
+                continue
+
+            try:
+                dependency_pkg = spack.repo.get(dependency_name)
+            except spack.repo.UnknownPackageError:
+                # This dependency is completely missing, so report
+                # and continue the analysis
+                summary = (pkg_name + ": unknown package '{0}' in "
+                           "'depends_on' directive".format(dependency_name))
+                details = [
+                    " in " + filename
+                ]
+                errors.append(error_cls(summary=summary, details=details))
+                continue
+
+            for _, dependency_edge in dependency_data.items():
+                dependency_variants = dependency_edge.spec.variants
+                for name, value in dependency_variants.items():
+                    try:
+                        dependency_pkg.variants[name].validate_or_raise(
+                            value, pkg=dependency_pkg
+                        )
+                    except Exception as e:
+                        summary = (pkg_name + ": wrong variant used for a "
+                                   "dependency in a 'depends_on' directive")
+                        error_msg = str(e).strip()
+                        if isinstance(e, KeyError):
+                            error_msg = ('the variant {0} does not '
+                                         'exist'.format(error_msg))
+                        error_msg += " in package '" + dependency_name + "'"
+
+                        errors.append(error_cls(
+                            summary=summary, details=[error_msg, 'in ' + filename]
+                        ))
+
+    return errors
+
+
+def _analyze_variants_in_directive(pkg, constraint, directive, error_cls):
+    import spack.variant
+    variant_exceptions = (
+        spack.variant.InconsistentValidationError,
+        spack.variant.MultipleValuesInExclusiveVariantError,
+        spack.variant.InvalidVariantValueError,
+        KeyError
+    )
+    errors = []
+    for name, v in constraint.variants.items():
+        try:
+            pkg.variants[name].validate_or_raise(v, pkg=pkg)
+        except variant_exceptions as e:
+            summary = pkg.name + ': wrong variant in "{0}" directive'
+            summary = summary.format(directive)
+            filename = spack.repo.path.filename_for_package_name(pkg.name)
+
+            error_msg = str(e).strip()
+            if isinstance(e, KeyError):
+                error_msg = 'the variant {0} does not exist'.format(error_msg)
+
+            err = error_cls(summary=summary, details=[
+                error_msg, 'in ' + filename
+            ])
+
+            errors.append(err)
+
+    return errors

lib/spack/spack/binary_distribution.py

@@ -4,22 +4,21 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import codecs
+import glob
+import hashlib
+import json
 import os
 import re
+import shutil
 import sys
 import tarfile
-import shutil
 import tempfile
-import hashlib
-import glob
-from ordereddict_backport import OrderedDict
-
+import traceback
 from contextlib import closing
+
 import ruamel.yaml as yaml
-
-import json
-
-from six.moves.urllib.error import URLError, HTTPError
+from ordereddict_backport import OrderedDict
+from six.moves.urllib.error import HTTPError, URLError
 
 import llnl.util.lang
 import llnl.util.tty as tty
@@ -29,19 +28,20 @@
 import spack.config as config
 import spack.database as spack_db
 import spack.fetch_strategy as fs
-import spack.util.file_cache as file_cache
+import spack.hash_types as ht
+import spack.hooks.sbang
+import spack.mirror
 import spack.relocate as relocate
+import spack.util.file_cache as file_cache
 import spack.util.gpg
 import spack.util.spack_json as sjson
 import spack.util.spack_yaml as syaml
-import spack.mirror
 import spack.util.url as url_util
 import spack.util.web as web_util
 from spack.caches import misc_cache_location
 from spack.spec import Spec
 from spack.stage import Stage
 
-
 _build_cache_relative_path = 'build_cache'
 _build_cache_keys_relative_path = '_pgp'
 
@@ -207,7 +207,7 @@ def find_built_spec(self, spec):
         The cache can be updated by calling ``update()`` on the cache.
 
         Args:
-            spec (Spec): Concrete spec to find
+            spec (spack.spec.Spec): Concrete spec to find
 
         Returns:
             An list of objects containing the found specs and mirror url where
@@ -584,7 +584,7 @@ def get_buildfile_manifest(spec):
                     added = True
 
             if relocate.needs_binary_relocation(m_type, m_subtype):
-                if ((m_subtype in ('x-executable', 'x-sharedlib')
+                if ((m_subtype in ('x-executable', 'x-sharedlib', 'x-pie-executable')
                     and sys.platform != 'darwin') or
                    (m_subtype in ('x-mach-binary')
                     and sys.platform == 'darwin') or
@@ -616,9 +616,8 @@ def write_buildinfo_file(spec, workdir, rel=False):
         prefix_to_hash[str(d.prefix)] = d.dag_hash()
 
     # Create buildinfo data and write it to disk
-    import spack.hooks.sbang as sbang
     buildinfo = {}
-    buildinfo['sbang_install_path'] = sbang.sbang_install_path()
+    buildinfo['sbang_install_path'] = spack.hooks.sbang.sbang_install_path()
     buildinfo['relative_rpaths'] = rel
     buildinfo['buildpath'] = spack.store.layout.root
     buildinfo['spackprefix'] = spack.paths.prefix
@@ -712,12 +711,6 @@ def generate_package_index(cache_prefix):
     cache_prefix.  This page contains a link for each binary package (.yaml)
     under cache_prefix.
     """
-    tmpdir = tempfile.mkdtemp()
-    db_root_dir = os.path.join(tmpdir, 'db_root')
-    db = spack_db.Database(None, db_dir=db_root_dir,
-                           enable_transaction_locking=False,
-                           record_fields=['spec', 'ref_count', 'in_buildcache'])
-
     try:
         file_list = (
             entry
@@ -738,22 +731,90 @@ def generate_package_index(cache_prefix):
 
     tty.debug('Retrieving spec.yaml files from {0} to build index'.format(
         cache_prefix))
+
+    all_mirror_specs = {}
+
     for file_path in file_list:
         try:
             yaml_url = url_util.join(cache_prefix, file_path)
             tty.debug('fetching {0}'.format(yaml_url))
             _, _, yaml_file = web_util.read_from_url(yaml_url)
             yaml_contents = codecs.getreader('utf-8')(yaml_file).read()
-            # yaml_obj = syaml.load(yaml_contents)
-            # s = Spec.from_yaml(yaml_obj)
+            spec_dict = syaml.load(yaml_contents)
             s = Spec.from_yaml(yaml_contents)
-            db.add(s, None)
-            db.mark(s, 'in_buildcache', True)
+            all_mirror_specs[s.dag_hash()] = {
+                'yaml_url': yaml_url,
+                'spec': s,
+                'num_deps': len(list(s.traverse(root=False))),
+                'binary_cache_checksum': spec_dict['binary_cache_checksum'],
+                'buildinfo': spec_dict['buildinfo'],
+            }
         except (URLError, web_util.SpackWebError) as url_err:
             tty.error('Error reading spec.yaml: {0}'.format(file_path))
             tty.error(url_err)
 
+    sorted_specs = sorted(all_mirror_specs.keys(),
+                          key=lambda k: all_mirror_specs[k]['num_deps'])
+
+    tmpdir = tempfile.mkdtemp()
+    db_root_dir = os.path.join(tmpdir, 'db_root')
+    db = spack_db.Database(None, db_dir=db_root_dir,
+                           enable_transaction_locking=False,
+                           record_fields=['spec', 'ref_count', 'in_buildcache'])
+
     try:
+        tty.debug('Specs sorted by number of dependencies:')
+        for dag_hash in sorted_specs:
+            spec_record = all_mirror_specs[dag_hash]
+            s = spec_record['spec']
+            num_deps = spec_record['num_deps']
+            tty.debug('  {0}/{1} -> {2}'.format(
+                s.name, dag_hash[:7], num_deps))
+            if num_deps > 0:
+                # Check each of this spec's dependencies (which we have already
+                # processed), as they are the source of truth for their own
+                # full hash.  If the full hash we have for any deps does not
+                # match what those deps have themselves, then we need to splice
+                # this spec with those deps, and push this spliced spec
+                # (spec.yaml file) back to the mirror, as well as update the
+                # all_mirror_specs dictionary with this spliced spec.
+                to_splice = []
+                for dep in s.dependencies():
+                    dep_dag_hash = dep.dag_hash()
+                    if dep_dag_hash in all_mirror_specs:
+                        true_dep = all_mirror_specs[dep_dag_hash]['spec']
+                        if true_dep.full_hash() != dep.full_hash():
+                            to_splice.append(true_dep)
+
+                if to_splice:
+                    tty.debug('    needs the following deps spliced:')
+                    for true_dep in to_splice:
+                        tty.debug('      {0}/{1}'.format(
+                            true_dep.name, true_dep.dag_hash()[:7]))
+                        s = s.splice(true_dep, True)
+
+                    # Push this spliced spec back to the mirror
+                    spliced_yaml = s.to_dict(hash=ht.full_hash)
+                    for key in ['binary_cache_checksum', 'buildinfo']:
+                        spliced_yaml[key] = spec_record[key]
+
+                    temp_yaml_path = os.path.join(tmpdir, 'spliced.spec.yaml')
+                    with open(temp_yaml_path, 'w') as fd:
+                        fd.write(syaml.dump(spliced_yaml))
+
+                    spliced_yaml_url = spec_record['yaml_url']
+                    web_util.push_to_url(
+                        temp_yaml_path, spliced_yaml_url, keep_original=False)
+                    tty.debug('    spliced and wrote {0}'.format(
+                        spliced_yaml_url))
+                    spec_record['spec'] = s
+
+            db.add(s, None)
+            db.mark(s, 'in_buildcache', True)
+
+        # Now that we have fixed any old spec yamls that might have had the wrong
+        # full hash for their dependencies, we can generate the index, compute
+        # the hash, and push those files to the mirror.
         index_json_path = os.path.join(db_root_dir, 'index.json')
         with open(index_json_path, 'w') as f:
             db._write_to_file(f)
@@ -785,6 +846,7 @@ def generate_package_index(cache_prefix):
         msg = 'Encountered problem pushing package index to {0}: {1}'.format(
             cache_prefix, err)
         tty.warn(msg)
+        tty.debug('\n' + traceback.format_exc())
     finally:
         shutil.rmtree(tmpdir)
 
@@ -1017,14 +1079,14 @@ def download_tarball(spec, preferred_mirrors=None):
     path to downloaded tarball if successful, None otherwise.
 
     Args:
-        spec (Spec): Concrete spec
+        spec (spack.spec.Spec): Concrete spec
         preferred_mirrors (list): If provided, this is a list of preferred
-        mirror urls.  Other configured mirrors will only be used if the
-        tarball can't be retrieved from one of these.
+            mirror urls.  Other configured mirrors will only be used if the
+            tarball can't be retrieved from one of these.
 
     Returns:
         Path to the downloaded tarball, or ``None`` if the tarball could not
-            be downloaded from any configured mirrors.
+        be downloaded from any configured mirrors.
     """
     if not spack.mirror.MirrorCollection():
         tty.die("Please add a spack mirror to allow " +
@@ -1107,8 +1169,6 @@ def relocate_package(spec, allow_root):
     """
     Relocate the given package
     """
-    import spack.hooks.sbang as sbang
-
     workdir = str(spec.prefix)
     buildinfo = read_buildinfo_file(workdir)
     new_layout_root = str(spack.store.layout.root)
@@ -1147,7 +1207,8 @@ def relocate_package(spec, allow_root):
     prefix_to_prefix_bin = OrderedDict({})
 
     if old_sbang_install_path:
-        prefix_to_prefix_text[old_sbang_install_path] = sbang.sbang_install_path()
+        install_path = spack.hooks.sbang.sbang_install_path()
+        prefix_to_prefix_text[old_sbang_install_path] = install_path
 
     prefix_to_prefix_text[old_prefix] = new_prefix
     prefix_to_prefix_bin[old_prefix] = new_prefix
@@ -1161,7 +1222,7 @@ def relocate_package(spec, allow_root):
     # now a POSIX script that lives in the install prefix. Old packages
     # will have the old sbang location in their shebangs.
     orig_sbang = '#!/bin/bash {0}/bin/sbang'.format(old_spack_prefix)
-    new_sbang = sbang.sbang_shebang_line()
+    new_sbang = spack.hooks.sbang.sbang_shebang_line()
     prefix_to_prefix_text[orig_sbang] = new_sbang
 
     tty.debug("Relocating package from",
@@ -1393,7 +1454,7 @@ def get_mirrors_for_spec(spec=None, full_hash_match=False,
     indicating the mirrors on which it can be found
 
     Args:
-        spec (Spec): The spec to look for in binary mirrors
+        spec (spack.spec.Spec): The spec to look for in binary mirrors
         full_hash_match (bool): If True, only includes mirrors where the spec
             full hash matches the locally computed full hash of the ``spec``
             argument.  If False, any mirror which has a matching DAG hash
@@ -1670,11 +1731,11 @@ def check_specs_against_mirrors(mirrors, specs, output_file=None,
 
     Arguments:
         mirrors (dict): Mirrors to check against
-        specs (iterable): Specs to check against mirrors
-        output_file (string): Path to output file to be written.  If provided,
+        specs (typing.Iterable): Specs to check against mirrors
+        output_file (str): Path to output file to be written.  If provided,
             mirrors with missing or out-of-date specs will be formatted as a
             JSON object and written to this file.
-        rebuild_on_errors (boolean): Treat any errors encountered while
+        rebuild_on_errors (bool): Treat any errors encountered while
             checking specs as a signal to rebuild package.
 
     Returns: 1 if any spec was out-of-date on any mirror, 0 otherwise.

lib/spack/spack/bootstrap.py

@@ -3,8 +3,10 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import contextlib
+import json
 import os
 import sys
+
 try:
     import sysconfig  # novm
 except ImportError:
@@ -17,15 +19,226 @@
 import llnl.util.tty as tty
 
 import spack.architecture
+import spack.binary_distribution
 import spack.config
+import spack.main
 import spack.paths
 import spack.repo
 import spack.spec
 import spack.store
 import spack.user_environment as uenv
 import spack.util.executable
+import spack.util.path
 from spack.util.environment import EnvironmentModifications
 
+#: Map a bootstrapper type to the corresponding class
+_bootstrap_methods = {}
+
+
+def _bootstrapper(type):
+    """Decorator to register classes implementing bootstrapping
+    methods.
+
+    Args:
+        type (str): string identifying the class
+    """
+    def _register(cls):
+        _bootstrap_methods[type] = cls
+        return cls
+    return _register
+
+
+def _try_import_from_store(module, abstract_spec_str):
+    """Return True if the module can be imported from an already
+    installed spec, False otherwise.
+
+    Args:
+        module: Python module to be imported
+        abstract_spec_str: abstract spec that may provide the module
+    """
+    bincache_platform = spack.architecture.real_platform()
+    if str(bincache_platform) == 'cray':
+        bincache_platform = spack.platforms.linux.Linux()
+        with spack.architecture.use_platform(bincache_platform):
+            abstract_spec_str = str(spack.spec.Spec(abstract_spec_str))
+
+    # We have to run as part of this python interpreter
+    abstract_spec_str += ' ^' + spec_for_current_python()
+
+    installed_specs = spack.store.db.query(abstract_spec_str, installed=True)
+
+    for candidate_spec in installed_specs:
+        lib_spd = candidate_spec['python'].package.default_site_packages_dir
+        lib64_spd = lib_spd.replace('lib/', 'lib64/')
+        module_paths = [
+            os.path.join(candidate_spec.prefix, lib_spd),
+            os.path.join(candidate_spec.prefix, lib64_spd)
+        ]
+        sys.path.extend(module_paths)
+
+        try:
+            if _python_import(module):
+                msg = ('[BOOTSTRAP MODULE {0}] The installed spec "{1}/{2}" '
+                       'provides the "{0}" Python module').format(
+                    module, abstract_spec_str, candidate_spec.dag_hash()
+                )
+                tty.debug(msg)
+                return True
+        except Exception as e:
+            msg = ('unexpected error while trying to import module '
+                   '"{0}" from spec "{1}" [error="{2}"]')
+            tty.warn(msg.format(module, candidate_spec, str(e)))
+        else:
+            msg = "Spec {0} did not provide module {1}"
+            tty.warn(msg.format(candidate_spec, module))
+
+        sys.path = sys.path[:-2]
+
+    return False
+
+
+@_bootstrapper(type='buildcache')
+class _BuildcacheBootstrapper(object):
+    """Install the software needed during bootstrapping from a buildcache."""
+    def __init__(self, conf):
+        self.name = conf['name']
+        self.url = conf['info']['url']
+
+    def try_import(self, module, abstract_spec_str):
+        # This import is local since it is needed only on Cray
+        import spack.platforms.linux
+
+        if _try_import_from_store(module, abstract_spec_str):
+            return True
+
+        # Try to install from an unsigned binary cache
+        abstract_spec = spack.spec.Spec(
+            abstract_spec_str + ' ^' + spec_for_current_python()
+        )
+
+        # On Cray we want to use Linux binaries if available from mirrors
+        bincache_platform = spack.architecture.real_platform()
+        if str(bincache_platform) == 'cray':
+            bincache_platform = spack.platforms.linux.Linux()
+            with spack.architecture.use_platform(bincache_platform):
+                abstract_spec = spack.spec.Spec(
+                    abstract_spec_str + ' ^' + spec_for_current_python()
+                )
+
+        # Read information on verified clingo binaries
+        json_filename = '{0}.json'.format(module)
+        json_path = os.path.join(
+            spack.paths.share_path, 'bootstrap', self.name, json_filename
+        )
+        with open(json_path) as f:
+            data = json.load(f)
+
+        buildcache = spack.main.SpackCommand('buildcache')
+        # Ensure we see only the buildcache being used to bootstrap
+        mirror_scope = spack.config.InternalConfigScope(
+            'bootstrap', {'mirrors:': {self.name: self.url}}
+        )
+        with spack.config.override(mirror_scope):
+            # This index is currently needed to get the compiler used to build some
+            # specs that wwe know by dag hash.
+            spack.binary_distribution.binary_index.regenerate_spec_cache()
+            index = spack.binary_distribution.update_cache_and_get_specs()
+            for item in data['verified']:
+                candidate_spec = item['spec']
+                python_spec = item['python']
+                # Skip specs which are not compatible
+                if not abstract_spec.satisfies(candidate_spec):
+                    continue
+
+                if python_spec not in abstract_spec:
+                    continue
+
+                for pkg_name, pkg_hash, pkg_sha256 in item['binaries']:
+                    msg = ('[BOOTSTRAP MODULE {0}] Try installing "{1}" from binary '
+                           'cache at "{2}"')
+                    tty.debug(msg.format(module, pkg_name, self.url))
+                    index_spec = next(x for x in index if x.dag_hash() == pkg_hash)
+                    # Reconstruct the compiler that we need to use for bootstrapping
+                    compiler_entry = {
+                        "modules": [],
+                        "operating_system": str(index_spec.os),
+                        "paths": {
+                            "cc": "/dev/null",
+                            "cxx": "/dev/null",
+                            "f77": "/dev/null",
+                            "fc": "/dev/null"
+                        },
+                        "spec": str(index_spec.compiler),
+                        "target": str(index_spec.target.family)
+                    }
+                    with spack.architecture.use_platform(bincache_platform):
+                        with spack.config.override(
+                                'compilers', [{'compiler': compiler_entry}]
+                        ):
+                            spec_str = '/' + pkg_hash
+                            install_args = [
+                                'install',
+                                '--sha256', pkg_sha256,
+                                '-a', '-u', '-o', '-f', spec_str
+                            ]
+                            buildcache(*install_args, fail_on_error=False)
+                # TODO: undo installations that didn't complete?
+
+                if _try_import_from_store(module, abstract_spec_str):
+                    return True
+        return False
+
+
+@_bootstrapper(type='install')
+class _SourceBootstrapper(object):
+    """Install the software needed during bootstrapping from sources."""
+    def __init__(self, conf):
+        self.conf = conf
+
+    @staticmethod
+    def try_import(module, abstract_spec_str):
+        if _try_import_from_store(module, abstract_spec_str):
+            return True
+
+        # Try to build and install from sources
+        with spack_python_interpreter():
+            # Add hint to use frontend operating system on Cray
+            if str(spack.architecture.platform()) == 'cray':
+                abstract_spec_str += ' os=fe'
+
+            concrete_spec = spack.spec.Spec(
+                abstract_spec_str + ' ^' + spec_for_current_python()
+            )
+
+            if module == 'clingo':
+                # TODO: remove when the old concretizer is deprecated
+                concrete_spec._old_concretize()
+            else:
+                concrete_spec.concretize()
+
+        msg = "[BOOTSTRAP MODULE {0}] Try installing '{1}' from sources"
+        tty.debug(msg.format(module, abstract_spec_str))
+
+        # Install the spec that should make the module importable
+        concrete_spec.package.do_install()
+
+        return _try_import_from_store(module, abstract_spec_str=abstract_spec_str)
+
+
+def _make_bootstrapper(conf):
+    """Return a bootstrap object built according to the
+    configuration argument
+    """
+    btype = conf['type']
+    return _bootstrap_methods[btype](conf)
+
+
+def _source_is_trusted(conf):
+    trusted, name = spack.config.get('bootstrap:trusted'), conf['name']
+    if name not in trusted:
+        return False
+    return trusted[name]
+
 
 def spec_for_current_python():
     """For bootstrapping purposes we are just interested in the Python
@@ -66,69 +279,58 @@ def spack_python_interpreter():
         yield
 
 
-def make_module_available(module, spec=None, install=False):
-    """Ensure module is importable"""
-    # If we already can import it, that's great
-    try:
-        __import__(module)
+def ensure_module_importable_or_raise(module, abstract_spec=None):
+    """Make the requested module available for import, or raise.
+
+    This function tries to import a Python module in the current interpreter
+    using, in order, the methods configured in bootstrap.yaml.
+
+    If none of the methods succeed, an exception is raised. The function exits
+    on first success.
+
+    Args:
+        module (str): module to be imported in the current interpreter
+        abstract_spec (str): abstract spec that might provide the module. If not
+            given it defaults to "module"
+
+    Raises:
+        ImportError: if the module couldn't be imported
+    """
+    # If we can import it already, that's great
+    tty.debug("[BOOTSTRAP MODULE {0}] Try importing from Python".format(module))
+    if _python_import(module):
         return
-    except ImportError:
-        pass
 
-    # If it's already installed, use it
-    # Search by spec
-    spec = spack.spec.Spec(spec or module)
+    abstract_spec = abstract_spec or module
+    source_configs = spack.config.get('bootstrap:sources', [])
+    for current_config in source_configs:
+        if not _source_is_trusted(current_config):
+            msg = ('[BOOTSTRAP MODULE {0}] Skipping source "{1}" since it is '
+                   'not trusted').format(module, current_config['name'])
+            tty.debug(msg)
+            continue
 
-    # We have to run as part of this python
-    # We can constrain by a shortened version in place of a version range
-    # because this spec is only used for querying or as a placeholder to be
-    # replaced by an external that already has a concrete version. This syntax
-    # is not sufficient when concretizing without an external, as it will
-    # concretize to python@X.Y instead of python@X.Y.Z
-    python_requirement = '^' + spec_for_current_python()
-    spec.constrain(python_requirement)
-    installed_specs = spack.store.db.query(spec, installed=True)
-
-    for ispec in installed_specs:
-        # TODO: make sure run-environment is appropriate
-        module_path = os.path.join(ispec.prefix,
-                                   ispec['python'].package.site_packages_dir)
-        module_path_64 = module_path.replace('/lib/', '/lib64/')
+        b = _make_bootstrapper(current_config)
         try:
-            sys.path.append(module_path)
-            sys.path.append(module_path_64)
-            __import__(module)
-            return
-        except ImportError:
-            tty.warn("Spec %s did not provide module %s" % (ispec, module))
-            sys.path = sys.path[:-2]
+            if b.try_import(module, abstract_spec):
+                return
+        except Exception as e:
+            msg = '[BOOTSTRAP MODULE {0}] Unexpected error "{1}"'
+            tty.debug(msg.format(module, str(e)))
 
-    def _raise_error(module_name, module_spec):
-        error_msg = 'cannot import module "{0}"'.format(module_name)
-        if module_spec:
-            error_msg += ' from spec "{0}'.format(module_spec)
-        raise ImportError(error_msg)
+    # We couldn't import in any way, so raise an import error
+    msg = 'cannot bootstrap the "{0}" Python module'.format(module)
+    if abstract_spec:
+        msg += ' from spec "{0}"'.format(abstract_spec)
+    raise ImportError(msg)
 
-    if not install:
-        _raise_error(module, spec)
 
-    with spack_python_interpreter():
-        # We will install for ourselves, using this python if needed
-        # Concretize the spec
-        spec.concretize()
-    spec.package.do_install()
-
-    module_path = os.path.join(spec.prefix,
-                               spec['python'].package.site_packages_dir)
-    module_path_64 = module_path.replace('/lib/', '/lib64/')
+def _python_import(module):
     try:
-        sys.path.append(module_path)
-        sys.path.append(module_path_64)
         __import__(module)
-        return
     except ImportError:
-        sys.path = sys.path[:-2]
-        _raise_error(module, spec)
+        return False
+    return True
 
 
 def get_executable(exe, spec=None, install=False):
@@ -136,13 +338,14 @@ def get_executable(exe, spec=None, install=False):
 
     Args:
         exe (str): needed executable name
-        spec (Spec or str): spec to search for exe in (default exe)
+        spec (spack.spec.Spec or str): spec to search for exe in (default exe)
         install (bool): install spec if not available
 
     When ``install`` is True, Spack will use the python used to run Spack as an
     external. The ``install`` option should only be used with packages that
     install quickly (when using external python) or are guaranteed by Spack
-    organization to be in a binary mirror (clingo)."""
+    organization to be in a binary mirror (clingo).
+    """
     # Search the system first
     runner = spack.util.executable.which(exe)
     if runner:
@@ -215,9 +418,10 @@ def _bootstrap_config_scopes():
 
 @contextlib.contextmanager
 def ensure_bootstrap_configuration():
+    bootstrap_store_path = store_path()
     with spack.architecture.use_platform(spack.architecture.real_platform()):
         with spack.repo.use_repositories(spack.paths.packages_path):
-            with spack.store.use_store(spack.paths.user_bootstrap_store):
+            with spack.store.use_store(bootstrap_store_path):
                 # Default configuration scopes excluding command line
                 # and builtin but accounting for platform specific scopes
                 config_scopes = _bootstrap_config_scopes()
@@ -226,6 +430,23 @@ def ensure_bootstrap_configuration():
                         yield
 
 
+def store_path():
+    """Path to the store used for bootstrapped software"""
+    enabled = spack.config.get('bootstrap:enable', True)
+    if not enabled:
+        msg = ('bootstrapping is currently disabled. '
+               'Use "spack bootstrap enable" to enable it')
+        raise RuntimeError(msg)
+
+    bootstrap_root_path = spack.config.get(
+        'bootstrap:root', spack.paths.user_bootstrap_path
+    )
+    bootstrap_store_path = spack.util.path.canonicalize_path(
+        os.path.join(bootstrap_root_path, 'store')
+    )
+    return bootstrap_store_path
+
+
 def clingo_root_spec():
     # Construct the root spec that will be used to bootstrap clingo
     spec_str = 'clingo-bootstrap@spack+python'
@@ -237,14 +458,17 @@ def clingo_root_spec():
     else:
         spec_str += ' %gcc'
 
-    # Add hint to use frontend operating system on Cray
-    if str(spack.architecture.platform()) == 'cray':
-        spec_str += ' os=fe'
-
     # Add the generic target
     generic_target = archspec.cpu.host().family
     spec_str += ' target={0}'.format(str(generic_target))
 
     tty.debug('[BOOTSTRAP ROOT SPEC] clingo: {0}'.format(spec_str))
 
-    return spack.spec.Spec(spec_str)
+    return spec_str
+
+
+def ensure_clingo_importable_or_raise():
+    """Ensure that the clingo module is available for import."""
+    ensure_module_importable_or_raise(
+        module='clingo', abstract_spec=clingo_root_spec()
+    )

lib/spack/spack/build_environment.py

@@ -33,44 +33,52 @@
 calls you can make from within the install() function.
 """
 import inspect
-import re
 import multiprocessing
 import os
+import re
 import shutil
 import sys
 import traceback
 import types
+
 from six import StringIO
 
 import llnl.util.tty as tty
-from llnl.util.tty.color import cescape, colorize
-from llnl.util.filesystem import mkdirp, install, install_tree
+from llnl.util.filesystem import install, install_tree, mkdirp
 from llnl.util.lang import dedupe
+from llnl.util.tty.color import cescape, colorize
 from llnl.util.tty.log import MultiProcessFd
 
+import spack.architecture as arch
 import spack.build_systems.cmake
 import spack.build_systems.meson
 import spack.config
+import spack.install_test
 import spack.main
-import spack.paths
 import spack.package
+import spack.paths
 import spack.repo
 import spack.schema.environment
 import spack.store
-import spack.install_test
 import spack.subprocess_context
-import spack.architecture as arch
 import spack.util.path
-from spack.util.string import plural
-from spack.util.environment import (
-    env_flag, filter_system_paths, get_path, is_system_path,
-    EnvironmentModifications, validate, preserve_environment)
-from spack.util.environment import system_dirs
-from spack.error import NoLibrariesError, NoHeadersError
-from spack.util.executable import Executable
-from spack.util.module_cmd import load_module, path_from_modules, module
-from spack.util.log_parse import parse_log_events, make_log_context
+from spack.error import NoHeadersError, NoLibrariesError
 from spack.util.cpus import cpus_available
+from spack.util.environment import (
+    EnvironmentModifications,
+    env_flag,
+    filter_system_paths,
+    get_path,
+    is_system_path,
+    preserve_environment,
+    system_dirs,
+    validate,
+)
+from spack.util.executable import Executable
+from spack.util.log_parse import make_log_context, parse_log_events
+from spack.util.module_cmd import load_module, module, path_from_modules
+from spack.util.string import plural
+
 #
 # This can be set by the user to globally disable parallel builds.
 #
@@ -78,7 +86,7 @@
 
 #
 # These environment variables are set by
-# set_build_environment_variables and used to pass parameters to
+# set_wrapper_variables and used to pass parameters to
 # Spack's compiler wrappers.
 #
 SPACK_ENV_PATH = 'SPACK_ENV_PATH'
@@ -159,6 +167,12 @@ def clean_environment():
     env.unset('CPLUS_INCLUDE_PATH')
     env.unset('OBJC_INCLUDE_PATH')
 
+    env.unset('CMAKE_PREFIX_PATH')
+
+    # Avoid that libraries of build dependencies get hijacked.
+    env.unset('LD_PRELOAD')
+    env.unset('DYLD_INSERT_LIBRARIES')
+
     # On Cray "cluster" systems, unset CRAY_LD_LIBRARY_PATH to avoid
     # interference with Spack dependencies.
     # CNL requires these variables to be set (or at least some of them,
@@ -306,111 +320,20 @@ def set_compiler_environment_variables(pkg, env):
     return env
 
