Merge branch 'main' of github.com:keller-mark/scanpy into keller-mark…

…/densmap-2

.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"
 
@@ -103,6 +103,12 @@ jobs:
       testResultsFormat: NUnit
       testRunTitle: 'Publish test results for $(Agent.JobName)'
 
+  - task: PublishBuildArtifacts@1
+    inputs:
+      pathToPublish: '.pytest_cache/d/debug'
+      artifactName: debug-data
+    condition: eq(variables['TEST_TYPE'], 'coverage')
+
   - script: bash <(curl -s https://codecov.io/bash)
     displayName: 'Upload to codecov.io'
     condition: eq(variables['TEST_TYPE'], 'coverage')

.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 }}

.github/workflows/check-pr.yml

@@ -49,13 +49,13 @@ jobs:
         with:
           fetch-depth: 0
           filter: blob:none
-      - name: Find out if relevant release notes are modified
-        uses: dorny/paths-filter@v2
+      - name: Find out if a relevant release fragment is added
+        uses: dorny/paths-filter@v3
         id: changes
         with:
           filters: | # this is intentionally a string
-            relnotes: 'docs/release-notes/${{ github.event.pull_request.milestone.title }}.md'
-      - name: Check if relevant release notes are modified
+            relnotes: 'docs/release-notes/${{ github.event.pull_request.number }}.*.md'
+      - name: Check if a relevant release fragment is added
         uses: flying-sheep/check@v1
         with:
           success: ${{ steps.changes.outputs.relnotes }}

.gitignore

@@ -18,7 +18,6 @@
 /tests/**/*failed-diff.png
 
 # Environment management
-/hatch.toml
 /Pipfile
 /Pipfile.lock
 /requirements*.lock
@@ -29,6 +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: v0.5.6
+    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

.readthedocs.yml

@@ -2,9 +2,16 @@ version: 2
 submodules:
   include: all
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
     python: '3.12'
+  jobs:
+    post_checkout:
+      # unshallow so version can be derived from tag
+      - git fetch --unshallow || true
+    pre_build:
+      # run towncrier to preview the next version’s release notes
+      - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
 sphinx:
   fail_on_warning: true # do not change or you will be fired
   configuration: docs/conf.py
@@ -14,4 +21,5 @@ python:
     path: .
     extra_requirements:
     - doc
+    - dev  # for towncrier
     - leiden

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 +1,17 @@
-#!python3
+#!/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 pathlib import Path
 from typing import TYPE_CHECKING
 
@@ -16,7 +24,7 @@
 from packaging.version import Version
 
 if TYPE_CHECKING:
-    from collections.abc import Generator, Iterable
+    from collections.abc import Generator, Iterable, Sequence
 
 
 def min_dep(req: Requirement) -> Requirement:
@@ -27,18 +35,21 @@ 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)
@@ -65,12 +76,19 @@ def extract_min_deps(
             yield min_dep(req)
 
 
-def main():
+class Args(argparse.Namespace):
+    path: Path
+    output: Path | None
+    extras: list[str]
+
+
+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 directly passable to `pip install`.""",
+        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(
@@ -79,8 +97,18 @@ def main():
     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()
+    args = parser.parse_args(argv, Args())
 
     pyproject = tomllib.loads(args.path.read_text())
 
@@ -92,7 +120,10 @@ def main():
 
     min_deps = extract_min_deps(deps, pyproject=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

@@ -0,0 +1,111 @@
+#!/usr/bin/env python3
+# /// script
+# dependencies = [ "towncrier", "packaging" ]
+# ///
+
+from __future__ import annotations
+
+import argparse
+import subprocess
+from typing import TYPE_CHECKING
+
+from packaging.version import Version
+
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
+
+class Args(argparse.Namespace):
+    version: str
+    dry_run: bool
+
+
+def parse_args(argv: Sequence[str] | None = None) -> Args:
+    parser = argparse.ArgumentParser(
+        prog="towncrier-automation",
+        description=(
+            "This script runs towncrier for a given version, "
+            "creates a branch off of the current one, "
+            "and then creates a PR into the original branch with the changes. "
+            "The PR will be backported to main if the current branch is not main."
+        ),
+    )
+    parser.add_argument(
+        "version",
+        type=str,
+        help=(
+            "The new version for the release must have at least three parts, like `major.minor.patch` and no `major.minor`. "
+            "It can have a suffix like `major.minor.patch.dev0` or `major.minor.0rc1`."
+        ),
+    )
+    parser.add_argument(
+        "--dry-run",
+        help="Whether or not to dry-run the actual creation of the pull request",
+        action="store_true",
+    )
+    args = parser.parse_args(argv, Args())
+    # validate the version
+    if len(Version(args.version).release) != 3:
+        msg = f"Version argument {args.version} must contain major, minor, and patch version."
+        raise ValueError(msg)
+    return args
+
+
+def main(argv: Sequence[str] | None = None) -> None:
+    args = parse_args(argv)
+
+    # Run towncrier
+    subprocess.run(
+        ["towncrier", "build", f"--version={args.version}", "--yes"], check=True
+    )
+
+    # Check if we are on the main branch to know if we need to backport
+    base_branch = subprocess.run(
+        ["git", "rev-parse", "--abbrev-ref", "HEAD"],
+        capture_output=True,
+        text=True,
+        check=True,
+    ).stdout.strip()
+    pr_description = "" if base_branch == "main" else "@meeseeksdev backport to main"
+    branch_name = f"release_notes_{args.version}"
+
+    # Create a new branch + commit
+    subprocess.run(["git", "switch", "-c", branch_name], check=True)
+    subprocess.run(["git", "add", "docs/release-notes"], check=True)
+    pr_title = f"(chore): generate {args.version} release notes"
+    subprocess.run(["git", "commit", "-m", pr_title], check=True)
+
+    # push
+    if not args.dry_run:
+        subprocess.run(
+            ["git", "push", "--set-upstream", "origin", branch_name], check=True
+        )
+    else:
+        print("Dry run, not pushing")
+
+    # Create a PR
+    subprocess.run(
+        [
+            "gh",
+            "pr",
+            "create",
+            f"--base={base_branch}",
+            f"--title={pr_title}",
+            f"--body={pr_description}",
+            *(["--label=no milestone"] if base_branch == "main" else []),
+            *(["--dry-run"] if args.dry_run else []),
+        ],
+        check=True,
+    )
+
+    # Enable auto-merge
+    if not args.dry_run:
+        subprocess.run(
+            ["gh", "pr", "merge", branch_name, "--auto", "--squash"], check=True
+        )
+    else:
+        print("Dry run, not merging")
+
+
+if __name__ == "__main__":
+    main()

docs/conf.py

@@ -79,6 +79,7 @@
     "scanpydoc",  # needs to be before sphinx.ext.linkcode
     "sphinx.ext.linkcode",
     "sphinx_design",
+    "sphinx_tabs.tabs",
     "sphinx_search.extension",
     "sphinxext.opengraph",
     *[p.stem for p in (HERE / "extensions").glob("*.py") if p.stem not in {"git_ref"}],