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[python] Python 3.12 support #3001

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[python] Python 3.12 support #3001

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3f5af11
[python] Python 3.12 support
johnkerl Sep 17, 2024
ad613ae
`python-ci-packaging`: consistent dep order
ryan-williams Oct 18, 2024
8b45396
use Typeguard@HEAD
ryan-williams Oct 18, 2024
b7db9ed
rm `soma@kerl/python-3.12` CI pin
ryan-williams Oct 18, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/python-ci-full.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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6 changes: 3 additions & 3 deletions .github/workflows/python-ci-minimal.yml
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Expand Up @@ -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
Expand All @@ -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
6 changes: 4 additions & 2 deletions .github/workflows/python-ci-packaging.yml
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Expand Up @@ -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: |
Expand Down Expand Up @@ -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())"

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2 changes: 2 additions & 0 deletions .github/workflows/python-packaging.yml
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Expand Up @@ -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
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5 changes: 4 additions & 1 deletion apis/python/requirements_dev.txt
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Expand Up @@ -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
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This would be the place for a TODO / issue link related to upgrading Typeguard. Do you want me to change this comment?

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Filed #3216 and referenced it here

types-setuptools
27 changes: 22 additions & 5 deletions apis/python/tests/test_dataframe.py
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Expand Up @@ -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
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Let's hvae a GitHub issue tracking the 'real' typeguard release, and let's put its URL here as a to-do comment

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This change isn't due to using Typeguard@HEAD; it will remain relevant when we move back to a proper Typeguard release.

The reason for it is: in 3.12, better type-checking was causing a TypeCheckError to occur before the TypeError we were verifying here.

I worked around it by disabling type-checking while triggering this error, so we can continue to verify what we were previously.

# raised (though that's not what would happen in production)
"throws": (TypeError, False),
},
{
"name": "bad index type bool",
Expand Down Expand Up @@ -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
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Ditto the above to-do URL/comment

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Same as above, todo related to upgrading Typeguard is not applicable here.

# `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()
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2 changes: 1 addition & 1 deletion apis/python/tests/test_sparse_nd_array.py
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Expand Up @@ -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())


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