autodoc inheritance

docs/conf.py

@@ -61,7 +61,12 @@
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
 
-autosummary_generate = True
+# Inherit docs from anndata
+autodoc_default_options = {
+    "inherited-members": True,
+}
+
+autosummary_generate = True  # Can disabled to avoid inheritance conflicts
 autodoc_member_order = "groupwise"
 default_role = "literal"
 napoleon_google_docstring = False
@@ -98,6 +103,7 @@
     "networkx": ("https://networkx.org/documentation/stable/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
     "h5py": ("https://docs.h5py.org/en/stable/", None),
+    "hdf5plugin": ("https://hdf5plugin.readthedocs.io/en/latest/", None),
 }
 
 # List of patterns, relative to source directory, that match files and

src/treedata/_core/treedata.py

@@ -26,14 +26,14 @@
 class TreeData(ad.AnnData):
     """AnnData with trees.
 
-    `TreeData` is a light-weight wrapper around :class:`~anndata.AnnData`
-    which adds two additional attributes, `obst` and `vart`, to
-    store trees for observations and variables A `TreeData`
+    :class:`~treedata.TreeData` is a light-weight wrapper around :class:`~anndata.AnnData`
+    which adds two additional attributes, :attr:`obst` and :attr:`vart`, to
+    store trees for observations and variables A :class:`~treedata.TreeData`
     object can be used just like an :class:`~anndata.AnnData` object and stores a
-    data matrix `X` together with annotations
-    of observations `obs` (`obsm`, `obsp`, `obst`),
-    variables `var` (`varm`, `varp`, `vart`),
-    and unstructured annotations `uns`.
+    data matrix :attr:`X` together with annotations
+    of observations :attr:`obs` (:attr:`obsm`, :attr:`obsp`, :attr:`obst`),
+    variables :attr:`var` (:attr:`varm`, :attr:`varp`, :attr:`vart`),
+    and unstructured annotations :attr:`uns`.
 
     Parameters
     ----------
@@ -133,7 +133,7 @@ def obst(self) -> AxisTrees:
         """Tree annotation of observations
 
         Stores for each key a :class:`~networkx.DiGraph` with leaf nodes in
-        `obs_names`. Is subset and pruned with `data` but behaves
+        :attr:`obs_names`. Is subset and pruned with `data` but behaves
         otherwise like a :term:`mapping`.
         """
         return self._obst
@@ -143,7 +143,7 @@ def vart(self):
         """Tree annotation of variables
 
         Stores for each key a :class:`~networkx.DiGraph` with leaf nodes in
-        `var_names`. Is subset and pruned with `data` but behaves
+        :attr:`var_names`. Is subset and pruned with `data` but behaves
         otherwise like a :term:`mapping`.
         """
         return self._vart
@@ -179,3 +179,7 @@ def __repr__(self) -> str:
     def __getitem__(self, index: Index) -> TreeData:
         """Returns a sliced view of the object."""
         raise NotImplementedError("Slicing not yet implemented")
+
+    def concatenate(self) -> None:
+        """Concatenate deprecated, use `treedata.concat` instead."""
+        raise NotImplementedError("Concatenation deprecated, use `treedata.concat` instead")