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bigbio / sdrf-pipelines

A repository to convert SDRF proteomics files into pipelines config files
Apache License 2.0
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Various fixes and adding conversion to Normalyzer #123

Closed veitveit closed 2 years ago

veitveit commented 2 years ago

Now the precursor tolerance for FirstSearchTol is set to 50 ppm or 0.01 Da depending on the unit of the given precursor mass. The fragment tolerance was added as MatchTolerance to all "instruments"

ypriverol commented 2 years ago

@veitveit when you are happy with you changes let me know to review the PR.

veitveit commented 2 years ago

@ypriverol Thanks, still some minor details to finish. Trying to pass all tests including the ones complaining about too complex functions.

veitveit commented 2 years ago

@ypriverol The updates are done now. Please revise.

fabianegli commented 2 years ago

Is the title still representative of the PR content? If not maybe consider updating it.

ypriverol commented 2 years ago

@veitveit this is still failing. I will wait for your changes and all the tests pass.

fabianegli commented 2 years ago

@veitveit Running black locally committing those changes will solve the failing test.

From the failing test:

Run mshick/add-pr-comment@v1
  with:
    message: ## Python linting (`black`) is failing
  To keep the code consistent with lots of contributors, we run automated code consistency checks.
  To fix this CI test, please run:
  * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
  * Fix formatting errors in your pipeline: `black .`
  Once you push these changes the test should pass, and you can hide this comment :+1:
  We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
  Thanks again for your contribution!
veitveit commented 2 years ago

@ypriverol @fabianegli Thanks for the help. Running black solved it.