Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add no_git=True when possible #1709

Merged
merged 7 commits into from
Jul 29, 2022
Merged

Add no_git=True when possible #1709

merged 7 commits into from
Jul 29, 2022

Conversation

mirpedrol
Copy link
Member

As mentioned in #1688 comment

I think in the case of nf-core lint you could actually pass no_git=True to PipelineCreate here, and skip making a git repository entirely, as the linter does not seem to require a git repository to compare the template files

The argument no_git=True can be added when a pipeline is created but there's no need to initialise a git repository.

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
Copy link

codecov bot commented Jul 28, 2022

Codecov Report

Merging #1709 (3bf6d70) into dev (880d627) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev    #1709   +/-   ##
=======================================
  Coverage   68.23%   68.23%           
=======================================
  Files          57       57           
  Lines        6744     6744           
=======================================
  Hits         4602     4602           
  Misses       2142     2142           
Impacted Files Coverage Δ
nf_core/lint/files_unchanged.py 72.61% <ø> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 880d627...3bf6d70. Read the comment docs.

@mirpedrol mirpedrol marked this pull request as ready for review July 29, 2022 07:22
Copy link
Contributor

@ErikDanielsson ErikDanielsson left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

We should do the same in tests/test_lint.py, tests/test_utils.py and tests/test_modules.py also right?

@mirpedrol
Copy link
Member Author

Thanks @ErikDanielsson, I forgot some tests!
I don't add it to tests/test_lint.py as the git repository is required there.

Copy link
Contributor

@ErikDanielsson ErikDanielsson left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good now!

@ErikDanielsson ErikDanielsson merged commit a627c7f into nf-core:dev Jul 29, 2022
@mirpedrol mirpedrol deleted the no-git branch July 29, 2022 12:17
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants