chore: switch to dependency groups (#3905)

Author: flying-sheep

.readthedocs.yml

@@ -10,16 +10,14 @@ build:
     post_checkout:
       # unshallow so version can be derived from tag
       - git fetch --unshallow || true
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
     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
-python:
-  install:
-  - method: pip
-    path: .
-    extra_requirements:
-    - doc
-    - dev  # for towncrier
+      - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true
+    build:
+      html:
+        - uvx hatch run docs:build
+        - mv docs/_build $READTHEDOCS_OUTPUT

ci/scripts/low-vers.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # /// script
 # requires-python = ">=3.11"
-# dependencies = [ "packaging" ]
+# dependencies = [ "packaging", "dependency-groups" ]
 # ///
 """Parse a pyproject.toml file and output a list of minimum dependency versions."""
 
@@ -16,6 +16,7 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+import dependency_groups
 from packaging.requirements import Requirement
 from packaging.version import Version
 
@@ -92,6 +93,8 @@ class Args(argparse.Namespace):
     output: Path | None
     _extras: list[str]
     _all_extras: bool
+    _groups: list[str]
+    _all_groups: bool
 
     @classmethod
     def parse(cls, argv: Sequence[str] | None = None) -> Self:
@@ -128,6 +131,21 @@ def parser(cls) -> argparse.ArgumentParser:
             action="store_true",
             help="get all extras",
         )
+        parser.add_argument(
+            "--groups",
+            dest="_groups",
+            metavar="GROUP",
+            type=str,
+            nargs="*",
+            default=(),
+            help="dependency groups to install",
+        )
+        parser.add_argument(
+            "--all-groups",
+            dest="_all_groups",
+            action="store_true",
+            help="get all dependency groups",
+        )
         parser.add_argument(
             *("--output", "-o"),
             metavar="FILE",
@@ -157,6 +175,17 @@ def extras(self) -> AbstractSet[str]:
             return set()
         return self.pyproject["project"]["optional-dependencies"].keys()
 
+    @cached_property
+    def groups(self) -> AbstractSet[str]:
+        """Return the dependency groups to install."""
+        if self._groups:
+            if self._all_groups:
+                sys.exit("Cannot specify both --groups and --all-groups")
+            return dict.fromkeys(self._groups).keys()
+        if not self._all_groups:
+            return set()
+        return self.pyproject["dependency-groups"].keys()
+
 
 def main(argv: Sequence[str] | None = None) -> None:
     """Run main entry point."""
@@ -166,6 +195,12 @@ def main(argv: Sequence[str] | None = None) -> None:
     deps = [
         *map(Requirement, args.pyproject["project"]["dependencies"]),
         *(Requirement(f"{project_name}[{extra}]") for extra in args.extras),
+        *map(
+            Requirement,
+            dependency_groups.resolve(
+                args.pyproject["dependency-groups"], *args.groups
+            ),
+        ),
     ]
 
     min_deps = extract_min_deps(deps, pyproject=args.pyproject)

docs/installation.md

@@ -75,7 +75,7 @@ If you are using `pip>=21.3`, an editable install can be made:
 ```console
 $ python -m venv .venv
 $ source .venv/bin/activate
-$ pip install -e '.[dev,test]'
+$ pip install --group=dev --group=test -e .
 ```
 :::
 
