genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2022-06-21	tests: test_file_utils: Replace pytest.mark.skip with unittest.skip	BonfaceKilz
	"python setup.py test" won't skip "pytest.mark.skip" thereby leading to build failure when you try to package gn3.
2022-06-21	test_file_utils: Disable test cases for "cache_ipfs_file"	BonfaceKilz
	* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip it. (test_cache_ipfs_file_cache_miss): Ditto.
2022-03-11	Fix some linting issues	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
2022-02-17	Use pytest's "mark" feature to categorise tests	Frederick Muriuki Muriithi
	Use pytest's `mark` feature to explicitly categorise the tests and run them per category
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...
2021-05-08	Add extra genotype test file	BonfaceKilz
	* tests/unit/test_data/genotype.txt: New file. * tests/unit/test_file_utils.py: Update failing test.
2021-03-23	Convert Path object to a str	BonfaceKilz
	* gn3/file_utils.py (cache_ipfs_file): Return a str instead of a path object. * tests/unit/test_file_utils.py: Update failing tests.
2021-03-23	Add function to cache ipfs files	BonfaceKilz

2021-03-23	Apply autopep-8	BonfaceKilz

2021-03-10	Apply yapf file formatting to file	BonfaceKilz

2021-03-10	Add extra tests for file utils	BonfaceKilz
	In test server, files were not extracted properly. This test exposes the bug.
2021-03-10	Run yapf-formatter against file	BonfaceKilz

2021-03-08	Delete "lookup_file" procedure	BonfaceKilz

2021-03-08	Extract files to "/TMPDIR/TOKEN"	BonfaceKilz
	TOKEN is the user token * gn3/file_utils.py (extract_uploaded_file): Add extra param "token". If a token is empty, create a new directory based off that token. * tests/unit/test_file_utils.py: Update failing tests.
2021-02-16	Add procedure for uploading gzipped file	BonfaceKilz
	* gn3/file_utils.py (extract_uploaded_file): New procedure. * tests/unit/test_file_utils.py: Test cases for ^^. * tests/unit/upload-data.tar.gz: New test data.
2021-02-12	Use sorted list of files when calculating md5sums of directory	BonfaceKilz
	* gn3/file_utils.py (get_dir_hash): Sort list of files before calculating their md5sums. * tests/unit/test_file_utils.py (test_get_dir_hash): Update test-case md5sum.
2021-02-12	Add new procedure to return a python dict from a json file	BonfaceKilz
	* gn3/file_utils.py (jsonfile_to_dict): New procedure * tests/unit/test_file_utils.py: New test-cases.
2021-02-12	Add new procedure for looking up files in a given ENV variable	BonfaceKilz
	* gn3/file_utils.py (lookup_file): New function. * tests/unit/test_file_utils.py: New test cases for ^^.
2021-02-12	Add function for computing the hash of a directory	BonfaceKilz