Modernize packaging & tooling from the scverse template#215
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| @@ -112,22 +143,22 @@ jobs: | |||
| shell: bash | |||
| run: | | |||
| set -euo pipefail | |||
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| BRANCH="${GITHUB_REF#refs/heads/}" | |||
| echo "Current branch: $BRANCH" | |||
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| git config user.name "github-actions[bot]" | |||
| git config user.email "github-actions[bot]@users.noreply.github.com" | |||
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| git add tests/pytest_results_py*.txt | |||
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| if git diff --cached --quiet; then | |||
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| git commit -m "CI: update pytest results ($BRANCH)" | |||
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| for attempt in 1 2 3 4 5; do | |||
| echo "Push attempt $attempt..." | |||
| git pull --rebase --autostash origin "$BRANCH" || true | |||
| @@ -136,7 +167,7 @@ jobs: | |||
| fi | |||
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| if [ "$code" != "0" ]; then | |||
| exit "$code" | |||
| fi | |||
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What's the purpose of this, @lauraluebbert?
Do we even need this?
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Adopt the modern parts of the scverse cookiecutter while preserving gget's mdbook docs, bundled binaries/data, and live-API test workflow. Packaging: - Consolidate setup.py + setup.cfg + requirements.txt + dev-requirements.txt + MANIFEST.in into a single pyproject.toml (hatchling backend, static version 0.30.6). Bundled binaries (gget/bins) and data (gget/constants) stay in the wheel; the `gget` console script is preserved. - Require Python >= 3.12; classifiers and CI cover 3.12 / 3.13 / 3.14. - Declare runtime deps in [project] and a [dependency-groups] `test` group; keep cellxgene-census in a separate optional `cellxgene` group (no wheels for newer Python yet) and have its test skip itself when the dep is absent. Linting / formatting: - Add the full scverse pre-commit config (biome, pyproject-fmt, ruff lint + format, standard hygiene hooks) plus the scverse ruff config. - Run ruff format + fixes across the tree; add docstrings, `raise ... from`, isinstance checks, and targeted noqa to reach a green `prek run --all-files`. - Vendored binaries, bundled data, test fixtures, and the CI report are excluded from formatting; Markdown hard line breaks are preserved. CI: - Modernize ci.yml (uv, pull_request trigger, 3.12/3.13/3.14 matrix, codecov, alls-green gate) while preserving the scheduled pytest-report commit-back. - Add build.yml (package build check) and release.yml (PyPI trusted publishing). Also fixes two latent bugs surfaced by ruff (undefined `Optional` in gget_cbio, use-before-assignment of `seqs` in gget_muscle) and a duplicate tearDown in the muscle tests. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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What & why
ggetstill used a pre-PEP-517 stack (setup.py+setup.cfg+requirements.txt+dev-requirements.txt+MANIFEST.in, no in-repo linter config, no pre-commit). This PR adopts the good parts of the scverse cookiecutter template while keeping the mdbook docs, the bundled binaries/data, and the existing live-API test workflow working.Packaging
pyproject.toml(hatchling backend, staticversion = 0.30.6). Verified the built wheel still bundles all 17gget/bins/**binaries +gget/constants/**data and theggetconsole script;twine check --strictpasses.[project]; test deps in a PEP 735[dependency-groups]testgroup.cellxgene-censuslives in a separate optionalcellxgenegroup because it has no wheels for 3.14 yet (itstiledbsomadep fails to build) — thegget cellxgenetest nowimportorskips itself when the dep is absent, so the suite stays green on 3.14.Linting / formatting
.pre-commit-config.yaml(biome, pyproject-fmt, ruff lint+format, standard hygiene hooks) and the scverse ruff config (verbatim ruleset incl. pydocstyle).CI / CD
ci.yml:uv, apull_requesttrigger (PRs didn't run tests before), 3.12/3.13/3.14 matrix, Codecov upload, and analls-greengate job — while preserving the scheduled run that saves & commitstests/pytest_results_py3.12.txt.build.yml(package build check) andrelease.yml(PyPI trusted publishing).Also
Optionalannotation ingget_cbio, and use-before-assignment ofseqsingget_muscle; plus a duplicatetearDownin the muscle tests.release.ymluses PyPI trusted publishing — it needs a one-time trusted publisher configured on PyPI forgget(workflowrelease.yml, environmentpypi) before the first tagged release.