@@ -87,7 +87,7 @@ $ pipx install beni
 $ beni pyproject.toml > environment.yml
 $ conda env create -f environment.yml
 $ conda activate scanpy
-$ pip install -e '.[dev,doc,test]'
+$ pip install --group=dev --group=test --group=doc -e .
 ```
 
 For instructions on how to work with the code, see the {ref}`contribution guide <contribution-guide>`.

docs/release-notes/3905.chore.md

@@ -0,0 +1 @@
+Remove development extras (`scanpy[test,dev]`) in favor of dependency groups {smaller}`P Angerer`

hatch.toml

@@ -1,10 +1,10 @@
 [envs.default]
 installer = "uv"
-features = [ "dev" ]
+dependency-groups = [ "dev" ]
 
 [envs.docs]
-features = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build -W --keep-going {args}"
+dependency-groups = [ "doc" ]
+scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
 scripts.open = "python3 -m webbrowser -t docs/_build/html/index.html"
 scripts.clean = "git clean -fdX -- {args:docs}"
 
@@ -15,7 +15,7 @@ scripts.clean = "git restore --source=HEAD --staged --worktree -- docs/release-n
 
 [envs.hatch-test]
 default-args = [  ]
-features = [ "dev", "test-min" ]
+dependency-groups = [ "dev", "test-min" ]
 extra-dependencies = [ "ipykernel" ]
 overrides.matrix.deps.env-vars = [
     { if = [ "pre" ], key = "UV_PRERELEASE", value = "allow" },
@@ -24,7 +24,7 @@ overrides.matrix.deps.env-vars = [
 overrides.matrix.deps.pre-install-commands = [
     { if = [
         "low-vers",
-    ], value = "uv run ci/scripts/low-vers.py pyproject.toml --all-extras -o ci/scanpy-low-vers.txt" },
+    ], value = "uv run ci/scripts/low-vers.py pyproject.toml --all-extras --all-groups -o ci/scanpy-low-vers.txt" },
 ]
 overrides.matrix.deps.python = [
     { if = [ "low-vers" ], value = "3.12" },
@@ -34,9 +34,9 @@ overrides.matrix.deps.python = [
     { if = [ "pre" ], value = "3.14" },
 ]
 overrides.matrix.deps.extra-dependencies = [
-    { if = [ "pre" ], value = "anndata[dev,test] @ git+https://github.com/scverse/anndata.git" },
+    { if = [ "pre" ], value = "anndata @ git+https://github.com/scverse/anndata.git" },
 ]
-overrides.matrix.deps.features = [
+overrides.matrix.deps.dependency-groups = [
     { if = [ "stable", "pre", "low-vers" ], value = "test" },
 ]
 

pyproject.toml

@@ -54,7 +54,7 @@ dependencies = [
     "numpy>=2",
     "fast-array-utils[accel,sparse]>=1.2.1",
     "matplotlib>=3.9",
-    "pandas >=2.2.2",
+    "pandas >=2.2.2, <3.0.0rc0",
     "scipy>=1.13",
     "seaborn>=0.13.2",
     "h5py>=3.11",
@@ -87,7 +87,7 @@ Twitter = "https://x.com/scverse_team"
 [project.scripts]
 scanpy = "scanpy.cli:console_main"
 
-[project.optional-dependencies]
+[dependency-groups]
 test-min = [
     "pytest",
     "pytest-mock",
@@ -96,9 +96,10 @@ test-min = [
     "pytest-randomly",
     "pytest-rerunfailures",
     "tuna",
+    "dependency-groups",    # for CI scripts doctests
 ]
 test = [
-    "scanpy[test-min]",
+    { include-group = "test-min" },
     # optional storage and processing modes
     "scanpy[dask]",
     "zarr>=2.18.7",
@@ -131,6 +132,8 @@ dev = [
     "towncrier",   # release note management
     "scipy-stubs", # static typing and IDE support
 ]
+
+[project.optional-dependencies]
 # Algorithms
 paga = [ "igraph" ]
 louvain = [ "igraph", "louvain>=0.8.2", "setuptools" ] # Louvain community detection
@@ -152,7 +155,8 @@ packages = [ "src/testing", "src/scanpy" ]
 source = "vcs"
 raw-options.version_scheme = "release-branch-semver"
 
-[tool.pytest.ini_options]
+[tool.pytest]
+strict = true
 addopts = [
     "--import-mode=importlib",
     "--strict-markers",
@@ -162,7 +166,6 @@ addopts = [
 ]
 testpaths = [ "./tests", "./ci", "scanpy" ]
 norecursedirs = [ "tests/_images" ]
-xfail_strict = true
 junit_family = "xunit1"
 markers = [
     "internet: tests which rely on internet resources (enable with `--internet-tests`)",

tests/test_normalization.py

@@ -118,12 +118,16 @@ def test_normalize_pearson_residuals_warnings(pbmc3k_parametrized):
 @pytest.mark.parametrize(
     ("params", "match"),
     [
-        pytest.param(dict(theta=0), r"Pearson residuals require theta > 0", id="theta"),
         pytest.param(
-            dict(theta=-1), r"Pearson residuals require theta > 0", id="theta"
+            dict(theta=0), r"Pearson residuals require theta > 0", id="theta=0"
         ),
         pytest.param(
-            dict(clip=-1), r"Pearson residuals require `clip>=0` or `clip=None`."
+            dict(theta=-1), r"Pearson residuals require theta > 0", id="theta=-1"
+        ),
+        pytest.param(
+            dict(clip=-1),
+            r"Pearson residuals require `clip>=0` or `clip=None`.",
+            id="clip=-1",
         ),
     ],
 )