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Add pygrep-hooks and mdformat to pre-commit hooks #9644

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@Armavica Armavica commented Oct 18, 2024

Towards #8239. This mainly addresses problems in rst and markdown files.

- [ ] Tests added
- [ ] User visible changes (including notable bug fixes) are documented in `whats-new.rst`
- [ ] New functions/methods are listed in `api.rst`
- \[ \] Closes #xxxx
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Are we confident this still displays correctly?

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It seems to be fine, though I also find that surprising.

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Indeed!

Though it seems a bit confusing since people will be directly editing it...

> [!NOTE]
This is the boolean "summarization matrix" referred to in the classic Iverson (1980, Section 4.3)\[^2\] and "nub sieve" in [various APLs](https://aplwiki.com/wiki/Nub_Sieve).

> \[!NOTE\]
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Same here — are we sure these should be escaped? Looks like a directive (though not sure what...)


## Copyright

This document has been placed in the public domain.

## References and footnotes

[^1]: Wickham, H. (2011). The split-apply-combine strategy for data analysis. https://vita.had.co.nz/papers/plyr.html
[^2]: Iverson, K.E. (1980). Notation as a tool of thought. Commun. ACM 23, 8 (Aug. 1980), 444–465. https://doi.org/10.1145/358896.358899
\[^1\]: Wickham, H. (2011). The split-apply-combine strategy for data analysis. https://vita.had.co.nz/papers/plyr.html
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and here; seems unlikely this is correct

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A bunch of changes in this file look quite good!

@max-sixty
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Overall looks great!

We should check some of those, I added a couple of comments, though not a complete review.

To the extent that some might interfere with mypy or ruff, etc, that's not good — we don't want to be in a situation where code can't get through both checkers. Are we OK there?

The markdown & rst checkers look overall great!

@TomNicholas TomNicholas added the CI Continuous Integration tools label Oct 19, 2024
- repo: https://github.com/executablebooks/mdformat
rev: 0.7.18
hooks:
- id: mdformat
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apparently, we can fix (some of) the surprising bracket escapes with

Suggested change
- id: mdformat
- id: mdformat
additional_dependencies: [mdformat-gfm]

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@keewis keewis Oct 19, 2024

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though I wonder if instead of using mdformat we should rely on prettier to format markdown, as that can also format json and yaml?

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FWIW in prql we quite successfully use prettier to format all non-core code, including yaml / json / md; would recommend: https://github.com/PRQL/prql/blob/86becc591eb1a6421695ccccdf67dd8ab5c775ec/.pre-commit-config.yaml#L18-L22

...and it has a nice VS Code extension (and I guess emacs for the pros among us...)

@headtr1ck
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Why don't we instead try to rely on ruff and enable these rules there?
Many seems supported already, rules start with PGH*.

@max-sixty
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Why don't we instead try to rely on ruff and enable these rules there? Many seems supported already, rules start with PGH*.

Definitely preferable for the python ones. (though formatting non-python files would still be part of this sort of effort...)

@@ -69,7 +69,7 @@ Here’s a typical workflow for triaging a newly opened issue or discussion:
The issue tracker is many people’s first interaction with the xarray project itself, beyond just using the library.
It may also be their first open-source contribution of any kind. As such, we want it to be a welcoming, pleasant experience.

2. **Is the necessary information provided?**
1. **Is the necessary information provided?**
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This 1. and the below ones looks wrong.

git pull upstream main
```

1. Add a list of contributors.
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Forgotten the enumeration again.

2. The CI job will be started. Checks will appear in the usual dashboard panel above the comment box.
3. If more commits are added, the label checks will be grouped with the last commit checks _before_ you added the label.
4. Alternatively, you can always go to the `Actions` tab in the repo and [filter for `workflow:Benchmark`](https://github.com/scikit-image/scikit-image/actions?query=workflow%3ABenchmark). Your username will be assigned to the `actor` field, so you can also filter the results with that if you need it.
1. The CI job will be started. Checks will appear in the usual dashboard panel above the comment box.
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Forgotten enumeration.

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6 participants