add docs to commit new files before pytest

[mirpedrol]

The command nf-core modules test runs tests using pytest. We use the pytest argument --git-aware.
This argument is used to avoid copying the whole .git directory and files ignored by git.
It will only include files listed by git ls-files.
In order to test a new module or subworkflow, the new files have to be committed, otherwise they will be ignored. This was reported in #2235 and nf-core Slack.
This PR adds documentation to advise committing changes before running the command, as it is better to keep the argument --git-aware.

It throws a warning if there are uncommitted changes:

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[mashehu]

Nice! we could also print a warning if we see uncommited modules or do you think that is not that easy to check?

[codecov]

Codecov Report

Merging #2316 (b4e8f82) into dev (1e39535) will decrease coverage by 0.13%.
The diff coverage is 14.28%.

@@            Coverage Diff             @@
##              dev    #2316      +/-   ##
==========================================
- Coverage   73.05%   72.93%   -0.13%     
==========================================
  Files          78       78              
  Lines        8732     8763      +31     
==========================================
+ Hits         6379     6391      +12     
- Misses       2353     2372      +19     

Impacted Files	Coverage Δ
nf_core/components/components_test.py	52.80% <14.28%> (-3.29%)	⬇️

... and 2 files with indirect coverage changes

[mirpedrol]

We don't use git in this command, so we would need to import GitPython, but we already have it in requirements for the sync command :) I will try to add the warning

[MatthiasZepper]

Nice! we could also print a warning if we see uncommited modules or do you think that is not that easy to check?

One can definitively check if there are uncommitted changes in the whole working tree with Repo.is_dirty(). Might be a bit more complicated to restrict it to modules only, but is_dirty() accepts os.PathLike argument, so might be feasible.

[mashehu]

Can we set an option to ignore this? Sorry for being particular 🙂

[mirpedrol]

It is only a warning, do we need to ignore it? Maybe better to capture possible errors, so it doesn't fail, in case someone doesn't have a repo or something similar