 
-def _place_externals_last(spec_container):
+def set_wrapper_variables(pkg, env):
+    """Set environment variables used by the Spack compiler wrapper
+       (which have the prefix `SPACK_`) and also add the compiler wrappers
+       to PATH.
+
+       This determines the injected -L/-I/-rpath options; each
+       of these specifies a search order and this function computes these
+       options in a manner that is intended to match the DAG traversal order
+       in `modifications_from_dependencies`: that method uses a post-order
+       traversal so that `PrependPath` actions from dependencies take lower
+       precedence; we use a post-order traversal here to match the visitation
+       order of `modifications_from_dependencies` (so we are visiting the
+       lowest priority packages first).
     """
-    For a (possibly unordered) container of specs, return an ordered list
-    where all external specs are at the end of the list. External packages
-    may be installed in merged prefixes with other packages, and so
-    they should be deprioritized for any search order (i.e. in PATH, or
-    for a set of -L entries in a compiler invocation).
-    """
-    # Establish an arbitrary but fixed ordering of specs so that resulting
-    # environment variable values are stable
-    spec_container = sorted(spec_container, key=lambda x: x.name)
-    first = list(x for x in spec_container if not x.external)
-    second = list(x for x in spec_container if x.external)
-    return first + second
-
-
-def set_build_environment_variables(pkg, env, dirty):
-    """Ensure a clean install environment when we build packages.
-
-    This involves unsetting pesky environment variables that may
-    affect the build. It also involves setting environment variables
-    used by Spack's compiler wrappers.
-
-    Args:
-        pkg: The package we are building
-        env: The build environment
-        dirty (bool): Skip unsetting the user's environment settings
-    """
-    # Gather information about various types of dependencies
-    build_deps      = set(pkg.spec.dependencies(deptype=('build', 'test')))
-    link_deps       = set(pkg.spec.traverse(root=False, deptype=('link')))
-    build_link_deps = build_deps | link_deps
-    rpath_deps      = get_rpath_deps(pkg)
-    # This includes all build dependencies and any other dependencies that
-    # should be added to PATH (e.g. supporting executables run by build
-    # dependencies)
-    build_and_supporting_deps = set()
-    for build_dep in build_deps:
-        build_and_supporting_deps.update(build_dep.traverse(deptype='run'))
-
-    # External packages may be installed in a prefix which contains many other
-    # package installs. To avoid having those installations override
-    # Spack-installed packages, they are placed at the end of search paths.
-    # System prefixes are removed entirely later on since they are already
-    # searched.
-    build_deps = _place_externals_last(build_deps)
-    link_deps = _place_externals_last(link_deps)
-    build_link_deps = _place_externals_last(build_link_deps)
-    rpath_deps = _place_externals_last(rpath_deps)
-    build_and_supporting_deps = _place_externals_last(
-        build_and_supporting_deps)
-
-    link_dirs = []
-    include_dirs = []
-    rpath_dirs = []
-
-    # The top-level package is always RPATHed. It hasn't been installed yet
-    # so the RPATHs are added unconditionally (e.g. even though lib64/ may
-    # not be created for the install).
-    for libdir in ['lib', 'lib64']:
-        lib_path = os.path.join(pkg.prefix, libdir)
-        rpath_dirs.append(lib_path)
-
-    # Set up link, include, RPATH directories that are passed to the
-    # compiler wrapper
-    for dep in link_deps:
-        if is_system_path(dep.prefix):
-            continue
-        query = pkg.spec[dep.name]
-        dep_link_dirs = list()
-        try:
-            dep_link_dirs.extend(query.libs.directories)
-        except NoLibrariesError:
-            tty.debug("No libraries found for {0}".format(dep.name))
-
-        for default_lib_dir in ['lib', 'lib64']:
-            default_lib_prefix = os.path.join(dep.prefix, default_lib_dir)
-            if os.path.isdir(default_lib_prefix):
-                dep_link_dirs.append(default_lib_prefix)
-
-        link_dirs.extend(dep_link_dirs)
-        if dep in rpath_deps:
-            rpath_dirs.extend(dep_link_dirs)
-
-        try:
-            include_dirs.extend(query.headers.directories)
-        except NoHeadersError:
-            tty.debug("No headers found for {0}".format(dep.name))
-
-    link_dirs = list(dedupe(filter_system_paths(link_dirs)))
-    include_dirs = list(dedupe(filter_system_paths(include_dirs)))
-    rpath_dirs = list(dedupe(filter_system_paths(rpath_dirs)))
-
-    env.set(SPACK_LINK_DIRS, ':'.join(link_dirs))
-    env.set(SPACK_INCLUDE_DIRS, ':'.join(include_dirs))
-    env.set(SPACK_RPATH_DIRS, ':'.join(rpath_dirs))
-
-    build_and_supporting_prefixes = filter_system_paths(
-        x.prefix for x in build_and_supporting_deps)
-    build_link_prefixes = filter_system_paths(
-        x.prefix for x in build_link_deps)
-
-    # Add dependencies to CMAKE_PREFIX_PATH
-    env.set_path('CMAKE_PREFIX_PATH', get_cmake_prefix_path(pkg))
-
     # Set environment variables if specified for
     # the given compiler
     compiler = pkg.compiler
@@ -420,16 +343,6 @@ def set_build_environment_variables(pkg, env, dirty):
         extra_rpaths = ':'.join(compiler.extra_rpaths)
         env.set('SPACK_COMPILER_EXTRA_RPATHS', extra_rpaths)
 
-    # Add bin directories from dependencies to the PATH for the build.
-    # These directories are added to the beginning of the search path, and in
-    # the order given by 'build_and_supporting_prefixes' (the iteration order
-    # is reversed because each entry is prepended)
-    for prefix in reversed(build_and_supporting_prefixes):
-        for dirname in ['bin', 'bin64']:
-            bin_dir = os.path.join(prefix, dirname)
-            if os.path.isdir(bin_dir):
-                env.prepend_path('PATH', bin_dir)
-
     # Add spack build environment path with compiler wrappers first in
     # the path. We add the compiler wrapper path, which includes default
     # wrappers (cc, c++, f77, f90), AND a subdirectory containing
@@ -449,6 +362,7 @@ def set_build_environment_variables(pkg, env, dirty):
         if os.path.isdir(ci):
             env_paths.append(ci)
 
+    tty.debug("Adding compiler bin/ paths: " + " ".join(env_paths))
     for item in env_paths:
         env.prepend_path('PATH', item)
     env.set_path(SPACK_ENV_PATH, env_paths)
@@ -467,14 +381,69 @@ def set_build_environment_variables(pkg, env, dirty):
             raise RuntimeError("No ccache binary found in PATH")
         env.set(SPACK_CCACHE_BINARY, ccache)
 
-    # Add any pkgconfig directories to PKG_CONFIG_PATH
-    for prefix in reversed(build_link_prefixes):
-        for directory in ('lib', 'lib64', 'share'):
-            pcdir = os.path.join(prefix, directory, 'pkgconfig')
-            if os.path.isdir(pcdir):
-                env.prepend_path('PKG_CONFIG_PATH', pcdir)
+    # Gather information about various types of dependencies
+    link_deps  = set(pkg.spec.traverse(root=False, deptype=('link')))
+    rpath_deps = get_rpath_deps(pkg)
 
-    return env
+    link_dirs = []
+    include_dirs = []
+    rpath_dirs = []
+
+    def _prepend_all(list_to_modify, items_to_add):
+        # Update the original list (creating a new list would be faster but
+        # may not be convenient)
+        for item in reversed(list(items_to_add)):
+            list_to_modify.insert(0, item)
+
+    def update_compiler_args_for_dep(dep):
+        if dep in link_deps and (not is_system_path(dep.prefix)):
+            query = pkg.spec[dep.name]
+            dep_link_dirs = list()
+            try:
+                dep_link_dirs.extend(query.libs.directories)
+            except NoLibrariesError:
+                tty.debug("No libraries found for {0}".format(dep.name))
+
+            for default_lib_dir in ['lib', 'lib64']:
+                default_lib_prefix = os.path.join(
+                    dep.prefix, default_lib_dir)
+                if os.path.isdir(default_lib_prefix):
+                    dep_link_dirs.append(default_lib_prefix)
+
+            _prepend_all(link_dirs, dep_link_dirs)
+            if dep in rpath_deps:
+                _prepend_all(rpath_dirs, dep_link_dirs)
+
+            try:
+                _prepend_all(include_dirs, query.headers.directories)
+            except NoHeadersError:
+                tty.debug("No headers found for {0}".format(dep.name))
+
+    for dspec in pkg.spec.traverse(root=False, order='post'):
+        if dspec.external:
+            update_compiler_args_for_dep(dspec)
+
+    # Just above, we prepended entries for -L/-rpath for externals. We
+    # now do this for non-external packages so that Spack-built packages
+    # are searched first for libraries etc.
+    for dspec in pkg.spec.traverse(root=False, order='post'):
+        if not dspec.external:
+            update_compiler_args_for_dep(dspec)
+
+    # The top-level package is always RPATHed. It hasn't been installed yet
+    # so the RPATHs are added unconditionally (e.g. even though lib64/ may
+    # not be created for the install).
+    for libdir in ['lib64', 'lib']:
+        lib_path = os.path.join(pkg.prefix, libdir)
+        rpath_dirs.insert(0, lib_path)
+
+    link_dirs = list(dedupe(filter_system_paths(link_dirs)))
+    include_dirs = list(dedupe(filter_system_paths(include_dirs)))
+    rpath_dirs = list(dedupe(filter_system_paths(rpath_dirs)))
+
+    env.set(SPACK_LINK_DIRS, ':'.join(link_dirs))
+    env.set(SPACK_INCLUDE_DIRS, ':'.join(include_dirs))
+    env.set(SPACK_RPATH_DIRS, ':'.join(rpath_dirs))
 
 
 def determine_number_of_jobs(
@@ -486,11 +455,11 @@ def determine_number_of_jobs(
     cap to the number of CPUs available to avoid oversubscription.
 
     Parameters:
-        parallel (bool): true when package supports parallel builds
-        command_line (int/None): command line override
-        config_default (int/None): config default number of jobs
-        max_cpus (int/None): maximum number of CPUs available. When None, this
-                             value is automatically determined.
+        parallel (bool or None): true when package supports parallel builds
+        command_line (int or None): command line override
+        config_default (int or None): config default number of jobs
+        max_cpus (int or None): maximum number of CPUs available. When None, this
+            value is automatically determined.
     """
     if not parallel:
         return 1
@@ -712,27 +681,18 @@ def get_rpaths(pkg):
     return list(dedupe(filter_system_paths(rpaths)))
 
 
-def get_cmake_prefix_path(pkg):
-    build_deps      = set(pkg.spec.dependencies(deptype=('build', 'test')))
-    link_deps       = set(pkg.spec.traverse(root=False, deptype=('link')))
-    build_link_deps = build_deps | link_deps
-    build_link_deps = _place_externals_last(build_link_deps)
-    build_link_prefixes = filter_system_paths(x.prefix for x in build_link_deps)
-    return build_link_prefixes
-
-
 def get_std_cmake_args(pkg):
     """List of standard arguments used if a package is a CMakePackage.
 
     Returns:
-        list of str: standard arguments that would be used if this
+        list: standard arguments that would be used if this
         package were a CMakePackage instance.
 
     Args:
-        pkg (PackageBase): package under consideration
+        pkg (spack.package.PackageBase): package under consideration
 
     Returns:
-        list of str: arguments for cmake
+        list: arguments for cmake
     """
     return spack.build_systems.cmake.CMakePackage._std_args(pkg)
 
@@ -741,14 +701,14 @@ def get_std_meson_args(pkg):
     """List of standard arguments used if a package is a MesonPackage.
 
     Returns:
-        list of str: standard arguments that would be used if this
+        list: standard arguments that would be used if this
         package were a MesonPackage instance.
 
     Args:
-        pkg (PackageBase): package under consideration
+        pkg (spack.package.PackageBase): package under consideration
 
     Returns:
-        list of str: arguments for meson
+        list: arguments for meson
     """
     return spack.build_systems.meson.MesonPackage._std_args(pkg)
 
@@ -778,7 +738,7 @@ def load_external_modules(pkg):
     associated with them.
 
     Args:
-        pkg (PackageBase): package to load deps for
+        pkg (spack.package.PackageBase): package to load deps for
     """
     for dep in list(pkg.spec.traverse()):
         external_modules = dep.external_modules or []
@@ -788,42 +748,40 @@ def load_external_modules(pkg):
 
 def setup_package(pkg, dirty, context='build'):
     """Execute all environment setup routines."""
+    if context not in ['build', 'test']:
+        raise ValueError(
+            "'context' must be one of ['build', 'test'] - got: {0}"
+            .format(context))
+
+    set_module_variables_for_package(pkg)
+
     env = EnvironmentModifications()
 
     if not dirty:
         clean_environment()
 
-    # setup compilers and build tools for build contexts
+    # setup compilers for build contexts
     need_compiler = context == 'build' or (context == 'test' and
                                            pkg.test_requires_compiler)
     if need_compiler:
         set_compiler_environment_variables(pkg, env)
-        set_build_environment_variables(pkg, env, dirty)
+        set_wrapper_variables(pkg, env)
+
+    env.extend(modifications_from_dependencies(
+        pkg.spec, context, custom_mods_only=False))
 
     # architecture specific setup
     pkg.architecture.platform.setup_platform_environment(pkg, env)
 
     if context == 'build':
-        # recursive post-order dependency information
-        env.extend(
-            modifications_from_dependencies(pkg.spec, context=context)
-        )
+        pkg.setup_build_environment(env)
 
         if (not dirty) and (not env.is_unset('CPATH')):
             tty.debug("A dependency has updated CPATH, this may lead pkg-"
                       "config to assume that the package is part of the system"
                       " includes and omit it when invoked with '--cflags'.")
-
-        # setup package itself
-        set_module_variables_for_package(pkg)
-        pkg.setup_build_environment(env)
     elif context == 'test':
-        import spack.user_environment as uenv  # avoid circular import
-        env.extend(uenv.environment_modifications_for_spec(pkg.spec))
-        env.extend(
-            modifications_from_dependencies(pkg.spec, context=context)
-        )
-        set_module_variables_for_package(pkg)
+        pkg.setup_run_environment(env)
         env.prepend_path('PATH', '.')
 
     # Loading modules, in particular if they are meant to be used outside
@@ -865,39 +823,173 @@ def setup_package(pkg, dirty, context='build'):
     env.apply_modifications()
 
 
-def modifications_from_dependencies(spec, context):
+def _make_runnable(pkg, env):
+    # Helper method which prepends a Package's bin/ prefix to the PATH
+    # environment variable
+    prefix = pkg.prefix
+
+    for dirname in ['bin', 'bin64']:
+        bin_dir = os.path.join(prefix, dirname)
+        if os.path.isdir(bin_dir):
+            env.prepend_path('PATH', bin_dir)
+
+
+def modifications_from_dependencies(spec, context, custom_mods_only=True):
     """Returns the environment modifications that are required by
     the dependencies of a spec and also applies modifications
     to this spec's package at module scope, if need be.
 
+    Environment modifications include:
+
+    - Updating PATH so that executables can be found
+    - Updating CMAKE_PREFIX_PATH and PKG_CONFIG_PATH so that their respective
+      tools can find Spack-built dependencies
+    - Running custom package environment modifications
+
+    Custom package modifications can conflict with the default PATH changes
+    we make (specifically for the PATH, CMAKE_PREFIX_PATH, and PKG_CONFIG_PATH
+    environment variables), so this applies changes in a fixed order:
+
+    - All modifications (custom and default) from external deps first
+    - All modifications from non-external deps afterwards
+
+    With that order, `PrependPath` actions from non-external default
+    environment modifications will take precedence over custom modifications
+    from external packages.
+
+    A secondary constraint is that custom and default modifications are
+    grouped on a per-package basis: combined with the post-order traversal this
+    means that default modifications of dependents can override custom
+    modifications of dependencies (again, this would only occur for PATH,
+    CMAKE_PREFIX_PATH, or PKG_CONFIG_PATH).
+
     Args:
-        spec (Spec): spec for which we want the modifications
+        spec (spack.spec.Spec): spec for which we want the modifications
         context (str): either 'build' for build-time modifications or 'run'
             for run-time modifications
     """
+    if context not in ['build', 'run', 'test']:
+        raise ValueError(
+            "Expecting context to be one of ['build', 'run', 'test'], "
+            "got: {0}".format(context))
+
     env = EnvironmentModifications()
-    pkg = spec.package
 
-    # Maps the context to deptype and method to be called
-    deptype_and_method = {
-        'build': (('build', 'link', 'test'),
-                  'setup_dependent_build_environment'),
-        'run': (('link', 'run'), 'setup_dependent_run_environment'),
-        'test': (('link', 'run', 'test'), 'setup_dependent_run_environment')
-    }
-    deptype, method = deptype_and_method[context]
+    # Note: see computation of 'custom_mod_deps' and 'exe_deps' later in this
+    # function; these sets form the building blocks of those collections.
+    build_deps      = set(spec.dependencies(deptype=('build', 'test')))
+    link_deps       = set(spec.traverse(root=False, deptype='link'))
+    build_link_deps = build_deps | link_deps
+    build_and_supporting_deps = set()
+    for build_dep in build_deps:
+        build_and_supporting_deps.update(build_dep.traverse(deptype='run'))
+    run_and_supporting_deps = set(
+        spec.traverse(root=False, deptype=('run', 'link')))
+    test_and_supporting_deps = set()
+    for test_dep in set(spec.dependencies(deptype='test')):
+        test_and_supporting_deps.update(test_dep.traverse(deptype='run'))
 
