ci: use Python 3.14 more

.github/workflows/ci.yml

@@ -32,7 +32,7 @@ jobs:
               select(.key | startswith("hatch-test"))
               | {
                 name: .key,
-                "test-type": (if (.key | test("pre|min")) then "coverage" else null end),
+                "test-type": (if (.key | test("pre|low-vers")) then "coverage" else null end),
                 python: .value.python
               }
             )')
@@ -44,6 +44,8 @@ jobs:
     strategy:
       matrix:
         env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+    permissions:
+      id-token: write  # for codecov OIDC
     steps:
       - uses: actions/checkout@v6
         with: { filter: 'blob:none', fetch-depth: 0 }
@@ -77,24 +79,26 @@ jobs:
           hatch run ${{ matrix.env.name }}:run-cov
           hatch run ${{ matrix.env.name }}:cov-combine
           hatch run ${{ matrix.env.name }}:coverage xml
+          hatch run ${{ matrix.env.name }}:cov-report
 
       - name: Upload coverage data
         if: ${{ !cancelled() && matrix.env.test-type == 'coverage' }}
         uses: codecov/codecov-action@v5
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
           flags: ${{ matrix.env.name }}
-          fail_ci_if_error: true
           files: test-data/coverage.xml
+          use_oidc: true
+          fail_ci_if_error: true
 
       - name: Upload test results
         if: ${{ !cancelled() }}
-        uses: codecov/test-results-action@v1
+        uses: codecov/codecov-action@v5
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+          report_type: test_results
           flags: ${{ matrix.env.name }}
+          files: test-data/test-results.xml
+          use_oidc: true
           fail_ci_if_error: true
-          file: test-data/test-results.xml
 
       - name: Publish debug artifacts
         if: ${{ !cancelled() }}

docs/conf.py

@@ -126,6 +126,7 @@
 ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg"
 
 typehints_defaults = "braces"
+always_use_bars_union = True  # Don’t use `Union` even when building with Python ≤3.14
 
 pygments_style = "default"
 pygments_dark_style = "native"
@@ -157,11 +158,7 @@
     pydeseq2=("https://pydeseq2.readthedocs.io/en/stable/", None),
     pynndescent=("https://pynndescent.readthedocs.io/en/latest/", None),
     pytest=("https://docs.pytest.org/en/latest/", None),
-    python=(
-        # TODO: switch to `/3` once docs are built with Python 3.14
-        "https://docs.python.org/3.13",
-        None,
-    ),
+    python=("https://docs.python.org/3", None),
     rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None),
     scipy=("https://docs.scipy.org/doc/scipy/", None),
     seaborn=("https://seaborn.pydata.org/", None),

hatch.toml

@@ -14,6 +14,7 @@ scripts.build = "python3 ci/scripts/towncrier_automation.py {args}"
 scripts.clean = "git restore --source=HEAD --staged --worktree -- docs/release-notes"
 
 [envs.hatch-test]
+python = "3.14"
 default-args = [  ]
 dependency-groups = [ "dev", "test-min" ]
 extra-dependencies = [ "ipykernel" ]
@@ -28,10 +29,6 @@ overrides.matrix.deps.pre-install-commands = [
 ]
 overrides.matrix.deps.python = [
     { if = [ "low-vers" ], value = "3.12" },
-    { if = [ "stable", "few-extras" ], value = "3.13" },
-    # numba doesn’t support 3.14 in a stable release yet:
-    # https://github.com/numba/numba/issues/9957
-    { if = [ "pre" ], value = "3.14" },
 ]
 overrides.matrix.deps.extra-dependencies = [
     { if = [ "pre" ], value = "anndata @ git+https://github.com/scverse/anndata.git" },

src/scanpy/external/pl.py

@@ -7,11 +7,8 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-from anndata import AnnData  # noqa: TC002
-from matplotlib.axes import Axes  # noqa: TC002
-from sklearn.utils import deprecated
 
-from .._compat import old_positionals
+from .._compat import deprecated, old_positionals
 from .._utils import _doc_params
 from .._utils._doctests import doctest_needs
 from ..plotting import _scrublet, _utils, embedding
@@ -28,6 +25,9 @@
     from collections.abc import Collection
     from typing import Any
 
+    from anndata import AnnData
+    from matplotlib.axes import Axes
+
 
 __all__ = [
     "harmony_timeseries",

src/scanpy/external/pp/__init__.py

@@ -2,8 +2,7 @@
 
 from __future__ import annotations
 
-from sklearn.utils import deprecated
-
+from ..._compat import deprecated
 from ...preprocessing import _scrublet
 from ._bbknn import bbknn
 from ._dca import dca

src/scanpy/external/pp/_harmony_integrate.py

@@ -2,7 +2,6 @@
 
 from __future__ import annotations
 
-from collections.abc import Sequence  # noqa: TC003
 from typing import TYPE_CHECKING
 
 import numpy as np
@@ -11,6 +10,8 @@
 from ..._utils._doctests import doctest_needs
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
+
     from anndata import AnnData
 
