Merge branch 'main' into ig/refactor_base_class

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
     -   id: black
 - repo: https://github.com/charliermarsh/ruff-pre-commit
   # Ruff version.
-  rev: 'v0.0.265'
+  rev: 'v0.0.270'
   hooks:
     - id: ruff
       args: ["--fix"]

anndata/_core/anndata.py

@@ -100,15 +100,19 @@ def _check_2d_shape(X):
 @singledispatch
 def _gen_dataframe(anno, length, index_names):
     if anno is None or len(anno) == 0:
-        return pd.DataFrame({}, index=pd.RangeIndex(0, length, name=None).astype(str))
+        anno = {}
     for index_name in index_names:
         if index_name in anno:
             return pd.DataFrame(
                 anno,
                 index=anno[index_name],
                 columns=[k for k in anno.keys() if k != index_name],
             )
-    return pd.DataFrame(anno, index=pd.RangeIndex(0, length, name=None).astype(str))
+    return pd.DataFrame(
+        anno,
+        index=pd.RangeIndex(0, length, name=None).astype(str),
+        columns=None if len(anno) else [],
+    )
 
 
 @_gen_dataframe.register(pd.DataFrame)
@@ -117,6 +121,8 @@ def _(anno, length, index_names):
     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
 
 
@@ -764,6 +770,8 @@ def _set_dim_df(self, value: pd.DataFrame, attr: str):
             self._init_as_actual(self.copy())
         setattr(self, f"_{attr}", value)
         self._set_dim_index(value_idx, attr)
+        if not len(value.columns):
+            value.columns = value.columns.astype(str)
 
     def _prep_dim_index(self, value, attr: str) -> pd.Index:
         """Prepares index to be uses as obs_names or var_names for AnnData object.AssertionError

anndata/_io/specs/methods.py

@@ -589,7 +589,7 @@ def read_dataframe(elem, _reader):
     df = pd.DataFrame(
         {k: _reader.read_elem(elem[k]) for k in columns},
         index=_reader.read_elem(elem[idx_key]),
-        columns=list(columns),
+        columns=columns if len(columns) else None,
     )
     if idx_key != "_index":
         df.index.name = idx_key
@@ -612,7 +612,7 @@ def read_dataframe_partial(
     df = pd.DataFrame(
         {k: read_elem_partial(elem[k], indices=indices[0]) for k in columns},
         index=read_elem_partial(elem[idx_key], indices=indices[0]),
-        columns=list(columns),
+        columns=columns if len(columns) else None,
     )
     if idx_key != "_index":
         df.index.name = idx_key
@@ -630,7 +630,7 @@ def read_dataframe_0_1_0(elem, _reader):
     df = pd.DataFrame(
         {k: read_series(elem[k]) for k in columns},
         index=read_series(elem[idx_key]),
-        columns=list(columns),
+        columns=columns if len(columns) else None,
     )
     if idx_key != "_index":
         df.index.name = idx_key

anndata/tests/test_concatenate.py

@@ -1086,11 +1086,9 @@ def test_concatenate_uns(unss, merge_strategy, result, value_gen):
     print(merge_strategy, "\n", unss, "\n", result)
     result, *unss = permute_nested_values([result] + unss, value_gen)
     adatas = [uns_ad(uns) for uns in unss]
-    assert_equal(
-        adatas[0].concatenate(adatas[1:], uns_merge=merge_strategy).uns,
-        result,
-        elem_name="uns",
-    )
+    with pytest.warns(FutureWarning, match=r"concatenate method is deprecated"):
+        merged = AnnData.concatenate(*adatas, uns_merge=merge_strategy).uns
+    assert_equal(merged, result, elem_name="uns")
 
 
 def test_transposed_concat(array_type, axis, join_type, merge_strategy, fill_val):

pyproject.toml

@@ -110,7 +110,7 @@ omit = [
 [tool.pytest.ini_options]
 addopts = "--doctest-modules"
 python_files = "test_*.py"
-testpaths = ["anndata", "docs/concatenation.rst"]
+testpaths = ["anndata/tests", "docs/concatenation.rst"]
 filterwarnings = [
     'ignore:X\.dtype being converted to np.float32:FutureWarning'
 ]