v3.0.0

What's Changed

What's Changed

• build(deps): update pydoclint requirement from <0.7.0,>=0.3.8 to >=0.3.8,<0.8.0 by @dependabot[bot] in #1121
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1122
• build(deps): update pytest-sugar requirement from <1.1.0,>=0.9.5 to >=0.9.5,<1.2.0 by @dependabot[bot] in #1120
• build(deps): update deptry requirement from <0.23.0,>=0.22.0 to >=0.22.0,<0.24.0 by @dependabot[bot] in #1117
• chore(deps): bump python-semantic-release/publish-action from 10.3.0 to 10.4.0 by @dependabot[bot] in #1118
• ci: fixes for dockerized gentropy by @project-defiant in #1131
• feat: capturing study date by @DSuveges in #1137
• fix: adding new exception for fine-mapping by @addramir in #1138
• feat: tweaking colocalisation step to limit the right-hand side of the overlaps step by @Daniel-Considine in #1034
• build(deps): update ruff requirement from <0.13.0,>=0.8.1 to >=0.8.1,<0.15.0 by @dependabot[bot] in #1135
• feat(consequence): vep consequence scoring by @project-defiant in #1114
• feat: finngen ukbb mvp meta analysis ingestion by @project-defiant in #1132
• chore(deps): bump actions/download-artifact from 5 to 6 by @dependabot[bot] in #1141
• feat: interval ingestion by @xyg123 in #1049
• chore(deps): bump actions/upload-artifact from 4 to 5 by @dependabot[bot] in #1140
• fix: fixing efo parsing for gwas catalog study index by @DSuveges in #1133
• fix: fix p-value in fine-mapping object by @addramir in #1142
• fix: ignoring multi ancestry studies in susie by @addramir in #1145
• feat: implementing coloc-pip by @Daniel-Considine in #1127
• build(deps): update google-cloud-secret-manager requirement from <2.25.0,>=2.12.6 to >=2.12.6,<2.26.0 by @dependabot[bot] in #1139
• chore(deps): bump astral-sh/setup-uv from 6 to 7 by @dependabot[bot] in #1134
• build(deps): update pytest-cov requirement from <7.0,>=4.1 to >=4.1,<8.0 by @dependabot[bot] in #1126
• build(deps): update mypy requirement from <1.18,>=1.13 to >=1.13,<1.19 by @dependabot[bot] in #1125
• chore(deps): bump actions/setup-python from 4 to 6 by @dependabot[bot] in #1116
• build(deps): update typing-extensions requirement from <4.15.0,>=4.12.2 to >=4.12.2,<4.16.0 by @dependabot[bot] in #1119
• docs: add coloc pip to docs by @project-defiant in #1146
• feat: ensure coloc_pip_ecaviar can be reused to build L2G features by @project-defiant in #1148
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1128
• build(deps): update wandb requirement from <0.22.0,>=0.19.4 to >=0.19.4,<0.23.0 by @dependabot[bot] in #1129
• refactor: migrate skops.hub_utils to huggingface_hub by @ireneisdoomed in #1151
• fix(finemapper): remove backdoor for beta and SE extraction by @project-defiant in #1153
• fix(ld_paths): add ld_matrix_paths to the finemapper config by @project-defiant in #1152
• feat: switch output format to Parquet by @DSuveges in #1161
• chore(deps): bump python-semantic-release/publish-action from 10.4.0 to 10.5.1 by @dependabot[bot] in #1160
• chore(deps): bump docker/setup-qemu-action from 3.6.0 to 3.7.0 by @dependabot[bot] in #1159
• build(deps-dev): update mkdocs-git-revision-date-localized-plugin requirement from <1.5.0,>=1.2.2 to >=1.2.2,<1.6.0 by @dependabot[bot] in #1158
• build(deps-dev): update pydoclint requirement from <0.8.0,>=0.3.8 to >=0.3.8,<0.9.0 by @dependabot[bot] in #1157
• build(deps-dev): update pytest requirement from <9.0.0,>=7.4.4 to >=7.4.4,<10.0.0 by @dependabot[bot] in #1156
• build(deps-dev): update deptry requirement from <0.24.0,>=0.22.0 to >=0.22.0,<0.25.0 by @dependabot[bot] in #1154
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1149
• build(deps): update shap requirement from <0.49,>=0.46 to >=0.46,<0.50 by @dependabot[bot] in #1155
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1162
• chore!: deprecate numpy < 2.0 and python < 3.11 by @project-defiant in #1163
• feat: adding new class for drug enrichment analysis by @addramir in #1032
• chore: trigger release process by @github-actions[bot] in #1123

Full Changelog: v2.4.1...v3.0.0