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HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
176 stars 32 forks source link

Styling formatting rework #245

Closed ThijsMaas closed 7 months ago

ThijsMaas commented 7 months ago

Hi @HadrienG, As promised, here is the PR that includes only the restyling and formatting of the code base. It is formatted using black and isort and I also checked the codestyle with flake8 and fixed the errors it found.

These tools have setting files, which contain some defaults. Specifically, I set the line-length to 120, which is higher than the default 88 of black, but in my opinion this is very reasonable with our large screen sizes and modern IDEs.

I'm trying to add the checking functionality of each of these tools to the github action. They currently run in our ENPICOM fork, so they don't show up here.

HadrienG commented 7 months ago

@ThijsMaas LGTM but I see that the tests are failing on your fork (due to a missing dependency for black?)

ThijsMaas commented 7 months ago

@HadrienG The lint tests work now, apparently Black has different dependencies below Python version 3.11. I don't have the secrets for codecov, so that part still fails, not sure if there is a way around that?

HadrienG commented 7 months ago

@HadrienG The lint tests work now, apparently Black has different dependencies below Python version 3.11. I don't have the secrets for codecov, so that part still fails, not sure if there is a way around that?

You could try to add if: github.event.repository.fork == false between line 28 and 29 in .github/workflows/pythonpackage.yml (if block same indentation as name and uses)

ThijsMaas commented 7 months ago

That solved it, thanks!