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path: root/tests/unit/computations/test_correlation.py
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2021-10-29Feature/biweight reimplementation (#47)...* add biweight reimplementation with pingouin * delete biweight scripts and tests * add python-pingouin to guix file * delete biweight paths * mypy fix:pingouin mising imports * pep8 formatting && pylint fixesAlexander Kabui
2021-08-20Minor correlation fixes (#36)...* fix key error for (*tissue_cor) tissue correlation * update tests for tissue correlation * rename speed_compute to fast_compute * pep8 formattingAlexander Kabui
2021-08-11use normal function for correlation (#34)...* use normal function for correlation + rename functions * update test for sample correlation * use normal function for tissue correlation + rename functionsAlexander Kabui
2021-07-26Fix issues caught by pylint...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix a myriad of issues caught by pylint to ensure the code passes all tests. Muriithi Frederick Muriuki
2021-07-20Add test for code to move over from GN1...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * .gitignore: ignore emacs temporary files * gn3/computations/correlations2.py: add a dummy function * tests/unit/computations/test_correlation.py: add unit tests for the function As part of the move of the clustering and heatmap code over from GN1 to GN3, this commit begins by providing some unit tests for the correlation function used to ensure that the implementation that is built up here corresponds, and produces the same results as the original. This tests and the function might change in the new system, but for now, we try and maintain bug-to-bug compatibility. Muriithi Frederick Muriuki
2021-06-20make requested changes to biweightAlexander Kabui
2021-06-14add biweight r script and testsAlexander Kabui
2021-05-30fix index error (#16)Alexander Kabui
2021-05-15index lit tuple resultAlexander Kabui
2021-05-12delete unused functionsAlexander Kabui
2021-05-12rename lit_correlation_for_trait_list to lit_correlation_for_traitAlexander Kabui
2021-05-12rename tissue_correlation_for_trait_list with tissue_correlation_for_traitAlexander Kabui
2021-05-12rename p_val ro tissue_p_value for tissue_resultsAlexander Kabui
2021-05-03minor fixes for tiss correlation tests and namingAlexander Kabui
2021-05-03replace database with connAlexander Kabui
2021-04-18refactor:return trait_name in corr_resultsAlexander Kabui
2021-04-17ad pep8 formattingAlexander Kabui
2021-04-17refactor tests for litAlexander Kabui
2021-04-15optimization for sample correlationAlexander Kabui
2021-04-12fix tests for lit correlationAlexander Kabui
2021-04-12fix merge conflictAlexander Kabui
2021-04-12Integrate correlation API...- add new api for gn2-gn3 sample r integration - delete map for sample list to values - add db util file - add python msql-client dependency - add db for fetching lit correlation results - add unittests for db utils - add tests for db_utils - modify api for fetching lit correlation results - refactor Mock Database Connector and unittests - add sql url parser - add SQL URI env variable - refactor code for db utils - modify return data for lit correlation - refactor tissue correlation endpoint - replace db_instance with connAlexander Kabui
2021-04-06fix DocstringsAlexander Kabui
2021-03-16Refactor/clean up correlations (#4)...* initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>Alexander Kabui