-    root = context == 'test'
-    for dspec in spec.traverse(order='post', root=root, deptype=deptype):
-        dpkg = dspec.package
-        set_module_variables_for_package(dpkg)
-        # Allow dependencies to modify the module
-        dpkg.setup_dependent_package(pkg.module, spec)
-        getattr(dpkg, method)(env, spec)
+    # All dependencies that might have environment modifications to apply
+    custom_mod_deps = set()
+    if context == 'build':
+        custom_mod_deps.update(build_and_supporting_deps)
+        # Tests may be performed after build
+        custom_mod_deps.update(test_and_supporting_deps)
+    else:
+        # test/run context
+        custom_mod_deps.update(run_and_supporting_deps)
+        if context == 'test':
+            custom_mod_deps.update(test_and_supporting_deps)
+    custom_mod_deps.update(link_deps)
+
+    # Determine 'exe_deps': the set of packages with binaries we want to use
+    if context == 'build':
+        exe_deps = build_and_supporting_deps | test_and_supporting_deps
+    elif context == 'run':
+        exe_deps = set(spec.traverse(deptype='run'))
+    elif context == 'test':
+        exe_deps = test_and_supporting_deps
+
+    def default_modifications_for_dep(dep):
+        if (dep in build_link_deps and
+                not is_system_path(dep.prefix) and
+                context == 'build'):
+            prefix = dep.prefix
+
+            env.prepend_path('CMAKE_PREFIX_PATH', prefix)
+
+            for directory in ('lib', 'lib64', 'share'):
+                pcdir = os.path.join(prefix, directory, 'pkgconfig')
+                if os.path.isdir(pcdir):
+                    env.prepend_path('PKG_CONFIG_PATH', pcdir)
+
+        if dep in exe_deps and not is_system_path(dep.prefix):
+            _make_runnable(dep, env)
+
+    def add_modifications_for_dep(dep):
+        # Some callers of this function only want the custom modifications.
+        # For callers that want both custom and default modifications, we want
+        # to perform the default modifications here (this groups custom
+        # and default modifications together on a per-package basis).
+        if not custom_mods_only:
+            default_modifications_for_dep(dep)
+
+        # Perform custom modifications here (PrependPath actions performed in
+        # the custom method override the default environment modifications
+        # we do to help the build, namely for PATH, CMAKE_PREFIX_PATH, and
+        # PKG_CONFIG_PATH)
+        if dep in custom_mod_deps:
+            dpkg = dep.package
+            set_module_variables_for_package(dpkg)
+            # Allow dependencies to modify the module
+            dpkg.setup_dependent_package(spec.package.module, spec)
+            if context == 'build':
+                dpkg.setup_dependent_build_environment(env, spec)
+            else:
+                dpkg.setup_dependent_run_environment(env, spec)
+
+    # Note that we want to perform environment modifications in a fixed order.
+    # The Spec.traverse method provides this: i.e. in addition to
+    # the post-order semantics, it also guarantees a fixed traversal order
+    # among dependencies which are not constrained by post-order semantics.
+    for dspec in spec.traverse(root=False, order='post'):
+        if dspec.external:
+            add_modifications_for_dep(dspec)
+
+    for dspec in spec.traverse(root=False, order='post'):
+        # Default env modifications for non-external packages can override
+        # custom modifications of external packages (this can only occur
+        # for modifications to PATH, CMAKE_PREFIX_PATH, and PKG_CONFIG_PATH)
+        if not dspec.external:
+            add_modifications_for_dep(dspec)
 
     return env
 
 
+def get_cmake_prefix_path(pkg):
+    # Note that unlike modifications_from_dependencies, this does not include
+    # any edits to CMAKE_PREFIX_PATH defined in custom
+    # setup_dependent_build_environment implementations of dependency packages
+    build_deps      = set(pkg.spec.dependencies(deptype=('build', 'test')))
+    link_deps       = set(pkg.spec.traverse(root=False, deptype=('link')))
+    build_link_deps = build_deps | link_deps
+    spack_built = []
+    externals = []
+    # modifications_from_dependencies updates CMAKE_PREFIX_PATH by first
+    # prepending all externals and then all non-externals
+    for dspec in pkg.spec.traverse(root=False, order='post'):
+        if dspec in build_link_deps:
+            if dspec.external:
+                externals.insert(0, dspec)
+            else:
+                spack_built.insert(0, dspec)
+
+    ordered_build_link_deps = spack_built + externals
+    build_link_prefixes = filter_system_paths(
+        x.prefix for x in ordered_build_link_deps)
+    return build_link_prefixes
+
+
 def _setup_pkg_and_run(serialized_pkg, function, kwargs, child_pipe,
                        input_multiprocess_fd):
 
@@ -970,9 +1062,9 @@ def start_build_process(pkg, function, kwargs):
 
     Args:
 
-        pkg (PackageBase): package whose environment we should set up the
+        pkg (spack.package.PackageBase): package whose environment we should set up the
             child process for.
-        function (callable): argless function to run in the child
+        function (typing.Callable): argless function to run in the child
             process.
 
     Usage::
@@ -1057,7 +1149,7 @@ def get_package_context(traceback, context=3):
     """Return some context for an error message when the build fails.
 
     Args:
-        traceback (traceback): A traceback from some exception raised during
+        traceback: A traceback from some exception raised during
             install
 
         context (int): Lines of context to show before and after the line

lib/spack/spack/build_systems/aspell_dict.py

@@ -6,6 +6,7 @@
 # Why doesn't this work for me?
 # from spack import *
 from llnl.util.filesystem import filter_file
+
 from spack.build_systems.autotools import AutotoolsPackage
 from spack.directives import extends
 from spack.package import ExtensionError

lib/spack/spack/build_systems/autotools.py

@@ -7,13 +7,13 @@
 import os
 import os.path
 import stat
-from subprocess import PIPE
-from subprocess import check_call
+from subprocess import PIPE, check_call
 from typing import List  # novm
 
-import llnl.util.tty as tty
 import llnl.util.filesystem as fs
-from llnl.util.filesystem import working_dir, force_remove
+import llnl.util.tty as tty
+from llnl.util.filesystem import force_remove, working_dir
+
 from spack.package import PackageBase, run_after, run_before
 from spack.util.executable import Executable
 
@@ -30,7 +30,7 @@ class AutotoolsPackage(PackageBase):
 
     They all have sensible defaults and for many packages the only thing
     necessary will be to override the helper method
-    :py:meth:`~.AutotoolsPackage.configure_args`.
+    :meth:`~spack.build_systems.autotools.AutotoolsPackage.configure_args`.
     For a finer tuning you may also override:
 
         +-----------------------------------------------+--------------------+
@@ -331,7 +331,7 @@ def flags_to_build_system_args(self, flags):
 
     def configure(self, spec, prefix):
         """Runs configure with the arguments specified in
-        :py:meth:`~.AutotoolsPackage.configure_args`
+        :meth:`~spack.build_systems.autotools.AutotoolsPackage.configure_args`
         and an appropriately set prefix.
         """
         options = getattr(self, 'configure_flag_args', [])
@@ -345,8 +345,11 @@ def build(self, spec, prefix):
         """Makes the build targets specified by
         :py:attr:``~.AutotoolsPackage.build_targets``
         """
+        # See https://autotools.io/automake/silent.html
+        params = ['V=1']
+        params += self.build_targets
         with working_dir(self.build_directory):
-            inspect.getmodule(self).make(*self.build_targets)
+            inspect.getmodule(self).make(*params)
 
     def install(self, spec, prefix):
         """Makes the install targets specified by
@@ -373,8 +376,8 @@ def _activate_or_not(
             activation_value=None
     ):
         """This function contains the current implementation details of
-        :py:meth:`~.AutotoolsPackage.with_or_without` and
-        :py:meth:`~.AutotoolsPackage.enable_or_disable`.
+        :meth:`~spack.build_systems.autotools.AutotoolsPackage.with_or_without` and
+        :meth:`~spack.build_systems.autotools.AutotoolsPackage.enable_or_disable`.
 
         Args:
             name (str): name of the variant that is being processed
@@ -382,7 +385,7 @@ def _activate_or_not(
                 case of ``with_or_without``)
             deactivation_word (str): the default deactivation word ('without'
                 in the case of ``with_or_without``)
-            activation_value (callable): callable that accepts a single
+            activation_value (typing.Callable): callable that accepts a single
                 value. This value is either one of the allowed values for a
                 multi-valued variant or the name of a bool-valued variant.
                 Returns the parameter to be used when the value is activated.
@@ -417,7 +420,7 @@ def _activate_or_not(
             for ``<spec-name> foo=x +bar``
 
         Returns:
-            list of strings that corresponds to the activation/deactivation
+            list: list of strings that corresponds to the activation/deactivation
             of the variant that has been processed
 
         Raises:
@@ -498,7 +501,7 @@ def with_or_without(self, name, activation_value=None):
 
         Args:
             name (str): name of a valid multi-valued variant
-            activation_value (callable): callable that accepts a single
+            activation_value (typing.Callable): callable that accepts a single
                 value and returns the parameter to be used leading to an entry
                 of the type ``--with-{name}={parameter}``.
 
@@ -511,12 +514,13 @@ def with_or_without(self, name, activation_value=None):
         return self._activate_or_not(name, 'with', 'without', activation_value)
 
     def enable_or_disable(self, name, activation_value=None):
-        """Same as :py:meth:`~.AutotoolsPackage.with_or_without` but substitute
-        ``with`` with ``enable`` and ``without`` with ``disable``.
+        """Same as
+        :meth:`~spack.build_systems.autotools.AutotoolsPackage.with_or_without`
+        but substitute ``with`` with ``enable`` and ``without`` with ``disable``.
 
         Args:
             name (str): name of a valid multi-valued variant
-            activation_value (callable): if present accepts a single value
+            activation_value (typing.Callable): if present accepts a single value
                 and returns the parameter to be used leading to an entry of the
                 type ``--enable-{name}={parameter}``
 

lib/spack/spack/build_systems/cached_cmake.py

@@ -4,8 +4,8 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
 
-from llnl.util.filesystem import install, mkdirp
 import llnl.util.tty as tty
+from llnl.util.filesystem import install, mkdirp
 
 from spack.build_systems.cmake import CMakePackage
 from spack.package import run_after
@@ -108,21 +108,6 @@ def initconfig_compiler_entries(self):
         if fflags:
             entries.append(cmake_cache_string("CMAKE_Fortran_FLAGS", fflags))
 
-        # Override XL compiler family
-        familymsg = ("Override to proper compiler family for XL")
-        if "xlf" in (self.compiler.fc or ''):  # noqa: F821
-            entries.append(cmake_cache_string(
-                "CMAKE_Fortran_COMPILER_ID", "XL",
-                familymsg))
-        if "xlc" in self.compiler.cc:  # noqa: F821
-            entries.append(cmake_cache_string(
-                "CMAKE_C_COMPILER_ID", "XL",
-                familymsg))
-        if "xlC" in self.compiler.cxx:  # noqa: F821
-            entries.append(cmake_cache_string(
-                "CMAKE_CXX_COMPILER_ID", "XL",
-                familymsg))
-
         return entries
 
     def initconfig_mpi_entries(self):

lib/spack/spack/build_systems/cmake.py

@@ -10,10 +10,11 @@
 import re
 from typing import List  # novm
 
-import spack.build_environment
 from llnl.util.filesystem import working_dir
-from spack.directives import depends_on, variant, conflicts
-from spack.package import PackageBase, InstallError, run_after
+
+import spack.build_environment
+from spack.directives import conflicts, depends_on, variant
+from spack.package import InstallError, PackageBase, run_after
 
 # Regex to extract the primary generator from the CMake generator
 # string.
@@ -235,7 +236,7 @@ def define_from_variant(self, cmake_var, variant=None):
         of ``cmake_var``.
 
         This utility function is similar to
-        :py:meth:`~.AutotoolsPackage.with_or_without`.
+        :meth:`~spack.build_systems.autotools.AutotoolsPackage.with_or_without`.
 
         Examples:
 
@@ -253,9 +254,9 @@ def define_from_variant(self, cmake_var, variant=None):
 
             .. code-block:: python
 
-                [define_from_variant('BUILD_SHARED_LIBS', 'shared'),
-                 define_from_variant('CMAKE_CXX_STANDARD', 'cxxstd'),
-                 define_from_variant('SWR')]
+                [self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
+                 self.define_from_variant('CMAKE_CXX_STANDARD', 'cxxstd'),
+                 self.define_from_variant('SWR')]
 
             will generate the following configuration options:
 

lib/spack/spack/build_systems/cuda.py

@@ -3,10 +3,9 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack.package import PackageBase
-from spack.directives import depends_on, variant, conflicts
-
 import spack.variant
+from spack.directives import conflicts, depends_on, variant
+from spack.package import PackageBase
 
 
 class CudaPackage(PackageBase):
@@ -79,47 +78,46 @@ def cuda_flags(arch_list):
     depends_on('cuda@11.0:',    when='cuda_arch=80')
     depends_on('cuda@11.1:',    when='cuda_arch=86')
 
-    # There are at least three cases to be aware of for compiler conflicts
-    # 1. Linux x86_64
-    # 2. Linux ppc64le
-    # 3. Mac OS X
-    # CUDA-compiler conflicts are version-to-version specific and are
-    # difficult to express with the current Spack conflict syntax
+    # From the NVIDIA install guide we know of conflicts for particular
+    # platforms (linux, darwin), architectures (x86, powerpc) and compilers
+    # (gcc, clang). We don't restrict %gcc and %clang conflicts to
+    # platform=linux, since they should also apply to platform=cray, and may
+    # apply to platform=darwin. We currently do not provide conflicts for
+    # platform=darwin with %apple-clang.
 
     # Linux x86_64 compiler conflicts from here:
     # https://gist.github.com/ax3l/9489132
-    arch_platform = ' target=x86_64: platform=linux'
-    conflicts('%gcc@5:', when='+cuda ^cuda@:7.5' + arch_platform)
-    conflicts('%gcc@6:', when='+cuda ^cuda@:8' + arch_platform)
-    conflicts('%gcc@7:', when='+cuda ^cuda@:9.1' + arch_platform)
-    conflicts('%gcc@8:', when='+cuda ^cuda@:10.0.130' + arch_platform)
-    conflicts('%gcc@9:', when='+cuda ^cuda@:10.2.89' + arch_platform)
-    conflicts('%gcc@:4', when='+cuda ^cuda@11.0.2:' + arch_platform)
-    conflicts('%gcc@10:', when='+cuda ^cuda@:11.0.2' + arch_platform)
-    conflicts('%gcc@11:', when='+cuda ^cuda@:11.1.0' + arch_platform)
-    conflicts('%pgi@:14.8', when='+cuda ^cuda@:7.0.27' + arch_platform)
-    conflicts('%pgi@:15.3,15.5:', when='+cuda ^cuda@7.5' + arch_platform)
-    conflicts('%pgi@:16.2,16.0:16.3', when='+cuda ^cuda@8' + arch_platform)
-    conflicts('%pgi@:15,18:', when='+cuda ^cuda@9.0:9.1' + arch_platform)
-    conflicts('%pgi@:16,19:', when='+cuda ^cuda@9.2.88:10' + arch_platform)
+    conflicts('%gcc@5:', when='+cuda ^cuda@:7.5 target=x86_64:')
+    conflicts('%gcc@6:', when='+cuda ^cuda@:8 target=x86_64:')
+    conflicts('%gcc@7:', when='+cuda ^cuda@:9.1 target=x86_64:')
+    conflicts('%gcc@8:', when='+cuda ^cuda@:10.0.130 target=x86_64:')
+    conflicts('%gcc@9:', when='+cuda ^cuda@:10.2.89 target=x86_64:')
+    conflicts('%gcc@:4', when='+cuda ^cuda@11.0.2: target=x86_64:')
+    conflicts('%gcc@10:', when='+cuda ^cuda@:11.0.3 target=x86_64:')
+    conflicts('%gcc@11:', when='+cuda ^cuda@:11.1.0 target=x86_64:')
+    conflicts('%pgi@:14.8', when='+cuda ^cuda@:7.0.27 target=x86_64:')
+    conflicts('%pgi@:15.3,15.5:', when='+cuda ^cuda@7.5 target=x86_64:')
+    conflicts('%pgi@:16.2,16.0:16.3', when='+cuda ^cuda@8 target=x86_64:')
+    conflicts('%pgi@:15,18:', when='+cuda ^cuda@9.0:9.1 target=x86_64:')
+    conflicts('%pgi@:16,19:', when='+cuda ^cuda@9.2.88:10 target=x86_64:')
     conflicts('%pgi@:17,20:',
-              when='+cuda ^cuda@10.1.105:10.2.89' + arch_platform)
+              when='+cuda ^cuda@10.1.105:10.2.89 target=x86_64:')
     conflicts('%pgi@:17,21:',
-              when='+cuda ^cuda@11.0.2:11.1.0' + arch_platform)
-    conflicts('%clang@:3.4', when='+cuda ^cuda@:7.5' + arch_platform)
+              when='+cuda ^cuda@11.0.2:11.1.0 target=x86_64:')
+    conflicts('%clang@:3.4', when='+cuda ^cuda@:7.5 target=x86_64:')
     conflicts('%clang@:3.7,4:',
-              when='+cuda ^cuda@8.0:9.0' + arch_platform)
+              when='+cuda ^cuda@8.0:9.0 target=x86_64:')
     conflicts('%clang@:3.7,4.1:',
-              when='+cuda ^cuda@9.1' + arch_platform)
-    conflicts('%clang@:3.7,5.1:', when='+cuda ^cuda@9.2' + arch_platform)
-    conflicts('%clang@:3.7,6.1:', when='+cuda ^cuda@10.0.130' + arch_platform)
-    conflicts('%clang@:3.7,7.1:', when='+cuda ^cuda@10.1.105' + arch_platform)
+              when='+cuda ^cuda@9.1 target=x86_64:')
+    conflicts('%clang@:3.7,5.1:', when='+cuda ^cuda@9.2 target=x86_64:')
+    conflicts('%clang@:3.7,6.1:', when='+cuda ^cuda@10.0.130 target=x86_64:')
+    conflicts('%clang@:3.7,7.1:', when='+cuda ^cuda@10.1.105 target=x86_64:')
     conflicts('%clang@:3.7,8.1:',
-              when='+cuda ^cuda@10.1.105:10.1.243' + arch_platform)
-    conflicts('%clang@:3.2,9:', when='+cuda ^cuda@10.2.89' + arch_platform)
-    conflicts('%clang@:5', when='+cuda ^cuda@11.0.2:' + arch_platform)
-    conflicts('%clang@10:', when='+cuda ^cuda@:11.0.2' + arch_platform)
-    conflicts('%clang@11:', when='+cuda ^cuda@:11.1.0' + arch_platform)
+              when='+cuda ^cuda@10.1.105:10.1.243 target=x86_64:')
+    conflicts('%clang@:3.2,9:', when='+cuda ^cuda@10.2.89 target=x86_64:')
+    conflicts('%clang@:5', when='+cuda ^cuda@11.0.2: target=x86_64:')
+    conflicts('%clang@10:', when='+cuda ^cuda@:11.0.3 target=x86_64:')
+    conflicts('%clang@11:', when='+cuda ^cuda@:11.1.0 target=x86_64:')
 
