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Use dependency groups for development dependencies - #564
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #564 +/- ##
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Coverage 78.20% 78.20%
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Files 68 68
Lines 7845 7845
Branches 1400 1400
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Hits 6135 6135
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dweindl
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| "ipython>=7.21.0, !=8.7.0", | ||
| "pysb", | ||
| ] | ||
| lint = [ |
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Maybe a bad name for this group since we also have petablint/linting in general is relevant to petab users.
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Dropped that group. Now part of dev.
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Move development-only dependencies from extras to dependency groups (`test`, `doc`, `dev`), keep feature extras (`antimony`, `combine`, `reports`, `sciml`, `vis`) and add an `all` extra. * `dev` (`test` + `pre-commit`) is the default group for `uv sync`. * Merge the former `ci` group into `test`, since the test suite requires `petabtests` and `benchmark_models_petab`. * Use pysb from master via `tool.uv.sources`. * Relax the `Jinja2` pin in `reports`. * Drop the unused `sphinxcontrib-napoleon`. * Read the Docs: install via `uv sync --group doc`. * CI: fetch the BNGL test corpus without syncing the project. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Move development-only dependencies from extras to dependency groups, since they don't need to be part of the published package metadata.
test,doc, anddev(=test+pre-commit).devis the default group, so a plainuv syncgives a development environment.cigroup is merged intotest, since the test suite requirespetabtestsandbenchmark_models_petab.antimony,combine,reports,sciml,visare kept; a newallextra includes all of them.tests,doc, andqualityare removed (→pip install petab[tests]no longer works).[tool.uv.sources](not part of the published metadata).Jinja2pin inreports(old nbsphinx workaround) is relaxed.sphinxcontrib-napoleonis dropped (sphinx.ext.napoleonis used).uv sync --group doc.uv run --no-project, avoiding a sync of the default group before the actual test environment sync.🤖 Generated with Claude Code