feat: Allow using accessors in sc.get.aggregate

ci/scripts/low-vers.py

@@ -14,7 +14,7 @@
 from contextlib import ExitStack
 from functools import cached_property
 from pathlib import Path
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, assert_never
 
 import dependency_groups
 from packaging.requirements import Requirement
@@ -93,6 +93,7 @@ class Args(argparse.Namespace):
     output: Path | None
     _extras: list[str]
     _all_extras: bool
+    _skip_extras: list[str]
     _groups: list[str]
     _all_groups: bool
 
@@ -121,7 +122,7 @@ def parser(cls) -> argparse.ArgumentParser:
             dest="_extras",
             metavar="EXTRA",
             type=str,
-            nargs="*",
+            nargs="+",
             default=(),
             help="extras to install",
         )
@@ -131,6 +132,15 @@ def parser(cls) -> argparse.ArgumentParser:
             action="store_true",
             help="get all extras",
         )
+        parser.add_argument(
+            "--skip-extras",
+            dest="_skip_extras",
+            metavar="EXTRA",
+            type=str,
+            nargs="+",
+            default=(),
+            help="extras to skip when `--all-extras` is set",
+        )
         parser.add_argument(
             "--groups",
             dest="_groups",
@@ -167,13 +177,20 @@ def pyproject(self) -> dict[str, Any]:
     @cached_property
     def extras(self) -> AbstractSet[str]:
         """Return the extras to install."""
-        if self._extras:
-            if self._all_extras:
+        match self._extras, self._all_extras, self._skip_extras:
+            case [], True, skip:
+                return dict.fromkeys(
+                    self.pyproject["project"]["optional-dependencies"].keys()
+                    - set(skip)
+                ).keys()
+            case extras, False, []:
+                return dict.fromkeys(extras).keys()
+            case _, True, _:
                 sys.exit("Cannot specify both --extras and --all-extras")
-            return dict.fromkeys(self._extras).keys()
-        if not self._all_extras:
-            return set()
-        return self.pyproject["project"]["optional-dependencies"].keys()
+            case _, False, _:
+                sys.exit("Cannot specify --skip-extras without --all-extras")
+            case never:
+                assert_never(never)
 
     @cached_property
     def groups(self) -> AbstractSet[str]:

docs/conf.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import os
 import shutil
 import sys
 from datetime import datetime
@@ -126,6 +127,7 @@
 nb_execution_excludepatterns = [
     f"{d}{'/*' * n}" for d in ["tutorials", "how-to"] for n in (1, 2, 3)
 ]
+nb_execution_show_tb = bool(os.environ.get("READTHEDOCS"))
 nb_merge_streams = True
 
 ogp_site_url = "https://scanpy.scverse.org/en/stable/"
@@ -140,7 +142,8 @@
 katex_prerender = shutil.which(NODEJS_BINARY) is not None
 
 intersphinx_mapping = dict(
-    anndata=("https://anndata.scverse.org/en/stable/", None),
+    # Needs latest until `.acc` is released in 0.13
+    anndata=("https://anndata.scverse.org/en/latest/", None),
     bbknn=("https://bbknn.readthedocs.io/en/latest/", None),
     cuml=("https://docs.rapids.ai/api/cuml/stable/", None),
     cycler=("https://matplotlib.org/cycler/", None),

docs/release-notes/1.6.0.md

@@ -40,7 +40,7 @@ This release includes an overhaul of {func}`~scanpy.pl.dotplot`, {func}`~scanpy.
 
 #### Additions
 
-- {func}`~anndata.concat` is now exported from scanpy, see {doc}`anndata:concatenation` for more info. {pr}`1338` {smaller}`I Virshup`
+- {func}`~anndata.concat` is now exported from scanpy, see {doc}`anndata:tutorials/concatenation` for more info. {pr}`1338` {smaller}`I Virshup`
 - Added highly variable gene selection strategy from Seurat v3 {pr}`1204` {smaller}`A Gayoso`
 - Added [CellRank](https://github.com/theislab/cellrank/) to scanpy ecosystem {pr}`1304` {smaller}`giovp`
 - Added `backup_url` param to {func}`~scanpy.read_10x_h5` {pr}`1296` {smaller}`A Gayoso`

docs/release-notes/4199.feat.md

@@ -0,0 +1 @@
+Add {mod}`anndata.acc` support to {func}`scanpy.get.aggregate`. {smaller}`P Angerer`