     # x86_64 vs. ppc64le differ according to NVidia docs
     # Linux ppc64le compiler conflicts from Table from the docs below:
@@ -129,27 +127,26 @@ def cuda_flags(arch_list):
     # https://docs.nvidia.com/cuda/archive/9.0/cuda-installation-guide-linux/index.html
     # https://docs.nvidia.com/cuda/archive/8.0/cuda-installation-guide-linux/index.html
 
-    arch_platform = ' target=ppc64le: platform=linux'
     # information prior to CUDA 9 difficult to find
-    conflicts('%gcc@6:', when='+cuda ^cuda@:9' + arch_platform)
-    conflicts('%gcc@8:', when='+cuda ^cuda@:10.0.130' + arch_platform)
-    conflicts('%gcc@9:', when='+cuda ^cuda@:10.1.243' + arch_platform)
+    conflicts('%gcc@6:', when='+cuda ^cuda@:9 target=ppc64le:')
+    conflicts('%gcc@8:', when='+cuda ^cuda@:10.0.130 target=ppc64le:')
+    conflicts('%gcc@9:', when='+cuda ^cuda@:10.1.243 target=ppc64le:')
     # officially, CUDA 11.0.2 only supports the system GCC 8.3 on ppc64le
-    conflicts('%gcc@:4', when='+cuda ^cuda@11.0.2:' + arch_platform)
-    conflicts('%gcc@10:', when='+cuda ^cuda@:11.0.2' + arch_platform)
-    conflicts('%gcc@11:', when='+cuda ^cuda@:11.1.0' + arch_platform)
-    conflicts('%pgi', when='+cuda ^cuda@:8' + arch_platform)
-    conflicts('%pgi@:16', when='+cuda ^cuda@:9.1.185' + arch_platform)
-    conflicts('%pgi@:17', when='+cuda ^cuda@:10' + arch_platform)
-    conflicts('%clang@4:', when='+cuda ^cuda@:9.0.176' + arch_platform)
-    conflicts('%clang@5:', when='+cuda ^cuda@:9.1' + arch_platform)
-    conflicts('%clang@6:', when='+cuda ^cuda@:9.2' + arch_platform)
-    conflicts('%clang@7:', when='+cuda ^cuda@10.0.130' + arch_platform)
-    conflicts('%clang@7.1:', when='+cuda ^cuda@:10.1.105' + arch_platform)
-    conflicts('%clang@8.1:', when='+cuda ^cuda@:10.2.89' + arch_platform)
-    conflicts('%clang@:5', when='+cuda ^cuda@11.0.2:' + arch_platform)
-    conflicts('%clang@10:', when='+cuda ^cuda@:11.0.2' + arch_platform)
-    conflicts('%clang@11:', when='+cuda ^cuda@:11.1.0' + arch_platform)
+    conflicts('%gcc@:4', when='+cuda ^cuda@11.0.2: target=ppc64le:')
+    conflicts('%gcc@10:', when='+cuda ^cuda@:11.0.3 target=ppc64le:')
+    conflicts('%gcc@11:', when='+cuda ^cuda@:11.1.0 target=ppc64le:')
+    conflicts('%pgi', when='+cuda ^cuda@:8 target=ppc64le:')
+    conflicts('%pgi@:16', when='+cuda ^cuda@:9.1.185 target=ppc64le:')
+    conflicts('%pgi@:17', when='+cuda ^cuda@:10 target=ppc64le:')
+    conflicts('%clang@4:', when='+cuda ^cuda@:9.0.176 target=ppc64le:')
+    conflicts('%clang@5:', when='+cuda ^cuda@:9.1 target=ppc64le:')
+    conflicts('%clang@6:', when='+cuda ^cuda@:9.2 target=ppc64le:')
+    conflicts('%clang@7:', when='+cuda ^cuda@10.0.130 target=ppc64le:')
+    conflicts('%clang@7.1:', when='+cuda ^cuda@:10.1.105 target=ppc64le:')
+    conflicts('%clang@8.1:', when='+cuda ^cuda@:10.2.89 target=ppc64le:')
+    conflicts('%clang@:5', when='+cuda ^cuda@11.0.2: target=ppc64le:')
+    conflicts('%clang@10:', when='+cuda ^cuda@:11.0.3 target=ppc64le:')
+    conflicts('%clang@11:', when='+cuda ^cuda@:11.1.0 target=ppc64le:')
 
     # Intel is mostly relevant for x86_64 Linux, even though it also
     # exists for Mac OS X. No information prior to CUDA 3.2 or Intel 11.1
@@ -171,15 +168,8 @@ def cuda_flags(arch_list):
     conflicts('%xl@:12,14:15,17:', when='+cuda ^cuda@9.2')
     conflicts('%xl@:12,17:', when='+cuda ^cuda@:11.1.0')
 
-    # Mac OS X
-    # platform = ' platform=darwin'
-    # Apple XCode clang vs. LLVM clang are difficult to specify
-    # with spack syntax. Xcode clang name is `clang@x.y.z-apple`
-    # which precludes ranges being specified. We have proposed
-    # rename XCode clang to `clang@apple-x.y.z` or even
-    # `clang-apple@x.y.z as a possible fix.
-    # Compiler conflicts will be eventual taken from here:
-    # https://docs.nvidia.com/cuda/cuda-installation-guide-mac-os-x/index.html#abstract
+    # Darwin.
+    # TODO: add missing conflicts for %apple-clang cuda@:10
     conflicts('platform=darwin', when='+cuda ^cuda@11.0.2:')
 
     # Make sure cuda_arch can not be used without +cuda

lib/spack/spack/build_systems/gnu.py

@@ -3,8 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import spack.util.url
 import spack.package
+import spack.util.url
 
 
 class GNUMirrorPackage(spack.package.PackageBase):

lib/spack/spack/build_systems/intel.py

@@ -4,26 +4,32 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
-import os
-import sys
 import glob
-import tempfile
-import re
 import inspect
+import os
+import re
+import sys
+import tempfile
 import xml.etree.ElementTree as ElementTree
+
 import llnl.util.tty as tty
+from llnl.util.filesystem import (
+    HeaderList,
+    LibraryList,
+    ancestor,
+    filter_file,
+    find_headers,
+    find_libraries,
+    find_system_libraries,
+    install,
+)
 
-from llnl.util.filesystem import \
-    install, ancestor, filter_file, \
-    HeaderList, find_headers, \
-    LibraryList, find_libraries, find_system_libraries
-
-from spack.version import Version, ver
-from spack.package import PackageBase, run_after, InstallError
+from spack.build_environment import dso_suffix
+from spack.package import InstallError, PackageBase, run_after
 from spack.util.environment import EnvironmentModifications
 from spack.util.executable import Executable
 from spack.util.prefix import Prefix
-from spack.build_environment import dso_suffix
+from spack.version import Version, ver
 
 # A couple of utility functions that might be useful in general. If so, they
 # should really be defined elsewhere, unless deemed heretical.
@@ -362,7 +368,7 @@ def normalize_suite_dir(self, suite_dir_name, version_globs=['*.*.*']):
                 toplevel psxevars.sh or equivalent file to source (and thus by
                 the modulefiles that Spack produces).
 
-            version_globs (list of str): Suffix glob patterns (most specific
+            version_globs (list): Suffix glob patterns (most specific
                 first) expected to qualify suite_dir_name to its fully
                 version-specific install directory (as opposed to a
                 compatibility directory or symlink).
@@ -1089,7 +1095,7 @@ def _setup_dependent_env_callback(
                 # Intel MPI since 2019 depends on libfabric which is not in the
                 # lib directory but in a directory of its own which should be
                 # included in the rpath
-                if self.version >= ver('2019'):
+                if self.version_yearlike >= ver('2019'):
                     d = ancestor(self.component_lib_dir('mpi'))
                     libfabrics_path = os.path.join(d, 'libfabric', 'lib')
                     env.append_path('SPACK_COMPILER_EXTRA_RPATHS',

lib/spack/spack/build_systems/makefile.py

@@ -9,6 +9,7 @@
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import working_dir
+
 from spack.package import PackageBase, run_after
 
 

lib/spack/spack/build_systems/maven.py

@@ -5,6 +5,7 @@
 
 
 from llnl.util.filesystem import install_tree, working_dir
+
 from spack.directives import depends_on
 from spack.package import PackageBase, run_after
 from spack.util.executable import which

lib/spack/spack/build_systems/meson.py

@@ -9,6 +9,7 @@
 from typing import List  # novm
 
 from llnl.util.filesystem import working_dir
+
 from spack.directives import depends_on, variant
 from spack.package import PackageBase, run_after
 
@@ -101,9 +102,9 @@ def _std_args(pkg):
 
         strip = 'true' if '+strip' in pkg.spec else 'false'
 
-        if 'libs=static,shared' in pkg.spec:
+        if 'default_library=static,shared' in pkg.spec:
             default_library = 'both'
-        elif 'libs=static' in pkg.spec:
+        elif 'default_library=static' in pkg.spec:
             default_library = 'static'
         else:
             default_library = 'shared'

lib/spack/spack/build_systems/oneapi.py

@@ -8,16 +8,16 @@
 """
 
 import getpass
+import platform
 import shutil
-from sys import platform
 from os.path import basename, dirname, isdir
 
+from llnl.util.filesystem import find_headers, find_libraries, join_path
+
 from spack.package import Package
 from spack.util.environment import EnvironmentModifications
 from spack.util.executable import Executable
 
-from llnl.util.filesystem import find_headers, find_libraries, join_path
-
 
 class IntelOneApiPackage(Package):
     """Base class for Intel oneAPI packages."""
@@ -48,7 +48,7 @@ def install(self, spec, prefix, installer_path=None):
         if installer_path is None:
             installer_path = basename(self.url_for_version(spec.version))
 
-        if platform == 'linux':
+        if platform.system() == 'Linux':
             # Intel installer assumes and enforces that all components
             # are installed into a single prefix. Spack wants to
             # install each component in a separate prefix. The
@@ -69,6 +69,9 @@ def install(self, spec, prefix, installer_path=None):
 
             # Installer writes files in ~/intel set HOME so it goes to prefix
             bash.add_default_env('HOME', prefix)
+            # Installer checks $XDG_RUNTIME_DIR/.bootstrapper_lock_file as well
+            bash.add_default_env('XDG_RUNTIME_DIR',
+                                 join_path(self.stage.path, 'runtime'))
 
             bash(installer_path,
                  '-s', '-a', '-s', '--action', 'install',

lib/spack/spack/build_systems/perl.py

@@ -7,10 +7,11 @@
 import inspect
 import os
 
+from llnl.util.filesystem import filter_file
+
 from spack.directives import extends
 from spack.package import PackageBase, run_after
 from spack.util.executable import Executable
-from llnl.util.filesystem import filter_file
 
 
 class PerlPackage(PackageBase):

lib/spack/spack/build_systems/python.py

@@ -6,14 +6,20 @@
 import os
 import shutil
 
+import llnl.util.tty as tty
+from llnl.util.filesystem import (
+    filter_file,
+    find,
+    get_filetype,
+    path_contains_subdirectory,
+    same_path,
+    working_dir,
+)
+from llnl.util.lang import match_predicate
+
 from spack.directives import extends
 from spack.package import PackageBase, run_after
 
-from llnl.util.filesystem import (working_dir, get_filetype, filter_file,
-                                  path_contains_subdirectory, same_path, find)
-from llnl.util.lang import match_predicate
-import llnl.util.tty as tty
-
 
 class PythonPackage(PackageBase):
     """Specialized class for packages that are built using Python
@@ -121,24 +127,22 @@ def import_modules(self):
             list: list of strings of module names
         """
         modules = []
+        root = self.spec['python'].package.get_python_lib(prefix=self.prefix)
 
-        # Python libraries may be installed in lib or lib64
-        # See issues #18520 and #17126
-        for lib in ['lib', 'lib64']:
-            root = os.path.join(self.prefix, lib, 'python{0}'.format(
-                self.spec['python'].version.up_to(2)), 'site-packages')
-            # Some Python libraries are packages: collections of modules
-            # distributed in directories containing __init__.py files
-            for path in find(root, '__init__.py', recursive=True):
-                modules.append(path.replace(root + os.sep, '', 1).replace(
-                    os.sep + '__init__.py', '').replace('/', '.'))
-            # Some Python libraries are modules: individual *.py files
-            # found in the site-packages directory
-            for path in find(root, '*.py', recursive=False):
-                modules.append(path.replace(root + os.sep, '', 1).replace(
-                    '.py', '').replace('/', '.'))
+        # Some Python libraries are packages: collections of modules
+        # distributed in directories containing __init__.py files
+        for path in find(root, '__init__.py', recursive=True):
+            modules.append(path.replace(root + os.sep, '', 1).replace(
+                os.sep + '__init__.py', '').replace('/', '.'))
+
+        # Some Python libraries are modules: individual *.py files
+        # found in the site-packages directory
+        for path in find(root, '*.py', recursive=False):
+            modules.append(path.replace(root + os.sep, '', 1).replace(
+                '.py', '').replace('/', '.'))
 
         tty.debug('Detected the following modules: {0}'.format(modules))
+
         return modules
 
     def setup_file(self):
@@ -248,15 +252,12 @@ def install_args(self, spec, prefix):
         # Get all relative paths since we set the root to `prefix`
         # We query the python with which these will be used for the lib and inc
         # directories. This ensures we use `lib`/`lib64` as expected by python.
-        python = spec['python'].package.command
-        command_start = 'print(distutils.sysconfig.'
-        commands = ';'.join([
-            'import distutils.sysconfig',
-            command_start + 'get_python_lib(plat_specific=False, prefix=""))',
-            command_start + 'get_python_lib(plat_specific=True, prefix=""))',
-            command_start + 'get_python_inc(plat_specific=True, prefix=""))'])
-        pure_site_packages_dir, plat_site_packages_dir, inc_dir = python(
-            '-c', commands, output=str, error=str).strip().split('\n')
+        pure_site_packages_dir = spec['python'].package.get_python_lib(
+            plat_specific=False, prefix='')
+        plat_site_packages_dir = spec['python'].package.get_python_lib(
+            plat_specific=True, prefix='')
+        inc_dir = spec['python'].package.get_python_inc(
+            plat_specific=True, prefix='')
 
         args += ['--root=%s' % prefix,
                  '--install-purelib=%s' % pure_site_packages_dir,

lib/spack/spack/build_systems/qmake.py

@@ -7,6 +7,7 @@
 import inspect
 
 from llnl.util.filesystem import working_dir
+
 from spack.directives import depends_on
 from spack.package import PackageBase, run_after
 

lib/spack/spack/build_systems/rocm.py

@@ -75,10 +75,9 @@
 #    does not like its directory structure.
 #
 
-from spack.package import PackageBase
-from spack.directives import depends_on, variant, conflicts
-
 import spack.variant
+from spack.directives import conflicts, depends_on, variant
+from spack.package import PackageBase
 
 
 class ROCmPackage(PackageBase):

lib/spack/spack/build_systems/sip.py

@@ -6,10 +6,11 @@
 import inspect
 import os
 
-from llnl.util.filesystem import find, working_dir, join_path
+import llnl.util.tty as tty
+from llnl.util.filesystem import find, join_path, working_dir
+
 from spack.directives import depends_on, extends
 from spack.package import PackageBase, run_after
-import llnl.util.tty as tty
 
 
 class SIPPackage(PackageBase):
@@ -63,24 +64,22 @@ def import_modules(self):
             list: list of strings of module names
         """
         modules = []
+        root = self.spec['python'].package.get_python_lib(prefix=self.prefix)
 
