Merge branch 'udev' into odev

teonnik · Feb 1, 2022 · 2654545 · 2654545
2 parents 88fbef2 + 4b52f0e
commit 2654545
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diff --git a/.github/workflows/bootstrap.yml b/.github/workflows/bootstrap.yml
@@ -158,7 +158,7 @@ jobs:
         run: |
           brew install tree
       - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-      - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+      - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
         with:
           python-version: ${{ matrix.python-version }}
       - name: Bootstrap clingo
@@ -175,7 +175,7 @@ jobs:
         python-version: ['2.7', '3.5', '3.6', '3.7', '3.8', '3.9']
     steps:
       - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-      - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+      - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
         with:
           python-version: ${{ matrix.python-version }}
       - name: Setup repo and non-root user

diff --git a/.github/workflows/build-containers.yml b/.github/workflows/build-containers.yml
@@ -12,6 +12,7 @@ on:
       - develop
     paths:
       - '.github/workflows/build-containers.yml'
+      - 'share/spack/docker/*'
   # Let's also build & tag Spack containers on releases.
   release:
     types: [published]
@@ -66,20 +67,21 @@ jobs:
         uses: docker/setup-buildx-action@94ab11c41e45d028884a99163086648e898eed25 # @v1
 
       - name: Log in to GitHub Container Registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 # @v1
+        uses: docker/login-action@42d299face0c5c43a0487c477f595ac9cf22f1a7 # @v1
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Log in to DockerHub
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 # @v1
+        if: ${{ github.event_name != 'pull_request' }}
+        uses: docker/login-action@42d299face0c5c43a0487c477f595ac9cf22f1a7 # @v1
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build & Deploy ${{ matrix.dockerfile[1] }}
-        uses: docker/build-push-action@a66e35b9cbcf4ad0ea91ffcaf7bbad63ad9e0229 # @v2
+        uses: docker/build-push-action@1814d3dfb36d6f84174e61f4a4b05bd84089a4b9 # @v2
         with:
           file: share/spack/docker/${{matrix.dockerfile[1]}}
           platforms: ${{ matrix.dockerfile[2] }}

diff --git a/.github/workflows/install_spack.sh b/.github/workflows/install_spack.sh
@@ -2,19 +2,7 @@
 . share/spack/setup-env.sh
 echo -e "config:\n  build_jobs: 2" > etc/spack/config.yaml
 spack config add "packages:all:target:[x86_64]"
-# TODO: remove this explicit setting once apple-clang detection is fixed
-cat <<EOF > etc/spack/compilers.yaml
-compilers:
-- compiler:
-    spec: apple-clang@11.0.3
-    paths:
-      cc: /usr/bin/clang
-      cxx: /usr/bin/clang++
-      f77: /usr/local/bin/gfortran-9
-      fc: /usr/local/bin/gfortran-9
-    modules: []
-    operating_system: catalina
-    target: x86_64
-EOF
+spack compiler find
 spack compiler info apple-clang
 spack debug report
+spack solve zlib
diff --git a/.github/workflows/macos_python.yml b/.github/workflows/macos_python.yml
@@ -25,7 +25,7 @@ jobs:
     runs-on: macos-latest
     steps:
     - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-    - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
       with:
         python-version: 3.9
     - name: spack install
@@ -40,7 +40,7 @@ jobs:
     timeout-minutes: 700
     steps:
     - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-    - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
       with:
         python-version: 3.9
     - name: spack install
@@ -53,7 +53,7 @@ jobs:
     runs-on: macos-latest
     steps:
     - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-    - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
       with:
         python-version: 3.9
     - name: spack install

diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
-    - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
       with:
         python-version: 3.9
     - name: Install Python Packages
@@ -34,7 +34,7 @@ jobs:
     - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
       with:
         python-version: 3.9
     - name: Install Python packages
@@ -97,12 +97,19 @@ jobs:
     strategy:
       matrix:
         python-version: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9]
-        concretizer: ['original', 'clingo']
+        concretizer: ['clingo']
+        include:
+        - python-version: 2.7
+          concretizer: original
+        - python-version: 3.6
+          concretizer: original
+        - python-version: 3.9
+          concretizer: original
     steps:
     - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install System packages
@@ -114,7 +121,7 @@ jobs:
               patchelf cmake bison libbison-dev kcov
     - name: Install Python packages
       run: |
-          pip install --upgrade pip six setuptools pytest codecov coverage[toml]
+          pip install --upgrade pip six setuptools pytest codecov "coverage[toml]<=6.2"
           # 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
@@ -163,7 +170,7 @@ jobs:
     - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
       with:
         python-version: 3.9
     - name: Install System packages
@@ -173,7 +180,7 @@ jobs:
           sudo apt-get install -y coreutils kcov csh zsh tcsh fish dash bash
     - name: Install Python packages
       run: |
-          pip install --upgrade pip six setuptools pytest codecov coverage[toml]
+          pip install --upgrade pip six setuptools pytest codecov coverage[toml]==6.2
     - name: Setup git configuration
       run: |
           # Need this for the git tests to succeed.
@@ -229,7 +236,7 @@ jobs:
     - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
       with:
         python-version: 3.9
     - name: Install System packages
@@ -241,7 +248,7 @@ jobs:
               patchelf kcov
     - name: Install Python packages
       run: |
-          pip install --upgrade pip six setuptools pytest codecov coverage[toml] clingo
+          pip install --upgrade pip six setuptools pytest codecov coverage[toml]==6.2 clingo
     - name: Setup git configuration
       run: |
           # Need this for the git tests to succeed.
@@ -278,13 +285,13 @@ jobs:
     - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@dc73133d4da04e56a135ae2246682783cc7c7cb6 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Python packages
       run: |
           pip install --upgrade pip six setuptools
-          pip install --upgrade pytest codecov coverage[toml]
+          pip install --upgrade pytest codecov coverage[toml]==6.2
     - name: Setup Homebrew packages
       run: |
         brew install dash fish gcc gnupg2 kcov
@@ -314,3 +321,32 @@ jobs:
       with:
         files: ./coverage.xml
         flags: unittests,macos
+
+  # Run audits on all the packages in the built-in repository
+  package-audits:
+    needs: [ validate, style, changes ]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
+    - uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
+      with:
+        python-version: 3.9
+    - name: Install Python packages
+      run: |
+        pip install --upgrade pip six setuptools pytest codecov coverage[toml]==6.2
+    - name: Package audits (with coverage)
+      if: ${{ needs.changes.outputs.with_coverage == 'true' }}
+      run: |
+          . share/spack/setup-env.sh
+          coverage run $(which spack) audit packages
+          coverage combine
+          coverage xml
+    - name: Package audits (wwithout coverage)
+      if: ${{ needs.changes.outputs.with_coverage == 'false' }}
+      run: |
+          . share/spack/setup-env.sh
+          $(which spack) audit packages
+    - uses: codecov/codecov-action@f32b3a3741e1053eb607407145bc9619351dc93b # @v2.1.0
+      if: ${{ needs.changes.outputs.with_coverage == 'true' }}
+      with:
+        flags: unittests,linux,audits
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,28 @@
+# v0.17.1 (2021-12-23)
+
+### Spack Bugfixes
+* Allow locks to work under high contention (#27846)
+* Improve errors messages from clingo (#27707 #27970)
+* Respect package permissions for sbang (#25764)
+* Fix --enable-locks behavior (#24675)
+* Fix log-format reporter ignoring install errors (#25961)
+* Fix overloaded argparse keys (#27379)
+* Allow style commands to run with targets other than "develop" (#27472)
+* Log lock messages to debug level, instead of verbose level (#27408)
+* Handle invalid unicode while logging (#21447)
+* spack audit: fix API calls to variants (#27713)
+* Provide meaningful message for empty environment installs (#28031)
+* Added opensuse leap containers to spack containerize (#27837)
+* Revert "patches: make re-applied patches idempotent" (#27625)
+* MANPATH can use system defaults (#21682)
+* Add "setdefault" subcommand to `spack module tcl` (#14686)
+* Regenerate views when specs already installed (#28113)
+
+### Package bugfixes
+* Fix external package detection for OpenMPI (#27255)
+* Update the UPC++ package to 2021.9.0 (#26996)
+* Added py-vermin v1.3.2 (#28072)
+
 # v0.17.0 (2021-11-05)
 
 `v0.17.0` is a major feature release.

