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Feature/auto add up new #4

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@jcharkow jcharkow commented Dec 6, 2023

Description

Checklist

  • Make sure that you are listed in the AUTHORS file
  • Add relevant changes and new features to the CHANGELOG file
  • I have commented my code, particularly in hard-to-understand areas
  • New and existing unit tests pass locally with my changes
  • Updated or added python bindings for changed or new classes (Tick if no updates were necessary.)

How can I get additional information on failed tests during CI

Click to expand If your PR is failing you can check out
  • The details of the action statuses at the end of the PR or the "Checks" tab.
  • http://cdash.openms.de/index.php?project=OpenMS and look for your PR. Use the "Show filters" capability on the top right to search for your PR number.
    If you click in the column that lists the failed tests you will get detailed error messages.

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  • /reformat (experimental) applies the clang-format style changes as additional commit. Note: your branch must have a different name (e.g., yourrepo:feature/XYZ) than the receiving branch (e.g., OpenMS:develop). Otherwise, reformat fails to push.
  • setting the label "NoJenkins" will skip tests for this PR on jenkins (saves resources e.g., on edits that do not affect tests)
  • commenting with rebuild jenkins will retrigger Jenkins-based CI builds

⚠️ Note: Once you opened a PR try to minimize the number of pushes to it as every push will trigger CI (automated builds and test) and is rather heavy on our infrastructure (e.g., if several pushes per day are performed).

turn OpenSwathWorkflow -Scoring:add_up_spectra for DIA scorign parameter into an "auto-set" parameter
which will add up all spectra based on rt boundaries
Add to OSW file FEATURE_MS2 table the NUM_SPEC_ADD column which the number of spectra added by the autoAdd.
If -Scoring:add_up_spectra is a positive number, all entries of will be
this positive number. If -Scoring:add_up_spectra is -1 than this column
will be variable based on peak width.
error with osw because num_spec_added was expected but not present
update featureXML files to have numSpectraAdd which is a new output
added
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