-        # Python libraries may be installed in lib or lib64
-        # See issues #18520 and #17126
-        for lib in ['lib', 'lib64']:
-            root = os.path.join(self.prefix, lib, 'python{0}'.format(
-                self.spec['python'].version.up_to(2)), 'site-packages')
-            # Some Python libraries are packages: collections of modules
-            # distributed in directories containing __init__.py files
-            for path in find(root, '__init__.py', recursive=True):
-                modules.append(path.replace(root + os.sep, '', 1).replace(
-                    os.sep + '__init__.py', '').replace('/', '.'))
-            # Some Python libraries are modules: individual *.py files
-            # found in the site-packages directory
-            for path in find(root, '*.py', recursive=False):
-                modules.append(path.replace(root + os.sep, '', 1).replace(
-                    '.py', '').replace('/', '.'))
+        # Some Python libraries are packages: collections of modules
+        # distributed in directories containing __init__.py files
+        for path in find(root, '__init__.py', recursive=True):
+            modules.append(path.replace(root + os.sep, '', 1).replace(
+                os.sep + '__init__.py', '').replace('/', '.'))
+
+        # Some Python libraries are modules: individual *.py files
+        # found in the site-packages directory
+        for path in find(root, '*.py', recursive=False):
+            modules.append(path.replace(root + os.sep, '', 1).replace(
+                '.py', '').replace('/', '.'))
 
         tty.debug('Detected the following modules: {0}'.format(modules))
+
         return modules
 
     def python(self, *args, **kwargs):

lib/spack/spack/build_systems/sourceforge.py

@@ -3,8 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import spack.util.url
 import spack.package
+import spack.util.url
 
 
 class SourceforgePackage(spack.package.PackageBase):

lib/spack/spack/build_systems/sourceware.py

@@ -3,8 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import spack.util.url
 import spack.package
+import spack.util.url
 
 
 class SourcewarePackage(spack.package.PackageBase):

lib/spack/spack/build_systems/waf.py

@@ -6,11 +6,11 @@
 
 import inspect
 
+from llnl.util.filesystem import working_dir
+
 from spack.directives import depends_on
 from spack.package import PackageBase, run_after
 
-from llnl.util.filesystem import working_dir
-
 
 class WafPackage(PackageBase):
     """Specialized class for packages that are built using the

lib/spack/spack/build_systems/xorg.py

@@ -3,8 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import spack.util.url
 import spack.package
+import spack.util.url
 
 
 class XorgPackage(spack.package.PackageBase):

lib/spack/spack/caches.py

@@ -9,10 +9,10 @@
 import llnl.util.lang
 from llnl.util.filesystem import mkdirp
 
-import spack.error
-import spack.paths
 import spack.config
+import spack.error
 import spack.fetch_strategy
+import spack.paths
 import spack.util.file_cache
 import spack.util.path
 

lib/spack/spack/ci.py

@@ -17,10 +17,10 @@
 from six import iteritems
 from six.moves.urllib.error import HTTPError, URLError
 from six.moves.urllib.parse import urlencode
-from six.moves.urllib.request import build_opener, HTTPHandler, Request
+from six.moves.urllib.request import HTTPHandler, Request, build_opener
 
-import llnl.util.tty as tty
 import llnl.util.filesystem as fs
+import llnl.util.tty as tty
 
 import spack
 import spack.binary_distribution as bindist
@@ -28,18 +28,17 @@
 import spack.compilers as compilers
 import spack.config as cfg
 import spack.environment as ev
-from spack.error import SpackError
 import spack.main
 import spack.mirror
 import spack.paths
 import spack.repo
-from spack.spec import Spec
 import spack.util.executable as exe
-import spack.util.spack_yaml as syaml
-import spack.util.web as web_util
 import spack.util.gpg as gpg_util
+import spack.util.spack_yaml as syaml
 import spack.util.url as url_util
-
+import spack.util.web as web_util
+from spack.error import SpackError
+from spack.spec import Spec
 
 JOB_RETRY_CONDITIONS = [
     'always',
@@ -81,7 +80,8 @@ def _create_buildgroup(opener, headers, url, project, group_name, group_type):
     if response_code != 200 and response_code != 201:
         msg = 'Creating buildgroup failed (response code = {0}'.format(
             response_code)
-        raise SpackError(msg)
+        tty.warn(msg)
+        return None
 
     response_text = response.read()
     response_json = json.loads(response_text)
@@ -110,7 +110,8 @@ def populate_buildgroup(job_names, group_name, project, site,
     if not parent_group_id or not group_id:
         msg = 'Failed to create or retrieve buildgroups for {0}'.format(
             group_name)
-        raise SpackError(msg)
+        tty.warn(msg)
+        return
 
     data = {
         'project': project,
@@ -133,7 +134,7 @@ def populate_buildgroup(job_names, group_name, project, site,
     if response_code != 200:
         msg = 'Error response code ({0}) in populate_buildgroup'.format(
             response_code)
-        raise SpackError(msg)
+        tty.warn(msg)
 
 
 def is_main_phase(phase_name):
@@ -507,7 +508,7 @@ def format_job_needs(phase_name, strip_compilers, dep_jobs,
                 'job': get_job_name(phase_name,
                                     strip_compilers,
                                     dep_job,
-                                    osname,
+                                    dep_job.architecture,
                                     build_group),
                 'artifacts': enable_artifacts_buildcache,
             })
@@ -549,9 +550,8 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
     generate_job_name = os.environ.get('CI_JOB_NAME', None)
     parent_pipeline_id = os.environ.get('CI_PIPELINE_ID', None)
 
-    is_pr_pipeline = (
-        os.environ.get('SPACK_IS_PR_PIPELINE', '').lower() == 'true'
-    )
+    spack_pipeline_type = os.environ.get('SPACK_PIPELINE_TYPE', None)
+    is_pr_pipeline = spack_pipeline_type == 'spack_pull_request'
 
     spack_pr_branch = os.environ.get('SPACK_PR_BRANCH', None)
     pr_mirror_url = None
@@ -706,14 +706,9 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
                 root_spec = spec_record['rootSpec']
                 pkg_name = pkg_name_from_spec_label(spec_label)
                 release_spec = root_spec[pkg_name]
-
-                # Check if this spec is in our list of known failures.
-                if broken_specs_url:
-                    full_hash = release_spec.full_hash()
-                    broken_spec_path = url_util.join(broken_specs_url, full_hash)
-                    if web_util.url_exists(broken_spec_path):
-                        known_broken_specs_encountered.append('{0} ({1})'.format(
-                            release_spec, full_hash))
+                release_spec_full_hash = release_spec.full_hash()
+                release_spec_dag_hash = release_spec.dag_hash()
+                release_spec_build_hash = release_spec.build_hash()
 
                 runner_attribs = find_matching_config(
                     release_spec, gitlab_ci)
@@ -746,8 +741,7 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
                     job_script.insert(0, 'cd {0}'.format(concrete_env_dir))
 
                 job_script.extend([
-                    'spack ci rebuild --prepare',
-                    './install.sh'
+                    'spack ci rebuild'
                 ])
 
                 if 'script' in runner_attribs:
@@ -776,7 +770,9 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
                 job_vars = {
                     'SPACK_ROOT_SPEC': format_root_spec(
                         root_spec, main_phase, strip_compilers),
-                    'SPACK_JOB_SPEC_DAG_HASH': release_spec.dag_hash(),
+                    'SPACK_JOB_SPEC_DAG_HASH': release_spec_dag_hash,
+                    'SPACK_JOB_SPEC_BUILD_HASH': release_spec_build_hash,
+                    'SPACK_JOB_SPEC_FULL_HASH': release_spec_full_hash,
                     'SPACK_JOB_SPEC_PKG_NAME': release_spec.name,
                     'SPACK_COMPILER_ACTION': compiler_action
                 }
@@ -877,6 +873,15 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
                 if prune_dag and not rebuild_spec:
                     continue
 
+                # Check if this spec is in our list of known failures, now that
+                # we know this spec needs a rebuild
+                if broken_specs_url:
+                    broken_spec_path = url_util.join(
+                        broken_specs_url, release_spec_full_hash)
+                    if web_util.url_exists(broken_spec_path):
+                        known_broken_specs_encountered.append('{0} ({1})'.format(
+                            release_spec, release_spec_full_hash))
+
                 if artifacts_root:
                     job_dependencies.append({
                         'job': generate_job_name,
@@ -1069,7 +1074,7 @@ def generate_gitlab_ci_yaml(env, print_summary, output_file,
             'SPACK_JOB_LOG_DIR': rel_job_log_dir,
             'SPACK_JOB_REPRO_DIR': rel_job_repro_dir,
             'SPACK_LOCAL_MIRROR_DIR': rel_local_mirror_dir,
-            'SPACK_IS_PR_PIPELINE': str(is_pr_pipeline)
+            'SPACK_PIPELINE_TYPE': str(spack_pipeline_type)
         }
 
         if pr_mirror_url:
@@ -1256,7 +1261,8 @@ def register_cdash_build(build_name, base_url, project, site, track):
 
     if response_code != 200 and response_code != 201:
         msg = 'Adding build failed (response code = {0}'.format(response_code)
-        raise SpackError(msg)
+        tty.warn(msg)
+        return (None, None)
 
     response_text = response.read()
     response_json = json.loads(response_text)
@@ -1293,8 +1299,9 @@ def relate_cdash_builds(spec_map, cdash_base_url, job_build_id, cdash_project,
                 tty.debug('Did not find cdashid for {0} on {1}'.format(
                     dep_pkg_name, url))
         else:
-            raise SpackError('Did not find cdashid for {0} anywhere'.format(
+            tty.warn('Did not find cdashid for {0} anywhere'.format(
                 dep_pkg_name))
+            return
 
         payload = {
             "project": cdash_project,
@@ -1309,16 +1316,20 @@ def relate_cdash_builds(spec_map, cdash_base_url, job_build_id, cdash_project,
 
         request = Request(cdash_api_url, data=enc_data, headers=headers)
 
-        response = opener.open(request)
-        response_code = response.getcode()
+        try:
+            response = opener.open(request)
+            response_code = response.getcode()
 
-        if response_code != 200 and response_code != 201:
-            msg = 'Relate builds ({0} -> {1}) failed (resp code = {2})'.format(
-                job_build_id, dep_build_id, response_code)
-            raise SpackError(msg)
+            if response_code != 200 and response_code != 201:
+                msg = 'Relate builds ({0} -> {1}) failed (resp code = {2})'.format(
+                    job_build_id, dep_build_id, response_code)
+                tty.warn(msg)
+                return
 
-        response_text = response.read()
-        tty.debug('Relate builds response: {0}'.format(response_text))
+            response_text = response.read()
+            tty.debug('Relate builds response: {0}'.format(response_text))
+        except Exception as e:
+            print("Relating builds in CDash failed: {0}".format(e))
 
 
 def write_cdashid_to_mirror(cdashid, spec, mirror_url):
@@ -1338,7 +1349,16 @@ def write_cdashid_to_mirror(cdashid, spec, mirror_url):
         tty.debug('pushing cdashid to url')
         tty.debug('  local file path: {0}'.format(local_cdash_path))
         tty.debug('  remote url: {0}'.format(remote_url))
-        web_util.push_to_url(local_cdash_path, remote_url)
+
+        try:
+            web_util.push_to_url(local_cdash_path, remote_url)
+        except Exception as inst:
+            # No matter what went wrong here, don't allow the pipeline to fail
+            # just because there was an issue storing the cdashid on the mirror
+            msg = 'Failed to write cdashid {0} to mirror {1}'.format(
+                cdashid, mirror_url)
+            tty.warn(inst)
+            tty.warn(msg)
 
 
 def read_cdashid_from_mirror(spec, mirror_url):
@@ -1356,40 +1376,34 @@ def read_cdashid_from_mirror(spec, mirror_url):
     return int(contents)
 
 
-def push_mirror_contents(env, spec, yaml_path, mirror_url, build_id,
-                         sign_binaries):
-    if mirror_url:
-        try:
-            unsigned = not sign_binaries
-            tty.debug('Creating buildcache ({0})'.format(
-                'unsigned' if unsigned else 'signed'))
-            spack.cmd.buildcache._createtarball(
-                env, spec_yaml=yaml_path, add_deps=False,
-                output_location=mirror_url, force=True, allow_root=True,
-                unsigned=unsigned)
-            if build_id:
-                tty.debug('Writing cdashid ({0}) to remote mirror: {1}'.format(
-                    build_id, mirror_url))
-                write_cdashid_to_mirror(build_id, spec, mirror_url)
-        except Exception as inst:
-            # If the mirror we're pushing to is on S3 and there's some
-            # permissions problem, for example, we can't just target
-            # that exception type here, since users of the
-            # `spack ci rebuild' may not need or want any dependency
-            # on boto3.  So we use the first non-boto exception type
-            # in the heirarchy:
-            #     boto3.exceptions.S3UploadFailedError
-            #     boto3.exceptions.Boto3Error
-            #     Exception
-            #     BaseException
-            #     object
-            err_msg = 'Error msg: {0}'.format(inst)
-            if 'Access Denied' in err_msg:
-                tty.msg('Permission problem writing to {0}'.format(
-                    mirror_url))
-                tty.msg(err_msg)
-            else:
-                raise inst
+def push_mirror_contents(env, spec, yaml_path, mirror_url, sign_binaries):
+    try:
+        unsigned = not sign_binaries
+        tty.debug('Creating buildcache ({0})'.format(
+            'unsigned' if unsigned else 'signed'))
+        spack.cmd.buildcache._createtarball(
+            env, spec_yaml=yaml_path, add_deps=False,
+            output_location=mirror_url, force=True, allow_root=True,
+            unsigned=unsigned)
+    except Exception as inst:
+        # If the mirror we're pushing to is on S3 and there's some
+        # permissions problem, for example, we can't just target
+        # that exception type here, since users of the
+        # `spack ci rebuild' may not need or want any dependency
+        # on boto3.  So we use the first non-boto exception type
+        # in the heirarchy:
+        #     boto3.exceptions.S3UploadFailedError
+        #     boto3.exceptions.Boto3Error
+        #     Exception
+        #     BaseException
+        #     object
+        err_msg = 'Error msg: {0}'.format(inst)
+        if any(x in err_msg for x in ['Access Denied', 'InvalidAccessKeyId']):
+            tty.msg('Permission problem writing to {0}'.format(
+                mirror_url))
+            tty.msg(err_msg)
+        else:
+            raise inst
 
 
 def copy_stage_logs_to_artifacts(job_spec, job_log_dir):

lib/spack/spack/cmd/__init__.py

@@ -5,19 +5,20 @@
 
 from __future__ import print_function
 
+import argparse
 import os
 import re
 import sys
-import argparse
-import ruamel.yaml as yaml
 
+import ruamel.yaml as yaml
 import six
+from ruamel.yaml.error import MarkedYAMLError
 
 import llnl.util.tty as tty
+from llnl.util.filesystem import join_path
 from llnl.util.lang import attr_setdefault, index_by
 from llnl.util.tty.colify import colify
 from llnl.util.tty.color import colorize
-from llnl.util.filesystem import join_path
 
 import spack.config
 import spack.error
@@ -27,8 +28,6 @@
 import spack.store
 import spack.util.spack_json as sjson
 import spack.util.string
-from ruamel.yaml.error import MarkedYAMLError
-
 
 # cmd has a submodule called "list" so preserve the python list module
 python_list = list
@@ -217,10 +216,10 @@ def disambiguate_spec(spec, env, local=False, installed=True, first=False):
         spec (spack.spec.Spec): a spec to disambiguate
         env (spack.environment.Environment): a spack environment,
             if one is active, or None if no environment is active
-        local (boolean, default False): do not search chained spack instances
-        installed (boolean or any, or spack.database.InstallStatus or iterable
-            of spack.database.InstallStatus): install status argument passed to
-            database query. See ``spack.database.Database._query`` for details.
+        local (bool): do not search chained spack instances
+        installed (bool or spack.database.InstallStatus or typing.Iterable):
+            install status argument passed to database query.
+            See ``spack.database.Database._query`` for details.
     """
     hashes = env.all_hashes() if env else None
     return disambiguate_spec_from_hashes(spec, hashes, local, installed, first)
@@ -232,11 +231,11 @@ def disambiguate_spec_from_hashes(spec, hashes, local=False,
 
     Arguments:
         spec (spack.spec.Spec): a spec to disambiguate
-        hashes (iterable): a set of hashes of specs among which to disambiguate
-        local (boolean, default False): do not search chained spack instances
-        installed (boolean or any, or spack.database.InstallStatus or iterable
-            of spack.database.InstallStatus): install status argument passed to
-            database query. See ``spack.database.Database._query`` for details.
+        hashes (typing.Iterable): a set of hashes of specs among which to disambiguate
+        local (bool): do not search chained spack instances
+        installed (bool or spack.database.InstallStatus or typing.Iterable):
+            install status argument passed to database query.
+            See ``spack.database.Database._query`` for details.
     """
     if local:
         matching_specs = spack.store.db.query_local(spec, hashes=hashes,
@@ -334,9 +333,8 @@ def display_specs(specs, args=None, **kwargs):
     namespace.
 
