remove circularity and implicit module members (#1396)

anndata/__init__.py

@@ -1,4 +1,5 @@
 """Annotated multivariate observation data."""
+
 from __future__ import annotations
 
 try:  # See https://github.com/maresb/hatch-vcs-footgun-example
@@ -45,6 +46,9 @@
 # Experimental needs to be imported last
 from . import experimental  # isort: skip
 
+# We use these in tests by attribute access
+from . import _io, logging  # noqa: F401 isort: skip
+
 
 def read(*args, **kwargs):
     import warnings

anndata/_core/aligned_df.py

@@ -0,0 +1,104 @@
+from __future__ import annotations
+
+import warnings
+from functools import singledispatch
+from typing import TYPE_CHECKING, Any, Literal
+
+import pandas as pd
+from pandas.api.types import is_string_dtype
+
+from .._warnings import ImplicitModificationWarning
+
+if TYPE_CHECKING:
+    from collections.abc import Iterable, Mapping
+
+
+@singledispatch
+def _gen_dataframe(
+    anno: Mapping[str, Any],
+    index_names: Iterable[str],
+    *,
+    source: Literal["X", "shape"],
+    attr: Literal["obs", "var"],
+    length: int | None = None,
+) -> pd.DataFrame:
+    if anno is None or len(anno) == 0:
+        anno = {}
+
+    def mk_index(l: int) -> pd.Index:
+        return pd.RangeIndex(0, l, name=None).astype(str)
+
+    for index_name in index_names:
+        if index_name not in anno:
+            continue
+        df = pd.DataFrame(
+            anno,
+            index=anno[index_name],
+            columns=[k for k in anno.keys() if k != index_name],
+        )
+        break
+    else:
+        df = pd.DataFrame(
+            anno,
+            index=None if length is None else mk_index(length),
+            columns=None if len(anno) else [],
+        )
+
+    if length is None:
+        df.index = mk_index(len(df))
+    elif length != len(df):
+        raise _mk_df_error(source, attr, length, len(df))
+    return df
+
+
+@_gen_dataframe.register(pd.DataFrame)
+def _gen_dataframe_df(
+    anno: pd.DataFrame,
+    index_names: Iterable[str],
+    *,
+    source: Literal["X", "shape"],
+    attr: Literal["obs", "var"],
+    length: int | None = None,
+):
+    if length is not None and length != len(anno):
+        raise _mk_df_error(source, attr, length, len(anno))
+    anno = anno.copy(deep=False)
+    if not is_string_dtype(anno.index):
+        warnings.warn("Transforming to str index.", ImplicitModificationWarning)
+        anno.index = anno.index.astype(str)
+    if not len(anno.columns):
+        anno.columns = anno.columns.astype(str)
+    return anno
+
+
+@_gen_dataframe.register(pd.Series)
+@_gen_dataframe.register(pd.Index)
+def _gen_dataframe_1d(
+    anno: pd.Series | pd.Index,
+    index_names: Iterable[str],
+    *,
+    source: Literal["X", "shape"],
+    attr: Literal["obs", "var"],
+    length: int | None = None,
+):
+    raise ValueError(f"Cannot convert {type(anno)} to {attr} DataFrame")
+
+
+def _mk_df_error(
+    source: Literal["X", "shape"],
+    attr: Literal["obs", "var"],
+    expected: int,
+    actual: int,
+):
+    if source == "X":
+        what = "row" if attr == "obs" else "column"
+        msg = (
+            f"Observations annot. `{attr}` must have as many rows as `X` has {what}s "
+            f"({expected}), but has {actual} rows."
+        )
+    else:
+        msg = (
+            f"`shape` is inconsistent with `{attr}` "
+            "({actual} {what}s instead of {expected})"
+        )
+    return ValueError(msg)

anndata/_core/anndata.py

@@ -1,6 +1,7 @@
 """\
 Main class and helper functions.
 """
+
 from __future__ import annotations
 
 import collections.abc as cabc
@@ -9,7 +10,7 @@
 from collections.abc import Iterable, Mapping, MutableMapping, Sequence
 from copy import copy, deepcopy
 from enum import Enum
-from functools import partial, singledispatch
+from functools import partial
 from pathlib import Path
 from textwrap import dedent
 from typing import (  # Meta  # Generic ABCs  # Generic
@@ -23,12 +24,10 @@
 import pandas as pd
 from natsort import natsorted
 from numpy import ma
-from pandas.api.types import infer_dtype, is_string_dtype
+from pandas.api.types import infer_dtype
 from scipy import sparse
 from scipy.sparse import issparse
 
