GeneNetwork3 REST API for data science and machine learning http://git.genenetwork.org/genenetwork3/atom?h=technical-specification 2022-03-15T11:08:39+00:00 2022-03-15T11:08:39+00:00 Alexander Kabui 2022-03-15T11:08:39+00:00 urn:sha1:16367dab9248d3aa2660e0b5cafdce25e8f7067c * compute zscore function * test case for computing zscore * function to compute pca * generate scree plot data * generate new pca trait data from zscores and eigen_vec * remove redundant functions * generate factor loading table data * generate pca temp dataset dict * variable naming and error fixes * unit test for processing factor loadings * minor fixes for generating temp pca dataset * pass datetime as argument to generate_pca temp dataset function * add unittest for caching pca datasets * cache temp datasets * ignore missing imports for sklearn * mypy fixes * pylint fixes * refactor tests for pca * remove ununsed imports * fix for generating pca traits vals * mypy and code refactoring * pep8 formatting and add docstrings * remove comments /pep8 formatting * sort eigen vectors based on eigen values * minor fix for zscores * fix for rounding variance ratios * refactor tests * rename module to pca * rename datasets to traits * fix failing tests * fix caching function * fixes return x and y coordinates for scree plot * expand exception scope * fix for deprecated numpy.matrix function * fix for failing tests * pep8 fixes * remove comments * fix merge conflict * pylint fixes * rename module name to test_pca 2022-03-08T05:18:32+00:00 Frederick Muriuki Muriithi 2022-03-08T05:18:32+00:00 urn:sha1:a7696cc668e00215e1d5af2425765451811bca9d 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. 2022-02-21T13:23:06+00:00 Frederick Muriuki Muriithi 2022-02-21T13:23:06+00:00 urn:sha1:a35fce27875d9db80dce1976b6f8ee8c00ecfe0a * 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 2022-02-17T03:37:30+00:00 Frederick Muriuki Muriithi 2022-02-14T03:56:32+00:00 urn:sha1:74044f3c7985308b4996da3a52f91c5c20a19194 Use pytest's `mark` feature to explicitly categorise the tests and run them per category 2022-02-17T03:37:30+00:00 Frederick Muriuki Muriithi 2022-02-10T08:36:10+00:00 urn:sha1:67f517aa0f44f55dc691ffd791bf22ef7af0b02c Add property tests using pytest and hypothesis to test that the expected properties hold for the `gn3.computations.partial_correlations.dictify_by_samples` function. 2021-12-14T10:53:30+00:00 Frederick Muriuki Muriithi 2021-12-14T10:53:30+00:00 urn:sha1:ed87184929eec6614c2cca0105c335ad24bf2720 2021-12-10T06:58:29+00:00 Alexander Kabui 2021-11-28T21:27:19+00:00 urn:sha1:bc1b310503d63555ffe9d2da0a881f11b666fa3b 2021-12-10T06:58:29+00:00 Alexander Kabui 2021-11-28T20:30:09+00:00 urn:sha1:d253a9bc5e4831da03df45c7b0b73ed4456853b9 2021-11-29T11:02:56+00:00 Frederick Muriuki Muriithi 2021-11-29T11:02:56+00:00 urn:sha1:4c3863a6fd5d1864c135bddfe02d06c98a19ca18 Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi