feat: create scanpy2 extra for dependencies

pyproject.toml

@@ -99,6 +99,7 @@ scanorama = [ "scanorama" ]
 scrublet = [ "scikit-image>=0.23.1" ]
 # highly_variable_genes method 'seurat_v3'
 skmisc = [ "scikit-misc>=0.5.1" ]
+scanpy2 = [ "igraph>=0.10.8", "leidenalg>=0.10.1", "scikit-misc>=0.5.1" ]
 
 [dependency-groups]
 dev = [

src/scanpy/_settings/__init__.py

@@ -105,7 +105,12 @@ def preset(cls) -> Preset:
 
     @preset.setter
     def preset(cls, preset: Preset | str) -> None:
-        cls._preset = Preset(preset)
+        from .presets import _check_scanpy_v2_deps
+
+        new_preset = Preset(preset)
+        if new_preset is Preset.ScanpyV2Preview:
+            _check_scanpy_v2_deps()
+        cls._preset = new_preset
 
     @property
     def verbosity(cls) -> Verbosity:

src/scanpy/_settings/presets.py

@@ -8,6 +8,8 @@
 from functools import cached_property, partial, wraps
 from typing import TYPE_CHECKING, Literal, NamedTuple
 
+from .._utils._doctests import doctest_needs
+
 if TYPE_CHECKING:
     from collections.abc import Callable, Generator, Mapping
 
@@ -128,6 +130,30 @@ def get(self: Preset) -> NT:
     return prop
 
 
+def _check_scanpy_v2_deps() -> None:
+    from importlib.metadata import packages_distributions, requires
+    from importlib.util import find_spec
+
+    from packaging.requirements import Requirement
+
+    dist_to_module = {d: m for m, ds in packages_distributions().items() for d in ds}
+    missing = [
+        r.name
+        for r in map(Requirement, requires("scanpy"))
+        if r.marker
+        and r.marker.evaluate({"extra": "scanpy2"})
+        and find_spec(dist_to_module.get(r.name, r.name.replace("-", "_"))) is None
+    ]
+    if missing:
+        missing_str = ", ".join(f"’{m}’" for m in missing)
+        msg = (
+            f"Setting preset to {Preset.ScanpyV2Preview!r} requires optional "
+            f"dependencies that are not installed: {missing_str}. "
+            "Install them with: pip install `scanpy[scanpy2]`"
+        )
+        raise ImportError(msg)
+
+
 class Preset(enum.StrEnum):
     """Presets for :attr:`scanpy.settings.preset`.
 
@@ -198,6 +224,7 @@ def leiden() -> Mapping[Preset, LeidenPreset]:
         }
 
     @contextmanager
+    @doctest_needs("igraph")
     def override(self, preset: Preset) -> Generator[Preset, None, None]:
         """Temporarily override :attr:`scanpy.settings.preset`.
 

src/scanpy/_utils/__init__.py

@@ -34,7 +34,6 @@
 
 from .. import logging as logg
 from .._compat import CSBase, DaskArray, _CSArray, pkg_version, warn
-from .._settings import settings
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Iterable, KeysView, Mapping
@@ -340,6 +339,8 @@ def compute_association_matrix_of_groups(
         reference labels, entries are proportional to degree of association.
 
     """
+    from .._settings import settings
+
     if normalization not in {"prediction", "reference"}:
         msg = '`normalization` needs to be either "prediction" or "reference".'
         raise ValueError(msg)

tests/test_settings.py

@@ -1,6 +1,10 @@
 from __future__ import annotations
 
+from importlib.metadata import packages_distributions, requires
+from importlib.util import find_spec
+
 import pytest
+from packaging.requirements import Requirement
 
 import scanpy as sc
 
@@ -17,3 +21,21 @@ def test_resets(_attempt: int) -> None:
 def test_set_figure_params_warns() -> None:
     with pytest.warns(FutureWarning, match=r"scanpy\.set_figure_params"):
         sc.settings.set_figure_params()
+
+
+def test_preset_scanpy_v2_preview_checks_deps() -> None:
+    _dist_to_module = {d: m for m, ds in packages_distributions().items() for d in ds}
+    _scanpy2_deps_missing = any(
+        find_spec(_dist_to_module.get(r.name, r.name.replace("-", "_"))) is None
+        for r in map(Requirement, requires("scanpy"))
+        if r.marker and r.marker.evaluate({"extra": "scanpy2"})
+    )
+
+    if _scanpy2_deps_missing:
+        with pytest.raises(ImportError, match=r"scanpy\[scanpy2\]"):
+            sc.settings.preset = sc.Preset.ScanpyV2Preview
+    else:
+        sc.settings.preset = sc.Preset.ScanpyV2Preview
+        assert sc.settings.preset is sc.Preset.ScanpyV2Preview
+        sc.settings.preset = sc.Preset.ScanpyV1
+    assert sc.settings.preset == sc.Preset.ScanpyV1