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 nf-test and fix stub happy/sompy #6285

Merged

Conversation

kubranarci
Copy link
Contributor

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@kubranarci kubranarci requested a review from a team as a code owner August 23, 2024 14:52
@kubranarci kubranarci requested review from louperelo and removed request for a team August 23, 2024 14:52
@kubranarci kubranarci linked an issue Aug 23, 2024 that may be closed by this pull request
2 tasks
Comment on lines 42 to 45
{ assert snapshot(process.out.stats).match("stats_1") },
{ assert snapshot(process.out.versions).match("versions_1") },
{ assert snapshot(file(process.out.metrics[0][1]).name).match("metrics_1")},
{ assert snapshot(file(process.out.features[0][1]).name).match("features_1")}
Copy link
Contributor

Choose a reason for hiding this comment

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

Can you put all the snapshots into one: (indentation probably needs fixing)

Suggested change
{ assert snapshot(process.out.stats).match("stats_1") },
{ assert snapshot(process.out.versions).match("versions_1") },
{ assert snapshot(file(process.out.metrics[0][1]).name).match("metrics_1")},
{ assert snapshot(file(process.out.features[0][1]).name).match("features_1")}
{ assert snapshot(
process.out.stats,
process.out.versions,
file(process.out.metrics[0][1]).name,
file(process.out.features[0][1]).name
).match() },

Copy link
Contributor Author

Choose a reason for hiding this comment

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

when I don't separate "versions", lint gives an error. that is why I put it like this.

Copy link
Contributor

Choose a reason for hiding this comment

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

Hmm, shouldn't be an issue like this, I've done it on a number of modules

Copy link
Contributor Author

Choose a reason for hiding this comment

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

I dont know what was that, but it works out inside one match now

@kubranarci kubranarci added this pull request to the merge queue Aug 26, 2024
Merged via the queue into master with commit 5f5f9f7 Aug 26, 2024
11 checks passed
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.

[FEATURE] add nf-test to happy/sompy and fix stub
2 participants