actions{cache,checkout,setup-python} upgrades (#2856)

* CI: use `pip` directly (instead of `python -m pip`) * CI: checkout@v4, setup-python@v5 cache@v4 * disable setup-python cache for lint/pre-commit See actions/setup-python#919; setup-python cache likely doesn't help much here, as we only `pip install pre-commit`, and cache `~/.cache/pre-commit` separately using `actions/cache`. * bump to codecov-action@v4 rm coverage/uploader pin added in #2827, per codecov/uploader#1673 (comment) * `s/MacOS/macOS/ * fix typo from #2854
single-cell-data · Aug 8, 2024 · 7742bff · 7742bff
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diff --git a/.github/workflows/libtiledb-ci.yml b/.github/workflows/libtiledb-ci.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: macos-latest
     steps:
     - name: Checkout TileDB-SOMA
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Build libTileDB-SOMA
       run: TILEDBSOMA_COVERAGE="--coverage" ./scripts/bld --no-tiledb-deprecated=true
     - name: Run libTileDB-SOMA unittests

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -23,7 +23,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v1
         with:

diff --git a/.github/workflows/python-ci-packaging.yml b/.github/workflows/python-ci-packaging.yml
@@ -101,8 +101,8 @@ jobs:
         run: |
           python --version
           python -m venv ./venv-soma
-          ./venv-soma/bin/python -m pip install --prefer-binary pybind11-global typeguard sparse wheel
-          ./venv-soma/bin/python -m pip list
+          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel
+          ./venv-soma/bin/pip list
       - name: Build wheel
         run: |
           echo env vars: $LD_LIBRARY_PATH $PKG_CONFIG_PATH $TILEDB_PATH $TILEDBSOMA_PATH
@@ -133,7 +133,7 @@ jobs:
             exit 1
           fi
       - name: Install wheel
-        run: ./venv-soma/bin/python -m pip install --prefer-binary apis/python/dist/tiledbsoma-*.whl
+        run: ./venv-soma/bin/pip install --prefer-binary apis/python/dist/tiledbsoma-*.whl
       - name: Check linking and RPATH
         run: |
           ldd ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so
@@ -201,8 +201,8 @@ jobs:
         run: |
           python --version
           python -m venv ./venv-soma
-          ./venv-soma/bin/python -m pip install --prefer-binary pybind11-global typeguard sparse wheel setuptools
-          ./venv-soma/bin/python -m pip list
+          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel setuptools
+          ./venv-soma/bin/pip list
       - name: Build wheel
         run: |
           echo env vars: $DYLD_LIBRARY_PATH $PKG_CONFIG_PATH $TILEDB_PATH $TILEDBSOMA_PATH
@@ -233,7 +233,7 @@ jobs:
             exit 1
           fi
       - name: Install wheel
-        run: ./venv-soma/bin/python -m pip install --prefer-binary apis/python/dist/tiledbsoma-*.whl
+        run: ./venv-soma/bin/pip install --prefer-binary apis/python/dist/tiledbsoma-*.whl
       - name: Check linking and RPATH
         run: otool -L ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so
       - name: Runtime test
@@ -302,8 +302,8 @@ jobs:
         run: |
           python --version
           python -m venv ./venv-soma
-          ./venv-soma/bin/python -m pip install --prefer-binary pybind11-global typeguard sparse wheel setuptools
-          ./venv-soma/bin/python -m pip list
+          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel setuptools
+          ./venv-soma/bin/pip list
       - name: Install TileDB-SOMA-Py with setuptools and --libtiledbsoma
         run: |
           cd apis/python
@@ -323,7 +323,7 @@ jobs:
           otool -L ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so
           otool -l ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so
       - name: Install runtime dependencies
-        run: ./venv-soma/bin/python -m pip install --prefer-binary `grep -v '^\[' apis/python/src/tiledbsoma.egg-info/requires.txt`
+        run: ./venv-soma/bin/pip install --prefer-binary `grep -v '^\[' apis/python/src/tiledbsoma.egg-info/requires.txt`
       - name: Runtime test
         run: ./venv-soma/bin/python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
 
@@ -363,7 +363,7 @@ jobs:
         with:
           python-version: "3.11"
       - name: Install dependencies
-        run: python -m pip install --prefer-binary pybind11 wheel
+        run: pip install --prefer-binary pybind11 wheel
       - name: Build source tarball (sdist)
         run: |
           cd TileDB-SOMA/apis/python
@@ -378,5 +378,5 @@ jobs:
           python setup.py bdist_wheel
       - name: Install wheel
         run: |
-          python -m pip install --prefer-binary tiledbsoma-*/dist/tiledbsoma-*.whl
+          pip install --prefer-binary tiledbsoma-*/dist/tiledbsoma-*.whl
           python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
diff --git a/.github/workflows/python-ci-single.yml b/.github/workflows/python-ci-single.yml
@@ -33,26 +33,24 @@ jobs:
     runs-on: ${{ inputs.os }}
     steps:
     - name: Checkout TileDB-SOMA
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ inputs.python_version }}
-        cache: pip
-        cache-dependency-path: ./.github/workflows/python-ci-single.yml
 