 

src/scanpy/plotting/_tools/scatterplots.py

@@ -1,44 +1,28 @@
 from __future__ import annotations
 
 import inspect
-from collections.abc import Mapping, Sequence  # noqa: TC003
+import re
+import textwrap
+from collections.abc import Sequence
 from copy import copy
-from functools import partial
+from functools import cache, partial
 from itertools import combinations, product
 from numbers import Integral
-from typing import (
-    TYPE_CHECKING,
-    Any,  # noqa: TC003
-    Literal,  # noqa: TC003
-)
+from typing import TYPE_CHECKING
 
 import numpy as np
 import pandas as pd
-from anndata import AnnData  # noqa: TC002
-from cycler import Cycler  # noqa: TC002
 from matplotlib import colormaps, colors, patheffects, rcParams
 from matplotlib import pyplot as plt
-from matplotlib.axes import Axes  # noqa: TC002
-from matplotlib.colors import (
-    Colormap,  # noqa: TC002
-    Normalize,
-)
-from matplotlib.figure import Figure  # noqa: TC002
+from matplotlib.colors import Normalize
 from matplotlib.markers import MarkerStyle
-from numpy.typing import NDArray  # noqa: TC002
 
 from ... import logging as logg
 from ..._compat import deprecated
 from ..._settings import settings
-from ..._utils import (
-    Empty,  # noqa: TC001
-    _doc_params,
-    _empty,
-    sanitize_anndata,
-)
+from ..._utils import _doc_params, _empty, sanitize_anndata
 from ..._utils._doctests import doctest_internet
 from ...get import _check_mask
-from ...tools._draw_graph import _Layout  # noqa: TC001
 from .. import _utils
 from .._docs import (
     doc_adata_color_etc,
@@ -47,19 +31,23 @@
     doc_scatter_spatial,
     doc_show_save_ax,
 )
-from .._utils import (
-    ColorLike,  # noqa: TC001
-    VBound,  # noqa: TC001
-    _FontSize,  # noqa: TC001
-    _FontWeight,  # noqa: TC001
-    _LegendLoc,  # noqa: TC001
-    check_colornorm,
-    check_projection,
-    circles,
-)
+from .._utils import check_colornorm, check_projection, circles
 
 if TYPE_CHECKING:
-    from collections.abc import Collection
+    from collections.abc import Callable, Collection, Mapping
+    from types import FunctionType
+    from typing import Any, Literal
+
+    from anndata import AnnData
+    from cycler import Cycler
+    from matplotlib.axes import Axes
+    from matplotlib.colors import Colormap
+    from matplotlib.figure import Figure
+    from numpy.typing import NDArray
+
+    from ..._utils import Empty
+    from ...tools._draw_graph import _Layout
+    from .._utils import ColorLike, VBound, _FontSize, _FontWeight, _LegendLoc
 
 
 @_doc_params(
@@ -600,10 +588,29 @@ def _get_vboundnorm(
     return tuple(out)
 
 
-def _wraps_plot_scatter(wrapper):
+_TYPE_GUARD_IMPORT_RE = re.compile(r"\nif TYPE_CHECKING:[^\n]*([\s\S]*?)(?=\n\S)")
+
+
+@cache
+def _get_guarded_imports(obj: FunctionType) -> Mapping[str, Any]:
+    """Simplified version from `sphinx-autodoc-typehints`."""
+    module = inspect.getmodule(obj)
+    assert module
+    code = inspect.getsource(module)
+    rv: dict[str, Any] = {}
+    for m in _TYPE_GUARD_IMPORT_RE.finditer(code):
+        guarded_code = textwrap.dedent(m.group(1))
+        rv.update(obj.__globals__)
+        exec(guarded_code, rv)
+        for k in obj.__globals__:
+            del rv[k]
+    return rv
+
+
+def _wraps_plot_scatter[**P, R](wrapper: Callable[P, R]) -> Callable[P, R]:
     """Update the wrapper function to use the correct signature."""
-    params = inspect.signature(embedding, eval_str=True).parameters.copy()
-    wrapper_sig = inspect.signature(wrapper, eval_str=True)
+    params = inspect.signature(embedding).parameters.copy()
+    wrapper_sig = inspect.signature(wrapper)
     wrapper_params = wrapper_sig.parameters.copy()
 
     params.pop("basis")
@@ -619,6 +626,14 @@ def _wraps_plot_scatter(wrapper):
     if wrapper_sig.return_annotation is not inspect.Signature.empty:
         annotations["return"] = wrapper_sig.return_annotation
 
+    # `sphinx-autodoc-typehints` can execute `if TYPECHECKING` blocks,
+    # but all all users of `_wraps_plot_scatter` that aren’t in this module
+    # won’t have any imports. So we execute and inject the imports here.
+    wrapper.__globals__.update({
+        k: v
+        for k, v in {**embedding.__globals__, **_get_guarded_imports(embedding)}.items()
+        if k not in wrapper.__globals__
+    })
     wrapper.__signature__ = inspect.Signature(
         list(params.values()), return_annotation=wrapper_sig.return_annotation
     )