gentropy 2.3.0

v2.3.0

on Python PyPI

What's Changed

• fix: addressing #3800 and #3799 by @DSuveges in #1017
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1018
• Fix: Ensure qualityControls and analysisFlags columns are always added when curation_table is None by @ffrnz in #1020
• refactor(l2g): make wandb logging optional by @ireneisdoomed in #1019
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1022
• chore: offline check uv lock by @project-defiant in #1024
• chore: skip uv-lock on pre-commit ci by @project-defiant in #1027
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1028
• build(deps): update shap requirement by @dependabot[bot] in #1016
• feat: (coloc) parameterise the small overlaps filtering criteria so they can be specified in orchestration by @Daniel-Considine in #1030
• feat: slimmer docker image by @ffrnz in #1023
• chore(deps): bump actions/create-github-app-token from 1 to 2 by @dependabot[bot] in #1033
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1031
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1036
• fix: remove trans molQTLs from FM by @addramir in #1038
• docs: remove roadmap section by @d0choa in #1042
• chore(VEP): Update Ensembl to 144 by @DSuveges in #1043
• refactor(summary_statistics_qc): Summary Statistics QC dataset by @project-defiant in #1040
• fix: correction of the code for calculating log10BF for credible sets by @Daniel-Considine in #1041
• fix: ensure the coloc method name is not added to the output by @project-defiant in #1044
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1037
• chore(deps): bump astral-sh/setup-uv from 5 to 6 by @dependabot[bot] in #1035
• chore: remove vep image and artifact build by @project-defiant in #1045
• fix: fix isProteincoding by @addramir in #1046
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1047
• fix(changelog): ensure the changelog template is reused by @project-defiant in #1048
• fix(l2g): half of the feature matrix have distance features larger than 1 by @ireneisdoomed in #1053
• feat: pass partition number to the step by @project-defiant in #1054
• feat(sumstat): rescue standard error from p-value and beta by @project-defiant in #1059
• feat: standard error from ci by @project-defiant in #1061
• fix: spark plan optimisation by @DSuveges in #1055
• fix: neglog func fix by @addramir in #1062
• chore: adding pubmed identifier to evidence by @DSuveges in #1068
• fix: adding rsids to GnomAD variants by @DSuveges in #1060
• feat: adding pmid to finngen studies by @DSuveges in #1069
• chore: trigger release process by @github-actions[bot] in #1021

New Contributors

• @ffrnz made their first contribution in #1020

Full Changelog: v2.2.0...v2.3.0