| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-12-06 | mypy and pylint fixes | Alexander_Kabui | |
| 2022-12-02 | correlations: return `None` rather than zero for missing lit corrs | Frederick Muriuki Muriithi | |
| * gn3/computations/correlations.py: Return `None` for missing literature correlations rather than zero. Update the sorting key to avoid issues with comparing floats to NoneType objects | |||
| 2022-07-29 | Fix failing tests | Frederick Muriuki Muriithi | |
| * gn3/computations/correlations.py: rename function * mypy.ini: deactivate mypy error about missing imports * tests/integration/test_correlation.py: mock correct function * tests/unit/computations/test_correlation.py: test correct function | |||
| 2022-07-28 | Update sample correlations code to use multiprocessing | Frederick Muriuki Muriithi | |
| * To help speed up the processing of the correlations, convert the `compute_all_sample_correlation` function to use the multiprocessing module. | |||
| 2022-02-25 | Fix issue where 0's were treated as False for the primary trait in | zsloan | |
| correlations In the original version of the if statement* I believe it was interpreted as "if a_val and (b_val is not None)". This caused values of 0 for a_val (the primary trait's values) to be evaluated as False. I changed it to compare both a_val and b_val to None. This seems to have fixed the issue. * if (a_val and b_val is not None) | |||
| 2022-01-12 | Update return type. Remove duplicate import. | Frederick Muriuki Muriithi | |
| The function is a generator function, since it uses a `yield` statement, and thus returns a generator object, that contains a tuple object. This fixes that. We also remove a duplicate import. | |||
| 2022-01-05 | Merge pull request #64 from jgarte/type-hint-normalize-values | BonfaceKilz | |
| Adds type hint for normalize_values function | |||
| 2021-12-24 | Fix typing errors | Frederick Muriuki Muriithi | |
| 2021-12-24 | Fix linting errors | Frederick Muriuki Muriithi | |
| 2021-12-14 | Adds type hint for normalize_values function | jgart | |
| 2021-12-10 | format normalize function doc string | Alexander Kabui | |
| 2021-12-10 | minor pr fixes | Alexander Kabui | |
| 2021-12-10 | rename variables | Alexander Kabui | |
| 2021-12-10 | try and catch for non matching sample keys | Alexander Kabui | |
| 2021-12-10 | update function docs for normalizing strain values | Alexander Kabui | |
| 2021-12-10 | fix bug:unpacking error when generator returns empty list | Alexander Kabui | |
| 2021-11-11 | pylint fixes and pep8 formatting | Alexander Kabui | |
| 2021-11-11 | fix target and base sample data order | Alexander Kabui | |
| 2021-11-11 | fix:spawned processes memory issues | Alexander Kabui | |
| 2021-11-11 | replace list with generators | Alexander Kabui | |
| 2021-10-29 | Feature/biweight reimplementation (#47) | Alexander Kabui | |
| * 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 fixes | |||
| 2021-08-20 | Minor correlation fixes (#36) | Alexander Kabui | |
| * fix key error for (*tissue_cor) tissue correlation * update tests for tissue correlation * rename speed_compute to fast_compute * pep8 formatting | |||
| 2021-08-18 | Fix obvious linting errors | Muriithi Frederick Muriuki | |
| * Fix linting errors that do not change the function of the code. | |||
| 2021-08-11 | use normal function for correlation (#34) | Alexander Kabui | |
| * use normal function for correlation + rename functions * update test for sample correlation * use normal function for tissue correlation + rename functions | |||
| 2021-07-26 | Check if corr_coefficient is NaN, since apparently it's stored as NaN ↵ | zsloan | |
| instead of None when it can't be calculcated (which was messing up sorting); it may also be okay to remove the None check, but leaving it for now (#28) | |||
| 2021-06-20 | merge main | Alexander Kabui | |
| 2021-06-20 | make requested changes to biweight | Alexander Kabui | |
| 2021-06-16 | Fixed spelling of coeffient to coefficient | zsloan | |
| 2021-06-14 | add biweight r script and tests | Alexander Kabui | |
| 2021-05-30 | fix index error (#16) | Alexander Kabui | |
| 2021-05-15 | resolve merge conflict | Alexander Kabui | |
| 2021-05-15 | Merge branch 'main' into feature/minor-fixes | Alexander Kabui | |
| 2021-05-15 | index lit tuple result | Alexander Kabui | |
| 2021-05-13 | computations: correlations: Apply pep-8 | BonfaceKilz | |
| 2021-05-12 | delete unused functions | Alexander Kabui | |
| 2021-05-12 | rename lit_correlation_for_trait_list to lit_correlation_for_trait | Alexander Kabui | |
| 2021-05-12 | rename tissue_correlation_for_trait_list with tissue_correlation_for_trait | Alexander Kabui | |
| 2021-05-12 | rename p_val ro tissue_p_value for tissue_results | Alexander Kabui | |
| 2021-05-03 | add default no of cores | Alexander Kabui | |
| 2021-05-03 | add trait_id fix mypy issues | Alexander Kabui | |
| 2021-05-03 | minor fixes for tiss correlation tests and naming | Alexander Kabui | |
| 2021-05-03 | replace database with conn | Alexander Kabui | |
| 2021-04-20 | pep8 formatting | Alexander Kabui | |
| 2021-04-20 | add experiment function for computing tissue correlation using multiprocessing | Alexander Kabui | |
| 2021-04-18 | refactor:return trait_name in corr_results | Alexander Kabui | |
| 2021-04-17 | ad pep8 formatting | Alexander Kabui | |
| 2021-04-17 | add sort for correlation results | Alexander Kabui | |
| refactor return data type for tissue and lit | |||
| 2021-04-16 | add benchmark function for sample r | Alexander Kabui | |
| 2021-04-16 | benchmark normal function for sample r | Alexander Kabui | |
| 2021-04-15 | optimization for sample correlation | Alexander Kabui | |
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