chore: bump cookiecutter-scverse template to v0.7.0#20
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Apply the still-relevant diffs from the v0.7.0 template update on top of current main (replaces the stale auto-PR #18). - `.cruft.json`: bump commit + checkout to `v0.7.0`. - Issue templates: `labels:` → `type:` (Bug, Enhancement); collapse one bug-report bullet onto a single line. - Workflows: drop the redundant top-level `defaults.run.shell` block, bump `actions/checkout@v4` → `@v5` and `astral-sh/setup-uv@v5` → `@v7`, drop `cache-dependency-glob` (uv handles it). Add `continue-on-error: ${{ contains(matrix.env.name, 'pre') }}` to the test matrix so pre-release runs do not block CI. - `.readthedocs.yaml`: python `3.12` → `3.13`, add `nodejs: latest` for KaTeX prerendering. - `docs/conf.py`: replace `sphinx.ext.mathjax` with `sphinxcontrib.katex`, enable `katex_prerender` when a Node binary is available, rename the local `project_name` to `project`. Pin the python intersphinx target to `3.13` until RTD ships 3.14. - `docs/contributing.md`: bump example versions (`py3.10`/`py3.13` → `py3.11`/`py3.14`). - `pyproject.toml`: migrate `dev`, `doc`, `test` from `[project.optional-dependencies]` to `[dependency-groups]` (PEP 735). Drop the `optional-dependencies.test` extra entirely; CPU+GPU coverage in CI now comes from `features = ["cpu", "gpu"]` on the hatch-test env combined with `dependency-groups = ["dev", "test"]`. Bump matrix Python to `["3.11", "3.14"]`. Add `sphinxcontrib-katex` to the doc group. Codecov upload stays token-based (intentionally not switching to OIDC in this PR).
This was referenced Apr 30, 2026
PyPI has quarantined the `lightning` distribution (https://pypi.org/simple/lightning/ -> project-status: quarantined, zero installable files). `scvi-tools>=1.3` depends on `lightning>=2.0`, so any hatch-test env that includes the `[gpu]` extra fails uv resolution with 'no versions of lightning'. This is independent of the v0.7.0 template bump but blocks PR #20 because the new test matrix exercises a fresh resolve on Python 3.11 and 3.14. Pre-existing main CI only passed on cached envs. Add a [tool.uv.sources] redirect to the upstream GitHub monorepo at tag 2.6.2 (>=2.0, satisfies scvi-tools). The override only takes effect for direct deps, so list `lightning` explicitly in the [gpu] extra. Drop both lines once PyPI restores the package.
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Bump pinned hook versions and run `pre-commit run --all-files`. Replaces the stale auto-PR #19. Stacked on top of #20 since pyproject-fmt v2.21 reformats the `[dependency-groups]` layout introduced there. - biomejs/pre-commit v2.3.10 → v2.4.13 - tox-dev/pyproject-fmt v2.11.1 → v2.21.1 - astral-sh/ruff-pre-commit v0.14.10 → v0.15.12 The `pyproject.toml` reformat (flatten `[tool.pytest.ini_options]` into `ini_options.*` keys under `[tool.pytest]`, same for `[tool.coverage]`) is purely the new pyproject-fmt's preferred layout.
Marius1311
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PyPI has quarantined the `lightning` distribution; `scvi-tools` depends on `lightning>=2.0`, so any hatch-test env with the `[gpu]` extra fails uv resolution. Cherry of the fix that lands on PR #20; included so this PR's CI is green independently. Drop once PyPI restores the package.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #20 +/- ##
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Coverage 78.51% 78.51%
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Files 11 11
Lines 1303 1303
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Hits 1023 1023
Misses 280 280 🚀 New features to boost your workflow:
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Marius1311
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* chore: pre-commit autoupdate Bump pinned hook versions and run `pre-commit run --all-files`. Replaces the stale auto-PR #19. Stacked on top of #20 since pyproject-fmt v2.21 reformats the `[dependency-groups]` layout introduced there. - biomejs/pre-commit v2.3.10 → v2.4.13 - tox-dev/pyproject-fmt v2.11.1 → v2.21.1 - astral-sh/ruff-pre-commit v0.14.10 → v0.15.12 The `pyproject.toml` reformat (flatten `[tool.pytest.ini_options]` into `ini_options.*` keys under `[tool.pytest]`, same for `[tool.coverage]`) is purely the new pyproject-fmt's preferred layout. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Summary
Apply the still-relevant diffs from cookiecutter-scverse
v0.7.0on top ofcurrent
main. Replaces the stale auto-PR #18 (which is now far enoughbehind that a clean cherry-pick is simpler than a rebase).
Behavior or invariants changed
[project.optional-dependencies].testis removed. Test tooling nowlives in
[dependency-groups].test(PEP 735). The hatch-test env keepsCPU + GPU coverage via
features = ["cpu", "gpu"]plusdependency-groups = ["dev", "test"]. Anyone previously runningpip install scembed[test]should switch touv sync --group test(orinstall
cpu/gpuextras directly).["3.11", "3.13"]→["3.11", "3.14"].continue-on-error: truewhen the env name contains
pre).Out of scope (intentionally not adopted)
we want it.
follow-up PR that branches off this one.
.github/copilot-instructions.mdrewrite:separate docs PR.
Tests run
uvx hatch env show -ilists the newhatch-test.py3.11andhatch-test.py3.14envs withfeatures = [cpu, gpu]anddependency-groups = [dev, test].uvx hatch run docs:buildsucceeds locally (KaTeX + sphinxcontrib-katexinstall correctly into the docs env).
the new
pyproject.tomlonce merged).Reviewer focus
pyproject.toml: theoptional-dependencies.testremoval and thehatch-test env layout (CPU+GPU features + dev/test groups).
docs/conf.py: KaTeX swap and thekatex_prerenderguard.defaults.run.shellblock doesn't breakany multi-line
run:step.Closes
Supersedes #18.