Docstrings #289

lill28 · 2023-10-24T21:11:04Z

Add and update docstrings and create documentation from the docstrings

PR checklist

main-branch has been merged into local branch to resolve conflicts
tests and linter have passed AFTER local merge
at least one other dev reviewed and approved
documentation
tests

github-actions · 2023-10-24T21:14:52Z

Coverage report

The coverage rate went from 71.58% to 70.25% ⬇️
The branch rate is 63%.

100% of new lines are covered.

Diff Coverage details (click to unfold)

protzilla/constants/location_mapping.py

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

protzilla/data_analysis/classification.py

100% of new lines are covered (48.05% of the complete file).

protzilla/data_analysis/clustering.py

100% of new lines are covered (82.66% of the complete file).

protzilla/data_analysis/differential_expression_anova.py

100% of new lines are covered (94.73% of the complete file).

protzilla/data_analysis/differential_expression_linear_model.py

100% of new lines are covered (84.74% of the complete file).

protzilla/data_analysis/differential_expression_t_test.py

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

protzilla/data_analysis/dimension_reduction.py

100% of new lines are covered (86.04% of the complete file).

protzilla/data_analysis/model_evaluation.py

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

protzilla/data_analysis/model_evaluation_plots.py

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

protzilla/data_analysis/plots.py

100% of new lines are covered (93.8% of the complete file).

protzilla/data_analysis/protein_graphs.py

100% of new lines are covered (88.92% of the complete file).

protzilla/data_integration/database_download.py

100% of new lines are covered (0% of the complete file).

protzilla/data_integration/database_integration.py

100% of new lines are covered (85.55% of the complete file).

protzilla/data_integration/database_query.py

100% of new lines are covered (60% of the complete file).

protzilla/data_integration/di_plots.py

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protzilla/data_integration/enrichment_analysis.py

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protzilla/data_integration/enrichment_analysis_gsea.py

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protzilla/data_integration/enrichment_analysis_helper.py

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protzilla/data_preprocessing/filter_proteins.py

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protzilla/data_preprocessing/filter_samples.py

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protzilla/data_preprocessing/imputation.py

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protzilla/data_preprocessing/normalisation.py

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protzilla/data_preprocessing/outlier_detection.py

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protzilla/data_preprocessing/peptide_filter.py

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protzilla/data_preprocessing/plots.py

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protzilla/data_preprocessing/transformation.py

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protzilla/history.py

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protzilla/run.py

100% of new lines are covered (85.35% of the complete file).

protzilla/utilities/clustergram.py

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protzilla/utilities/dunn_score.py

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protzilla/utilities/transform_dfs.py

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protzilla/utilities/utilities.py

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ui/main/upload_handler.py

100% of new lines are covered (0% of the complete file).

ui/runs/fields.py

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ui/runs/views.py

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hendraet · 2023-10-25T05:24:06Z

Looking forward to this PR :)

BelanaZ

I reviewed in the order provided by GitHub until (and including) the data_analysis package -> So overall: the docs, source, constants and data_analysis packages. Thus, some changes still need to be reviewed.

docs/source/conf.py

protzilla/data_analysis/classification.py

protzilla/data_analysis/clustering.py

protzilla/data_analysis/differential_expression_t_test.py

protzilla/data_analysis/dimension_reduction.py

protzilla/data_analysis/plots.py

fynnkroeger

I reviewed the rest except for

protzilla/data_integration/database_integration.py
protzilla/data_integration/database_query.py
ui/main/upload_handler.py

which I wrote, so someone else should please do it.

Mostly small changes and formatting to do, great work :)

protzilla/data_preprocessing/filter_proteins.py

protzilla/data_preprocessing/imputation.py

protzilla/data_preprocessing/normalisation.py

ui/runs/views.py

lill28

Reviewed the remaining 3 files (database_integration.py, database_query.py and upload_handler.py) and just suggested some minor changes.

