What's Changed
✨ Feature
- [airflow] include COLOC as a node in the DAG (#530) @Irene López
- check for if no overlapping variants in LD index (#594) @Daniel-Considine
- add purity qc metrics to fine-mapping (#592) @Yakov
- lighter dockerfile (#585) @David Ochoa
- github action to upload docker image to registry (#588) @David Ochoa
- functionality added to StudyLocus.find_overlaps() for finding within-study overlaps (#587) @Daniel-Considine
- susie_finemapper_one_studylocus_row_v3_dev_ss_gathered (#586) @Yakov
- [sumstat qc] adding methods for QC of summary statistics (#455) @Yakov
- changing locus window to locus radius to be consistent with other functions (#582) @Daniel-Considine
- updating step config file (#580) @Daniel-Considine
- dockerise gentropy python package (#579) @Irene López
- adding init to finemapping step (#577) @Daniel-Considine
- adding notebook for mapping EFOs for the FinnGen study index (#575) @Yakov
- add benchmarking for fine-mapping using Alzheimer as example (#572) @Yakov
- add FM step with carma and sumstat imputation (#568) @Yakov
- susie_finemapper_ss_gathered() (#567) @Daniel-Considine
- the FineMapper function for one locus (#564) @Yakov
- LD index and block matrix extraction for a studyLocus (#463) @Daniel-Considine
- add the step class for fine-mapping (#554) @Yakov
- notebook to run qc metrics each release (#541) @xyg123
- [l2g] distance features based on weighted score (#545) @Irene López
- [sumstat imputation] adding class for sumstat imputation (#490) @Yakov
- [coloc] single SNP case (#511) @xyg123
- extract credible sets and studies from all eQTL Catalogue finemapping results (#518) @Irene López
🐛 Fix
- fix python-semantic-release version (again) @David Ochoa
- fix python-semantic-release version @David Ochoa
- docker action fixes v3 (#591) @David Ochoa
- docker action fixes (#590) @David Ochoa
- docker action fixes (#589) @David Ochoa
- updating config.py argument for finemapper (#584) @Daniel-Considine
- minor updates and bug fixes (#543) @Daniel Suveges
- update error in config.py (#583) @Daniel-Considine
- removing all duplicated variants in sumstats for finemapping functions (#574) @Daniel-Considine
- adding deduplication for GWAS in locus (#573) @Yakov
- [sumstats] correct study id for dir of finngen studies (#551) @Joris Louwen
- [coloc] handle cases when the bayes factors are null (#556) @Irene López
- small fixes in susie defaults (#552) @Yakov
- read function for thurman data to include first line (#534) @Joris Louwen
- pin version of commitlint (#533) @Joris Louwen
- pr labeller patterns (#523) @David Ochoa
♻️ Refactor
- moving all variant coordinates to GnomAD (#566) @Daniel Suveges
⚡️ Performance
- [l2g] optimise extraction of features from colocalisation results (#553) @Irene López
- [clump] refactored window based clumping (#492) @David Ochoa
- [l2g] streamline feature generation (#544) @Irene López
✅ Test
🏗 Build
- [deps-dev] bump mypy from 1.9.0 to 1.10.0 (#604) @dependabot[bot]
- [deps-dev] bump ipython from 8.22.1 to 8.24.0 (#603) @dependabot[bot]
- [deps] bump typing-extensions from 4.10.0 to 4.11.0 (#602) @dependabot[bot]
- [deps-dev] bump ruff from 0.3.2 to 0.4.3 (#596) @dependabot[bot]
- [deps-dev] bump pytest-xdist from 3.5.0 to 3.6.1 (#597) @dependabot[bot]
- [deps-dev] bump pytest from 8.1.0 to 8.2.0 (#598) @dependabot[bot]
- [deps-dev] bump interrogate from 1.5.0 to 1.7.0 (#599) @dependabot[bot]
- [deps-dev] bump pymdown-extensions from 10.7 to 10.8.1 (#600) @dependabot[bot]
- [deps-dev] bump python-semantic-release from 9.1.0 to 9.4.1 (#571) @dependabot[bot]
- [deps-dev] bump pytest-cov from 4.1.0 to 5.0.0 (#560) @dependabot[bot]
- [deps-dev] bump pre-commit from 3.6.0 to 3.7.0 (#559) @dependabot[bot]
- [deps-dev] bump lxml from 5.1.0 to 5.2.1 (#569) @dependabot[bot]
- [deps-dev] bump deptry from 0.14.0 to 0.16.1 (#570) @dependabot[bot]
- [deps-dev] bump mkdocstrings-python from 1.8.0 to 1.9.0 (#549) @dependabot[bot]
- [deps-dev] bump deptry from 0.12.0 to 0.14.0 (#548) @dependabot[bot]
- [deps-dev] bump mypy from 1.8.0 to 1.9.0 (#532) @dependabot[bot]
- [deps-dev] bump ruff from 0.2.0 to 0.3.2 (#531) @dependabot[bot]
👷♂️ Ci
- bugfix in PR labeller (#537) @David Ochoa
🚀 Chore
- pre-commit autoupdate (#601) @pre-commit-ci[bot]
- pre-commit autoupdate (#593) @pre-commit-ci[bot]
- pre-commit autoupdate (#561) @pre-commit-ci[bot]
- pre-commit autoupdate (#550) @pre-commit-ci[bot]
- [l2g] log annotated gold standards in w&b (#546) @Irene López
- pre-commit autoupdate (#539) @pre-commit-ci[bot]
- update ruff pre-commit and rules (#522) @David Ochoa
- add sqtl, tuqtl, pqtl features to l2g inclusion list @Irene López
- add tuqtl features to L2Gfeaturematrix schema @Irene López