hatch.toml

@@ -26,13 +26,14 @@ overrides.matrix.deps.env-vars = [
 overrides.matrix.deps.pre-install-commands = [
     { if = [
         "low-vers",
-    ], value = "uv run ci/scripts/low-vers.py pyproject.toml --all-extras --groups=test -o ci/scanpy-low-vers.txt" },
+    ], value = "uv run ci/scripts/low-vers.py pyproject.toml --all-extras --skip-extras=scanpy2 --groups=test -o ci/scanpy-low-vers.txt" },
 ]
 overrides.matrix.deps.python = [
     { if = [ "low-vers" ], value = "3.12" },
 ]
 overrides.matrix.deps.extra-dependencies = [
     { if = [ "stable" ], value = "scipy>=1.17" },
+    { if = [ "pre" ], value = "scanpy[scanpy2]" },
     { if = [ "pre" ], value = "anndata @ git+https://github.com/scverse/anndata.git" },
     { if = [ "pre" ], value = "pandas>=3" },
 ]

pyproject.toml

@@ -99,7 +99,7 @@ scrublet = [ "scikit-image>=0.25" ]
 # highly_variable_genes method 'seurat_v3'
 skmisc = [ "scikit-misc>=0.5.1" ]
 illico = [ "illico>=0.6" ]
-scanpy2 = [ "igraph>=0.10.8", "scanpy[illico]", "scikit-misc>=0.5.1" ]
+scanpy2 = [ "anndata>=0.13", "igraph>=0.10.8", "scanpy[illico]", "scikit-misc>=0.5.1" ]
 
 [dependency-groups]
 dev = [
@@ -118,14 +118,14 @@ test = [
     { include-group = "test-min" },
 ]
 docs = [
-    "ipython>=8.27",                        # for nbsphinx code highlighting
+    "ipython>=8.27",                                         # for nbsphinx code highlighting
     "myst-nb>=1.4",
     "myst-parser>=2",
     "nbsphinx>=0.9",
-    "numpy>=2.4",                           # type aliases
+    "numpy>=2.4",                                            # type aliases
     "sam-algorithm",
     # TODO: remove necessity for being able to import doc-linked classes
-    "scanpy[dask-ml,leiden,paga,plotting]",
+    "scanpy[dask-ml,leiden,paga,plotting,scanpy2,scrublet]",
     "scanpydoc>=0.16.1",
     "scverse-misc[sphinx]",
     "sphinx>=9.1",
@@ -137,7 +137,7 @@ docs = [
     "sphinx-issues>=5.0.1",
     "sphinxcontrib-bibtex",
     "sphinxcontrib-katex",
-    "sphinxext-opengraph",                  # for nice cards when sharing on social
+    "sphinxext-opengraph",                                   # for nice cards when sharing on social
 ]
 test-min = [
     "dependency-groups",    # for CI scripts doctests
@@ -274,6 +274,8 @@ filterwarnings = [
     "ignore:is_categorical_dtype is deprecated:FutureWarning",
     # Ignore numba PEP 456 warning specific to ARM machines
     "ignore:FNV hashing is not implemented in Numba.*:UserWarning",
+    # Ignore numba macOS warnings
+    "ignore:Detected unsupported threading environment:UserWarning",
     # we want to see and eventually fix these
     "default::numba.core.errors.NumbaPerformanceWarning",
     # we should set init=obsm["X_pca"] or so

src/scanpy/_settings/presets.py

@@ -5,7 +5,7 @@
 import re
 from contextlib import contextmanager
 from dataclasses import dataclass
-from functools import cached_property, partial, wraps
+from functools import cache, cached_property, partial, wraps
 from importlib.metadata import distributions, requires
 from typing import TYPE_CHECKING, Literal, NamedTuple
 
@@ -17,8 +17,11 @@
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Generator, Mapping
+    from collections.abc import Set as AbstractSet
     from typing import Self
 
+    from packaging.utils import NormalizedName
+
 
 __all__ = [
     "DETest",
@@ -312,14 +315,18 @@ def check(self) -> Self:
                 return self
 
 
+@cache
+def dist_names() -> AbstractSet[NormalizedName]:
+    return dict.fromkeys(canonicalize_name(d.name) for d in distributions()).keys()
+
+
 def _missing_scanpy2_deps() -> list[Requirement]:
-    dist_names = {canonicalize_name(d.name) for d in distributions()}
     return [
         r
         for r in map(Requirement, requires("scanpy") or ())
         if r.marker
         and r.marker.evaluate({"extra": "scanpy2"}, "requirement")
-        and canonicalize_name(r.name) not in dist_names
+        and canonicalize_name(r.name) not in dist_names()
     ]