v3.3.0

What's Changed

• feat: remove ambiguous variants from decode sumstats by @project-defiant in #1212
• feat: add recursive_file_lookup parameter to wbc by @project-defiant in #1213
• fix(decode): enhancements post test run by @project-defiant in #1214
• perf(ty): add environment configuration by @project-defiant in #1215
• refactor(coloc): colocalisation step cleanup by @project-defiant in #1216
• feat: feature/trans pqtl coloc feature by @addramir in #1210
• feat(l2g): add option to retrain final model on full dataset by @addramir in #1220
• fix: remove old notebooks by @addramir in #1223
• feat(dependencies): remove google secret manager by @project-defiant in #1209
• feat: initial commit with logic to run LDSC h2 estimates by @xyg123 in #1187
• feat(session): add external hadoop connector flags by @project-defiant in #1226
• fix(harmonisation): remove duplicated variantIds across study by @project-defiant in #1231
• feat(l2g): add LocusToGeneTrainTestSplitStep pipeline step by @addramir in #1227
• perf(coloc): native and fused coloc_pip_ecaviar by @d0choa in #1232
• fix: handle OmegaConf DictConfig in Session connectors by @project-defiant in #1238
• feat: extract shared genomics processing utilities by @project-defiant in #1236
• feat(study_index): gc lambda distinction by @project-defiant in #1240
• feat(intervals): flag non intersecting chromosome by @project-defiant in #1242
• chore(decode secret): add a static script to upload decode secret by @project-defiant in #1246
• refactor(decode): align deCODE harmonisation to shared config pattern and common/processing utilities by @project-defiant in #1244
• chore(deps): bump actions/attest-build-provenance from 3 to 4 by @dependabot[bot] in #1202
• chore(deps): bump actions/download-artifact from 7 to 8 by @dependabot[bot] in #1201
• chore(deps): bump docker/login-action from 3 to 4 by @dependabot[bot] in #1207
• chore(deps): bump docker/setup-buildx-action from 3 to 4 by @dependabot[bot] in #1206
• chore(deps): bump docker/setup-qemu-action from 3.7.0 to 4.0.0 by @dependabot[bot] in #1205
• build(deps): update scipy requirement from <1.16.0,>=1.11.4 to >=1.11.4,<1.18.0 by @dependabot[bot] in #1197
• build(deps-dev): update pyparsing requirement from <3.3.0,>=3.1.1 to >=3.1.1,<3.4.0 by @dependabot[bot] in #1200
• build(deps): update scikit-learn requirement from <1.8.0,>=1.6.1 to >=1.6.1,<1.10.0 by @dependabot[bot] in #1199
• build(deps-dev): update mypy requirement from <1.19,>=1.13 to >=1.13,<2.2 by @dependabot[bot] in #1234
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1203
• chore(deps): bump codecov/codecov-action from 5 to 7 by @dependabot[bot] in #1248
• chore(deps): bump actions/create-github-app-token from 2 to 3 by @dependabot[bot] in #1249
• chore(deps): bump docker/setup-qemu-action from 4.0.0 to 4.2.0 by @dependabot[bot] in #1250
• chore(deps): bump python-semantic-release/publish-action from 10.5.1 to 10.6.1 by @dependabot[bot] in #1251
• chore(deps): bump actions/checkout from 6 to 7 by @dependabot[bot] in #1252
• chore: trigger release process by @github-actions[bot] in #1211

Full Changelog: v3.2.0...v3.3.0