protzilla/data_integration/database_integration.py

protzilla/data_integration/database_query.py

* correct docstring syntax of data_analysis package * Fix docstring syntax in data_integration package * Fix docstring syntax in utilities package * Fix more docstring syntax * format code * add docstrings for database_integration.py * add returns for database_download.py * add docstrings for database_query.py * add docstrings for upload_handler.py * docstrings runs/views part1 * docstrings 2 runs/views.py * docstrings for runs/fields.py * docstrings for clustergram copy * docstrings for data_analysis/dimension_reduction.py * docstrings for data_analysis/classification.py * add __init__.py * Fix run docstring * Add docs build instructions and packages * update docs build instructions * Implement review suggestions * remove \ in data_preprocessing docstrings * remove more \ in docstrings * adopt PR suggestions --------- Co-authored-by: Fynn <[email protected]> Co-authored-by: BelanaZ <[email protected]> Co-authored-by: Sara Grau <[email protected]> Co-authored-by: antonneubauer <[email protected]>

lill28 and others added 19 commits October 5, 2023 19:46

correct docstring syntax of data_analysis package

ad6bf10

Fix docstring syntax in data_integration package

1f7663a

Fix docstring syntax in utilities package

0257f1e

Fix more docstring syntax

f12d039

format code

0dc3094

add docstrings for database_integration.py

314651c

add returns for database_download.py

362f76f

add docstrings for database_query.py

6c8ede6

add docstrings for upload_handler.py

a868bed

docstrings runs/views part1

7b38978

docstrings 2 runs/views.py

5270f4e

docstrings for runs/fields.py

e419e28

docstrings for clustergram copy

171cc90

docstrings for data_analysis/dimension_reduction.py

ff5607e

docstrings for data_analysis/classification.py

f7546d7

add __init__.py

c69ec4f

Fix run docstring

4821e3a

Add docs build instructions and packages

1b9058b

Merge branch 'main' into docstrings

f9dd53b

update docs build instructions

5079deb

BelanaZ reviewed Oct 26, 2023

View reviewed changes

fynnkroeger reviewed Oct 30, 2023

View reviewed changes

lill28 commented Oct 31, 2023

View reviewed changes

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protzilla/data_integration/database_query.py Outdated Show resolved Hide resolved

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lill28 added 3 commits October 31, 2023 17:21

Implement review suggestions

e4b002a

remove \ in data_preprocessing docstrings

d3a7943

remove more \ in docstrings

69c7535

fynnkroeger assigned antonneubauer Nov 16, 2023

adopt PR suggestions

b045bc0

Merge branch 'main' into docstrings

f931f49

antonneubauer merged commit 67c3a6f into main Nov 25, 2023
1 check passed

antonneubauer deleted the docstrings branch November 25, 2023 08:56

Docstrings #289

Docstrings #289

Conversation

lill28 commented Oct 24, 2023 • edited by antonneubauer Loading

PR checklist

github-actions bot commented Oct 24, 2023 • edited Loading

Coverage report

protzilla/constants/location_mapping.py

protzilla/data_analysis/classification.py

protzilla/data_analysis/clustering.py

protzilla/data_analysis/differential_expression_anova.py

protzilla/data_analysis/differential_expression_linear_model.py

protzilla/data_analysis/differential_expression_t_test.py

protzilla/data_analysis/dimension_reduction.py

protzilla/data_analysis/model_evaluation.py

protzilla/data_analysis/model_evaluation_plots.py

protzilla/data_analysis/plots.py

protzilla/data_analysis/protein_graphs.py

protzilla/data_integration/database_download.py

protzilla/data_integration/database_integration.py

protzilla/data_integration/database_query.py

protzilla/data_integration/di_plots.py

protzilla/data_integration/enrichment_analysis.py

protzilla/data_integration/enrichment_analysis_gsea.py

protzilla/data_integration/enrichment_analysis_helper.py

protzilla/data_preprocessing/filter_proteins.py

protzilla/data_preprocessing/filter_samples.py

protzilla/data_preprocessing/imputation.py

protzilla/data_preprocessing/normalisation.py

protzilla/data_preprocessing/outlier_detection.py

protzilla/data_preprocessing/peptide_filter.py

protzilla/data_preprocessing/plots.py

protzilla/data_preprocessing/transformation.py

protzilla/history.py

protzilla/run.py

protzilla/utilities/clustergram.py

protzilla/utilities/dunn_score.py

protzilla/utilities/transform_dfs.py

protzilla/utilities/utilities.py

ui/main/upload_handler.py

ui/runs/fields.py

ui/runs/views.py

hendraet commented Oct 25, 2023

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lill28 commented Oct 24, 2023 •

edited by antonneubauer

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