| 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 | |
| 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 | |
| 2022-02-24 | gn3: Explicitly specify UTF-8 to be the file encoding. | Arun Isaac | |
| When the encoding is not specified explicitly, the system default encoding is used. This is not recommended. * gn3/computations/ctl.py (call_ctl_script), gn3/computations/gemma.py (generate_pheno_txt_file), gn3/computations/parsers.py (parse_genofile), gn3/computations/partial_correlations.py (partial_correlations_fast), gn3/computations/rqtl.py (process_rqtl_output, process_perm_output), gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script), gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file encoding. * tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file), tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test for call to open with encoding='utf-8' argument. | |||
| 2021-05-13 | Rename file_utils to fs_helpers | BonfaceKilz | |
| Generally avoid naming things with a "utils" prefix/ suffix since it encourages contributors to dump any new functions there; and over time, as the code grows, things get messy... | |||
| 2021-03-10 | Fix k-compute command when "loco" is true | BonfaceKilz | |
| 2021-03-08 | Remove unused imports | BonfaceKilz | |
| 2021-03-08 | Delete "generate_gemma_computation_cmd" | BonfaceKilz | |
| 2021-03-08 | Add generic fn for computing k and gwa values | BonfaceKilz | |
| 2021-03-08 | Apply pep-8 formatting | BonfaceKilz | |
| Began using elpy's format code fn | |||
| 2021-03-08 | Move "generate_random_n_string" to file_utils | BonfaceKilz | |
| * gn3/computations/gemma.py (generaten_random_n_string): Move to... * gn3/file_utils.py: ... here. | |||
| 2021-03-08 | Fix failing tests | BonfaceKilz | |
| 2021-02-24 | Create a new helper function for generating k_values and GWA | BonfaceKilz | |
| 2021-02-24 | Add procedure that checks whether a list of paths exist | BonfaceKilz | |
| 2021-02-24 | Check if phenotype exists before creating one | BonfaceKilz | |
| 2021-02-24 | Add new procedure that computes the hash of an array of strings | BonfaceKilz | |
| 2021-02-24 | Add mypy-typing to function | BonfaceKilz | |
| * gn3/computations/gemma.py (generate_random_n_string): Add typing to function. | |||
| 2021-02-24 | Append random 6 chars to generated phenotype file | BonfaceKilz | |
| 2021-02-24 | Create a new method for generating a valid phenotype file on the fly | BonfaceKilz | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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