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bigbio / sdrf-pipelines

A repository to convert SDRF proteomics files into pipelines config files
Apache License 2.0
16 stars 21 forks source link

Refactor testing and arbitrary extension handling #149

Closed jspaezp closed 11 months ago

jspaezp commented 11 months ago

The main purpose of this PR is to increase the test cases in the repo and make it easier to maintain.

In addition,

  1. it fixes an issue where failing tests would never be reported as failed (since it checked for strings whose case didnt match, Error != ERROR).
  2. Documents better what each file attempts to test.
  3. Removes a false positive where failed runs generated incomplete/empty openms.tsv or experimental designs.
  4. Documents a deprecation warning and fixes another one.
  5. Updates pre-commit versions.

EDIT:

  1. Now it also extends the handling of file extension variants to allow things like .gz -> .d or .d.zip -> .d, while at the same time handling graciously cases where the passed conversions are not used (ie, raw:mzml does not error out if there are both .raw and .mzml files)
jspaezp commented 11 months ago

@ypriverol LMK what you think

jspaezp commented 11 months ago

@ypriverol as we talked about, I added the extended handling of extensions