     Args:
-        specs (list of spack.spec.Spec): the specs to display
-        args (optional argparse.Namespace): namespace containing
-            formatting arguments
+        specs (list): the specs to display
+        args (argparse.Namespace or None): namespace containing formatting arguments
 
     Keyword Args:
         paths (bool): Show paths with each displayed spec
@@ -349,9 +347,9 @@ def display_specs(specs, args=None, **kwargs):
         indent (int): indent each line this much
         groups (bool): display specs grouped by arch/compiler (default True)
         decorators (dict): dictionary mappng specs to decorators
-        header_callback (function): called at start of arch/compiler groups
+        header_callback (typing.Callable): called at start of arch/compiler groups
         all_headers (bool): show headers even when arch/compiler aren't defined
-        output (stream): A file object to write to. Default is ``sys.stdout``
+        output (typing.IO): A file object to write to. Default is ``sys.stdout``
 
     """
     def get_arg(name, default=None):

lib/spack/spack/cmd/add.py

@@ -9,7 +9,6 @@
 import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 
-
 description = 'add a spec to an environment'
 section = "environments"
 level = "long"

lib/spack/spack/cmd/analyze.py

@@ -17,7 +17,6 @@
 import spack.paths
 import spack.report
 
-
 description = "run analyzers on installed packages"
 section = "analysis"
 level = "long"
@@ -59,9 +58,9 @@ def analyze_spec(spec, analyzers=None, outdir=None, monitor=None, overwrite=Fals
     analyze_spec(spec, args.analyzers, args.outdir, monitor)
 
     Args:
-        spec (Spec): spec object of installed package
+        spec (spack.spec.Spec): spec object of installed package
         analyzers (list): list of analyzer (keys) to run
-        monitor (monitor.SpackMonitorClient): a monitor client
+        monitor (spack.monitor.SpackMonitorClient): a monitor client
         overwrite (bool): overwrite result if already exists
     """
     analyzers = analyzers or list(spack.analyzers.analyzer_types.keys())

lib/spack/spack/cmd/arch.py

@@ -8,8 +8,10 @@
 import collections
 
 import archspec.cpu
+
 import llnl.util.tty.colify as colify
 import llnl.util.tty.color as color
+
 import spack.architecture as architecture
 
 description = "print architecture information about this machine"

lib/spack/spack/cmd/audit.py

@@ -0,0 +1,80 @@
+# Copyright 2013-2021 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)
+import llnl.util.tty.color as cl
+
+import spack.audit
+import spack.repo
+
+description = "audit configuration files, packages, etc."
+section = "system"
+level = "short"
+
+
+def setup_parser(subparser):
+    # Top level flags, valid for every audit class
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='subcommand')
+
+    # Audit configuration files
+    sp.add_parser('configs', help='audit configuration files')
+
+    # Audit package recipes
+    pkg_parser = sp.add_parser('packages', help='audit package recipes')
+    pkg_parser.add_argument(
+        'name', metavar='PKG', nargs='*',
+        help='package to be analyzed (if none all packages will be processed)',
+    )
+
+    # List all checks
+    sp.add_parser('list', help='list available checks and exits')
+
+
+def configs(parser, args):
+    reports = spack.audit.run_group(args.subcommand)
+    _process_reports(reports)
+
+
+def packages(parser, args):
+    pkgs = args.name or spack.repo.path.all_package_names()
+    reports = spack.audit.run_group(args.subcommand, pkgs=pkgs)
+    _process_reports(reports)
+
+
+def list(parser, args):
+    for subcommand, check_tags in spack.audit.GROUPS.items():
+        print(cl.colorize('@*b{' + subcommand + '}:'))
+        for tag in check_tags:
+            audit_obj = spack.audit.CALLBACKS[tag]
+            print('  ' + audit_obj.description)
+            if args.verbose:
+                for idx, fn in enumerate(audit_obj.callbacks):
+                    print('    {0}. '.format(idx + 1) + fn.__doc__)
+                print()
+        print()
+
+
+def audit(parser, args):
+    subcommands = {
+        'configs': configs,
+        'packages': packages,
+        'list': list
+    }
+    subcommands[args.subcommand](parser, args)
+
+
+def _process_reports(reports):
+    for check, errors in reports:
+        if errors:
+            msg = '{0}: {1} issue{2} found'.format(
+                check, len(errors), '' if len(errors) == 1 else 's'
+            )
+            header = '@*b{' + msg + '}'
+            print(cl.colorize(header))
+            for idx, error in enumerate(errors):
+                print(str(idx + 1) + '. ' + str(error))
+            raise SystemExit(1)
+        else:
+            msg = '{0}: 0 issues found.'.format(check)
+            header = '@*b{' + msg + '}'
+            print(cl.colorize(header))

lib/spack/spack/cmd/blame.py

@@ -8,16 +8,15 @@
 import sys
 
 import llnl.util.tty as tty
-from llnl.util.lang import pretty_date
 from llnl.util.filesystem import working_dir
+from llnl.util.lang import pretty_date
 from llnl.util.tty.colify import colify_table
-import spack.util.spack_json as sjson
 
 import spack.paths
 import spack.repo
-from spack.util.executable import which
+import spack.util.spack_json as sjson
 from spack.cmd import spack_is_git_repo
-
+from spack.util.executable import which
 
 description = "show contributors to packages"
 section = "developer"

lib/spack/spack/cmd/bootstrap.py

@@ -0,0 +1,218 @@
+# Copyright 2013-2021 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)
+import os.path
+import shutil
+
+import llnl.util.tty
+import llnl.util.tty.color
+
+import spack.cmd.common.arguments
+import spack.config
+import spack.main
+import spack.util.path
+
+description = "manage bootstrap configuration"
+section = "system"
+level = "long"
+
+
+def _add_scope_option(parser):
+    scopes = spack.config.scopes()
+    scopes_metavar = spack.config.scopes_metavar
+    parser.add_argument(
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        help="configuration scope to read/modify"
+    )
+
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(dest='subcommand')
+
+    enable = sp.add_parser('enable', help='enable bootstrapping')
+    _add_scope_option(enable)
+
+    disable = sp.add_parser('disable', help='disable bootstrapping')
+    _add_scope_option(disable)
+
+    reset = sp.add_parser(
+        'reset', help='reset bootstrapping configuration to Spack defaults'
+    )
+    spack.cmd.common.arguments.add_common_arguments(
+        reset, ['yes_to_all']
+    )
+
+    root = sp.add_parser(
+        'root', help='get/set the root bootstrap directory'
+    )
+    _add_scope_option(root)
+    root.add_argument(
+        'path', nargs='?', default=None,
+        help='set the bootstrap directory to this value'
+    )
+
+    list = sp.add_parser(
+        'list', help='list the methods available for bootstrapping'
+    )
+    _add_scope_option(list)
+
+    trust = sp.add_parser(
+        'trust', help='trust a bootstrapping method'
+    )
+    _add_scope_option(trust)
+    trust.add_argument(
+        'name', help='name of the method to be trusted'
+    )
+
+    untrust = sp.add_parser(
+        'untrust', help='untrust a bootstrapping method'
+    )
+    _add_scope_option(untrust)
+    untrust.add_argument(
+        'name', help='name of the method to be untrusted'
+    )
+
+
+def _enable_or_disable(args):
+    # Set to True if we called "enable", otherwise set to false
+    value = args.subcommand == 'enable'
+    spack.config.set('bootstrap:enable', value, scope=args.scope)
+
+
+def _reset(args):
+    if not args.yes_to_all:
+        msg = [
+            "Bootstrapping configuration is being reset to Spack's defaults. "
+            "Current configuration will be lost.\n",
+            "Do you want to continue?"
+        ]
+        ok_to_continue = llnl.util.tty.get_yes_or_no(
+            ''.join(msg), default=True
+        )
+        if not ok_to_continue:
+            raise RuntimeError('Aborting')
+
+    for scope in spack.config.config.file_scopes:
+        # The default scope should stay untouched
+        if scope.name == 'defaults':
+            continue
+
+        # If we are in an env scope we can't delete a file, but the best we
+        # can do is nullify the corresponding configuration
+        if (scope.name.startswith('env') and
+                spack.config.get('bootstrap', scope=scope.name)):
+            spack.config.set('bootstrap', {}, scope=scope.name)
+            continue
+
+        # If we are outside of an env scope delete the bootstrap.yaml file
+        bootstrap_yaml = os.path.join(scope.path, 'bootstrap.yaml')
+        backup_file = bootstrap_yaml + '.bkp'
+        if os.path.exists(bootstrap_yaml):
+            shutil.move(bootstrap_yaml, backup_file)
+
+
+def _root(args):
+    if args.path:
+        spack.config.set('bootstrap:root', args.path, scope=args.scope)
+
+    root = spack.config.get('bootstrap:root', default=None, scope=args.scope)
+    if root:
+        root = spack.util.path.canonicalize_path(root)
+    print(root)
+
+
+def _list(args):
+    sources = spack.config.get(
+        'bootstrap:sources', default=None, scope=args.scope
+    )
+
+    if not sources:
+        llnl.util.tty.msg(
+            "No method available for bootstrapping Spack's dependencies"
+        )
+        return
+
+    def _print_method(source, trusted):
+        color = llnl.util.tty.color
+
+        def fmt(header, content):
+            header_fmt = "@*b{{{0}:}} {1}"
+            color.cprint(header_fmt.format(header, content))
+
+        trust_str = "@*y{UNKNOWN}"
+        if trusted is True:
+            trust_str = "@*g{TRUSTED}"
+        elif trusted is False:
+            trust_str = "@*r{UNTRUSTED}"
+
+        fmt("Name", source['name'] + ' ' + trust_str)
+        print()
+        fmt("  Type", source['type'])
+        print()
+
+        info_lines = ['\n']
+        for key, value in source.get('info', {}).items():
+            info_lines.append(' ' * 4 + '@*{{{0}}}: {1}\n'.format(key, value))
+        if len(info_lines) > 1:
+            fmt("  Info", ''.join(info_lines))
+
+        description_lines = ['\n']
+        for line in source['description'].split('\n'):
+            description_lines.append(' ' * 4 + line + '\n')
+
+        fmt("  Description", ''.join(description_lines))
+
+    trusted = spack.config.get('bootstrap:trusted', {})
+    for s in sources:
+        _print_method(s, trusted.get(s['name'], None))
+
+
+def _write_trust_state(args, value):
+    name = args.name
+    sources = spack.config.get('bootstrap:sources')
+
+    matches = [s for s in sources if s['name'] == name]
+    if not matches:
+        names = [s['name'] for s in sources]
+        msg = ('there is no bootstrapping method named "{0}". Valid '
+               'method names are: {1}'.format(name, ', '.join(names)))
+        raise RuntimeError(msg)
+
+    if len(matches) > 1:
+        msg = ('there is more than one bootstrapping method named "{0}". '
+               'Please delete all methods but one from bootstrap.yaml '
+               'before proceeding').format(name)
+        raise RuntimeError(msg)
+
+    # Setting the scope explicitly is needed to not copy over to a new scope
+    # the entire default configuration for bootstrap.yaml
+    scope = args.scope or spack.config.default_modify_scope('bootstrap')
+    spack.config.add(
+        'bootstrap:trusted:{0}:{1}'.format(name, str(value)), scope=scope
+    )
+
+
+def _trust(args):
+    _write_trust_state(args, value=True)
+    msg = '"{0}" is now trusted for bootstrapping'
+    llnl.util.tty.msg(msg.format(args.name))
+
+
+def _untrust(args):
+    _write_trust_state(args, value=False)
+    msg = '"{0}" is now untrusted and will not be used for bootstrapping'
+    llnl.util.tty.msg(msg.format(args.name))
+
+
+def bootstrap(parser, args):
+    callbacks = {
+        'enable': _enable_or_disable,
+        'disable': _enable_or_disable,
+        'reset': _reset,
+        'root': _root,
+        'list': _list,
+        'trust': _trust,
+        'untrust': _untrust
+    }
+    callbacks[args.subcommand](args)

lib/spack/spack/cmd/buildcache.py

@@ -2,34 +2,36 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
+import argparse
 import os
 import shutil
 import sys
+import tempfile
 
 import llnl.util.tty as tty
+
 import spack.architecture
 import spack.binary_distribution as bindist
 import spack.cmd
 import spack.cmd.common.arguments as arguments
+import spack.config
 import spack.environment as ev
+import spack.fetch_strategy as fs
 import spack.hash_types as ht
 import spack.mirror
 import spack.relocate
 import spack.repo
 import spack.spec
 import spack.store
-import spack.config
-import spack.repo
-import spack.store
+import spack.util.crypto
 import spack.util.url as url_util
-
+import spack.util.web as web_util
+from spack.cmd import display_specs
 from spack.error import SpecError
 from spack.spec import Spec, save_dependency_spec_yamls
+from spack.stage import Stage
 from spack.util.string import plural
 
-from spack.cmd import display_specs
-
 description = "create, download and install binary packages"
 section = "packaging"
 level = "long"
@@ -100,6 +102,8 @@ def setup_parser(subparser):
     install.add_argument('-o', '--otherarch', action='store_true',
                          help="install specs from other architectures" +
                               " instead of default platform and OS")
+    # This argument is needed by the bootstrapping logic to verify checksums
+    install.add_argument('--sha256', help=argparse.SUPPRESS)
 
     arguments.add_common_arguments(install, ['specs'])
     install.set_defaults(func=installtarball)
@@ -226,6 +230,36 @@ def setup_parser(subparser):
         help='Destination mirror url')
     copy.set_defaults(func=buildcache_copy)
 
+    # Sync buildcache entries from one mirror to another
+    sync = subparsers.add_parser('sync', help=buildcache_sync.__doc__)
+    source = sync.add_mutually_exclusive_group(required=True)
+    source.add_argument('--src-directory',
+                        metavar='DIRECTORY',
+                        type=str,
+                        help="Source mirror as a local file path")
+    source.add_argument('--src-mirror-name',
+                        metavar='MIRROR_NAME',
+                        type=str,
+                        help="Name of the source mirror")
+    source.add_argument('--src-mirror-url',
+                        metavar='MIRROR_URL',
+                        type=str,
+                        help="URL of the source mirror")
+    dest = sync.add_mutually_exclusive_group(required=True)
+    dest.add_argument('--dest-directory',
+                      metavar='DIRECTORY',
+                      type=str,
+                      help="Destination mirror as a local file path")
+    dest.add_argument('--dest-mirror-name',
+                      metavar='MIRROR_NAME',
+                      type=str,
+                      help="Name of the destination mirror")
+    dest.add_argument('--dest-mirror-url',
+                      metavar='MIRROR_URL',
+                      type=str,
+                      help="URL of the destination mirror")
+    sync.set_defaults(func=buildcache_sync)
+
     # Update buildcache index without copying any additional packages
     update_index = subparsers.add_parser(
         'update-index', help=buildcache_update_index.__doc__)
@@ -242,12 +276,13 @@ def find_matching_specs(pkgs, allow_multiple_matches=False, env=None):
        concretized specs given from cli
 
     Args:
-        pkgs (string): spec to be matched against installed packages
+        pkgs (str): spec to be matched against installed packages
         allow_multiple_matches (bool): if True multiple matches are admitted
-        env (Environment): active environment, or ``None`` if there is not one
+        env (spack.environment.Environment or None): active environment, or ``None``
+            if there is not one
 
     Return:
-        list of specs
+        list: list of specs
     """
     hashes = env.all_hashes() if env else None
 
@@ -497,6 +532,15 @@ def install_tarball(spec, args):
     else:
         tarball = bindist.download_tarball(spec)
         if tarball:
+            if args.sha256:
+                checker = spack.util.crypto.Checker(args.sha256)
+                msg = ('cannot verify checksum for "{0}"'
+                       ' [expected={1}]')
+                msg = msg.format(tarball, args.sha256)
+                if not checker.check(tarball):
+                    raise spack.binary_distribution.NoChecksumException(msg)
+                tty.debug('Verified SHA256 checksum of the build cache')
+
             tty.msg('Installing buildcache for spec %s' % spec.format())
             bindist.extract_tarball(spec, tarball, args.allow_root,
                                     args.unsigned, args.force)
@@ -769,6 +813,123 @@ def buildcache_copy(args):
         shutil.copyfile(cdashid_src_path, cdashid_dest_path)
 
