Adopt the Scientific Python deprecation schedule: (#3485)

.azure-pipelines.yml

@@ -3,7 +3,7 @@ trigger:
 - "*.*.x"
 
 variables:
-  python.version: '3.12'
+  python.version: '3.13'
   PYTEST_ADDOPTS: '-v --color=yes --internet-tests --nunit-xml=test-data/test-results.xml'
   TEST_EXTRA: 'test-full'
   DEPENDENCIES_VERSION: "latest"  # |"pre-release" | "minimum-version"
@@ -15,16 +15,16 @@ jobs:
     vmImage: 'ubuntu-22.04'
   strategy:
     matrix:
-      Python3.10:
-        python.version: '3.10'
-      Python3.12: {}
+      Python3.11:
+        python.version: '3.11'
+      Python3.13: {}
       minimal_dependencies:
         TEST_EXTRA: 'test-min'
       anndata_dev:
         DEPENDENCIES_VERSION: "pre-release"
         TEST_TYPE: "coverage"
       minimum_versions:
-        python.version: '3.10'
+        python.version: '3.11'
         DEPENDENCIES_VERSION: "minimum-version"
         TEST_TYPE: "coverage"
 
@@ -120,8 +120,8 @@ jobs:
 
   - task: UsePythonVersion@0
     inputs:
-      versionSpec: '3.12'
-    displayName: 'Use Python 3.12'
+      versionSpec: '3.13'
+    displayName: 'Use Python 3.13'
 
   - script: |
       python -m pip install --upgrade pip

.github/workflows/benchmark.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.12"]
+        python: ["3.13"]
         os: [ubuntu-latest]
 
     env:

.readthedocs.yml

@@ -4,7 +4,7 @@ submodules:
 build:
   os: ubuntu-24.04
   tools:
-    python: '3.12'
+    python: '3.13'
   jobs:
     post_checkout:
       # unshallow so version can be derived from tag

benchmarks/asv.conf.json

@@ -54,7 +54,7 @@
 
     // The Pythons you'd like to test against.  If not provided, defaults
     // to the current version of Python used to run `asv`.
-    // "pythons": ["3.10", "3.12"],
+    // "pythons": ["3.11", "3.13"],
 
     // The list of conda channel names to be searched for benchmark
     // dependency packages in the specified order

ci/scripts/min-deps.py

@@ -1,27 +1,21 @@
 #!/usr/bin/env python3
 # /// script
-# dependencies = [
-#   "tomli; python_version < '3.11'",
-#   "packaging",
-# ]
+# requires-python = ">=3.11"
+# dependencies = [ "packaging" ]
 # ///
 """Parse a pyproject.toml file and output a list of minimum dependencies."""
 
 from __future__ import annotations
 
 import argparse
 import sys
+import tomllib
 from collections import deque
 from contextlib import ExitStack
 from functools import cached_property
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-if sys.version_info >= (3, 11):
-    import tomllib
-else:
-    import tomli as tomllib
-
 from packaging.requirements import Requirement
 from packaging.version import Version
 
@@ -48,7 +42,8 @@ def min_dep(req: Requirement) -> Requirement:
         spec for spec in req.specifier if spec.operator in {"==", "~=", ">=", ">"}
     ]
     if not filter_specs:
-        return Requirement(req_name)
+        # TODO: handle markers
+        return Requirement(f"{req_name}{req.specifier}")
 
     min_version = Version("0.0.0.a1")
     for spec in filter_specs:

docs/conf.py

@@ -203,6 +203,7 @@ def setup(app: Sphinx):
 # -- Suppress link warnings ----------------------------------------------------
 
 qualname_overrides = {
+    "pathlib._local.Path": "pathlib.Path",
     "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.metrics.DistanceMetric",
     "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot",
     "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot",

docs/release-notes/3485.breaking.md

@@ -0,0 +1,2 @@
+Adopt the Scientific Python [deprecation schedule](https://scientific-python.org/specs/spec-0000/):
+remove Python 3.10 support and add Python 3.13 support, require anndata≥0.9 {smaller}`P Angerer`

hatch.toml

@@ -25,8 +25,8 @@ overrides.matrix.deps.pre-install-commands = [
     { if = [ "min" ], value = "uv run ci/scripts/min-deps.py pyproject.toml --all-extras -o ci/scanpy-min-deps.txt" },
 ]
 overrides.matrix.deps.python = [
-    { if = [ "min" ], value = "3.10" },
-    { if = [ "stable", "full", "pre" ], value = "3.12" },
+    { if = [ "min" ], value = "3.11" },
+    { if = [ "stable", "full", "pre" ], value = "3.13" },
 ]
 overrides.matrix.deps.features = [
     { if = [ "full" ], value = "test-full" },

