[python/ci] Test against older dependency versions (#3680)

* [python/ci] CI job with variant dependencies

* remove extraneities

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

@@ -0,0 +1,123 @@
+name: TileDB-SOMA Python CI with varying dependencies
+
+on:
+  push:
+    branches:
+      - main
+      - 'release-*'
+  pull_request:
+    paths-ignore:
+      - '**.md'
+      - 'apis/r/**'
+      - 'docs/**'
+  workflow_dispatch:
+
+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
+
+          - name: ensemble2
+            os: ubuntu-24.04
+            python_version: 3.9
+            cc: gcc-13
+            cxx: g++-13
+
+            anndata:  0.10.9
+            numba:    0.60.0
+            numpy:    1.25.0
+            pandas:   1.5.3
+            pyarrow:  12.0.1
+            scanpy:   1.10.3
+            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
+        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: Obtain test data
+        shell: bash
+        run: |
+          cd test
+          rm -rf soco
+          tar zxf soco.tgz
+          cd ..
+
+      - name: Run pytests for Python
+        shell: bash
+        run: python -m pytest apis/python/tests/*.py -v --durations=20 --maxfail=50