Merge branch 'main' into main

.azure-pipelines.yml

@@ -15,16 +15,16 @@ jobs:
     vmImage: 'ubuntu-22.04'
   strategy:
     matrix:
-      Python3.9:
-        python.version: '3.9'
+      Python3.10:
+        python.version: '3.10'
       Python3.12: {}
       minimal_dependencies:
         TEST_EXTRA: 'test-min'
       anndata_dev:
         DEPENDENCIES_VERSION: "pre-release"
         TEST_TYPE: "coverage"
       minimum_versions:
-        python.version: '3.9'
+        python.version: '3.10'
         DEPENDENCIES_VERSION: "minimum-version"
         TEST_TYPE: "coverage"
 

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -1,8 +1,8 @@
 name: Bug report
 description: Scanpy doesn’t do what it should? Please help us fix it!
 #title: ...
+type: Bug
 labels:
-- Bug 🐛
 - Triage 🩺
 #assignees: []
 body:

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,4 @@
-blank_issues_enabled: true
+blank_issues_enabled: false
 contact_links:
   - name: Scanpy Community Forum
     url: https://discourse.scverse.org/

.github/ISSUE_TEMPLATE/enhancement-request.yml

@@ -1,8 +1,8 @@
 name: Enhancement request
 description: Anything you’d like to see in scanpy?
 #title: ...
+type: Enhancement
 labels:
-- Enhancement ✨
 - Triage 🩺
 #assignees: []
 body:
@@ -14,6 +14,7 @@ body:
     - 'Additional function parameters / changed functionality / changed defaults?'
     - 'New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?'
     - 'New plotting function: A kind of plot you would like to seein `sc.pl`?'
+    - 'Improved documentation or error message?'
     - 'Other?'
   validations:
     required: true

.github/workflows/benchmark.yml

@@ -48,8 +48,7 @@ jobs:
           key: benchmark-state-${{ hashFiles('benchmarks/**') }}
 
       - name: Install dependencies
-        # TODO: revert once this PR is merged: https://github.com/airspeed-velocity/asv/pull/1397
-        run: pip install 'asv @ git+https://github.com/ivirshup/asv@fix-conda-usage'
+        run: pip install 'asv>=0.6.4'
 
       - name: Configure ASV
         working-directory: ${{ env.ASV_DIR }}

.gitignore

@@ -28,6 +28,7 @@
 # Python build files
 __pycache__/
 /src/scanpy/_version.py
+/ci/scanpy-min-deps.txt
 /dist/
 /*-env/
 /env-*/

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.8
+    rev: v0.8.2
     hooks:
     -   id: ruff
         types_or: [python, pyi, jupyter]
@@ -20,7 +20,7 @@ repos:
         - --sort-by-bibkey
         - --drop=abstract
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
         exclude: tests/_data

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": ["3.9", "3.12"],
+    // "pythons": ["3.10", "3.12"],
 
     // The list of conda channel names to be searched for benchmark
     // dependency packages in the specified order

benchmarks/benchmarks/_utils.py

@@ -14,15 +14,16 @@
 import scanpy as sc
 
 if TYPE_CHECKING:
-    from collections.abc import Callable, Sequence, Set
+    from collections.abc import Callable, Sequence
+    from collections.abc import Set as AbstractSet
     from typing import Literal, Protocol, TypeVar
 
     from anndata import AnnData
 
     C = TypeVar("C", bound=Callable)
 
     class ParamSkipper(Protocol):
-        def __call__(self, **skipped: Set) -> Callable[[C], C]: ...
+        def __call__(self, **skipped: AbstractSet) -> Callable[[C], C]: ...
 
     Dataset = Literal["pbmc68k_reduced", "pbmc3k", "bmmc", "lung93k"]
     KeyX = Literal[None, "off-axis"]
@@ -195,7 +196,7 @@ def param_skipper(
     b 5
     """
 
-    def skip(**skipped: Set) -> Callable[[C], C]:
+    def skip(**skipped: AbstractSet) -> Callable[[C], C]:
         skipped_combs = [
             tuple(record.values())
             for record in (

ci/scripts/min-deps.py

@@ -1,9 +1,18 @@
 #!/usr/bin/env python3
+# /// script
+# dependencies = [
+#   "tomli; python_version < '3.11'",
+#   "packaging",
+# ]
+# ///
+
 from __future__ import annotations
 
 import argparse
 import sys
 from collections import deque
+from contextlib import ExitStack
+from functools import cached_property
 from pathlib import Path
 from typing import TYPE_CHECKING
 
