Enforce common code style

Since most of us use different editors and/or have different coding habits there is an inconsistency in the format of the code pushed to the repo. One solution would be to run something like black before any push and add it to the CI/CD pipeline. I just tried it and though it works fine for python code, it's not working for Snakefiles. Do you have any idea of how to improve this?

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I had tried the same with flake8, which does not format the code like blackdoes, but will still warm about various code issues, including violations of PEP8. Same problem: doesn't really work with Snakemake files, because of their own non-standard Python syntax.

Tried to find a linter for Snakemake files, didn't find anything. Best I can suggest for the moment is to use a linter during coding (e.g., flake8 is pretty good, not too demanding) and fix all issues except for those that are caused by the specific Snakemake syntax. I've done a pass recently on the main Snakefile and ended up with only the Snakemake-specific code raising flags. Of course that was before the new code got merged on since Friday... :-)

Anyway, let's discuss this during the next session. We could at least enforce linter passes on any Python code that is not in the Snakemake files. And recommend people to use linters in their editors (also available for markdown, YAML etc)

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I think our problem might be soon resolved: https://github.com/snakemake/snakemake/pull/276

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Here it is for snakemake>=5.11:

https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html#best-practices

I think this will be the solution at the end: https://github.com/snakemake/snakefmt

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Enforce developer to use black before commiting test.

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This was set up on the ZARP cli repo. Linting of the Snakefile is still an open issue for the pipeline.

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I just tested https://github.com/snakemake/snakefmt but it does not work as described. I opened an issue here: https://github.com/snakemake/snakefmt/issues/112

<This is a tactical post, I want to get notifications on this issue.>

The issue is now gone in version 0.4.2 of snakefmt (https://github.com/snakemake/snakefmt/issues/112#issuecomment-902807805). In the coming days, I will try to integrate this into the CI.

I run into another issue with snakefmt. Here is the new issue: https://github.com/snakemake/snakefmt/issues/118

mentioned in issue #173 (closed)

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so we can leave this for now.

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