misc: Ruff

[JDBetteridge]

I'm trying to automate detection a lot of the "nitpick" code review comments and providing a route to automatically fixing the issues apriori.

What I have added to CI is equivalent to locally running:

isort --check-only --sort-reexports --multi-line VERTICAL_GRID_GROUPED --line-length 90 --force-alphabetical-sort-within-sections --project devito,examples .
ruff check --preview  --select E,W,F,B,UP,SIM,I,RUF022 --ignore F403,E226,E731,E275,F405,E722,E741,W605 --line-length=90 --output-format concise

Most command line arguments are included in the pyproject.toml and checking out this branch you can just run

isort --check-only .
ruff check --output-format concise

Fixing most linting issues is as simple as

isort .
ruff check --fix

if you trust the auto-formatter!

This PR also extends linting to Dockerfiles and Github actions too.

An excerpt from CONTRIBUTING.md:

Coding guidelines

Some coding rules are "enforced" (and automatically checked by our Continuous Integration systems), some are "strongly recommended", others are "optional" but welcome.

• We enforce PEP8, with a few exceptions, listed here
• We enforce a maximum line length of 90 characters.
• We enforce indentation via 4 spaces.
• We suggest to use flake8 to check the above points locally, before filing a Pull Request.
• We strongly recommend to document any new module, class, routine, ... with NumPy-like docstrings ("numpydoc").
• We strongly recommend imports to be at the top of a module, logically grouped and, within each group, to be alphabetically ordered. As an example, condider our init.py: the first group is imports from the standard library; then imports from third-party dependencies; finally, imports from devito modules.
• We strongly recommend to follow standard Python coding guidelines:
  • Use camel caps for class names, e.g. class FooBar.
  • Method names must start with a small letter; use underscores to separate words, e.g. def _my_meth_....
  • Private class attributes and methods must start with an underscore.
  • Variable names should be explicative (Devito prefers "long and clear" over "short but unclear").
  • Comment your code, and do not be afraid of being verbose. The first letter must be capitalized. Do not use punctuation (unless the comment consists of multiple sentences).
• We like that blank lines are used to logically split blocks of code implementing different (possibly sequential) tasks.

[codecov]

Codecov Report

❌ Patch coverage is 82.08517% with 244 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.19%. Comparing base (59c357b) to head (c8bb54c).

Files with missing lines	Patch %	Lines
devito/mpi/routines.py	18.60%	35 Missing ⚠️
tests/test_data.py	56.75%	16 Missing ⚠️
devito/mpi/distributed.py	37.50%	15 Missing ⚠️
devito/arch/compiler.py	50.00%	12 Missing and 2 partials ⚠️
tests/test_ir.py	48.14%	14 Missing ⚠️
tests/test_operator.py	41.66%	14 Missing ⚠️
benchmarks/user/benchmark.py	54.16%	11 Missing ⚠️
devito/data/data.py	38.46%	8 Missing ⚠️
devito/tools/data_structures.py	50.00%	8 Missing ⚠️
devito/data/utils.py	53.84%	5 Missing and 1 partial ⚠️
... and 58 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2771      +/-   ##
==========================================
+ Coverage   83.02%   83.19%   +0.16%     
==========================================
  Files         248      248              
  Lines       50804    50589     -215     
  Branches     4479     4392      -87     
==========================================
- Hits        42180    42087      -93     
+ Misses       7857     7753     -104     
+ Partials      767      749      -18     

Flag	Coverage Δ
pytest-gpu-aomp-amdgpuX	68.79% <71.39%> (+0.25%)	⬆️
pytest-gpu-nvc-nvidiaX	69.31% <71.41%> (+0.26%)	⬆️

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[FabioLuporini]

you look back 10 years ago or so there's a commit with message "FREEEEEEEEEEEEEDOOOMM" in which we are essentially removing isort from devito 😂

[JDBetteridge]

What was the motivation for removing?

[FabioLuporini]

if this is for

from X import (
A,
B,
C,
...
)

then I vote no

[JDBetteridge]

No this is in direct response to your comment on my other PR. This is specifically to avoid using ruff for the import formatting (see this issue)

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

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