Fix min-deps hatch config (#1807)

.azure-pipelines.yml

@@ -49,11 +49,7 @@ jobs:
           path: $(uv_cache_dir)
         displayName: Cache pip packages
 
-      # This prevents broken and slow back-tracking in dependency resolution
-      - script: printf "llvmlite>=0.43\nscanpy>=1.10.0rc1" | tee /tmp/constraints.txt
-        displayName: "Create constraints file for `pre-release` and `latest` jobs"
-
-      - script: uv pip install --system --compile "anndata[dev,test] @ ." -c /tmp/constraints.txt
+      - script: uv pip install --system --compile "anndata[dev,test] @ ." -c ci/constraints.txt
         displayName: "Install dependencies"
         condition: eq(variables['DEPENDENCIES_VERSION'], 'latest')
 
@@ -65,7 +61,7 @@ jobs:
         displayName: "Install minimum dependencies"
         condition: eq(variables['DEPENDENCIES_VERSION'], 'minimum')
 
-      - script: uv pip install -v --system --compile --pre "anndata[dev,test] @ ." -c /tmp/constraints.txt
+      - script: uv pip install -v --system --compile --pre "anndata[dev,test] @ ." -c ci/constraints.txt
         displayName: "Install dependencies release candidates"
         condition: eq(variables['DEPENDENCIES_VERSION'], 'pre-release')
 

.github/workflows/test-gpu.yml

@@ -72,9 +72,7 @@ jobs:
           cache-dependency-path: pyproject.toml
 
       - name: Install AnnData
-        run: |
-          printf "llvmlite>=0.43\nscanpy>=1.10.0rc1" | tee /tmp/constraints.txt
-          uv pip install --system -e ".[dev,test,cu12]" -c /tmp/constraints.txt
+        run: uv pip install --system -e ".[dev,test,cu12]" -c ci/constraints.txt
 
       - name: Env list
         run: pip list

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 
 # Distribution / packaging
 /dist/
+/ci/min-deps.txt
 /src/anndata/_version.py
 /requirements*.lock
 /.python-version

ci/constraints.txt

@@ -0,0 +1 @@
+numba>=0.56

ci/scripts/min-deps.py

@@ -11,6 +11,8 @@
 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
 
@@ -23,7 +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:
@@ -75,34 +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 +1,7 @@
 #!/usr/bin/env python3
+# /// script
+# dependencies = [ "towncrier", "packaging" ]
+# ///
 from __future__ import annotations
 
 import argparse

hatch.toml

@@ -4,21 +4,26 @@ features = ["dev"]
 
 [envs.docs]
 features = ["doc"]
-extra-dependencies = ["setuptools"]  # https://bitbucket.org/pybtex-devs/pybtex/issues/169
 scripts.build = "sphinx-build -M html docs docs/_build -W --keep-going {args}"
+scripts.open = "python3 -m webbrowser -t docs/_build/html/index.html"
 scripts.clean = "git clean -fdX -- {args:docs}"
 
 [envs.towncrier]
+scripts.create = "towncrier create {args}"
 scripts.build = "python3 ci/scripts/towncrier_automation.py {args}"
 scripts.clean = "git restore --source=HEAD --staged --worktree -- docs/release-notes"
 
 [envs.hatch-test]
 default-args = []
-extra-dependencies = ["ipykernel"]
 features = ["dev", "test"]
+extra-dependencies = ["ipykernel"]
+env-vars.UV_CONSTRAINT = "ci/constraints.txt"
 overrides.matrix.deps.env-vars = [
-    { key = "UV_PRERELEASE", value = "allow", if = ["pre"] },
-    { key = "UV_RESOLUTION", value = "lowest-direct", if = ["min"] },
+    { if = ["pre"], key = "UV_PRERELEASE", value = "allow" },
+    { if = ["min"], key = "UV_CONSTRAINT", value = "ci/constraints.txt ci/min-deps.txt" },
+]
+overrides.matrix.deps.pre-install-commands = [
+    { if = ["min"], value = "uv run ci/scripts/min-deps.py pyproject.toml --all-extras -o ci/min-deps.txt" },
 ]
 overrides.matrix.deps.python = [
     { if = ["min"], value = "3.10" },

pyproject.toml

@@ -42,7 +42,7 @@ dependencies = [
     "numpy>=1.23",
     # https://github.com/scverse/anndata/issues/1434
     "scipy >1.8",
-    "h5py>=3.6",
+    "h5py>=3.7",
     "exceptiongroup; python_version<'3.11'",
     "natsort",
     "packaging>=20.0",
@@ -74,7 +74,7 @@ doc = [
     "nbsphinx",
     "scanpydoc[theme,typehints] >=0.14.1",
     "zarr",
-    "awkward>=2.0.7",
+    "awkward>=2.3",
     "IPython",                          # For syntax highlighting in notebooks
     "myst_parser",
     "sphinx_design>=0.5.0",
@@ -93,7 +93,7 @@ test = [
     "openpyxl",
     "joblib",
     "boltons",
-    "scanpy",
+    "scanpy>=1.9.8",
     "httpx", # For data downloading
     "dask[distributed]",
     "awkward>=2.3",