Move calculation and plot methods

[saragrau]

PR for #9

The methods by_low_frequency, by_median, by_totalsum and by_reference_protein were moved to PROTzilla2. Each method has its corresponding function by_low_frequency_plot, by_median_plot, by_totalsum_plot and by_reference_protein_plot, that returns the plot for the corresponding method.

Also the tests for this methods were moved to PROTzilla2 and fixtures are now used for the setup.

Analogously to the perform_calculation_from_location and perform_calculation, the methods create_plot_from_location and create_plot call the corresponding plot with the appropriate parameters. For this purpose it also exists a plot_map.

[github-actions]

Coverage report

The coverage rate went from 79.67% to 84.05% ⬆️
The branch rate is 61%.

88.6% of new lines are covered.

Diff Coverage details (click to unfold)

protzilla/constants/paths.py

100% of new lines are covered (100% of the complete file).

protzilla/run_manager.py

0% of new lines are covered (0% of the complete file).
Missing lines: 1, 3, 4, 7, 8, 9, 11, 12, 13, 14, 16, 18, 20, 21, 22, 23, 25, 26, 27

protzilla/data_preprocessing/plots.py

90.14% of new lines are covered (90% of the complete file).
Missing lines: 368, 379, 380, 381, 389, 390, 392

protzilla/importing/ms_data_import.py

93.75% of new lines are covered (94.44% of the complete file).
Missing lines: 32

tests/protzilla/data_preprocessing/test_filter_proteins.py

93.75% of new lines are covered (88.88% of the complete file).
Missing lines: 48

protzilla/data_preprocessing/outlier_detection.py

92.85% of new lines are covered (83.33% of the complete file).
Missing lines: 151, 169, 178, 219

protzilla/data_preprocessing/normalisation.py

98.92% of new lines are covered (97.39% of the complete file).
Missing lines: 251

protzilla/utilities/transform_dfs.py

100% of new lines are covered (100% of the complete file).

tests/protzilla/data_preprocessing/test_transformation.py

94.28% of new lines are covered (89.74% of the complete file).
Missing lines: 122, 137

protzilla/workflow_manager.py

0% of new lines are covered (0% of the complete file).
Missing lines: 1, 4, 5, 6, 7, 8, 9

tests/protzilla/test_run.py

100% of new lines are covered (100% of the complete file).

protzilla/run.py

76.74% of new lines are covered (68.51% of the complete file).
Missing lines: 12, 13, 14, 15, 16, 17, 18, 64, 69, 70, 81, 82, 85, 119, 120, 121, 122, 123, 124, 125

protzilla/constants/constants.py

100% of new lines are covered (100% of the complete file).

protzilla/history.py

96.87% of new lines are covered (95.34% of the complete file).
Missing lines: 32, 133

protzilla/data_preprocessing/filter_samples.py

96.15% of new lines are covered (90% of the complete file).
Missing lines: 65

tests/protzilla/data_preprocessing/test_imputation.py

72.28% of new lines are covered (61.85% of the complete file).
Missing lines: 140, 141, 145, 154, 155, 165, 166, 170, 179, 180, 190, 191, 195, 204, 205, 216, 220, 233, 244, 245, 246, 258, 259

protzilla/data_preprocessing/filter_proteins.py

86.66% of new lines are covered (73.68% of the complete file).
Missing lines: 54, 55

tests/conftest.py

100% of new lines are covered (100% of the complete file).

protzilla/data_preprocessing/imputation.py

98.64% of new lines are covered (97.72% of the complete file).
Missing lines: 138

tests/protzilla/data_preprocessing/test_normalisation.py

93.33% of new lines are covered (88.23% of the complete file).
Missing lines: 309, 325, 342, 366

tests/protzilla/data_preprocessing/test_plots.py

82.97% of new lines are covered (79.36% of the complete file).
Missing lines: 21, 40, 57, 82, 117, 118, 119, 120

protzilla/data_preprocessing/transformation.py

90% of new lines are covered (82.14% of the complete file).
Missing lines: 31, 53

tests/protzilla/test_history.py

100% of new lines are covered (100% of the complete file).

protzilla/constants/location_mapping.py

100% of new lines are covered (100% of the complete file).

tests/protzilla/data_preprocessing/test_outlier_detection.py

86.95% of new lines are covered (79.31% of the complete file).
Missing lines: 43, 52, 59

tests/protzilla/data_preprocessing/test_filter_samples.py

93.1% of new lines are covered (87.87% of the complete file).
Missing lines: 73, 98

[antonneubauer]

I made a few small suggestions and commented on some ideas I had.
In addition: I think the tests for filter_samples is missing if I'm not mistaken. Was that by accident or am I overlooking them?

Good work!

changes adopted

[antonneubauer]

looks overall good apart from some minor changes that I think would make sense.
Also: the formatting is broken in many of the files and you should check if your pre-commit hook works properly.

Good work as far as I am concerned!

[antonneubauer]

idk how you managed to change almost all files without visibly changing them but the parts that actually did look good now!