fix such that anndata>=0.12.6 is acceptable

Author: eroell

docs/extensions/skip_inherited.py

@@ -33,15 +33,9 @@ def skip_member_handler(
 
 def setup(app: Sphinx) -> None:
     """Setup lamindb for CI."""
-    try:
-        import lamindb as ln
-    except ImportError:
-        # lamindb is currently incompatible with anndata>=0.12.13 (lamindb<=2.4.2
-        # caps anndata<=0.12.10), so it is excluded from the doc extras. Skip the
-        # CI bootstrap when it isn't installed.
-        pass
-    else:
-        with suppress(RuntimeError):
-            ln.setup.init(storage="/tmp/lamindb")
+    import lamindb as ln
+
+    with suppress(RuntimeError):
+        ln.setup.init(storage="/tmp/lamindb")
 
     app.connect("autodoc-skip-member", skip_member_handler)

pyproject.toml

@@ -23,7 +23,7 @@ classifiers = [
   "Programming Language :: Python :: 3.14",
 ]
 dependencies = [
-  "anndata>=0.12.13",
+  "anndata>=0.12.6",
   "duckdb",
   "fast-array-utils[sparse]",
   "filelock",
@@ -41,13 +41,7 @@ optional-dependencies.dev = [
 ]
 optional-dependencies.doc = [
   "docutils>=0.8,!=0.18.*,!=0.19.*",
-  # Do not include vitessce[all] in doc: https://github.com/keller-mark/esbuild-py/issues/19.
-  # Do not include ehrdata[lamin] in doc: every lamindb release through 2.4.2 caps
-  # anndata<=0.12.10 (via lamindb-core[full]), which conflicts with ehrdata's
-  # anndata>=0.12.13 pin. Notebooks aren't executed (nb_execution_mode = "off"), and
-  # the only references to lamindb in conf.py are an intersphinx URL and a qualname
-  # override, neither of which needs the package installed.
-  "ehrdata[torch]",
+  "ehrdata[lamin,torch]",            # do not include vitessce[all] in doc: https://github.com/keller-mark/esbuild-py/issues/19
   "ipykernel",
   "ipython",
   "myst-nb>=1.1",
@@ -72,6 +66,10 @@ optional-dependencies.lamin = [
 optional-dependencies.test = [
   "coverage>=7.10",
   "dask",
+  # No lamindb wheel/sdist is available for Python 3.14; pinning >=2.1 also prevents
+  # uv from backtracking to ancient lamindb 0.50.x (universal_pathlib==0.1.0, which
+  # imports `_PosixFlavour` removed in Python 3.12).
+  "lamindb>=2.1; python_version<'3.14'",
   "pytest",
   "pytest-cov",
   "torch",

src/ehrdata/core/ehrdata.py

@@ -202,7 +202,10 @@ class EHRData(AnnData):
     _t: pd.DataFrame | None
     _n_t: int
 
-    layers: AlignedMappingProperty3D = AlignedMappingProperty3D(Layers3D)
+    # Use keyword arguments so this works across the 0.12.x dataclass-field re-ordering:
+    # 0.12.6-0.12.11 require `(name, cls)`; 0.12.12+ make `name` optional (populated by
+    # `__set_name__`) and only require `cls`. Passing both by keyword satisfies both.
+    layers: AlignedMappingProperty3D = AlignedMappingProperty3D(name="layers", cls=Layers3D)
 
     def __init__(
         self,