Issue 0093 add lint at the actions

[Olender]

Description

This PR addresses Issue #93 by adding a linting step to the GitHub Actions workflow to ensure code quality and maintain consistency.

Changes Made

1. GitHub Actions Configuration (lint.yml):

   • Added a new workflow named "Run lint."
   • Configured the workflow to trigger on:
     • Push events to the master branch.
     • Pull requests.

2. Makefile Adjustments:

   • Added a format target to format the codebase using autopep8 with setup.cfg as the configuration file.
   • Added a lint target to run flake8 on setup.py, spyro/, and test/*.py.

3. Codebase Formatting:

   • Various files have been formatted according to the linting rules defined.

Additional Notes

• Developers should run make lint locally to catch issues before pushing to reduce CI errors.
• The formatting step (make format) ensures code consistency based on the settings defined in setup.cfg.

[Olender]

I based the flake8 parameters and the lint.yml file configuration on the ones used by the Firedrake project (see Firedrake's setup.cfg for reference).

[codecov]

Codecov Report

Attention: Patch coverage is 87.12871% with 13 lines in your changes missing coverage. Please review.

Project coverage is 84.23%. Comparing base (74bafaa) to head (9702d81).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
spyro/solvers/elastic_wave/isotropic_wave.py	57.14%	3 Missing ⚠️
spyro/meshing/meshing_functions.py	92.30%	2 Missing ⚠️
spyro/solvers/backward_time_integration.py	33.33%	2 Missing ⚠️
spyro/tools/input_models.py	33.33%	2 Missing ⚠️
spyro/receivers/changing_coordinates.py	92.85%	1 Missing ⚠️
spyro/solvers/elastic_wave/forms.py	0.00%	1 Missing ⚠️
spyro/solvers/inversion.py	75.00%	1 Missing ⚠️
spyro/solvers/wave.py	88.88%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #129      +/-   ##
==========================================
- Coverage   84.27%   84.23%   -0.05%     
==========================================
  Files          56       56              
  Lines        3733     3729       -4     
==========================================
- Hits         3146     3141       -5     
- Misses        587      588       +1     

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[SouzaEM]

Here I think that removing the big block of comments is more appropriate to make the code easier to navigate.

[Olender]

I have temporarily removed this section in the latest commit. However, I plan on adding an improved version if we ever work with hexahedrals not based on extruded meshes. Thanks for the suggestion!

[SouzaEM]

I see. In this case you could have left the comment, but the flag that you added is even better.

[SouzaEM]

Great work setting up the linter in the CI system! My only recommendation is to avoid big blocks of comments in the future. As the code is under version control, it is always possible to check previous implementations without leaving them commented.