GeneNetwork3 REST API for data science and machine learning http://git.genenetwork.org/genenetwork3/atom?h=ci-cd-scripts 2021-12-14T10:53:30+00:00 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 2021-11-19T07:56:35+00:00 Frederick Muriuki Muriithi 2021-11-19T07:56:35+00:00 urn:sha1:08c81b8892060353bb7fb15555875f03bbdcb46e Notes: https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918 * As mentioned in the notes, rather than rounding to an arbitrary number of decimal places, it is a much better practice to use approximate comparisons of floats for the tests. 2021-11-18T08:59:53+00:00 Frederick Muriuki Muriithi 2021-11-18T08:59:53+00:00 urn:sha1:3dd5fbda7e08999b6470cfe1fbbd19d767adea9b Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Fix some obvious linting errors and remove obsolete code 2021-11-18T07:58:34+00:00 Frederick Muriuki Muriithi 2021-11-18T07:58:34+00:00 urn:sha1:21fbbfd599c841f082d88ddfc5f4cb362e1eb869 Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Replace the code that was in the process of being migrated from R in GeneNetwork1 with calls to pingouin functions that achieve the same thing. Since the functions in this case are computing correlations and partial correlations, rather than having home-rolled functions to do that, this commit makes use of the tried and tested pingouin functions. This avoids complicating our code with edge-case checks, and leverages the performance optimisations done in pingouin. 2021-11-15T04:58:10+00:00 Frederick Muriuki Muriithi 2021-11-15T04:58:10+00:00 urn:sha1:29fc003070b45f61e7ab1048a818201b5beb9298 * gn3/computations/partial_correlations.py: Remove rounding. Fix computation of remaining covariates * tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt: reduce the number of covariates to between one (1) and three (3) * tests/unit/computations/test_partial_correlations.py: fix some minor bugs It turns out that the computation complexity increases exponentially, with the number of covariates. Therefore, to get a somewhat sensible test time, while retaining a large-ish number of tests, this commit reduces the number of covariates to between 1 and 3. 2021-11-15T04:06:58+00:00 Frederick Muriuki Muriithi 2021-11-15T04:06:58+00:00 urn:sha1:63b70daaffd2c3e095fde3ed59a07bb9ee894c4f Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * When the z value is a Sequence of sequences of values, each of the internal sequences should form a column of its own, and not a row, as it was originally set up to do. 2021-11-12T01:07:42+00:00 Frederick Muriuki Muriithi 2021-11-12T01:07:42+00:00 urn:sha1:d1617bd8af25bf7c7777be7a634559fd31b491ad