Peptide Data can now be imported and is then tagged along through the preprocessing (in every preprocessing step the peptide data is modified to match the peptide data)
(see the linked issues above to check how the different preprocessing steps should handle peptide data, as described by Chris)
Changes
all preprocessing methods were adapted to take a peptide dataframe, modify and return it, matching the peptide dataframe
all preprocessing tests were adapted to test the new functionality
the step classes were addapted to hand the peptide data from one preprocessing step to the next (if peptide data was imported)
the step evidence import was added to support the format of the evidence file (including tests for this new method and the necessary forms and step class)
Testing
step trough the run and check the peptide dataframes in the output trough brakepoints
PR checklist
Development
[x] If necessary, I have updated the documentation (README, docstrings, etc.)
[x] If necessary, I have created / updated tests.
Mergeability
[x] main-branch has been merged into local branch to resolve conflicts
[ ] The tests and linter have passed AFTER local merge
[ ] The code has been formatted with black
Code review
[x] I have self-reviewed my code.
[ ] At least one other developer reviewed and approved the changes
Description
fixes #452, #453, #454, #455, #456, #461
Changes
all preprocessing methods were adapted to take a peptide dataframe, modify and return it, matching the peptide dataframe
all preprocessing tests were adapted to test the new functionality
the step classes were addapted to hand the peptide data from one preprocessing step to the next (if peptide data was imported)
the step evidence import was added to support the format of the evidence file (including tests for this new method and the necessary forms and step class)
Testing
PR checklist
Development
Mergeability
blackCode review