genenetwork3/gn3/computations/gemma.py, branch auth/implement-authorization-code-flow GeneNetwork3 REST API for data science and machine learning http://git.genenetwork.org/genenetwork3/atom?h=auth%2Fimplement-authorization-code-flow 2022-02-24T08:34:06+00:00 gn3: Explicitly specify UTF-8 to be the file encoding. 2022-02-24T08:34:06+00:00 Arun Isaac 2022-02-24T08:16:34+00:00 urn:sha1:aaff8b8ac968bce9821d6fef22b1296247a9df09 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. Rename file_utils to fs_helpers 2021-05-13T08:18:57+00:00 BonfaceKilz 2021-05-11T14:00:26+00:00 urn:sha1:378d0fc7f4ff5df5e8e77617c37bcef2b26ddf02 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... Fix k-compute command when "loco" is true 2021-03-10T11:59:25+00:00 BonfaceKilz 2021-03-10T11:59:25+00:00 urn:sha1:8478bc9ee572224fe3b76696de85d1c9a7a89399 Remove unused imports 2021-03-08T18:09:58+00:00 BonfaceKilz 2021-03-08T12:27:47+00:00 urn:sha1:a92af15935847fd89d8702b46279ec9bc749915c Delete "generate_gemma_computation_cmd" 2021-03-08T18:09:58+00:00 BonfaceKilz 2021-03-08T12:26:33+00:00 urn:sha1:776598729bcff12bea933ff7cb4864e1c3eea0c8 Add generic fn for computing k and gwa values 2021-03-08T18:09:58+00:00 BonfaceKilz 2021-03-05T09:06:54+00:00 urn:sha1:8752937bc1e3cea84eefd3e363b429157f25acb5 Apply pep-8 formatting 2021-03-08T18:09:58+00:00 BonfaceKilz 2021-03-05T09:06:22+00:00 urn:sha1:5c56425d51ab6a6b4ffd6ec8f86121bd91ff5e63 Began using elpy's format code fn Move "generate_random_n_string" to file_utils 2021-03-08T18:09:58+00:00 BonfaceKilz 2021-03-01T09:57:47+00:00 urn:sha1:ff29ce04a1f10af819770ccafd347daaba6b2bf7 * gn3/computations/gemma.py (generaten_random_n_string): Move to... * gn3/file_utils.py: ... here. Fix failing tests 2021-03-08T18:09:58+00:00 BonfaceKilz 2021-03-01T08:47:21+00:00 urn:sha1:52e3569cca6b24d1318034f5ab004795e70135f5 Create a new helper function for generating k_values and GWA 2021-02-24T11:20:29+00:00 BonfaceKilz 2021-02-24T07:36:04+00:00 urn:sha1:2125450ffaf93e9500dc6360ecce8d6c7e8e4036