Actually working min-deps job (#3337)

.gitignore

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

ci/scripts/min-deps.py

@@ -11,6 +11,7 @@
 import argparse
 import sys
 from collections import deque
+from contextlib import ExitStack
 from pathlib import Path
 from typing import TYPE_CHECKING
 
@@ -23,7 +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:
@@ -75,12 +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(
@@ -89,8 +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())
 
@@ -102,7 +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

@@ -1,4 +1,8 @@
 #!/usr/bin/env python3
+# /// script
+# dependencies = [ "towncrier", "packaging" ]
+# ///
+
 from __future__ import annotations
 
 import argparse

hatch.toml

@@ -19,14 +19,17 @@ features = ["test", "dask-ml"]
 extra-dependencies = ["ipykernel"]
 overrides.matrix.deps.env-vars = [
     { if = ["pre"], key = "UV_PRERELEASE", value = "allow" },
-    { if = ["min"], key = "UV_RESOLUTION", value = "lowest-direct" },
+    { if = ["min"], key = "UV_CONSTRAINT", value = "ci/scanpy-min-deps.txt" },
+]
+overrides.matrix.deps.pre-install-commands = [
+    { if = ["min"], value = "uv run ci/scripts/min-deps.py pyproject.toml -o ci/scanpy-min-deps.txt" },
 ]
 overrides.matrix.deps.python = [
-    { if = ["min"] , value = "3.10" },
+    { if = ["min"], value = "3.10" },
     { if = ["stable", "full", "pre"], value = "3.12" },
 ]
 overrides.matrix.deps.features = [
-    { if = ["full"] , value = "test-full" },
+    { if = ["full"], value = "test-full" },
 ]
 
 [[envs.hatch-test.matrix]]

pyproject.toml

@@ -52,7 +52,7 @@ dependencies = [
     "pandas >=1.5",
     "scipy>=1.8",
     "seaborn>=0.13",
-    "h5py>=3.6",
+    "h5py>=3.7",
     "tqdm",
     "scikit-learn>=1.1",
     "statsmodels>=0.13",