     - name: Restore pre-commit cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pre-commit
         key: pre-commit-${{ inputs.os }}-${{ inputs.python_version }}-${{ hashFiles('.github/workflows/python-ci-single.yml', '.pre-commit-config.yaml') }}
 
     - name: Install pre-commit
-      run: python -m pip -v install pre-commit
+      run: pip -v install pre-commit
 
     - name: Log pip dependencies
-      run: python -m pip list
+      run: pip list
 
     - name: Run pre-commit hooks on all files
       run: pre-commit run -a -v
@@ -86,28 +84,28 @@ jobs:
         xcode-version: '13.4'
 
     - name: Checkout TileDB-SOMA
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0  # ensure we get all tags to inform package version determination
 
     - name: Set up Python ${{ inputs.python_version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ inputs.python_version }}
         cache: pip
         cache-dependency-path: ./apis/python/setup.py
 
-# Experiment for MacOS CI false negatives ...
+# Experiment for macOS CI false negatives ...
 #    - name: Cache native libraries
-#      uses: actions/cache@v3
+#      uses: actions/cache@v4
 #      with:
 #        path: |
 #          build
 #          dist
 #        key: libtiledbsoma-build-dist-${{ inputs.os }}-${{ inputs.python_version }}-${{ hashFiles('libtiledbsoma', 'scripts/bld') }}
 
     - name: Install tiledbsoma
-      run: python -m pip -v install -e apis/python[dev] -C "--build-option=--no-tiledb-deprecated"
+      run: pip -v install -e apis/python[dev] -C "--build-option=--no-tiledb-deprecated"
       env:
         CC: ${{ inputs.cc }}
         CXX: ${{ inputs.cxx }}
@@ -140,7 +138,7 @@ jobs:
 
     - name: Report coverage to Codecov
       if: inputs.report_codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         flags: python
         # Although Codecov isn't supposed to require an auth token for public repos like this one,
@@ -149,4 +147,3 @@ jobs:
         # As of this writing (8 Nov 2022) the CODECOV_TOKEN was generated by @aaronwolen in his
         # Codecov settings page for this repo, then filled into the GitHub Actions secrets.
         token: ${{ secrets.CODECOV_TOKEN }}
-        version: 'v0.7.3'
diff --git a/.github/workflows/python-packaging.yml b/.github/workflows/python-packaging.yml
@@ -78,7 +78,7 @@ jobs:
           echo matrix.platform: ${{ matrix.platform }}
           echo matrix.arch: ${{ matrix.arch }}
           # This bit is crucial since it's used to match up to a component of the wheel-file name
-          python -m pip install setuptools
+          pip install setuptools
           python -c 'from distutils import util; print("distutil.util.get_platform:", util.get_platform())'
           python -c 'import platform; print("platform.platform()", platform.platform())'
       - name: Build wheels
@@ -139,7 +139,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Set up Python ${{ matrix.python.dotted-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python.dotted-version }}
       - name: Download artifacts

diff --git a/.github/workflows/r-ci.yml b/.github/workflows/r-ci.yml
@@ -10,7 +10,7 @@ on:
       - '!.pre-commit-config.yaml'
       - '!apis/python/**'
       - '!docs/**'
-      - '!LICENSE''
+      - '!LICENSE'
   push:
     branches:
       - main
@@ -44,7 +44,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Show matrix OS
         run: echo "matrix.os:" ${{ matrix.os }}

diff --git a/.github/workflows/r-python-interop-testing.yml b/.github/workflows/r-python-interop-testing.yml
@@ -25,7 +25,7 @@ jobs:
 
     steps:
       - name: Checkout TileDB-SOMA
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0  # ensure we get all tags to inform package version determination
 
@@ -93,14 +93,14 @@ jobs:
         run: Rscript -e 'tiledbsoma::show_package_versions()'
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           cache: pip
           cache-dependency-path: ./apis/python/setup.py
 
       - name: Install tiledbsoma
-        run: python -m pip -v install -e apis/python[dev] -C "--build-option=--no-tiledb-deprecated"
+        run: pip -v install -e apis/python[dev] -C "--build-option=--no-tiledb-deprecated"
 
       - name: Show Python package versions
         run: |

diff --git a/.github/workflows/r-valgrind.yaml b/.github/workflows/r-valgrind.yaml
@@ -13,7 +13,7 @@ jobs:
     container:
       image: rocker/r2u:latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: SessionInfo
         run: R -q -e 'sessionInfo()'