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2024-02-25Disable too-many-arguments for "run_reaper"....* gn3/computations/qtlreaper.py: Disable "too-many-arguments" pylint check. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-19Pass qtlreaper command path as argument to run_reaper...Originally the system would get the path from the environment zsloan
2023-10-27Remove reimport "Optional"....* gn3/computations/gemma.py: Delete reimport "Qptional". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-27Make implicit optional type hints PEP 484 compliant....Ran the command: pipx run no_implicit_optional ./ in the root directory. Munyoki Kilyungi
2023-10-26Fix errors caught by mypy.Frederick Muriuki Muriithi
2023-10-06pylint: fix variable name.Frederick Muriuki Muriithi
2023-10-06Get `CORRELATION_COMMAND` from current_app not `gn3.settings`...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`. Frederick Muriuki Muriithi
2023-09-05Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-01-25Some commentsPjotr Prins
2022-12-21gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts....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 Frederick Muriuki Muriithi
2022-12-06mypy and pylint fixesAlexander_Kabui
2022-12-02correlations: return `None` rather than zero for missing lit corrs...* 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 Frederick Muriuki Muriithi
2022-11-29remove trailing whitespaceAlexanderKabui
2022-11-29remove unused function parameterAlexanderKabui
2022-11-08Fix issue where only primary samples were used when all samples are...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. zsloan
2022-10-22fix issue;parsing sample data (#102)Alexander Kabui
2022-10-06DEBUG: Collect more info for debuggingFrederick Muriuki Muriithi
2022-10-06DEBUG: Collect more information on possible failure.Frederick Muriuki Muriithi
2022-10-03Bug: 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
2022-09-30Add escape char to avoid error notice.Frederick Muriuki Muriithi
2022-09-29Use 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
2022-08-25revert for commit 6db3b2af8fc09999996d3acc09890a06f179c669;BugAlexander_Kabui
2022-08-12Add mandatory/expected fields to parsed data.Frederick Muriuki Muriithi
2022-08-10Fix returned value for 'parse_correlation_output'...* Always return dict * Fix internal '__parse_line__' to always have a valid return Frederick Muriuki Muriithi
2022-08-10code refactoringFrederick Muriuki Muriithi
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10code refactoringFrederick Muriuki Muriithi
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10enhancements for rust tissueFrederick Muriuki Muriithi
2022-08-10pylint fixesAlexander_Kabui
2022-08-10code refactoringAlexander_Kabui
2022-08-10remove unnessary codeAlexander_Kabui
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10merge for resultsAlexander_Kabui
2022-08-10enhancements for rust tissueAlexander_Kabui
2022-08-03Refactor: Remove unnecessary whitespace and nameFrederick Muriuki Muriithi
2022-08-03Refactor: Remove unnecessary iterations and name...* remove extra iteration that is unnecessary * remove unnecessary variables Frederick Muriuki Muriithi
2022-07-29Fix 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
2022-07-28Update 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
2022-07-22mypy fixesAlexander_Kabui
2022-07-22pep8 fixesAlexander_Kabui
2022-07-22linting and tests fixesAlexander_Kabui
2022-07-22compute num overlapAlexander_Kabui
2022-07-22fix for bug splitting list dataAlexander_Kabui
2022-07-22minor fixes for parsing dataAlexander_Kabui
2022-07-22code to parse tissue correlation inputAlexander_Kabui
2022-07-22mypy pylint fixesAlexander_Kabui
2022-07-22code to fetch correct sample corr dataAlexander_Kabui
2022-07-22delete dead_code;rename variablesAlexander_Kabui
2022-07-22minor fixesAlexander_Kabui