Add filtering of invalid intensity values in log transformation, add message to warn user

[henninggaertner]

Description

fixes #41
log(0) is infinite, which is not the desired outcome for such a value. Therefore, they need to be filtered and dropped from the data, while notifying the users about the dropped values and urging them to change their pre-processing pipeline.

Changes

Add filtering, dropping and message in transformation.py
Adjust and add tests in test_transformation.py

Testing

Create a run with both protein and peptide import. Then manually change some intensity values to be 0 or negative in the run's dataframe folder. Then do the log transformation with the "dirty" data.
You should see a message about the dropped 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					76-77, 161, 192
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
enrichment_analysis.py
protzilla/data_preprocessing
imputation.py
plots.py
protzilla/importing
ms_data_import.py					122, 276
protzilla/methods
data_analysis.py					21, 41, 123, 177, 200, 249, 284, 597, 615, 636, 651
importing.py					123
protzilla/utilities
utilities.py					184
ui/main
settings.py					131
ui/runs
fields.py
views.py					73-74, 180, 678, 683-687
views_helper.py
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
ui/settings
plot_template.py					84
Project Total

The report is truncated to 25 files out of 60. To see the full report, please visit the workflow summary page.

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

[ronjakrg]

I think we should use "workflow" here instead of "pipeline" to stay consistent? :)