pyproject.toml

@@ -5,7 +5,7 @@ requires = [ "hatchling", "hatch-vcs" ]
 [project]
 name = "scanpy"
 description = "Single-Cell Analysis in Python."
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = "BSD-3-clause"
 authors = [
     { name = "Alex Wolf" },
@@ -39,29 +39,29 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Visualization",
 ]
 dependencies = [
-    "anndata>=0.8",
-    "numpy>=1.24",
+    "anndata>=0.9",
+    "numpy>=1.25",
     "matplotlib>=3.6",
-    "pandas >=1.5",
-    "scipy>=1.8",
+    "pandas >=2.0",
+    "scipy>=1.11",
     "seaborn>=0.13",
-    "h5py>=3.7",
+    "h5py>=3.8",
     "tqdm",
-    "scikit-learn>=1.1,<1.6.0",
+    "scikit-learn>=1.1,<1.6",
     "statsmodels>=0.13",
     "patsy!=1.0.0",                               # https://github.com/pydata/patsy/issues/215
-    "networkx>=2.7",
+    "networkx>=2.8",
     "natsort",
     "joblib",
-    "numba>=0.57",
-    "umap-learn>=0.5,!=0.5.0",
+    "numba>=0.58",
+    "umap-learn>=0.5,!=0.5",
     "pynndescent>=0.5",
     "packaging>=21.3",
     "session-info2",
@@ -146,10 +146,10 @@ magic = [ "magic-impute>=2.0" ]                  # MAGIC imputation method
 skmisc = [ "scikit-misc>=0.1.3" ]                # highly_variable_genes method 'seurat_v3'
 harmony = [ "harmonypy" ]                        # Harmony dataset integration
 scanorama = [ "scanorama" ]                      # Scanorama dataset integration
-scrublet = [ "scikit-image" ]                    # Doublet detection with automatic thresholds
+scrublet = [ "scikit-image>=0.20" ]              # Doublet detection with automatic thresholds
 # Acceleration
 rapids = [ "cudf>=0.9", "cuml>=0.9", "cugraph>=0.9" ] # GPU accelerated calculation of neighbors
-dask = [ "dask[array]>=2022.09.2,<2024.8.0" ]         # Use the Dask parallelization engine
+dask = [ "dask[array]>=2023.5.1,<2024.8.0" ]          # Use the Dask parallelization engine
 dask-ml = [ "dask-ml", "scanpy[dask]" ]               # Dask-ML for sklearn-like API
 
 [tool.hatch.build.targets.wheel]

src/scanpy/_compat.py

@@ -1,12 +1,9 @@
 from __future__ import annotations
 
-import os
 import sys
 import warnings
-from dataclasses import dataclass, field
 from functools import WRAPPER_ASSIGNMENTS, cache, partial, wraps
 from importlib.util import find_spec
-from pathlib import Path
 from typing import TYPE_CHECKING, Literal, ParamSpec, TypeVar, cast, overload
 
 import numpy as np
@@ -63,25 +60,6 @@ def fullname(typ: type) -> str:
     return f"{module}.{name}"
 
 
-if sys.version_info >= (3, 11):
-    from contextlib import chdir
-else:
-    import os
-    from contextlib import AbstractContextManager
-
-    @dataclass
-    class chdir(AbstractContextManager):
-        path: Path
-        _old_cwd: list[Path] = field(default_factory=list)
-
-        def __enter__(self) -> None:
-            self._old_cwd.append(Path.cwd())
-            os.chdir(self.path)
-
-        def __exit__(self, *_excinfo) -> None:
-            os.chdir(self._old_cwd.pop())
-
-
 def pkg_metadata(package: str) -> PackageMetadata:
     from importlib.metadata import metadata
 
@@ -106,18 +84,6 @@ def old_positionals(*old_positionals: str):
         return lambda func: func
 
 
-if sys.version_info >= (3, 11):
-
-    def add_note(exc: BaseException, note: str) -> None:
-        exc.add_note(note)
-else:
-
-    def add_note(exc: BaseException, note: str) -> None:
-        if not hasattr(exc, "__notes__"):
-            exc.__notes__ = []
-        exc.__notes__.append(note)
-
-
 if sys.version_info >= (3, 13):
     from warnings import deprecated as _deprecated
 else:

src/scanpy/logging.py

@@ -4,7 +4,7 @@
 
 import logging
 import sys
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
 from functools import partial, update_wrapper
 from logging import CRITICAL, DEBUG, ERROR, INFO, WARNING
 from typing import TYPE_CHECKING, overload
@@ -45,7 +45,7 @@ def log(
     ) -> datetime:
         from ._settings import settings
 
-        now = datetime.now(timezone.utc)
+        now = datetime.now(UTC)
         time_passed: timedelta = None if time is None else now - time
         extra = {
             **(extra or {}),

src/scanpy/readwrite.py

@@ -36,7 +36,7 @@
 from matplotlib.image import imread
 
 from . import logging as logg
-from ._compat import add_note, deprecated, old_positionals
+from ._compat import deprecated, old_positionals
 from ._settings import settings
 from ._utils import _empty
 
@@ -1025,7 +1025,7 @@ def _download(url: str, path: Path):
             try:
                 from certifi import where
             except ImportError as e:
-                add_note(e, f"{msg} Please install `certifi` and try again.")
+                e.add_note(f"{msg} Please install `certifi` and try again.")
                 raise
             else:
                 logg.warning(f"{msg} Trying to use certifi.")

src/testing/scanpy/_pytest/fixtures/__init__.py

@@ -6,6 +6,7 @@
 from __future__ import annotations
 
 import warnings
+from contextlib import chdir
 from typing import TYPE_CHECKING
 
 import numpy as np
@@ -39,8 +40,6 @@ def float_dtype(request):
 
 @pytest.fixture
 def _doctest_env(cache: pytest.Cache, tmp_path: Path) -> Generator[None, None, None]:
-    from scanpy._compat import chdir
-
     showwarning_orig = warnings.showwarning
 
     def showwarning(message, category, filename, lineno, file=None, line=None):  # noqa: PLR0917

tests/test_package_structure.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import importlib
-import os
 from collections import defaultdict
 from inspect import Parameter, signature
 from pathlib import Path
@@ -54,16 +53,6 @@
 ]
 
 
-@pytest.fixture
-def in_project_dir():
-    wd_orig = Path.cwd()
-    os.chdir(proj_dir)
-    try:
-        yield proj_dir
-    finally:
-        os.chdir(wd_orig)
-
-
 @pytest.mark.xfail(reason="TODO: unclear if we want this to totally match, let’s see")
 def test_descend_classes_and_funcs():
     funcs = set(descend_classes_and_funcs(scanpy, "scanpy"))