Age | Commit message (Collapse) | Author | |
---|---|---|---|
2024-09-12 | Move assert_paths_exist into fs_helpers | Pjotr Prins | |
2024-09-12 | Change behavior of do_paths_exist to actually throw useful error | Pjotr Prins | |
2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins | |
2024-09-12 | Move assert_paths_exist into fs_helpers | Pjotr Prins | |
2024-09-12 | Change behavior of do_paths_exist to actually throw useful error | Pjotr Prins | |
2024-02-25 | Disable too-many-arguments for "run_reaper". | Munyoki Kilyungi | |
* gn3/computations/qtlreaper.py: Disable "too-many-arguments" pylint check. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
2024-02-19 | Pass qtlreaper command path as argument to run_reaper | zsloan | |
Originally the system would get the path from the environment | |||
2023-10-27 | Remove reimport "Optional". | Munyoki Kilyungi | |
* gn3/computations/gemma.py: Delete reimport "Qptional". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
2023-10-27 | Make implicit optional type hints PEP 484 compliant. | Munyoki Kilyungi | |
Ran the command: pipx run no_implicit_optional ./ in the root directory. | |||
2023-10-26 | Fix errors caught by mypy. | Frederick Muriuki Muriithi | |
2023-10-06 | pylint: fix variable name. | Frederick Muriuki Muriithi | |
2023-10-06 | Get `CORRELATION_COMMAND` from current_app not `gn3.settings` | Frederick Muriuki Muriithi | |
The default settings in `gn3.settings` are meant to be overridden thus the code should not be importing the setting from there, rather, the code should get its configurations settings from `flask.current_app.config`. | |||
2023-09-05 | Fix C3001: Lambda expression assigned to a variable | Munyoki Kilyungi | |
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
2023-01-25 | Some comments | Pjotr Prins | |
2022-12-21 | gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts. | Frederick Muriuki Muriithi | |
Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's `random` module. * gn3/random.py -> gn3/chancy.py: rename module * gn3/commands.py: update import * gn3/computations/partial_correlations.py: update import * gn3/computations/qtlreaper.py: update import * gn3/computations/rust_correlation.py: update import * gn3/db/correlations.py: update import * gn3/db/traits.py: update import * gn3/heatmaps.py: update import * tests/integration/conftest.py: update import | |||
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 | |||
2022-11-29 | remove trailing whitespace | AlexanderKabui | |
2022-11-29 | remove unused function parameter | AlexanderKabui | |
2022-11-08 | Fix issue where only primary samples were used when all samples are | zsloan | |
selected This is because base_samples was set to all_samples_ordered, which only includes primary samples + parents/f1s. Setting this to an empty list fixed the issue and caused it to use all samples again. | |||
2022-10-22 | fix issue;parsing sample data (#102) | Alexander Kabui | |
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 | Frederick Muriuki Muriithi | |
* 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. | |||
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 | Frederick Muriuki Muriithi | |
Use the built-in csv module for file output in order to avoid subtle errors in the formats. | |||
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' | Frederick Muriuki Muriithi | |
* Always return dict * Fix internal '__parse_line__' to always have a valid return | |||
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 | Frederick Muriuki Muriithi | |
* remove extra iteration that is unnecessary * remove unnecessary variables | |||
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. | |||
2022-07-22 | 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 | |