| Age | Commit message (Expand) | Author |
|---|
| 2022-10-06 | DEBUG: Collect more info for debugging | Frederick Muriuki Muriithi |
| 2022-10-06 | DEBUG: Collect more information on possible failure. | Frederick Muriuki Muriithi |
| 2022-10-03 | Bug: Do not process data for output too early...* gn3/computations/rust_correlation.py: (parse_tissue_corr_data): The function
was parsing data from a file, and then converting the parsed values into a
comma-separated string for output, despite the fact that the data parsed is
not output in this specific function. This is a really bad idea, and leads
to errors showing up down the line, far removed from the cause.
| Frederick Muriuki Muriithi |
| 2022-09-30 | Add escape char to avoid error notice. | Frederick Muriuki Muriithi |
| 2022-09-29 | Use the built-in csv module for file output...Use the built-in csv module for file output in order to avoid subtle errors in
the formats.
| Frederick Muriuki Muriithi |
| 2022-08-25 | revert for commit 6db3b2af8fc09999996d3acc09890a06f179c669;Bug | Alexander_Kabui |
| 2022-08-12 | Add mandatory/expected fields to parsed data. | Frederick Muriuki Muriithi |
| 2022-08-10 | Fix returned value for 'parse_correlation_output'...* Always return dict
* Fix internal '__parse_line__' to always have a valid return
| Frederick Muriuki Muriithi |
| 2022-08-10 | code refactoring | Frederick Muriuki Muriithi |
| 2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui |
| 2022-08-10 | code refactoring | Frederick Muriuki Muriithi |
| 2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui |
| 2022-08-10 | enhancements for rust tissue | Frederick Muriuki Muriithi |
| 2022-08-10 | pylint fixes | Alexander_Kabui |
| 2022-08-10 | code refactoring | Alexander_Kabui |
| 2022-08-10 | remove unnessary code | Alexander_Kabui |
| 2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui |
| 2022-08-10 | merge for results | Alexander_Kabui |
| 2022-08-10 | enhancements for rust tissue | Alexander_Kabui |
| 2022-08-03 | Refactor: Remove unnecessary whitespace and name | Frederick Muriuki Muriithi |
| 2022-08-03 | Refactor: Remove unnecessary iterations and name...* remove extra iteration that is unnecessary
* remove unnecessary variables
| Frederick Muriuki Muriithi |
| 2022-07-29 | Fix failing tests...* 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
| Frederick Muriuki Muriithi |
| 2022-07-28 | Update sample correlations code to use multiprocessing...* To help speed up the processing of the correlations, convert the
`compute_all_sample_correlation` function to use the multiprocessing module.
| Frederick Muriuki Muriithi |
| 2022-07-22 | mypy fixes | Alexander_Kabui |
| 2022-07-22 | pep8 fixes | Alexander_Kabui |
| 2022-07-22 | linting and tests fixes | Alexander_Kabui |
| 2022-07-22 | compute num overlap | Alexander_Kabui |
| 2022-07-22 | fix for bug splitting list data | Alexander_Kabui |
| 2022-07-22 | minor fixes for parsing data | Alexander_Kabui |
| 2022-07-22 | code to parse tissue correlation input | Alexander_Kabui |
| 2022-07-22 | mypy pylint fixes | Alexander_Kabui |
| 2022-07-22 | code to fetch correct sample corr data | Alexander_Kabui |
| 2022-07-22 | delete dead_code;rename variables | Alexander_Kabui |
| 2022-07-22 | minor fixes | Alexander_Kabui |
| 2022-06-29 | use explicit parameters | Alexander_Kabui |
| 2022-06-29 | fix issues | Alexander_Kabui |
| 2022-06-29 | pylint fixes | Alexander |
| 2022-06-29 | minor fixes | Alexander |
| 2022-06-29 | handle tmp files generation | Alexander |
| 2022-06-29 | parse output data | Alexander |
| 2022-06-29 | pep8 formatting | Alexander |
| 2022-06-29 | init rust correlation module | Alexander |
| 2022-05-30 | Pass trait data as args to `fix_strains` and fix some bugs...The `fix_strains` function works on the trait data, not the basic trait
info. This commit fixes the arguments passed to the function, and also some
bugs in the function.
| Frederick Muriuki Muriithi |
| 2022-05-24 | New script to compute partial correlations...* Add a new script to compute the partial correlations against:
- a select list of traits, or
- an entire dataset
depending on the specified subcommand. This new script is meant to supercede
the `scripts/partial_correlations.py` script.
* Fix the check for errors
* Reorganise the order of arguments for the
`partial_correlations_with_target_traits` function: move the `method`
argument before the `target_trait_names` argument so that the common
arguments in the partial correlation computation functions share the same
order.
| Frederick Muriuki Muriithi |
| 2022-05-21 | Use multiprocessing to improve performance | Frederick Muriuki Muriithi |
| 2022-05-21 | Process primary, target and control traits in a single iteration...Rework the code to process the traits in a single iteration to improve
performance.
| Frederick Muriuki Muriithi |
| 2022-05-21 | Return generator object rather than tuples...Return generator objects rather than pre-computed tuples to reduce the number
of iterations needed to process the data, and thus improve the performance of
the system somewhat.
| Frederick Muriuki Muriithi |
| 2022-05-06 | Fix linting and typing errors | Frederick Muriuki Muriithi |
| 2022-05-06 | Hook up pcorrs with target traits computations...Enable the endpoint to actually compute partial correlations with selected
target traits rather than against an entire dataset.
Fix some issues caused by recent refactor that broke pcorrs against a dataset
| Frederick Muriuki Muriithi |
| 2022-05-05 | Compute partial correlation with selected traits...Compute partial correlations against a selection of traits rather than against
an entire dataset.
| Frederick Muriuki Muriithi |
