[ci] Update github actions

.github/workflows/build-cpp.yml

@@ -15,14 +15,14 @@ jobs:
     runs-on: ${{ inputs.os }}
     steps:
       - name: Checkout TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Build and install libtiledbsoma
         run: |
           ./scripts/bld --no-tiledb-deprecated=true --werror=true --build ${{ inputs.build_type }}
 
       - name: Upload C++ build artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           # The name now includes the build type
           name: cpp-build-${{ inputs.build_type }}-${{ inputs.os }}

.github/workflows/ci-linters.yml

@@ -10,15 +10,15 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 
       - name: Restore pre-commit cache
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: ~/.cache/pre-commit
           key: pre-commit-ubuntu-24.04-3.12-${{ hashFiles('.github/workflows/lint-python.yml', '.pre-commit-config.yaml') }}

.github/workflows/ci-r-python-interop.yml

@@ -38,13 +38,13 @@ jobs:
 
     steps:
       - name: Checkout TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # Required to fetch tags: https://github.com/actions/checkout/issues/2199
           fetch-tags: true  # Tags used for Python package version.
 
       - name: Download pre-built C++ library
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: cpp-build-Release-${{ matrix.os }}
 
@@ -100,7 +100,7 @@ jobs:
         run: Rscript -e 'tiledbsoma::show_package_versions()'
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
           cache: pip

.github/workflows/pkgdown.yaml

@@ -23,7 +23,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/python-dependency-variation.yml

@@ -46,13 +46,13 @@ jobs:
 
     steps:
       - name: Check out TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # Required to fetch tags: https://github.com/actions/checkout/issues/2199
           fetch-tags: true  # Tags used for Python package version.
 
       - name: Checkout vcpkg
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: microsoft/vcpkg
           path: vcpkg
@@ -70,7 +70,7 @@ jobs:
         run: cat /proc/cpuinfo
 
       - name: Set up Python ${{ matrix.python_version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python_version }}
           cache: pip

.github/workflows/python-dockers.yml

@@ -45,7 +45,7 @@ jobs:
     name: ${{ matrix.img.name }}${{ matrix.os.suffix }}
     runs-on: ${{ matrix.os.runs-on }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: docker build
         run: |
           args=()
@@ -65,7 +65,7 @@ jobs:
     if: (failure() || cancelled()) && github.event_name == 'schedule' && github.run_attempt == 1
     steps:
       - name: Checkout TileDB-SOMA `main`
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Create Issue if Build Fails
         uses: JasonEtco/create-an-issue@v2
         env:

.github/workflows/python-packaging.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # Required to fetch tags: https://github.com/actions/checkout/issues/2199
           fetch-tags: true  # Tags needed for python API version number
@@ -34,7 +34,7 @@ jobs:
 
 
       - name: Upload sdist artifact to GitHub Actions storage
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: sdist
           path: apis/python/dist/
@@ -49,11 +49,11 @@ jobs:
         python_version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - name: Set up Python ${{ matrix.python_version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python_version }}
       - name: Download sdist artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: sdist
           path: apis/python/dist/
@@ -87,7 +87,7 @@ jobs:
 
     steps:
       - name: Checkout TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # Required to fetch tags: https://github.com/actions/checkout/issues/2199
           fetch-tags: true  # Tags needed for python API version number
@@ -118,7 +118,7 @@ jobs:
           pip list
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v3.1.1
+        uses: pypa/cibuildwheel@v3.4.0
         with:
           package-dir: apis/python/
           output-dir: wheelhouse
@@ -136,7 +136,7 @@ jobs:
         run: ls -l ./wheelhouse/*.whl
 
       - name: Upload wheel-${{ matrix.python_name }}-${{ matrix.platform }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: wheel-${{ matrix.python_name }}-${{ matrix.platform }}
           path: ./wheelhouse/*.whl
@@ -182,11 +182,11 @@ jobs:
       fail-fast: false
     steps:
       - name: Set up Python ${{ matrix.python_version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python_version }}
       - name: Download artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: wheel-${{ matrix.python_name }}-${{ matrix.platform }}
       - name: Install numba to prevent building from source
@@ -225,7 +225,7 @@ jobs:
     if: github.event_name == 'workflow_dispatch'
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
       - name: Create dist
         run: |
           set -x
@@ -252,7 +252,7 @@ jobs:
     if: github.event_name == 'release'
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
       - name: Create dist
         run: |
           set -x
@@ -273,7 +273,7 @@ jobs:
     if: (failure() || cancelled()) && github.event_name != 'workflow_dispatch' && github.event_name != 'pull_request' && github.run_attempt == 1
     steps:
       - name: Checkout TileDB-SOMA `main`
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Create Issue if Build Fails
         uses: JasonEtco/create-an-issue@v2
         env:

.github/workflows/python-remote-storage.yml

@@ -45,7 +45,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Show matrix OS
         run: echo "matrix.os:" ${{ matrix.os }}
@@ -55,19 +55,19 @@ jobs:
         run: cat /proc/cpuinfo
 
       - name: Set up Python ${{ matrix.python_version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python_version }}
           cache: pip
           cache-dependency-path: ./apis/python/setup.py
 
       - name: Check out TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # ensure we get all tags to inform package version determination
 
       - name: Download pre-built C++ library
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: cpp-build-Release-${{ matrix.os }}
 

.github/workflows/r-valgrind.yaml

@@ -17,7 +17,7 @@ jobs:
     container:
       image: rocker/r2u:latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: SessionInfo
         run: R -q -e 'sessionInfo()'

.github/workflows/test-cpp.yml

@@ -24,7 +24,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Download pre-built C++ library
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: cpp-build-Release-${{ inputs.os }}
 
@@ -50,7 +50,7 @@ jobs:
 
       - uses: actions/checkout@v4
       - name: Download C++ ASAN build artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: cpp-build-ASAN-${{ inputs.os }}
 

.github/workflows/test-python.yml

@@ -49,21 +49,21 @@ jobs:
           brew install automake llvm
 
       - name: Checkout TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # Required to fetch tags: https://github.com/actions/checkout/issues/2199
           fetch-tags: true  # Tags used for Python package version.
 
       - name: Download pre-built C++ library
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: cpp-build-Release-${{ inputs.os }}
 
       - name: Set up test data
         run: make data
 
       - name: Set up Python ${{ inputs.python_version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ inputs.python_version }}
           cache: pip

.github/workflows/test-r.yml

@@ -38,13 +38,13 @@ jobs:
 
     steps:
       - name: Checkout TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # Required to fetch tags: https://github.com/actions/checkout/issues/2199
           fetch-tags: true  # Tags used for Python package version.
 
       - name: Download pre-built C++ library
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: cpp-build-Release-${{ inputs.os }}
 
@@ -78,10 +78,10 @@ jobs:
     steps:
 
       - name: Checkout TileDB-SOMA
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Download pre-built C++ library
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: cpp-build-Release-${{ inputs.os }}
 

apis/python/setup.py

@@ -348,6 +348,7 @@ def run(self):
         "pyarrow",
         "scanpy>=1.9.2",
         "scipy",
+        "shapely",
         "typing-extensions>=4.5.0",  # Note "-" even though `import typing_extensions`
     ],
     extras_require={