@@ -16,7 +25,9 @@
 from packaging.version import Version
 
 if TYPE_CHECKING:
-    from collections.abc import Generator, Iterable
+    from collections.abc import Generator, Iterable, Sequence
+    from collections.abc import Set as AbstractSet
+    from typing import Any, Self
 
 
 def min_dep(req: Requirement) -> Requirement:
@@ -27,18 +38,21 @@ def min_dep(req: Requirement) -> Requirement:
     -------
 
     >>> min_dep(Requirement("numpy>=1.0"))
-    "numpy==1.0"
+    <Requirement('numpy==1.0.*')>
     """
     req_name = req.name
     if req.extras:
         req_name = f"{req_name}[{','.join(req.extras)}]"
 
-    if not req.specifier:
+    filter_specs = [
+        spec for spec in req.specifier if spec.operator in {"==", "~=", ">=", ">"}
+    ]
+    if not filter_specs:
         return Requirement(req_name)
 
     min_version = Version("0.0.0.a1")
-    for spec in req.specifier:
-        if spec.operator in [">", ">=", "~="]:
+    for spec in filter_specs:
+        if spec.operator in {">", ">=", "~="}:
             min_version = max(min_version, Version(spec.version))
         elif spec.operator == "==":
             min_version = Version(spec.version)
@@ -65,34 +79,92 @@ def extract_min_deps(
             yield min_dep(req)
 
 
-def main():
-    parser = argparse.ArgumentParser(
-        prog="min-deps",
-        description="""Parse a pyproject.toml file and output a list of minimum dependencies.
-
-        Output is directly passable to `pip install`.""",
-        usage="pip install `python min-deps.py pyproject.toml`",
-    )
-    parser.add_argument(
-        "path", type=Path, help="pyproject.toml to parse minimum dependencies from"
-    )
-    parser.add_argument(
-        "--extras", type=str, nargs="*", default=(), help="extras to install"
-    )
-
-    args = parser.parse_args()
-
-    pyproject = tomllib.loads(args.path.read_text())
+class Args(argparse.Namespace):
+    """\
+    Parse a pyproject.toml file and output a list of minimum dependencies.
+    Output is optimized for `[uv] pip install` (see `-o`/`--output` for details).
+    """
 
-    project_name = pyproject["project"]["name"]
+    _path: Path
+    output: Path | None
+    _extras: list[str]
+    _all_extras: bool
+
+    @classmethod
+    def parse(cls, argv: Sequence[str] | None = None) -> Self:
+        return cls.parser().parse_args(argv, cls())
+
+    @classmethod
+    def parser(cls) -> argparse.ArgumentParser:
+        parser = argparse.ArgumentParser(
+            prog="min-deps",
+            description=cls.__doc__,
+            usage="pip install `python min-deps.py pyproject.toml`",
+        )
+        parser.add_argument(
+            "_path",
+            metavar="pyproject.toml",
+            type=Path,
+            help="Path to pyproject.toml to parse minimum dependencies from",
+        )
+        parser.add_argument(
+            "--extras",
+            dest="_extras",
+            metavar="EXTRA",
+            type=str,
+            nargs="*",
+            default=(),
+            help="extras to install",
+        )
+        parser.add_argument(
+            "--all-extras",
+            dest="_all_extras",
+            action="store_true",
+            help="get all extras",
+        )
+        parser.add_argument(
+            *("--output", "-o"),
+            metavar="FILE",
+            type=Path,
+            default=None,
+            help=(
+                "output file (default: stdout). "
+                "Without this option, output is space-separated for direct passing to `pip install`. "
+                "With this option, output written to a file newline-separated file usable as `requirements.txt` or `constraints.txt`."
+            ),
+        )
+        return parser
+
+    @cached_property
+    def pyproject(self) -> dict[str, Any]:
+        return tomllib.loads(self._path.read_text())
+
+    @cached_property
+    def extras(self) -> AbstractSet[str]:
+        if self._extras:
+            if self._all_extras:
+                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()
+
+
+def main(argv: Sequence[str] | None = None) -> None:
+    args = Args.parse(argv)
+
+    project_name = args.pyproject["project"]["name"]
     deps = [
-        *map(Requirement, pyproject["project"]["dependencies"]),
+        *map(Requirement, args.pyproject["project"]["dependencies"]),
         *(Requirement(f"{project_name}[{extra}]") for extra in args.extras),
     ]
 
