Update template to v0.7.0#18
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Superseded by #20, which cherry-picks the still-relevant v0.7.0 template diffs onto current main. |
Marius1311
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Apr 30, 2026
* chore: bump cookiecutter-scverse template to v0.7.0 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). * ci: pull lightning from GitHub monorepo to bypass PyPI quarantine 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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cookiecutter-scversereleased v0.7.0.Changes
Changes
@flying-sheepin Switch to dependency groups scverse/cookiecutter-scverse#449@Zethsonin Use type instead of label for issue templates scverse/cookiecutter-scverse#444@flying-sheepin chore: use KaTeX Sphinx plugin scverse/cookiecutter-scverse#446Fixes
@ilia-katsin sphinx conf.py: use project instead of project_name scverse/cookiecutter-scverse#440@flying-sheepin Fix workflow badge and link in readme scverse/cookiecutter-scverse#441@grstin Enable OIDC in Codecov action scverse/cookiecutter-scverse#457Additional remarks
add
skip: truetotemplate-repos.ymlusing a PR or,if you never want to sync from the template again, delete the
.cruft.jsonfile in the root of your repository.Make sure to activate those apps if you haven't already.