 
+def buildcache_sync(args):
+    """ Syncs binaries (and associated metadata) from one mirror to another.
+    Requires an active environment in order to know which specs to sync.
+
+    Args:
+        src (str): Source mirror URL
+        dest (str): Destination mirror URL
+    """
+    # Figure out the source mirror
+    source_location = None
+    if args.src_directory:
+        source_location = args.src_directory
+        scheme = url_util.parse(source_location, scheme='<missing>').scheme
+        if scheme != '<missing>':
+            raise ValueError(
+                '"--src-directory" expected a local path; got a URL, instead')
+        # Ensure that the mirror lookup does not mistake this for named mirror
+        source_location = 'file://' + source_location
+    elif args.src_mirror_name:
+        source_location = args.src_mirror_name
+        result = spack.mirror.MirrorCollection().lookup(source_location)
+        if result.name == "<unnamed>":
+            raise ValueError(
+                'no configured mirror named "{name}"'.format(
+                    name=source_location))
+    elif args.src_mirror_url:
+        source_location = args.src_mirror_url
+        scheme = url_util.parse(source_location, scheme='<missing>').scheme
+        if scheme == '<missing>':
+            raise ValueError(
+                '"{url}" is not a valid URL'.format(url=source_location))
+
+    src_mirror = spack.mirror.MirrorCollection().lookup(source_location)
+    src_mirror_url = url_util.format(src_mirror.fetch_url)
+
+    # Figure out the destination mirror
+    dest_location = None
+    if args.dest_directory:
+        dest_location = args.dest_directory
+        scheme = url_util.parse(dest_location, scheme='<missing>').scheme
+        if scheme != '<missing>':
+            raise ValueError(
+                '"--dest-directory" expected a local path; got a URL, instead')
+        # Ensure that the mirror lookup does not mistake this for named mirror
+        dest_location = 'file://' + dest_location
+    elif args.dest_mirror_name:
+        dest_location = args.dest_mirror_name
+        result = spack.mirror.MirrorCollection().lookup(dest_location)
+        if result.name == "<unnamed>":
+            raise ValueError(
+                'no configured mirror named "{name}"'.format(
+                    name=dest_location))
+    elif args.dest_mirror_url:
+        dest_location = args.dest_mirror_url
+        scheme = url_util.parse(dest_location, scheme='<missing>').scheme
+        if scheme == '<missing>':
+            raise ValueError(
+                '"{url}" is not a valid URL'.format(url=dest_location))
+
+    dest_mirror = spack.mirror.MirrorCollection().lookup(dest_location)
+    dest_mirror_url = url_util.format(dest_mirror.fetch_url)
+
+    # Get the active environment
+    env = ev.get_env(args, 'buildcache sync', required=True)
+
+    tty.msg('Syncing environment buildcache files from {0} to {1}'.format(
+        src_mirror_url, dest_mirror_url))
+
+    build_cache_dir = bindist.build_cache_relative_path()
+    buildcache_rel_paths = []
+
+    tty.debug('Syncing the following specs:')
+    for s in env.all_specs():
+        tty.debug('  {0}{1}: {2}'.format(
+            '* ' if s in env.roots() else '  ', s.name, s.dag_hash()))
+
+        buildcache_rel_paths.extend([
+            os.path.join(
+                build_cache_dir, bindist.tarball_path_name(s, '.spack')),
+            os.path.join(
+                build_cache_dir, bindist.tarball_name(s, '.spec.yaml')),
+            os.path.join(
+                build_cache_dir, bindist.tarball_name(s, '.cdashid'))
+        ])
+
+    tmpdir = tempfile.mkdtemp()
+
+    try:
+        for rel_path in buildcache_rel_paths:
+            src_url = url_util.join(src_mirror_url, rel_path)
+            local_path = os.path.join(tmpdir, rel_path)
+            dest_url = url_util.join(dest_mirror_url, rel_path)
+
+            tty.debug('Copying {0} to {1} via {2}'.format(
+                src_url, dest_url, local_path))
+
+            stage = Stage(src_url,
+                          name="temporary_file",
+                          path=os.path.dirname(local_path),
+                          keep=True)
+
+            try:
+                stage.create()
+                stage.fetch()
+                web_util.push_to_url(
+                    local_path,
+                    dest_url,
+                    keep_original=True)
+            except fs.FetchError as e:
+                tty.debug('spack buildcache unable to sync {0}'.format(rel_path))
+                tty.debug(e)
+            finally:
+                stage.destroy()
+    finally:
+        shutil.rmtree(tmpdir)
+
+
 def update_index(mirror_url, update_keys=False):
     mirror = spack.mirror.MirrorCollection().lookup(mirror_url)
     outdir = url_util.format(mirror.push_url)

lib/spack/spack/cmd/checksum.py

@@ -15,7 +15,7 @@
 import spack.stage
 import spack.util.crypto
 from spack.util.naming import valid_fully_qualified_module_name
-from spack.version import ver, Version
+from spack.version import Version, ver
 
 description = "checksum available versions of a package"
 section = "packaging"

lib/spack/spack/cmd/ci.py

@@ -17,20 +17,21 @@
 
 import spack.binary_distribution as bindist
 import spack.ci as spack_ci
-import spack.config as cfg
 import spack.cmd.buildcache as buildcache
+import spack.config as cfg
 import spack.environment as ev
 import spack.hash_types as ht
 import spack.mirror
+import spack.util.spack_yaml as syaml
 import spack.util.url as url_util
 import spack.util.web as web_util
 
-
 description = "manage continuous integration pipelines"
 section = "build"
 level = "long"
 
 CI_REBUILD_INSTALL_BASE_ARGS = ['spack', '-d', '-v']
+INSTALL_FAIL_CODE = 1
 
 
 def get_env_var(variable_name):
@@ -196,8 +197,7 @@ def ci_rebuild(args):
     compiler_action = get_env_var('SPACK_COMPILER_ACTION')
     cdash_build_name = get_env_var('SPACK_CDASH_BUILD_NAME')
     related_builds = get_env_var('SPACK_RELATED_BUILDS_CDASH')
-    pr_env_var = get_env_var('SPACK_IS_PR_PIPELINE')
-    dev_env_var = get_env_var('SPACK_IS_DEVELOP_PIPELINE')
+    spack_pipeline_type = get_env_var('SPACK_PIPELINE_TYPE')
     pr_mirror_url = get_env_var('SPACK_PR_MIRROR_URL')
     remote_mirror_url = get_env_var('SPACK_REMOTE_MIRROR_URL')
 
@@ -231,7 +231,6 @@ def ci_rebuild(args):
         eq_idx = proj_enc.find('=') + 1
         cdash_project_enc = proj_enc[eq_idx:]
         cdash_site = ci_cdash['site']
-        cdash_id_path = os.path.join(repro_dir, 'cdash_id.txt')
         tty.debug('cdash_base_url = {0}'.format(cdash_base_url))
         tty.debug('cdash_project = {0}'.format(cdash_project))
         tty.debug('cdash_project_enc = {0}'.format(cdash_project_enc))
@@ -242,8 +241,11 @@ def ci_rebuild(args):
 
     # Is this a pipeline run on a spack PR or a merge to develop?  It might
     # be neither, e.g. a pipeline run on some environment repository.
-    spack_is_pr_pipeline = True if pr_env_var == 'True' else False
-    spack_is_develop_pipeline = True if dev_env_var == 'True' else False
+    spack_is_pr_pipeline = spack_pipeline_type == 'spack_pull_request'
+    spack_is_develop_pipeline = spack_pipeline_type == 'spack_protected_branch'
+
+    tty.debug('Pipeline type - PR: {0}, develop: {1}'.format(
+        spack_is_pr_pipeline, spack_is_develop_pipeline))
 
     # Figure out what is our temporary storage mirror: Is it artifacts
     # buildcache?  Or temporary-storage-url-prefix?  In some cases we need to
@@ -396,7 +398,7 @@ def ci_rebuild(args):
                 job_spec_pkg_name, matching_mirror))
             tty.debug('Downloading to {0}'.format(build_cache_dir))
             buildcache.download_buildcache_files(
-                job_spec, build_cache_dir, True, matching_mirror)
+                job_spec, build_cache_dir, False, matching_mirror)
 
         # Now we are done and successful
         sys.exit(0)
@@ -431,24 +433,21 @@ def ci_rebuild(args):
             cdash_build_name, cdash_base_url, cdash_project,
             cdash_site, job_spec_buildgroup)
 
-        cdash_upload_url = '{0}/submit.php?project={1}'.format(
-            cdash_base_url, cdash_project_enc)
+        if cdash_build_id is not None:
+            cdash_upload_url = '{0}/submit.php?project={1}'.format(
+                cdash_base_url, cdash_project_enc)
 
-        install_args.extend([
-            '--cdash-upload-url', cdash_upload_url,
-            '--cdash-build', cdash_build_name,
-            '--cdash-site', cdash_site,
-            '--cdash-buildstamp', cdash_build_stamp,
-        ])
+            install_args.extend([
+                '--cdash-upload-url', cdash_upload_url,
+                '--cdash-build', cdash_build_name,
+                '--cdash-site', cdash_site,
+                '--cdash-buildstamp', cdash_build_stamp,
+            ])
 
-        tty.debug('CDash: Relating build with dependency builds')
-        spack_ci.relate_cdash_builds(
-            spec_map, cdash_base_url, cdash_build_id, cdash_project,
-            [pipeline_mirror_url, pr_mirror_url, remote_mirror_url])
-
-        # store the cdash build id on disk for later
-        with open(cdash_id_path, 'w') as fd:
-            fd.write(cdash_build_id)
+            tty.debug('CDash: Relating build with dependency builds')
+            spack_ci.relate_cdash_builds(
+                spec_map, cdash_base_url, cdash_build_id, cdash_project,
+                [pipeline_mirror_url, pr_mirror_url, remote_mirror_url])
 
     # A compiler action of 'FIND_ANY' means we are building a bootstrap
     # compiler or one of its deps.
@@ -494,17 +493,28 @@ def ci_rebuild(args):
     # If a spec fails to build in a spack develop pipeline, we add it to a
     # list of known broken full hashes.  This allows spack PR pipelines to
     # avoid wasting compute cycles attempting to build those hashes.
-    if install_exit_code != 0 and spack_is_develop_pipeline:
+    if install_exit_code == INSTALL_FAIL_CODE and spack_is_develop_pipeline:
+        tty.debug('Install failed on develop')
         if 'broken-specs-url' in gitlab_ci:
             broken_specs_url = gitlab_ci['broken-specs-url']
             dev_fail_hash = job_spec.full_hash()
             broken_spec_path = url_util.join(broken_specs_url, dev_fail_hash)
+            tty.msg('Reporting broken develop build as: {0}'.format(
+                broken_spec_path))
             tmpdir = tempfile.mkdtemp()
             empty_file_path = os.path.join(tmpdir, 'empty.txt')
 
+            broken_spec_details = {
+                'broken-spec': {
+                    'job-url': get_env_var('CI_JOB_URL'),
+                    'pipeline-url': get_env_var('CI_PIPELINE_URL'),
+                    'concrete-spec-yaml': job_spec.to_dict(hash=ht.full_hash)
+                }
+            }
+
             try:
                 with open(empty_file_path, 'w') as efd:
-                    efd.write('')
+                    efd.write(syaml.dump(broken_spec_details))
                 web_util.push_to_url(
                     empty_file_path,
                     broken_spec_path,
@@ -541,17 +551,51 @@ def ci_rebuild(args):
 
         # Create buildcache in either the main remote mirror, or in the
         # per-PR mirror, if this is a PR pipeline
-        spack_ci.push_mirror_contents(
-            env, job_spec, job_spec_yaml_path, buildcache_mirror_url,
-            cdash_build_id, sign_binaries)
+        if buildcache_mirror_url:
+            spack_ci.push_mirror_contents(
+                env, job_spec, job_spec_yaml_path, buildcache_mirror_url,
+                sign_binaries)
+
+            if cdash_build_id:
+                tty.debug('Writing cdashid ({0}) to remote mirror: {1}'.format(
+                    cdash_build_id, buildcache_mirror_url))
+                spack_ci.write_cdashid_to_mirror(
+                    cdash_build_id, job_spec, buildcache_mirror_url)
 
         # Create another copy of that buildcache in the per-pipeline
         # temporary storage mirror (this is only done if either
         # artifacts buildcache is enabled or a temporary storage url
         # prefix is set)
-        spack_ci.push_mirror_contents(
-            env, job_spec, job_spec_yaml_path, pipeline_mirror_url,
-            cdash_build_id, sign_binaries)
+        if pipeline_mirror_url:
+            spack_ci.push_mirror_contents(
+                env, job_spec, job_spec_yaml_path, pipeline_mirror_url,
+                sign_binaries)
+
+            if cdash_build_id:
+                tty.debug('Writing cdashid ({0}) to remote mirror: {1}'.format(
+                    cdash_build_id, pipeline_mirror_url))
+                spack_ci.write_cdashid_to_mirror(
+                    cdash_build_id, job_spec, pipeline_mirror_url)
+
+        # If this is a develop pipeline, check if the spec that we just built is
+        # on the broken-specs list. If so, remove it.
+        if spack_is_develop_pipeline and 'broken-specs-url' in gitlab_ci:
+            broken_specs_url = gitlab_ci['broken-specs-url']
+            just_built_hash = job_spec.full_hash()
+            broken_spec_path = url_util.join(broken_specs_url, just_built_hash)
+            if web_util.url_exists(broken_spec_path):
+                tty.msg('Removing {0} from the list of broken specs'.format(
+                    broken_spec_path))
+                try:
+                    web_util.remove_url(broken_spec_path)
+                except Exception as err:
+                    # If we got some kind of S3 (access denied or other connection
+                    # error), the first non boto-specific class in the exception
+                    # hierarchy is Exception.  Just print a warning and return
+                    msg = 'Error removing {0} from broken specs list: {1}'.format(
+                        broken_spec_path, err)
+                    tty.warn(msg)
+
     else:
         tty.debug('spack install exited non-zero, will not create buildcache')
 
@@ -580,16 +624,16 @@ def ci_rebuild(args):
         print(reproduce_msg)
 
     # Tie job success/failure to the success/failure of building the spec
-    sys.exit(install_exit_code)
+    return install_exit_code
 
 
 def ci_reproduce(args):
     job_url = args.job_url
     work_dir = args.working_dir
 
-    spack_ci.reproduce_ci_job(job_url, work_dir)
+    return spack_ci.reproduce_ci_job(job_url, work_dir)
 
 
 def ci(parser, args):
     if args.func:
-        args.func(args)
+        return args.func(args)

lib/spack/spack/cmd/clean.py

@@ -9,16 +9,16 @@
 
 import llnl.util.tty as tty
 
+import spack.bootstrap
 import spack.caches
-import spack.config
-import spack.cmd.test
 import spack.cmd.common.arguments as arguments
+import spack.cmd.test
+import spack.config
 import spack.main
 import spack.repo
 import spack.stage
 from spack.paths import lib_path, var_path
 
-
 description = "remove temporary build files and/or downloaded archives"
 section = "build"
 level = "long"
@@ -103,7 +103,7 @@ def clean(parser, args):
 
     if args.bootstrap:
         msg = 'Removing software in "{0}"'
-        tty.msg(msg.format(spack.paths.user_bootstrap_store))
-        with spack.store.use_store(spack.paths.user_bootstrap_store):
+        tty.msg(msg.format(spack.bootstrap.store_path()))
+        with spack.store.use_store(spack.bootstrap.store_path()):
             uninstall = spack.main.SpackCommand('uninstall')
             uninstall('-a', '-y')

lib/spack/spack/cmd/commands.py

@@ -14,7 +14,9 @@
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 from llnl.util.argparsewriter import (
-    ArgparseWriter, ArgparseRstWriter, ArgparseCompletionWriter
+    ArgparseCompletionWriter,
+    ArgparseRstWriter,
+    ArgparseWriter,
 )
 from llnl.util.tty.colify import colify
 
@@ -23,7 +25,6 @@
 import spack.paths
 from spack.main import section_descriptions
 
-
 description = "list available spack commands"
 section = "developer"
 level = "long"

lib/spack/spack/cmd/common/env_utility.py

@@ -8,10 +8,11 @@
 import os
 
 import llnl.util.tty as tty
+
 import spack.build_environment as build_environment
-import spack.paths
 import spack.cmd
 import spack.cmd.common.arguments as arguments
+import spack.paths
 from spack.util.environment import dump_environment, pickle_environment