Log error when multiple remotes have the same org name

[anoronh4]

Addressing #2157

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

[codecov]

Codecov Report

Merging #2228 (3f44849) into dev (bb533fc) will increase coverage by 0.06%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##              dev    #2228      +/-   ##
==========================================
+ Coverage   72.98%   73.05%   +0.06%     
==========================================
  Files          78       77       -1     
  Lines        8384     8342      -42     
==========================================
- Hits         6119     6094      -25     
+ Misses       2265     2248      -17     

Impacted Files	Coverage Δ
nf_core/components/install.py	87.91% <100.00%> (+1.05%)	⬆️

... and 7 files with indirect coverage changes

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

[mirpedrol]

Thanks for this PR :)
I would throw an error instead of a warning in this case, and also reword a little bit the message to make it more clear.

[mirpedrol]

LGTM, only some last changes 🙂

[anoronh4]

@mirpedrol i think the function check_alternate_remotes is doing what it's supposed to be doing, but i think i've CI checks might be complaining because the module tests literally use alternate remotes with the same org_path! I suspect that i will have to change https://gitlab.com/nf-core/modules-test.git so that the org_path: nf-core-test, but i'm not sure if that will work with all the tests. any reason why the content of that repo can't be held on the main nf-core/modules repo?

[mirpedrol]

Some tests are failing due to log.err() which should be log.error().
This GitLab repo is used to test installing modules from other repos and from GitLab, so we still need to use it. For most of the failing tests, I think what we could do when installing modules in a pipeline is to remove all previously installed modules, the pipeline is created from the template which always includes fastqc and multiqc. And then add a test for this error. Sounds good?

[anoronh4]

Some tests are failing due to log.err() which should be log.error(). This GitLab repo is used to test installing modules from other repos and from GitLab, so we still need to use it. For most of the failing tests, I think what we could do when installing modules in a pipeline is to remove all previously installed modules, the pipeline is created from the template which always includes fastqc and multiqc. And then add a test for this error. Sounds good?

sorry, i may have caused confusion, i found the log.err already and fixed locally only without committing and pushing, and when i tested locally the new error message started popping up. yes that sounds like it could work! i'll try to implement that. sorry for all the back and forth, hopefully we can get this moving!

[anoronh4]

@mirpedrol i have implemented the changes we last discussed and it seems to pass all checks. however, i wonder if the better solution would have been to change the org_path in the gitlab repo, that way less time is spent removing default modules, and we would still have the ability to test out how tools behaves with multiple remotes. Having spent so much time on the current solution, I wanted to get someone else's thoughts before pursuing something different. If this solution is preferred I'm happy to approve this PR as-is.