[python] Typeguard not running as intended

[ryan-williams]

#2239 has a repro of typeguard failing to raise on non-test code with intentionally broken types.

I believe the issue is, in this block:

TileDB-SOMA/apis/python/tests/__init__.py

Lines 4 to 7 in 83bfd00

	# avoid typeguard by importing before calling install_import_hook
	from tiledbsoma import _query_condition # noqa: F401
	install_import_hook("tiledbsoma")

Line 5 is inadvertently importing ≈all of tiledbsoma (it executes tiledbsoma/__init__.py, which imports most things) before the typeguard hook is initialized, meaning ≈nothing is being checked by typeguard.

I suspect this has been the case since that line was added, in #496 (Nov '22).

Attempting to restore Typeguard checks

When I comment out the _query_condition line, typeguard raises in any pytest command that executes tiledbsoma/__init__.py, e.g.:

echo 'import tiledbsoma' > tests/test_typeguard.py
pytest tests/test_typeguard.py
# ERROR tests/test_typeguard.py - TypeError: Subscripted generics cannot be used with class and instance checks

Full stack trace

================================================== test session starts ==================================================
platform darwin -- Python 3.11.8, pytest-8.0.2, pluggy-1.4.0
rootdir: /Users/ryan/c/tiledb/tiledb-soma/apis/python
plugins: anyio-4.3.0, typeguard-2.13.3
collected 0 items / 1 error

======================================================== ERRORS =========================================================
_______________________________________ ERROR collecting tests/test_typeguard.py ________________________________________
tests/test_typeguard.py:3: in <module>
    import tiledbsoma
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:690: in _load_unlocked
    ???
/Users/ryan/.pyenv/versions/tiledb-soma-3.11.8/lib/python3.11/site-packages/typeguard/importhook.py:81: in exec_module
    return super().exec_module(module)
src/tiledbsoma/__init__.py:146: in <module>
    from ._collection import Collection
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:690: in _load_unlocked
    ???
/Users/ryan/.pyenv/versions/tiledb-soma-3.11.8/lib/python3.11/site-packages/typeguard/importhook.py:81: in exec_module
    return super().exec_module(module)
src/tiledbsoma/_collection.py:67: in <module>
    class CollectionBase(  # type: ignore[misc]  # __eq__ false positive
src/tiledbsoma/_collection.py:245: in CollectionBase
    @_funcs.forwards_kwargs_to(
/Users/ryan/.pyenv/versions/tiledb-soma-3.11.8/lib/python3.11/site-packages/typeguard/__init__.py:1032: in wrapper
    check_argument_types(memo)
/Users/ryan/.pyenv/versions/tiledb-soma-3.11.8/lib/python3.11/site-packages/typeguard/__init__.py:875: in check_argument_types
    raise TypeError(*exc.args) from None
E   TypeError: Subscripted generics cannot be used with class and instance checks
================================================ short test summary info ================================================
ERROR tests/test_typeguard.py - TypeError: Subscripted generics cannot be used with class and instance checks
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
=================================================== 1 error in 1.75s ====================================================

The culprit seems to be a @_funcs.forwards_kwargs_to annotation in _collection.py:

TileDB-SOMA/apis/python/src/tiledbsoma/_collection.py

Lines 245 to 250 in 83bfd00

	@_funcs.forwards_kwargs_to(
	DataFrame.create, exclude=("context", "tiledb_timestamp")
	)
	def add_new_dataframe(
	self, key: str, *, uri: Optional[str] = None, **kwargs: Any
	) -> DataFrame:

Adding @typeguard_ignore to the forwards_kwargs_to declaration didn't help, nor did adding it to the @_funcs.forwards_kwargs_to invocation above.

Open to discussion re: selectively ignoring/fixing problem cases, more explicitly enabling typeguard for known-compliant modules, etc.

[ryan-williams]

Thanks to #1116 (comment), my main mistake was thinking typeguard ran as part of a pytest invocation; it is actually run via pre-commit (source).

This (correctly) fails on my repro branch (#2239):

pre-commit run -v --files src/tiledbsoma/_sparse_nd_array.py

pre-commit not running pre-merge

However, it seems pre-commit doesn't run as part of pre-merge checks (python-ci-minimal.yml), which allowed my broken #2239 to pass CI.

"Lint" checks only run for Python 3.10:

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

Line 40 in 6b50fa9

run_lint: ${{ matrix.python-version == '3.10' }}

but the build matrix only includes 3.8 and 3.11:

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

Line 25 in 6b50fa9

python-version: ['3.8', '3.11']

Looks like this was inadvertent, when upgrading to 3.12 in February: 798ad5c.

I'll work on a PR restoring that, cc @johnkerl. (Update: #2247)