Adopt the current scverse cookiecutter template - #411
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Sync the repository with cookiecutter-scverse@707f3fa, including the mypy-based type checking the template now ships, and record the template state in `.cruft.json` so future syncs work. Packaging and tooling: - Drop Python 3.11 (SPEC 0, and `spatialdata` already requires >=3.12) and advertise 3.12-3.14 plus `Typing :: Typed`. - Replace the `dev`/`doc`/`test`/`pre` extras with dependency groups, and drive testing from a hatch matrix (3.12/3.14 stable, 3.14 pre-release) so local and CI runs share a single definition. - Adopt the template's ruff, coverage and pytest configuration, `biome.jsonc`, `.editorconfig`, `.gitignore`, `.codecov.yaml` and `CHANGELOG.md`, and delete the now-duplicated `.github/codecov.yml` and the broken `.bumpversion.cfg` (the version comes from git tags via hatch-vcs). - Rebuild the CI on the template's workflows: hatch-driven tests, a package build check, trusted publishing on release, pre-commit checks as a CI job, Dependabot for hooks and actions, and issue templates. The test-data artifact download is kept and now runs for every environment, so the 3.12 and pre-release jobs exercise the readers too. - Switch pre-commit to biome, pyproject-fmt, ruff-check and zizmor, and pin every action to a SHA so zizmor passes on `prepare_test_data.yaml` as well. Documentation: - Adopt the template's `conf.py` (scverse-misc, katex, opengraph, custom CSS) and drop the vendored `typed_returns` extension and autosummary template that scverse-misc replaces. - Merge the template's development guide into `docs/contributing.md` ahead of the existing reader-contribution guide, and describe the tag-based release flow instead of editing a version number. - `docs/changelog.md` now includes `CHANGELOG.md`. - Order `sphinx_click` before `sphinx_autodoc_typehints`: the latter imports `sphinx.ext.autodoc.mock` as a submodule, which shadows the callable of the same name that sphinx-click binds at import time. - Fix the references that made the strict build fail (`imageio.v2.imread`, the stereoseq `Notes` underline, the missing `Virshup_2023` entry) and inline `spatialdata`'s undocumented `Chunks_t` alias in `generic.image`, so the docs build clean with no nitpick exceptions. Typing: - Ship a `py.typed` marker and type-check `src` and `tests` with mypy, with no `# type: ignore`, no casts and no mypy settings beyond `ignore_missing_imports` for the dependencies that ship neither inline types nor stubs. Stubs are used wherever they exist (pandas, scipy, geopandas, shapely, tqdm, PyYAML, xmltodict). - This surfaced three real bugs: `cosmx`, `merscope` and `mcmicro` passed the `dtype=` argument that anndata removed in 0.11, so those readers raised `TypeError` at runtime; `mcmicro` now casts via `to_numpy(dtype=float)` to keep the previous behaviour. - `_get_translations` returned floats despite declaring `dict[str, int]`, which would have failed when used as `da.pad` widths. - Replace the remaining `# type: ignore` comments in `dbit` with real checks, and narrow the blind `except Exception` in `macsima` to the errors `parse_physical_size` actually raises. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #411 +/- ##
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- Coverage 63.41% 63.15% -0.26%
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Files 26 26
Lines 3217 3257 +40
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+ Hits 2040 2057 +17
- Misses 1177 1200 +23
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Under Python 3.14's dependency resolution, numpy types `ndarray.mean()` as `np.float64`, so mypy inferred that for the variable and rejected the `int` default in the other branch. Annotating the variable keeps both branches valid without changing the value or the log message. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Syncs the repo with
cookiecutter-scverse@707f3fa, including the mypy type checking the template now ships..cruft.jsonis recorded so futurecruft updateruns work.Breaking: Python 3.11 is dropped (SPEC 0;
spatialdatais already>=3.12).biome.jsonc,CHANGELOG.md,.codecov.yaml,.editorconfig,.gitignore. Removes the duplicate.github/codecov.ymland the broken.bumpversion.cfg; the version still comes from git tags via hatch-vcs.conf.py(scverse-misc, katex, opengraph); drops the vendoredtyped_returnsextension and autosummary template it replaces. Template dev guide merged above the existing reader-contribution guide.py.typedshipped;mypy src testsruns as a hook. No# type: ignore, no casts, no nitpick ignores, and no mypy settings beyondignore_missing_importsfor the deps that ship neither types nor stubs.Bugs this found
cosmx,merscopeandmcmicropasseddtype=toAnnData(...), removed in anndata 0.11 — those readers raisedTypeErrorat runtime.macsima._get_translationsreturned floats despite declaringdict[str, int]; the values are used asda.padwidths.# type: ignores indbithid that_check_pathcan returnNoneand thatpath=Nonesilently listed the working directory.Notes
.mypy.inipinnedpython_version = 3.10, so mypy aborted on numpy's stubs before checking anything.maincurrently fails the strict docs build (spatialdata.models.chunks_utils.TypeAliasTypehas no link target), which breaks RTD. Fixed at the source by inlining that alias ingeneric.image, plusimageio.v2.imread, a stereoseq section underline and the missingVirshup_2023entry.sphinx_clickis ordered beforesphinx_autodoc_typehints, which importssphinx.ext.autodoc.mockas a submodule and shadows the callable sphinx-click binds at import time. No version pin.[tool.pytest] strict = truerejects markers used by third-party test modules thatanndata.tests.helpersandspatialdata.testingimport, so four of them are declared inpyproject.toml.Verification
prek run --all-files,mypy src testsandsphinx -Wall clean on 3.14.pytestis 53 passed / 13 skipped / 22 failed, identical tomainlocally — the 22 areassert f.is_dir()on test data only CI has.