Merge branch 'main' into mem_fix

.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

.gitignore

@@ -27,7 +27,6 @@
 
 # Python build files
 __pycache__/
-/src/scanpy/_version.py
 /ci/scanpy-min-deps.txt
 /dist/
 /*-env/
@@ -42,7 +41,6 @@ Thumbs.db
 
 # IDEs and editors
 /.idea/
-/.vscode/
 
 # asv benchmark files
 /benchmarks/.asv

.pre-commit-config.yaml

@@ -1,16 +1,13 @@
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.4
+    rev: v0.9.2
     hooks:
     -   id: ruff
-        types_or: [python, pyi, jupyter]
         args: ["--fix"]
     -   id: ruff-format
-        types_or: [python, pyi, jupyter]
     # The following can be removed once PLR0917 is out of preview
     -   name: ruff preview rules
         id: ruff
-        types_or: [python, pyi, jupyter]
         args: ["--preview", "--select=PLR0917"]
 -   repo: https://github.com/flying-sheep/bibfmt
     rev: v4.3.0
@@ -19,6 +16,15 @@ repos:
         args:
         - --sort-by-bibkey
         - --drop=abstract
+-   repo: https://github.com/biomejs/pre-commit
+    rev: v0.6.1
+    hooks:
+    -   id: biome-format
+        additional_dependencies: ["@biomejs/[email protected]"]
+-   repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
+    hooks:
+    -   id: taplo-format
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
@@ -34,6 +40,3 @@ repos:
     -   id: detect-private-key
     -   id: no-commit-to-branch
         args: ["--branch=main"]
-
-ci:
-    autofix_prs: false

.taplo.toml

@@ -0,0 +1,5 @@
+[formatting]
+array_auto_collapse = false
+column_width = 120
+compact_arrays = false
+indent_string = '    '

.vscode/launch.json

@@ -0,0 +1,26 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": { "PYTEST_ADDOPTS": "--color=yes" },
+            "presentation": { "hidden": true },
+        },
+    ],
+}

.vscode/settings.json

@@ -0,0 +1,22 @@
+{
+    "[python][toml][json][jsonc]": {
+        "editor.formatOnSave": true,
+        "editor.codeActionsOnSave": {
+            "source.organizeImports": "explicit",
+            "source.fixAll": "explicit",
+        },
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+    },
+    "[toml]": {
+        "editor.defaultFormatter": "tamasfe.even-better-toml",
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+    "python.testing.pytestEnabled": true,
+    "python.terminal.activateEnvironment": true,
+}

benchmarks/asv.conf.json

@@ -78,7 +78,7 @@
         "natsort": [""],
         "pandas": [""],
         "memory_profiler": [""],
-        "zarr": [""],
+        "zarr": ["2.18.4"],
         "pytest": [""],
         "scanpy": [""],
         "python-igraph": [""],

biome.jsonc

@@ -0,0 +1,21 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": {
+        "indentStyle": "space",
+        "indentWidth": 4,
+    },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
+            "json": {
+                "formatter": {
+                    "trailingCommas": "all",
+                },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}

ci/scripts/min-deps.py

@@ -12,6 +12,7 @@
 import sys
 from collections import deque
 from contextlib import ExitStack
+from functools import cached_property
 from pathlib import Path
 from typing import TYPE_CHECKING
 
@@ -25,6 +26,8 @@
 
 if TYPE_CHECKING:
     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:
@@ -68,7 +71,9 @@ def extract_min_deps(
 
         # If we are referring to other optional dependency lists, resolve them
         if req.name == project_name:
-            assert req.extras, f"Project included itself as dependency, without specifying extras: {req}"
+            assert req.extras, (
+                f"Project included itself as dependency, without specifying extras: {req}"
+            )
             for extra in req.extras:
                 extra_deps = pyproject["project"]["optional-dependencies"][extra]
                 dependencies += map(Requirement, extra_deps)
@@ -77,48 +82,86 @@ def extract_min_deps(
 
 
 class Args(argparse.Namespace):
-    path: Path
+    """\
+    Parse a pyproject.toml file and output a list of minimum dependencies.
+    Output is optimized for `[uv] pip install` (see `-o`/`--output` for details).
+    """
+
+    _path: Path
     output: Path | None
-    extras: list[str]
+    _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:
-    parser = argparse.ArgumentParser(
-        prog="min-deps",
-        description=(
-            "Parse a pyproject.toml file and output a list of minimum dependencies. "
-            "Output is optimized for `[uv] pip install` (see `-o`/`--output` for details)."
-        ),
-        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"
-    )
-    parser.add_argument(
-        *("--output", "-o"),
-        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`."
-        ),
-    )
-
-    args = parser.parse_args(argv, Args())
-
-    pyproject = tomllib.loads(args.path.read_text())
+    args = Args.parse(argv)
 
-    project_name = pyproject["project"]["name"]
+    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)
 
     sep = "\n" if args.output else " "
     with ExitStack() as stack:

ci/scripts/towncrier_automation.py

@@ -92,7 +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
 ```
 
@@ -49,7 +49,7 @@ For visual quality control, see {func}`~scanpy.pl.highest_expr_genes` and
 
 ### Batch effect correction
 
-Also see [Data integration]. Note that a simple batch correction method is available via {func}`pp.regress_out`. Checkout {mod}`scanpy.external` for more.
+Also see {ref}`data-integration`. Note that a simple batch correction method is available via {func}`pp.regress_out`. Checkout {mod}`scanpy.external` for more.
 
 ```{eval-rst}
 .. autosummary::

docs/api/tools.md

@@ -48,6 +48,8 @@ Compute densities on embeddings.
    tl.paga
 ```
 
+(data-integration)=
+
 ### Data integration
 
 ```{eval-rst}

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),
 )
 
@@ -225,9 +227,6 @@ def setup(app: Sphinx):
     ("py:class", "scanpy._utils.Empty"),
     ("py:class", "numpy.random.mtrand.RandomState"),
     ("py:class", "scanpy.neighbors._types.KnnTransformerLike"),
-    # Will work once scipy 1.8 is released
-    ("py:class", "scipy.sparse.base.spmatrix"),
-    ("py:class", "scipy.sparse.csr.csr_matrix"),
 ]
 
 # Options for plot examples