Format yaml files

[timmens]

Closes #426.

[codecov]

Codecov Report

Merging #427 (98100fe) into main (9a2f3d6) will decrease coverage by 0.12%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #427      +/-   ##
==========================================
- Coverage   92.88%   92.76%   -0.12%     
==========================================
  Files         225      224       -1     
  Lines       17673    17134     -539     
==========================================
- Hits        16416    15895     -521     
+ Misses       1257     1239      -18     

Impacted Files	Coverage Δ
...c/estimagic/benchmarking/get_benchmark_problems.py	94.96% <ø> (ø)
src/estimagic/cli.py	100.00% <ø> (ø)
src/estimagic/config.py	77.77% <ø> (ø)
src/estimagic/dashboard/run_dashboard.py	33.33% <ø> (ø)
src/estimagic/examples/criterion_functions.py	100.00% <ø> (ø)
src/estimagic/examples/logit.py	100.00% <ø> (ø)
src/estimagic/exceptions.py	84.61% <ø> (ø)
src/estimagic/inference/bootstrap_outcomes.py	100.00% <ø> (ø)
src/estimagic/inference/bootstrap_samples.py	100.00% <ø> (ø)
src/estimagic/inference/ml_covs.py	84.14% <ø> (ø)
... and 176 more

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[timmens]

In order for yamllint to work I had to edit the configuration from

hyphens: enable

to

hypens:
   max-spaces-after: 3

which allows yaml files with nested lists like:

history_x:
  -   - 0.15
       - 0.008
       - 0.01
  -   - 0.25
       - 0.008
       - 0.01

where the potential problem is the spacing between the two hyphens. In principle, it might be possible to align the settings of yamlfix and yamllint here, but I could not find the yamlfix option which governs this behaviour.

[hmgaudecker]

Looks great to me, thanks a lot!!!

I would love to see common settings for the hooks across projects so one can easily spot differences. In particular, what would be good IMHO:

• Same order of hooks (if possible)
• Same settings for (basic) py / yaml / md linting and formatting
• Same sorting of environment files (alphabetically?)

Please append to the list if I am missing anything. I think estimagic is a good place to settle that because it's environment is close to being a superset of the others' environments.

@janosg @tobiasraabe I explicitly tagged you re the order, but it would be great if you could have a look at the other settings, too.

Partly related: yamlfix is based on ruyaml -- loading/dumping based on that would add another dependency but probably prevent some pre-commit surprises (and all of them if it could be configured according to the section in pyproject.toml). No strong opinion here, just wanted to toss it into the round.

[janosg]

In principle I like the standardization across projects, but we have tried that multiple times in the past and it always failed. Back then the idea was that there is one tiny project (I think it was called the OSE packaging guide) that always uses the latest version of pre-commits, CI and other infrastructure and each project copies from there. Typically nobody copied and thus at some point we stopped updating.

I think the only way we can implement something like that would be to automate it. I think Tobi does that to some extent for the many pytask repos. But probably after automatic updates we would still have to fix problems manually and I am not sure if people are willing to do that. There are also some things we probably cannot standardize. For example I would love to enable some more ruff rules in estimagic but fixing all issues in such a large codebase takes time. In small projects we can be stricter.

RE sorting: I think I prefer it if environment files are sorted by category (e.g. runtime dependencies, test dependencies, ...) but I don't have a strong opinion. I do like estimagic's new way of auto-generating variations of the development environment for testing, but probably most other packages don't need that.

If we start another real effort to standardize the whole infrastructure across OSE packages, we should probably discuss that in a larger group. Definitely out of scope for this PR.

[janosg]

BTW: The failing link will be fixed when you merge the main in this branch.

[timmens]

My only addition to Janos' comment is that we already sort alphabetically in each category, except for the first and last line of the dependencies.

[hmgaudecker]

In principle I like the standardization across projects, but we have tried that multiple times in the past and it always failed. Back then the idea was that there is one tiny project (I think it was called the OSE packaging guide) that always uses the latest version of pre-commits, CI and other infrastructure and each project copies from there. Typically nobody copied and thus at some point we stopped updating.

Yeah, fair enough, I remember that and I don't think we will be able to go fully automatic.

RE sorting: I think I prefer it if environment files are sorted by category (e.g. runtime dependencies, test dependencies, ...) but I don't have a strong opinion. I do like estimagic's new way of auto-generating variations of the development environment for testing, but probably most other packages don't need that.

Exactly. Different projects just have different needs. What I like to do to compare is to diff files from different projects. Three things were annoying in the past on that one:

1. Whitespace/formatting (solved by having the same formatters/linters and settings for them)
2. Different versions of hooks (solved by pre-commit CI)
3. Different order of the same things where order does not matter / is not crucial (could be solved by agreeing on a rule and starting with it in a project that has the largest numbers of hooks / settings)

Because of the last point, I think this is the right place to start.

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[hmgaudecker]

Looks good to me!

Disclaimer: Did not check all 281 files.