Initial setup of QA pre-commit tools [cf-units]

[ukmo-ccbunney]

🚀 Pull Request

Description

Added following pre-commit hooks:

• Extra "default" hooks from pre-commit (trailing whitespace, etc)
• MyPy
• codespell
• validate_pyproject
• numpydoc

sp-repo-review was already setup for cf-units, but have updated the ignore list as various tests now pass.

ruff was enabled, but with only selected tests. Have enabled "all" tests.

For all QA tools above, the results of any "auto-fixes" have been included in this repo, mainly fixes for:

• trailing whitespace
• missing newline at end of file
• docstring reformatting
• some code style linting from ruff

All other failing tests have been added to ignore lists. See separate issues:

• Address failing mypy tests #520
• Address failing numpydoc tests #521
• Address failing Ruff tests #526
• Address failing tests in repo-review #462

[codecov]

Codecov Report

Attention: Patch coverage is 81.48148% with 10 lines in your changes missing coverage. Please review.

Project coverage is 58.40%. Comparing base (4ad25ba) to head (2f88721).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
cf_units/__init__.py	80.76%	8 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #522      +/-   ##
==========================================
- Coverage   58.41%   58.40%   -0.02%     
==========================================
  Files          62       62              
  Lines        6435     6433       -2     
  Branches     1150     1150              
==========================================
- Hits         3759     3757       -2     
  Misses       2385     2385              
  Partials      291      291              

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---

🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[ukmo-ccbunney]

@pp-mo I Have resolved the issues I was having with pre-commit.ci.
I managed to reproduce the pre-commit.ci behaviour on my personal laptop which gave me a chance to investigate the issue.

I have reinstated the PY005 check ("has test folder") to the to [tool.repo-review] ignore list.

The MyPy behaviour was more difficult to debug. It turns out that adding files to the MyPy exclude list only stops them being passed as filenames to the MyPy call. However, these will still be checked if they are imported from some other module that is being checked.

There is a flag that can be passed to stop this --follow-imports=silent, but this is not supported via pyproject.toml.
However, I've found it can be set using the following too MyPy section:

[[tool.mypy.overrides]]
module = [
        "cf_units/_udunits2_parser/parser.*",
        "cf_units/_udunits2_parser/_antlr4_runtime.*",
]
ignore_errors = true

The combination of the above fix the errors on my personal laptop and the pre-commit.ci service, so this is ready for review now.

I don't know why the behaviour is different on the MO VDIs though (pre-commit and hook version numbers are same!)

[pp-mo]

--follow-imports=silent, but this is not supported via pyproject.toml

I don't think turning this totally off is a good idea, anyway.
Your approach to exclude certain files seems better to me.

[pp-mo]

Ok but a few nit-picky suggestions.

You should also create some PRs to track unfinished business.
Suggest one each for :

• re-order pre-commit entries based on updated tempate file : (can do this one right now)
• mypy
• ruff
• numpydocs-validation

[ukmo-ccbunney]

You should also create some PRs to track unfinished business. Suggest one each for :

I've already created Issues for these (not PRs), see links in description

• re-order pre-commit entries based on [updated tempate file]
  (Keep hook-repos in id order for easy template comparison. .github#29) : (can do this one right now)

Done; see d831bfb

[pp-mo]

I think removing "D212" from the ruff.lint select is worth doing,
not least because the comment is confusing + I think wrong!

otherwise all looks great now + good to go !

[ukmo-ccbunney]

Right - D212 is back in the Ruff select list after ALL.
Hopefully this is everything that is needed now for this PR.