Make EhrData subclass AnnData (#50)

* Make EhrData subclass AnnData

* Some init fixes

* some type fixes

* no useless privates

* repr fixes

* Fix tests

* fix docs

* improve typing

* Fix docs

* docs

* newer docs runner

* try uv for docs

* Fix docs

.readthedocs.yaml

@@ -1,16 +1,14 @@
 # https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.10"
+    python: "3.12"
+  jobs:
+    post_install:
+      - pip install uv
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install .[doc]
 sphinx:
   configuration: docs/conf.py
   # disable this for more lenient docs builds
   fail_on_warning: true
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - doc

docs/conf.py

@@ -106,6 +106,8 @@
     "anndata": ("https://anndata.readthedocs.io/en/stable", None),
     "scanpy": ("https://scanpy.readthedocs.io/en/stable", None),
     "numpy": ("https://numpy.org/doc/stable", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+    "pandas": ("https://pandas.pydata.org/docs", None),
     "zarr": ("https://zarr.readthedocs.io/en/stable", None),
     "vitessce": ("https://python-docs.vitessce.io", None),
     "lamin": ("https://docs.lamin.ai", None),
@@ -142,6 +144,8 @@
 nitpick_ignore = [
     # https://github.com/duckdb/duckdb-web/issues/3806
     ("py:class", "duckdb.duckdb.DuckDBPyConnection"),
+    # Is documented as a py:attribute instead
+    ("py:class", "numpy.int64"),
 ]
 
 # Redirect broken parameter annotation classes

docs/extensions/skip_inherited.py

@@ -0,0 +1,41 @@
+from __future__ import annotations
+
+from contextlib import suppress
+from typing import TYPE_CHECKING, Literal
+
+if TYPE_CHECKING:
+    from sphinx.application import Sphinx
+
+
+def skip_member_handler(
+    app: Sphinx,
+    what: Literal["module", "class", "exception", "function", "method", "attribute", "property"],
+    name: str,
+    obj: object,
+    skip: bool,
+    options,
+) -> bool | None:
+    """Skip inherited members."""
+    if what not in {"method", "attribute", "property"}:
+        return None
+    if isinstance(obj, property):
+        obj = obj.fget
+    if name == "__getitem__":
+        return False
+    if name.startswith("_"):
+        return True
+    if not hasattr(obj, "__module__"):
+        return None
+    if not obj.__module__.startswith("ehrdata"):
+        return True
+    return None
+
+
+def setup(app: Sphinx) -> None:
+    """Setup lamindb for CI."""
+    import lamindb as ln
+
+    with suppress(RuntimeError):
+        ln.setup.init(storage="/tmp/lamindb")
+
+    app.connect("autodoc-skip-member", skip_member_handler)