genenetwork3/gn3/computations, branch auth/implement-authorization-code-flow GeneNetwork3 REST API for data science and machine learning http://git.genenetwork.org/genenetwork3/atom?h=auth%2Fimplement-authorization-code-flow 2023-01-25T12:37:49+00:00 Some comments 2023-01-25T12:37:49+00:00 Pjotr Prins 2023-01-25T12:37:37+00:00 urn:sha1:9f8de83700a5aa1c19ec8d11b0978e8852b442db gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts. 2022-12-21T00:39:52+00:00 Frederick Muriuki Muriithi 2022-12-21T00:39:52+00:00 urn:sha1:daa3a9cade431b21bbc48b690c16dcb8746f3dce Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's `random` module. * gn3/random.py -> gn3/chancy.py: rename module * gn3/commands.py: update import * gn3/computations/partial_correlations.py: update import * gn3/computations/qtlreaper.py: update import * gn3/computations/rust_correlation.py: update import * gn3/db/correlations.py: update import * gn3/db/traits.py: update import * gn3/heatmaps.py: update import * tests/integration/conftest.py: update import mypy and pylint fixes 2022-12-05T21:45:58+00:00 Alexander_Kabui 2022-12-05T21:45:58+00:00 urn:sha1:e781996b952bc1ff9d9cd7703cb5e37e2a282162 correlations: return `None` rather than zero for missing lit corrs 2022-12-02T04:26:13+00:00 Frederick Muriuki Muriithi 2022-12-02T04:26:13+00:00 urn:sha1:156e6e4c372f3b4c24d5c07c02603a29d0d95412 * gn3/computations/correlations.py: Return `None` for missing literature correlations rather than zero. Update the sorting key to avoid issues with comparing floats to NoneType objects remove trailing whitespace 2022-11-29T14:54:59+00:00 AlexanderKabui 2022-11-29T14:54:59+00:00 urn:sha1:d1a425f924b2106115c05ac8054f2588c8e80446 remove unused function parameter 2022-11-29T14:46:38+00:00 AlexanderKabui 2022-11-29T14:46:38+00:00 urn:sha1:33f12bda728d9682abbe07b7ec6c603c5c67a1c5 Fix issue where only primary samples were used when all samples are 2022-11-08T20:30:44+00:00 zsloan 2022-11-08T20:30:44+00:00 urn:sha1:e66ca1919381261a0fcdb744d1fc12e8f51739d8 selected This is because base_samples was set to all_samples_ordered, which only includes primary samples + parents/f1s. Setting this to an empty list fixed the issue and caused it to use all samples again. fix issue;parsing sample data (#102) 2022-10-22T14:08:33+00:00 Alexander Kabui 2022-10-22T14:08:33+00:00 urn:sha1:544eae96a21848fbf400fa65b3eca40c0fc8fb87 DEBUG: Collect more info for debugging 2022-10-06T14:16:35+00:00 Frederick Muriuki Muriithi 2022-10-06T14:16:35+00:00 urn:sha1:660f125d3e448add6005e3998a782ce0d6b57151 DEBUG: Collect more information on possible failure. 2022-10-06T14:06:22+00:00 Frederick Muriuki Muriithi 2022-10-06T14:06:22+00:00 urn:sha1:f3ac628fd4e9ddb36f48c23186488bcef55f5e48