-from anndata._warnings import ImplicitModificationWarning
-
 from .. import utils
 from .._settings import settings
 from ..compat import (
@@ -42,6 +41,7 @@
 from ..logging import anndata_logger as logger
 from ..utils import convert_to_dict, deprecated, dim_len, ensure_df_homogeneous
 from .access import ElementRef
+from .aligned_df import _gen_dataframe
 from .aligned_mapping import (
     AxisArrays,
     AxisArraysView,
@@ -110,97 +110,6 @@ def _check_2d_shape(X):
         )
 
 
-def _mk_df_error(
-    source: Literal["X", "shape"],
-    attr: Literal["obs", "var"],
-    expected: int,
-    actual: int,
-):
-    if source == "X":
-        what = "row" if attr == "obs" else "column"
-        msg = (
-            f"Observations annot. `{attr}` must have as many rows as `X` has {what}s "
-            f"({expected}), but has {actual} rows."
-        )
-    else:
-        msg = (
-            f"`shape` is inconsistent with `{attr}` "
-            "({actual} {what}s instead of {expected})"
-        )
-    return ValueError(msg)
-
-
-@singledispatch
-def _gen_dataframe(
-    anno: Mapping[str, Any],
-    index_names: Iterable[str],
-    *,
-    source: Literal["X", "shape"],
-    attr: Literal["obs", "var"],
-    length: int | None = None,
-) -> pd.DataFrame:
-    if anno is None or len(anno) == 0:
-        anno = {}
-
-    def mk_index(l: int) -> pd.Index:
-        return pd.RangeIndex(0, l, name=None).astype(str)
-
-    for index_name in index_names:
-        if index_name not in anno:
-            continue
-        df = pd.DataFrame(
-            anno,
-            index=anno[index_name],
-            columns=[k for k in anno.keys() if k != index_name],
-        )
-        break
-    else:
-        df = pd.DataFrame(
-            anno,
-            index=None if length is None else mk_index(length),
-            columns=None if len(anno) else [],
-        )
-
-    if length is None:
-        df.index = mk_index(len(df))
-    elif length != len(df):
-        raise _mk_df_error(source, attr, length, len(df))
-    return df
-
-
-@_gen_dataframe.register(pd.DataFrame)
-def _gen_dataframe_df(
-    anno: pd.DataFrame,
-    index_names: Iterable[str],
-    *,
-    source: Literal["X", "shape"],
-    attr: Literal["obs", "var"],
-    length: int | None = None,
-):
-    if length is not None and length != len(anno):
-        raise _mk_df_error(source, attr, length, len(anno))
-    anno = anno.copy(deep=False)
-    if not is_string_dtype(anno.index):
-        warnings.warn("Transforming to str index.", ImplicitModificationWarning)
-        anno.index = anno.index.astype(str)
-    if not len(anno.columns):
-        anno.columns = anno.columns.astype(str)
-    return anno
-
-
-@_gen_dataframe.register(pd.Series)
-@_gen_dataframe.register(pd.Index)
-def _gen_dataframe_1d(
-    anno: pd.Series | pd.Index,
-    index_names: Iterable[str],
-    *,
-    source: Literal["X", "shape"],
-    attr: Literal["obs", "var"],
-    length: int | None = None,
-):
-    raise ValueError(f"Cannot convert {type(anno)} to {attr} DataFrame")
-
-
 class AnnData(metaclass=utils.DeprecationMixinMeta):
     """\
     An annotated data matrix.

anndata/_core/raw.py

@@ -8,6 +8,7 @@
 from scipy.sparse import issparse
 
 from ..compat import CupyArray, CupySparseMatrix
+from .aligned_df import _gen_dataframe
 from .aligned_mapping import AxisArrays
 from .index import _normalize_index, _subset, get_vector, unpack_index
 from .sparse_dataset import BaseCompressedSparseDataset, sparse_dataset
@@ -29,8 +30,6 @@ def __init__(
         var: pd.DataFrame | Mapping[str, Sequence] | None = None,
         varm: AxisArrays | Mapping[str, np.ndarray] | None = None,
     ):
-        from .anndata import _gen_dataframe
-
         self._adata = adata
         self._n_obs = adata.n_obs
         # construct manually

anndata/_io/__init__.py

@@ -20,6 +20,9 @@ def write_zarr(*args, **kw):
     return write_zarr(*args, **kw)
 
 
+# We use this in test by attribute access
+from . import specs  # noqa: F401, E402
+
 __all__ = [
     "read_csv",
     "read_excel",

anndata/tests/test_raw.py

@@ -4,7 +4,7 @@
 import pytest
 
 import anndata as ad
-from anndata._core.anndata import ImplicitModificationWarning
+from anndata import ImplicitModificationWarning
 from anndata.tests.helpers import GEN_ADATA_DASK_ARGS, assert_equal, gen_adata
 
 # -------------------------------------------------------------------------------