diff --git a/src/anndata/_core/anndata.py b/src/anndata/_core/anndata.py index 2c2f48f03..945d031d7 100644 --- a/src/anndata/_core/anndata.py +++ b/src/anndata/_core/anndata.py @@ -1429,13 +1429,13 @@ def to_memory(self, *, copy: bool = False) -> AnnData: ]: attr = getattr(self, attr_name, None) if attr is not None: - new[attr_name] = to_memory(attr, copy) + new[attr_name] = to_memory(attr, copy=copy) if self.raw is not None: new["raw"] = { - "X": to_memory(self.raw.X, copy), - "var": to_memory(self.raw.var, copy), - "varm": to_memory(self.raw.varm, copy), + "X": to_memory(self.raw.X, copy=copy), + "var": to_memory(self.raw.var, copy=copy), + "varm": to_memory(self.raw.varm, copy=copy), } if self.isbacked: diff --git a/src/anndata/tests/helpers.py b/src/anndata/tests/helpers.py index 724dfcf21..a915ff115 100644 --- a/src/anndata/tests/helpers.py +++ b/src/anndata/tests/helpers.py @@ -573,7 +573,7 @@ def assert_equal( def assert_equal_cupy( a: CupyArray, b: object, *, exact: bool = False, elem_name: str | None = None ): - assert_equal(b, a.get(), exact, elem_name) + assert_equal(b, a.get(), exact=exact, elem_name=elem_name) @assert_equal.register(np.ndarray) @@ -594,7 +594,10 @@ def assert_equal_ndarray( # Reshaping to allow >2d arrays assert a.shape == b.shape, format_msg(elem_name) assert_equal( - pd.DataFrame(a.reshape(-1)), pd.DataFrame(b.reshape(-1)), exact, elem_name + pd.DataFrame(a.reshape(-1)), + pd.DataFrame(b.reshape(-1)), + exact=exact, + elem_name=elem_name, ) else: assert np.all(a == b), format_msg(elem_name) @@ -617,14 +620,14 @@ def assert_equal_sparse( elem_name: str | None = None, ): a = asarray(a) - assert_equal(b, a, exact, elem_name=elem_name) + assert_equal(b, a, exact=exact, elem_name=elem_name) @assert_equal.register(SpArray) def assert_equal_sparse_array( a: SpArray, b: object, *, exact: bool = False, elem_name: str | None = None ): - return assert_equal_sparse(a, b, exact, elem_name) + return assert_equal_sparse(a, b, exact=exact, elem_name=elem_name) @assert_equal.register(CupySparseMatrix) @@ -632,7 +635,7 @@ def assert_equal_cupy_sparse( a: CupySparseMatrix, b: object, *, exact: bool = False, elem_name: str | None = None ): a = a.toarray() - assert_equal(b, a, exact, elem_name=elem_name) + assert_equal(b, a, exact=exact, elem_name=elem_name) @assert_equal.register(h5py.Dataset) @@ -641,14 +644,14 @@ def assert_equal_h5py_dataset( a: ArrayStorageType, b: object, *, exact: bool = False, elem_name: str | None = None ): a = asarray(a) - assert_equal(b, a, exact, elem_name=elem_name) + assert_equal(b, a, exact=exact, elem_name=elem_name) @assert_equal.register(DaskArray) def assert_equal_dask_array( a: DaskArray, b: object, *, exact: bool = False, elem_name: str | None = None ): - assert_equal(b, a.compute(), exact, elem_name) + assert_equal(b, a.compute(), exact=exact, elem_name=elem_name) @assert_equal.register(pd.DataFrame) @@ -656,7 +659,7 @@ def are_equal_dataframe( a: pd.DataFrame, b: object, *, exact: bool = False, elem_name: str | None = None ): if not isinstance(b, pd.DataFrame): - assert_equal(b, a, exact, elem_name) # , a.values maybe? + assert_equal(b, a, exact=exact, elem_name=elem_name) # , a.values maybe? report_name(pd.testing.assert_frame_equal)( a, @@ -690,7 +693,7 @@ def assert_equal_mapping( for k in a.keys(): if elem_name is None: elem_name = "" - assert_equal(a[k], b[k], exact, f"{elem_name}/{k}") + assert_equal(a[k], b[k], exact=exact, elem_name=f"{elem_name}/{k}") @assert_equal.register(AlignedMappingBase) @@ -783,8 +786,8 @@ def fmt_name(x): # There may be issues comparing views, since np.allclose # can modify ArrayViews if they contain `nan`s - assert_equal(a.obs_names, b.obs_names, exact, elem_name=fmt_name("obs_names")) - assert_equal(a.var_names, b.var_names, exact, elem_name=fmt_name("var_names")) + assert_equal(a.obs_names, b.obs_names, exact=exact, elem_name=fmt_name("obs_names")) + assert_equal(a.var_names, b.var_names, exact=exact, elem_name=fmt_name("var_names")) if not exact: # Reorder all elements if necessary idx = [slice(None), slice(None)] @@ -813,7 +816,7 @@ def fmt_name(x): assert_equal( getattr(a, attr), getattr(b, attr), - exact, + exact=exact, elem_name=fmt_name(attr), )