Simple CSV Import

[henninggaertner]

Description

fixes #573
Adds new method for importing proteomic data using a csv with a specified format.
Also runs black on the changed files, which unfortunately also changes formatting in different parts of the code.

Changes

The usual files when adding a new import method, see changes. Also added a comment for a related issue #574 and tests.

Testing

For example, pull one of the csvs added for testing and try to import it. The format should be the same as it would be for example for maxquant data.

PR checklist

Development

• If necessary, I have updated the documentation (README, docstrings, etc.)
• If necessary, I have created / updated tests.

Mergeability

• 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

• I have self-reviewed my code.
• At least one other developer reviewed and approved the changes

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
protzilla
disk_operator.py
run.py
run_helper.py
steps.py					79-80, 154
protzilla/data_analysis
plots.py
protein_graphs.py
ptm_analysis.py					56, 123-125
protzilla/data_integration
database_query.py					113-119
di_plots.py
protzilla/data_preprocessing
outlier_detection.py
plots.py
protzilla/importing
ms_data_import.py					122, 178, 189-190, 193, 195, 203, 211, 327, 337
protzilla/methods
data_analysis.py					21, 174, 250, 283, 308, 351, 916, 935
data_preprocessing.py
importing.py					67-68, 74, 160
protzilla/utilities
utilities.py					184
ui/main
settings.py					131
ui/runs
fields.py
views.py					21, 72-73, 185, 262, 712, 717-721
ui/runs/forms
base.py					107
custom_fields.py					119
data_analysis.py					323-327, 384, 414, 450, 473, 1188, 1226, 1248
data_integration.py
importing.py
ui/settings
plot_template.py					84
Project Total

The report is truncated to 25 files out of 62. To see the full report, please visit the workflow summary page.

This report was generated by python-coverage-comment-action