[python] Python 3.12 support (#3001)

* [python] Python 3.12 support * `python-ci-packaging`: consistent dep order * use Typeguard@HEAD for agronholm/typeguard#490, for Python 3.12 tests * rm `soma@kerl/python-3.12` CI pin --------- Co-authored-by: Ryan Williams <[email protected]>
single-cell-data · Oct 22, 2024 · 467cd7b · 467cd7b
1 parent f448271
commit 467cd7b
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diff --git a/.github/workflows/python-ci-full.yml b/.github/workflows/python-ci-full.yml
@@ -25,7 +25,7 @@ jobs:
         # os: [ubuntu-latest, macos-latest, windows-2019]
         # TODO: add 3.12
         # https://github.com/single-cell-data/TileDB-SOMA/issues/1849
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         include:
           - runs-on: ubuntu-latest
             cc: gcc-11

diff --git a/.github/workflows/python-ci-minimal.yml b/.github/workflows/python-ci-minimal.yml
@@ -29,7 +29,7 @@ jobs:
 
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.9', '3.11']
+        python-version: ['3.9', '3.12']
         include:
           - os: ubuntu-latest
             cc: gcc-11
@@ -43,6 +43,6 @@ jobs:
       python_version: ${{ matrix.python-version }}
       cc: ${{ matrix.cc }}
       cxx: ${{ matrix.cxx }}
-      report_codecov: ${{ matrix.python-version == '3.11' }}
-      run_lint: ${{ matrix.python-version == '3.11' }}
+      report_codecov: ${{ matrix.python-version == '3.12' }}
+      run_lint: ${{ matrix.python-version == '3.12' }}
     secrets: inherit
diff --git a/.github/workflows/python-ci-packaging.yml b/.github/workflows/python-ci-packaging.yml
@@ -102,7 +102,7 @@ jobs:
         run: |
           python --version
           python -m venv ./venv-soma
-          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse 'setuptools>=70.1' wheel
+          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel 'setuptools>=70.1'
           ./venv-soma/bin/pip list
       - name: Build wheel
         run: |
@@ -333,7 +333,9 @@ 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/pip install --prefer-binary `grep -v '^\[' apis/python/src/tiledbsoma.egg-info/requires.txt`
+        run: |
+          grep -v '^\[' apis/python/src/tiledbsoma.egg-info/requires.txt > runtime-reqs.txt
+          ./venv-soma/bin/pip install --prefer-binary -r runtime-reqs.txt
       - name: Runtime test
         run: ./venv-soma/bin/python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
 

diff --git a/.github/workflows/python-packaging.yml b/.github/workflows/python-packaging.yml
@@ -119,6 +119,8 @@ jobs:
             dotted-version: '3.10'
           - undotted-version: '311'
             dotted-version: '3.11'
+          - undotted-version: '312'
+            dotted-version: '3.12'
         wheel-name:
           - manylinux2014
           - macos-x86_64

diff --git a/apis/python/requirements_dev.txt b/apis/python/requirements_dev.txt
@@ -3,5 +3,8 @@ ruff
 pytest
 pytest-cov
 sparse
-typeguard==4.2.1
+# Python 3.12 support requires https://github.com/agronholm/typeguard/pull/490;
+# use Typeguard @ HEAD until that PR is included in a release. See also:
+# https://github.com/single-cell-data/TileDB-SOMA/issues/3216
+typeguard @ git+https://github.com/agronholm/typeguard
 types-setuptools
diff --git a/apis/python/tests/test_dataframe.py b/apis/python/tests/test_dataframe.py
@@ -783,7 +783,9 @@ def make_multiply_indexed_dataframe(
             "domain": [[-1000, 1000]],
             "coords": [{"bogus": True}],
             "A": None,
-            "throws": TypeError,
+            # Disable Typeguard while asserting this error, otherwise a typeguard.TypeCheckError is
+            # raised (though that's not what would happen in production)
+            "throws": (TypeError, False),
         },
         {
             "name": "bad index type bool",
@@ -890,15 +892,30 @@ def test_read_indexing(tmp_path, io):
         read_kwargs.update(
             {k: io[k] for k in ("coords", "partitions", "value_filter") if k in io}
         )
-        if io.get("throws", None):
-            with pytest.raises(io["throws"]):
+
+        # `throws` can be `Type[Exception]`, or `(Type[Exception], bool)` indicating explicitly
+        # whether Typeguard should be enabled during the `with raises` check.
+        throws = io.get("throws", None)
+        if throws:
+            if isinstance(throws, tuple) and not throws[1]:
+                # Disable Typeguard, verify actual runtime error type (avoid
+                # `typeguard.TypeCheckError` short-circuit)
+                throws = throws[0]
+                throws_ctx = raises_no_typeguard
+            else:
+                throws_ctx = pytest.raises
+        else:
+            throws_ctx = None
+
+        if throws_ctx:
+            with throws_ctx(throws):
                 next(sdf.read(**read_kwargs))
         else:
             table = next(sdf.read(**read_kwargs))
             assert table["A"].to_pylist() == io["A"]
 
-        if io.get("throws", None):
-            with pytest.raises(io["throws"]):
+        if throws_ctx:
+            with throws_ctx(throws):
                 next(sdf.read(**read_kwargs)).to_pandas()
         else:
             table = next(sdf.read(**read_kwargs)).to_pandas()

diff --git a/apis/python/tests/test_sparse_nd_array.py b/apis/python/tests/test_sparse_nd_array.py
@@ -1036,7 +1036,7 @@ def test_sparse_nd_array_error_corners(tmp_path):
 
     with soma.SparseNDArray.open(tmp_path.as_posix()) as a:
         # other coord types are illegal
-        with pytest.raises(TypeError):
+        with raises_no_typeguard(TypeError):
             next(a.read("hi").tables())