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Be explicit about test coverage and add footnotes #190

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merged 5 commits into from
Jul 26, 2024
Merged

Be explicit about test coverage and add footnotes #190

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Be explicit about test coverage and add footnotes
grst Jul 22, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 22, 2024
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Update README.md
grst Jul 26, 2024
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Merge branch 'main' into grst-patch-1
grst Jul 26, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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8 changes: 6 additions & 2 deletions README.md
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Expand Up @@ -40,8 +40,8 @@ How does the package use scverse data structures (please describe in a few sente
- [ ] The code is publicly available under an [OSI-approved](https://opensource.org/licenses/alphabetical) license
- [ ] The package provides versioned releases
- [ ] The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
- [ ] The package uses automated software tests and runs them via continuous integration (CI)
- [ ] The package provides API documentation via a website or README
- [ ] The package uses automated software tests that cover all public functions and runs them via continuous integration (CI)[^1]
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It is the correct expectation but a rather strong one. I'm fine with it but wonder what other people think. Maybe a quick question for zulip?

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It is strong, but maybe it can be made less imposing by adding a paragraph about what a public API should be.

I think we should advise people to rather make their public API smaller than to compromise its testing or documentation.

In anndata, we recently documented the callback parameter signature of anndata.experimental.read_dispatched and in the process discovered what we had made implicitly public (if experimental).

To avoid a bunch of private things being made public, we made it all more correct and slimmer, which improved clarity here a lot.

- [ ] The package provides API documentation via a website or README[^2]
- [ ] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
- [ ] I am an author or maintainer of the tool and agree on listing the package on the scverse website

Expand All @@ -55,3 +55,7 @@ How does the package use scverse data structures (please describe in a few sente
- Mastodon:
- [ ] The package provides tutorials (or "vignettes") that help getting users started quickly
- [ ] The package uses the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse).

[^1]: Continuous integration means that software tests are automatically executed on every push to the git repository. This guarantees they are always run and that they are run in a clean environment. Scverse ecosystem packages most commonly use [GitHub Actions](https://github.com/features/actions) for CI. For an example, check out our [cookiecutter template](https://github.com/scverse/cookiecutter-scverse).

[^2]: By API documentation, we mean an overview of _all_ public functions provided a package, with documentation of their parameters. For an example, see the [Scanpy documentation](https://scanpy.readthedocs.io/en/stable/api/preprocessing.html). In simple cases, this can be done manually in a README file. For anything more complex, we recommend the [Sphinx Autodoc plugin](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html)
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