-    min_deps = extract_min_deps(deps, pyproject=pyproject)
+    min_deps = extract_min_deps(deps, pyproject=args.pyproject)
 
-    print(" ".join(map(str, min_deps)))
+    sep = "\n" if args.output else " "
+    with ExitStack() as stack:
+        f = stack.enter_context(args.output.open("w")) if args.output else sys.stdout
+        print(sep.join(map(str, min_deps)), file=f)
 
 
 if __name__ == "__main__":

ci/scripts/towncrier_automation.py

@@ -1,4 +1,8 @@
 #!/usr/bin/env python3
+# /// script
+# dependencies = [ "towncrier", "packaging" ]
+# ///
+
 from __future__ import annotations
 
 import argparse
@@ -62,9 +66,7 @@ def main(argv: Sequence[str] | None = None) -> None:
         text=True,
         check=True,
     ).stdout.strip()
-    pr_description = (
-        "" if base_branch == "main" else "@meeseeksmachine backport to main"
-    )
+    pr_description = "" if base_branch == "main" else "@meeseeksdev backport to main"
     branch_name = f"release_notes_{args.version}"
 
     # Create a new branch + commit
@@ -90,7 +92,11 @@ def main(argv: Sequence[str] | None = None) -> None:
             f"--base={base_branch}",
             f"--title={pr_title}",
             f"--body={pr_description}",
-            *(["--label=no milestone"] if base_branch == "main" else []),
+            *(
+                ["--label=no milestone", "--label=Development Process 🚀"]
+                if base_branch == "main"
+                else []
+            ),
             *(["--dry-run"] if args.dry_run else []),
         ],
         check=True,

docs/api/deprecated.md

@@ -11,4 +11,5 @@
 
    pp.filter_genes_dispersion
    pp.normalize_per_cell
+   pp.subsample
 ```

docs/api/preprocessing.md

@@ -31,7 +31,7 @@ For visual quality control, see {func}`~scanpy.pl.highest_expr_genes` and
    pp.normalize_total
    pp.regress_out
    pp.scale
-   pp.subsample
+   pp.sample
    pp.downsample_counts
 ```
 

docs/conf.py

@@ -142,6 +142,8 @@
     rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None),
     scipy=("https://docs.scipy.org/doc/scipy/", None),
     seaborn=("https://seaborn.pydata.org/", None),
+    session_info2=("https://session-info2.readthedocs.io/en/stable/", None),
+    squidpy=("https://squidpy.readthedocs.io/en/stable/", None),
     sklearn=("https://scikit-learn.org/stable/", None),
 )
 

docs/release-notes/1.10.4.md

@@ -0,0 +1,17 @@
+(v1.10.4)=
+### 1.10.4 {small}`2024-11-12`
+
+### Breaking changes
+
+- Remove Python 3.9 support {smaller}`P Angerer` ({pr}`3283`)
+
+### Bug fixes
+
+- Fix {meth}`scanpy.pl.DotPlot.style`, {meth}`scanpy.pl.MatrixPlot.style`, and {meth}`scanpy.pl.StackedViolin.style` resetting all non-specified parameters {smaller}`P Angerer` ({pr}`3206`)
+- Accept `'group'` instead of `'obs'` for `standard_scale` parameter in {func}`~scanpy.pl.stacked_violin` {smaller}`P Angerer` ({pr}`3243`)
+- Use `density_norm` instead of of `scale` (cont. from {pr}`2844`) in {func}`~scanpy.pl.violin` and {func}`~scanpy.pl.stacked_violin` {smaller}`P Angerer` ({pr}`3244`)
+- Switched all compatibility adapters for positional parameters to {exc}`FutureWarning` {smaller}`P Angerer` ({pr}`3264`)
+- Catch `PerfectSeparationWarning` during {func}`~scanpy.pp.regress_out` {smaller}`J Wagner` ({pr}`3275`)
+- Fix {func}`scanpy.pp.highly_variable_genes` for batches of size 1 {smaller}`P Angerer` ({pr}`3286`)
+- Fix {func}`scanpy.pl.scatter`’s `color` parameter to take collections as advertised {smaller}`P Angerer` ({pr}`3299`)
+- Fix {func}`scanpy.pl.highest_expr_genes` when used with a categorical gene symbol column {smaller}`P Angerer` ({pr}`3302`)