genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2022-06-21	gn3: fs_helpers: Remove ipfshttpclient	BonfaceKilz
	This library pollutes the Genenetwork2 profile with an old version "dataclasses" thereby causing it to fail.
2022-03-11	Fix some linting issues	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.
2022-02-21	Fix minor issues introduced while fixing linting errors	Frederick Muriuki Muriithi

2022-02-21	Fix a myriad of linter issues	Frederick Muriuki Muriithi
	* Use `with` in place of plain `open` * Use f-strings in place of `str.format()` * Remove string interpolation from queries - provide data as query parameters * other minor fixes
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...