[python/ci] CI job with variant dependencies

.github/workflows/libtiledb-ci.yml

@@ -1,15 +1,16 @@
 name: libTileDB-SOMA CodeCov
 
 on:
-  pull_request:
-    paths-ignore:
-      - "apis/python/**"
-      - "apis/r/**"
-      - ".pre-commit-config.yaml"
-  push:
-    branches:
-      - main
-      - 'release-*'
+# XXX TEMP
+#  pull_request:
+#    paths-ignore:
+#      - "apis/python/**"
+#      - "apis/r/**"
+#      - ".pre-commit-config.yaml"
+#  push:
+#    branches:
+#      - main
+#      - 'release-*'
   workflow_dispatch:
 
 jobs:

.github/workflows/libtiledbsoma-asan-ci.yml

@@ -1,16 +1,17 @@
 name: libtiledbsoma ASAN
 
 on:
-  pull_request:
-    paths-ignore:
-      - "apis/python/**"
-      - "apis/r/**"
-      - ".pre-commit-config.yaml"
-  push:
-    branches:
-      - main
-      - 'release-*'
-  workflow_dispatch:
+# XXX TEMP
+#  pull_request:
+#    paths-ignore:
+#      - "apis/python/**"
+#      - "apis/r/**"
+#      - ".pre-commit-config.yaml"
+#  push:
+#    branches:
+#      - main
+#      - 'release-*'
+#  workflow_dispatch:
 
 jobs:
   asan:

.github/workflows/python-ci-minimal.yml

@@ -8,18 +8,19 @@ name: TileDB-SOMA Python CI (Minimal)
 # To test the full matrix on a working branch, invoke ./python-ci-full.yml from
 #   https://github.com/single-cell-data/TileDB-SOMA/actions/workflows/python-ci-full.yml
 on:
-  pull_request:
-    branches:
-      - main
-      - 'release-*'
-    paths:
-      - '**'
-      - '!**.md'
-      - '!apis/r/**'
-      - '!docs/**'
-      - '!.github/**'
-      - '.github/workflows/python-ci-minimal.yml'
-      - '.github/workflows/python-ci-single.yml'
+# XXX TEMP
+#  pull_request:
+#    branches:
+#      - main
+#      - 'release-*'
+#    paths:
+#      - '**'
+#      - '!**.md'
+#      - '!apis/r/**'
+#      - '!docs/**'
+#      - '!.github/**'
+#      - '.github/workflows/python-ci-minimal.yml'
+#      - '.github/workflows/python-ci-single.yml'
   workflow_dispatch:
 
 jobs:

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

@@ -0,0 +1,109 @@
+name: TileDB-SOMA Python CI with varying dependencies
+
+on:
+  workflow_dispatch:
+  #
+  # Not for regular use:
+  # TEMP
+  pull_request:
+  #
+  # TODO: a nightly cron
+
+env:
+  TILEDB_REST_TOKEN: ${{ secrets.TILEDB_REST_UNITTEST_TOKEN}}
+
+jobs:
+  ci:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: ensemble1
+            os: ubuntu-24.04
+            python_version: 3.9
+            cc: gcc-13
+            cxx: g++-13
+
+            anndata: 0.10.8
+            numba:   0.60.0
+            numpy:   1.25.0
+            pandas:  1.5.3
+            pyarrow: 11.0.0
+            scanpy:  1.9.8
+            scipy:   1.13.1
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Show matrix OS
+        run: echo "matrix.os:" ${{ matrix.os }}
+
+      - name: Linux CPU info
+        if: ${{ matrix.os == 'ubuntu-24.04' }}
+        run: cat /proc/cpuinfo
+
+      - name: MacOS CPU info
+        if: ${{ matrix.os == 'macOS-latest' }}
+        run: sysctl -a | grep cpu
+
+      - name: Select XCode version
+        if: startsWith(matrix.os, 'macos')
+        uses: maxim-lobanov/setup-xcode@v1
+        with:
+          xcode-version: '15.4'
+
+      - name: Set up Python ${{ matrix.python_version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python_version }}
+          cache: pip
+          cache-dependency-path: ./apis/python/setup.py
+
+      - name: Show XCode version
+        run: clang --version
+
+      - name: Check out TileDB-SOMA
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # ensure we get all tags to inform package version determination
+
+      - name: Log pip dependencies
+        run: pip list
+
+      - name: Install tiledbsoma
+        # If you'reiterating on the testing framework itself, install from PyPI to avoid the
+        # time-consuming build. If you're trying to evaluate the code modified by a PR,
+        # install from source.
+        #
+        # From PyPI:
+        run: pip install tiledbsoma==1.15.7
+        #
+        # From source:
+        # run: pip -v install -e apis/python[all] -C "--build-option=--no-tiledb-deprecated"
+        #
+        env:
+          CC: ${{ matrix.cc }}
+          CXX: ${{ matrix.cxx }}
+
+      - name: Install dependencies
+        run: pip install --prefer-binary pytest typeguard
+
+      - name: Install variant dependencies
+        run: |
+          pip install  \
+            anndata==${{matrix.anndata}} \
+            numba==${{matrix.numba}} \
+            numpy==${{matrix.numpy}} \
+            pandas==${{matrix.pandas}} \
+            pyarrow==${{matrix.pyarrow}} \
+            scanpy==${{matrix.scanpy}} \
+            scipy==${{matrix.scipy}}
+
+      - name: Show package versions
+        run: python scripts/show-versions.py
+
+      - name: Run pytests for Python
+        shell: bash
+        run: python -m pytest apis/python/tests -v --durations=20 --maxfail=50