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,58 @@
+# If you are referencing Spack in a publication, please cite the SC'15 paper
+# described here.
+#
+# Here's the raw citation:
+#
+#   Todd Gamblin, Matthew P. LeGendre, Michael R. Collette, Gregory L. Lee,
+#   Adam Moody, Bronis R. de Supinski, and W. Scott Futral.
+#   The Spack Package Manager: Bringing Order to HPC Software Chaos.
+#   In Supercomputing 2015 (SC’15), Austin, Texas, November 15-20 2015. LLNL-CONF-669890.
+#
+# Or, in BibTeX:
+#
+# @inproceedings{Gamblin_The_Spack_Package_2015,
+#     address = {Austin, Texas, USA},
+#     author = {Gamblin, Todd and LeGendre, Matthew and
+#               Collette, Michael R. and Lee, Gregory L. and
+#               Moody, Adam and de Supinski, Bronis R. and Futral, Scott},
+#     doi = {10.1145/2807591.2807623},
+#     month = {November 15-20},
+#     note = {LLNL-CONF-669890},
+#     series = {Supercomputing 2015 (SC’15)},
+#     title = {{The Spack Package Manager: Bringing Order to HPC Software Chaos}},
+#     url = {https://github.com/spack/spack},
+#     year = {2015}
+# }
+#
+# And here's the CITATION.cff format:
+#
+cff-version: 1.2.0
+message: "If you are referencing Spack in a publication, please cite the paper below."
+preferred-citation:
+  type: conference-paper
+  doi: "10.1145/2807591.2807623"
+  url: "https://github.com/spack/spack"
+  authors:
+  - family-names: "Gamblin"
+    given-names: "Todd"
+  - family-names: "LeGendre"
+    given-names: "Matthew"
+  - family-names: "Collette"
+    given-names: "Michael R."
+  - family-names: "Lee"
+    given-names: "Gregory L."
+  - family-names: "Moody"
+    given-names: "Adam"
+  - family-names: "de Supinski"
+    given-names: "Bronis R."
+  - family-names: "Futral"
+    given-names: "Scott"
+  title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
+  conference:
+    name: "Supercomputing 2015 (SC’15)"
+    city: "Austin"
+    region: "Texas"
+    country: "USA"
+  month: November 15-20
+  year: 2015
+  notes: LLNL-CONF-669890
diff --git a/COPYRIGHT b/COPYRIGHT
@@ -34,10 +34,22 @@ includes the sbang tool directly in bin/sbang. These packages are covered
 by various permissive licenses. A summary listing follows. See the
 license included with each package for full details.
 
+PackageName: altgraph
+PackageHomePage: https://altgraph.readthedocs.io/en/latest/index.html
+PackageLicenseDeclared: MIT
+
 PackageName: argparse
 PackageHomePage: https://pypi.python.org/pypi/argparse
 PackageLicenseDeclared: Python-2.0
 
+PackageName: astunparse
+PackageHomePage: https://github.com/simonpercivall/astunparse
+PackageLicenseDeclared: Python-2.0
+
+PackageName: attrs
+PackageHomePage: https://github.com/python-attrs/attrs
+PackageLicenseDeclared: MIT
+
 PackageName: ctest_log_parser
 PackageHomePage: https://github.com/Kitware/CMake
 PackageLicenseDeclared: BSD-3-Clause
@@ -46,8 +58,8 @@ PackageName: distro
 PackageHomePage: https://pypi.python.org/pypi/distro
 PackageLicenseDeclared: Apache-2.0
 
-PackageName: functools
-PackageHomePage: https://github.com/python/cpython/blob/2.7/Lib/functools.py
+PackageName: functools32
+PackageHomePage: https://github.com/MiCHiLU/python-functools32
 PackageLicenseDeclared: Python-2.0
 
 PackageName: jinja2
@@ -58,6 +70,10 @@ PackageName: jsonschema
 PackageHomePage: https://pypi.python.org/pypi/jsonschema
 PackageLicenseDeclared: MIT
 
+PackageName: macholib
+PackageHomePage: https://macholib.readthedocs.io/en/latest/index.html
+PackageLicenseDeclared: MIT
+
 PackageName: markupsafe
 PackageHomePage: https://pypi.python.org/pypi/MarkupSafe
 PackageLicenseDeclared: BSD-3-Clause
@@ -70,6 +86,10 @@ PackageName: py
 PackageHomePage: https://pypi.python.org/pypi/py
 PackageLicenseDeclared: MIT
 
+PackageName: pyrsistent
+PackageHomePage: http://github.com/tobgu/pyrsistent
+PackageLicenseDeclared: MIT
+
 PackageName: pytest
 PackageHomePage: https://pypi.python.org/pypi/pytest
 PackageLicenseDeclared: MIT
@@ -85,11 +105,3 @@ PackageLicenseDeclared: Apache-2.0 OR MIT
 PackageName: six
 PackageHomePage: https://pypi.python.org/pypi/six
 PackageLicenseDeclared: MIT
-
-PackageName: macholib
-PackageHomePage: https://macholib.readthedocs.io/en/latest/index.html
-PackageLicenseDeclared: MIT
-
-PackageName: altgraph
-PackageHomePage: https://altgraph.readthedocs.io/en/latest/index.html
-PackageLicenseDeclared: MIT
diff --git a/LICENSE-MIT b/LICENSE-MIT
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2013-2020 LLNS, LLC and other Spack Project Developers.
+Copyright (c) 2013-2022 LLNS, LLC and other Spack Project Developers.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal