diff --git a/pyproject.toml b/pyproject.toml index a7bcda91..4acd9115 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,6 +44,15 @@ force_single_line = true known_first_party = ["somacore"] single_line_exclusions = ["typing", "typing_extensions"] +[tool.mypy] +check_untyped_defs = true +enable_error_code = ["ignore-without-code"] +warn_redundant_casts = true +# We want to enable this but it won't work when running locally due to the +# presence of _version.py (which invalidates the ignore, which causes an error). +# +# warn_unused_ignores = true + [[tool.mypy.overrides]] # These dependencies do not currently have canonical type stubs. module = ["anndata", "numba", "pandas", "pyarrow", "scipy"] diff --git a/python-spec/src/somacore/query/_fast_csr.py b/python-spec/src/somacore/query/_fast_csr.py index 923724ab..b04240bf 100644 --- a/python-spec/src/somacore/query/_fast_csr.py +++ b/python-spec/src/somacore/query/_fast_csr.py @@ -165,7 +165,7 @@ def finalize(self) -> _CSRAccumulatorFinalResult: ) -@numba.jit(nopython=True, nogil=True) # type: ignore +@numba.jit(nopython=True, nogil=True) # type: ignore[attr-defined] def _accum_row_length( row_length: npt.NDArray[np.int64], row_ind: npt.NDArray[np.int64] ) -> None: @@ -173,7 +173,7 @@ def _accum_row_length( row_length[rind] += 1 -@numba.jit(nopython=True, nogil=True) # type: ignore +@numba.jit(nopython=True, nogil=True) # type: ignore[attr-defined] def _copy_chunk_range( row_ind_chunk: npt.NDArray[np.signedinteger], col_ind_chunk: npt.NDArray[np.signedinteger], @@ -194,7 +194,7 @@ def _copy_chunk_range( indptr[row] += 1 -@numba.jit(nopython=True, nogil=True) # type: ignore +@numba.jit(nopython=True, nogil=True) # type: ignore[attr-defined] def _copy_chunklist_range( chunk_list: numba.typed.List, data: npt.NDArray[np.number], @@ -219,7 +219,7 @@ def _copy_chunklist_range( ) -@numba.jit(nopython=True, nogil=True) # type: ignore +@numba.jit(nopython=True, nogil=True) # type: ignore[attr-defined] def _finalize_indptr(indptr: npt.NDArray[np.signedinteger]): prev = 0 for r in range(len(indptr)): diff --git a/python-spec/testing/test_collection.py b/python-spec/testing/test_collection.py index ce948c30..1e246c94 100644 --- a/python-spec/testing/test_collection.py +++ b/python-spec/testing/test_collection.py @@ -1,4 +1,5 @@ import unittest +from typing import Any from somacore import collection from somacore import experiment @@ -10,8 +11,8 @@ def test_basic(self): # Since the SimpleCollection implementation is straightforward this is # just to ensure that we actually fulfill everything. - coll = collection.SimpleCollection() - entry_a = collection.SimpleCollection() + coll = collection.SimpleCollection[Any]() + entry_a = collection.SimpleCollection[Any]() coll["a"] = entry_a self.assertIs(entry_a, coll["a"]) del coll["a"]