refactor: improve CI and local development

[skarzi]

This PR is quite big and changes several things:

• fix main deps declaration 52c86c5
• declare dev and test deps in pyproject.toml using flit extras
• add dev/test tools configuration to proper config files
• add linting and testing stages to Makefile
• removes tox support (flit and Makefile should be used for local development)
• merges main and lint_python workflows

Things to do (but probably in separate PRs):

• add better coverage configuration - @skarzi
• investigate why tests fail and fix them
• add .editorconfig and clean whitespaces in the codebase - check feat: add .editorconfig #158
• update .gitignore (e.g. with wily_report and foo)
• move codecov token to secrets - @tonybaloney
• set proper black configuration, apply it on the codebase and require it in Makefile
• set proper isort configuration, apply it on the codebase and require it in Makefile
• resolve flake8 issues and clean ignore in its config and set its proper configuration
• set proper codespell configuration, apply it on the codebase and require it in Makefile
• set proper mypy configuration, resolve its issues and require it in Makefile
• add some useful pytest plugins, like pytest-timeout or pytest-randomly

[codecov-commenter]

Codecov Report

Merging #157 (675eec4) into master (f33cbd7) will decrease coverage by 2.30%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #157      +/-   ##
==========================================
- Coverage   97.36%   95.05%   -2.31%     
==========================================
  Files          23       23              
  Lines        1213     1214       +1     
  Branches        0      290     +290     
==========================================
- Hits         1181     1154      -27     
- Misses         32       34       +2     
- Partials        0       26      +26     

Impacted Files	Coverage Δ
src/wily/__main__.py	95.48% <100.00%> (-2.83%)	⬇️
src/wily/commands/list_metrics.py	87.50% <0.00%> (-12.50%)	⬇️
src/wily/commands/build.py	86.81% <0.00%> (-8.80%)	⬇️
src/wily/archivers/git.py	87.50% <0.00%> (-5.00%)	⬇️
src/wily/state.py	95.29% <0.00%> (-3.52%)	⬇️
src/wily/operators/halstead.py	90.00% <0.00%> (-3.34%)	⬇️
src/wily/commands/rank.py	96.22% <0.00%> (-1.89%)	⬇️
src/wily/cache.py	98.18% <0.00%> (-1.82%)	⬇️
src/wily/commands/diff.py	88.75% <0.00%> (-1.25%)	⬇️
... and 2 more

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[skarzi]

I don't know why tests run on windows are failing, if you have any idea please share!

[tonybaloney]

There's a lot going on in this PR making it really hard to review. Could you please cherry-pick these commits into atomic changes i.e. one pull-request = one concern

[skarzi]

Yes, there is a log going on in this PR, but I have made atomic changes on the commit level, so you can review one commit after another. However, if it's still hard to review let me know and I will try to split it into multiple PRs with atomic changes ;)

[tonybaloney]

1 test is failing on Windows:

FAILED test/integration/test_complex_commits.py::test_skip_files

[skarzi]

Yes, but unfortunately, I don't know why it's failing at first sight and I don't have access to a windows machine so I can dig into this test more deeply.
It seems like for some reason the src\\test1.py is not included in the final report data.

[skarzi]

But this test is also failing on the main branch, let's check it here

[tonybaloney]

Ok. I have a windows machine, will test on that and make sure it's unrelated so we can merge this 👍🏻