genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2025-10-22	Fetch configs from app setting and pass them down	Frederick Muriuki Muriithi
	Fix the code to avoid using global variables holding configuration variables to avoid the failures caused by action-at-a-distance effects due to change of a value elsewhere. This way, all code consistently receives the same configuration values passed on from callers. We pass on the following configuration settings: * TMPDIR * SQL_URI * TEXTDIR
2024-09-27	Bug: Use absolute paths in place of relative paths.	Frederick Muriuki Muriithi
	Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51
2024-09-12	Modify script paths so they can be edited in Guix	Pjotr Prins

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.
2022-02-02	refactor code for invoking ctl script	Alexander Kabui

2022-02-02	pep8 formatting	Alexander Kabui

2022-02-02	new line fix	Alexander Kabui

2022-02-02	fix comprehension list	Alexander Kabui

2022-01-22	process ctl plot data img	Alexander Kabui

2022-01-22	read stdout data;handle exceptions	Alexander Kabui

2022-01-22	init file to call ctl script	Alexander Kabui