Gentropy

What's Changed


✨ Feature

- implement reading study locus paths from the manifest (706) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)








🏗 Build

- \[**deps-dev**\] bump mypy from 1.10.0 to 1.11.0 (713) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump deptry from 0.16.1 to 0.17.0 (714) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pytest from 8.2.2 to 8.3.1 (712) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)


👷‍♂️ Ci

- \[**release**\] use github app token for tag push (709) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)

What's Changed


✨ Feature

- allow image push [\Szymon Szyszkowski](mailto:ss60mib117351s.internal.sanger.ac.uk)
- \[**docker**\] drom jq [\Szymon Szyszkowski](mailto:ss60mib117351s.internal.sanger.ac.uk)
- explode loci to extract variants + tests [\Irene López](mailto:irene.lopezsprotonmail.com)


🐛 Fix

- \[**finemapping**\] typo in &34;elapsed_time&34; [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)
- typo in artifact file [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**docker**\] change JAVA_HOME env to `/usr` [\Szymon Szyszkowski](mailto:ss60mib117351s.internal.sanger.ac.uk)
- fix issue with gh commit not triggering artifact workflow [\Szymon Szyszkowski](mailto:ss60mib117351s.internal.sanger.ac.uk)








👷‍♂️ Ci

- authentication with github app [\Szymon Szyszkowski](mailto:ss60mib117351s.internal.sanger.ac.uk)


🚀 Chore

- pre-commit autoupdate [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)

What's Changed


✨ Feature

- full orchestration of the variant index dag (678) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**studyLocus validation**\] adding validation logic to studyLocus dataset (686) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- artifacts versionned by release (692) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)


🐛 Fix

- moving hl.init (687) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)








👷‍♂️ Ci

- revert semantic-release update (694) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- prevent user from rebasing in minimal way (691) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)


🚀 Chore

- \[**study_index**\] improve study definition for the eQTL Catalogue and Finngen (693) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)

What's Changed


✨ Feature

- \[**config**\] 24.06 data release fixes (639) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- credible set quality filtering (640) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- enable interface with gcp secrets manager (635) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- adding locus-breaker clumping method (634) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- \[**spark-helpers**\] enforce schema of returned objects (617) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- \[**qtl**\] ingest credible sets from single cell derived QTLs (630) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**data_release**\] preparation for 24.06 data release (633) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**config**\] extract gwas_significance parameter to step configuration (628) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**config**\] gnomAD steps configuration extraction and versioning (620) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- fine-mapping simulations class (618) [\Yakov](mailto:yt4sanger.ac.uk)


🐛 Fix

- \[**L2GPrediction**\] schema validation (642) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**docs**\] fixed typo in l2g_prediciton schema page (629) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**SummaryStatistics**\] fix in sanity_filter (623) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**susie_finemapper**\] fix in the fine-mapper in case of sum stat imputation is False (627) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**susie_finemapper**\] correct syntax for saving the logs df (625) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)
- \[**ld**\] correct syntax for the static method (624) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)
- \[**docs**\] update roadmap.md (622) [\buniello](mailto:30833755+buniellousers.noreply.github.com)
- \[**spark helpers**\] sorter function updated to avoid crash (613) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)







🏗 Build

- \[**deps-dev**\] bump dbldatagen from 0.3.5 to 0.4.0 (637) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] bump scikit-learn from 1.4.0 to 1.5.0 (638) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipython from 8.24.0 to 8.25.0 (636) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] bump wandb from 0.16.2 to 0.17.0 (606) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pep8-naming from 0.13.3 to 0.14.1 (616) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] bump typing-extensions from 4.11.0 to 4.12.1 (632) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] use pandas[gcp, parquet] (626) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)

What's Changed


✨ Feature

- \[**airflow**\] include COLOC as a node in the DAG (530) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- check for if no overlapping variants in LD index (594) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- add purity qc metrics to fine-mapping (592) [\Yakov](mailto:yt4sanger.ac.uk)
- lighter dockerfile (585) [\David Ochoa](mailto:ochoaebi.ac.uk)
- github action to upload docker image to registry (588) [\David Ochoa](mailto:ochoaebi.ac.uk)
- functionality added to StudyLocus.find_overlaps() for finding within-study overlaps (587) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- susie_finemapper_one_studylocus_row_v3_dev_ss_gathered (586) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**sumstat qc**\] adding methods for QC of summary statistics (455) [\Yakov](mailto:yt4sanger.ac.uk)
- changing locus window to locus radius to be consistent with other functions (582) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- updating step config file (580) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- dockerise gentropy python package (579) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- adding init to finemapping step (577) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- adding notebook for mapping EFOs for the FinnGen study index (575) [\Yakov](mailto:yt4sanger.ac.uk)
- add benchmarking for fine-mapping using Alzheimer as example (572) [\Yakov](mailto:yt4sanger.ac.uk)
- add FM step with carma and sumstat imputation (568) [\Yakov](mailto:yt4sanger.ac.uk)
- susie_finemapper_ss_gathered() (567) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- the FineMapper function for one locus (564) [\Yakov](mailto:yt4sanger.ac.uk)
- LD index and block matrix extraction for a studyLocus (463) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- add the step class for fine-mapping (554) [\Yakov](mailto:yt4sanger.ac.uk)
- notebook to run qc metrics each release (541) [\xyg123](mailto:33658607+xyg123users.noreply.github.com)
- \[**l2g**\] distance features based on weighted score (545) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**sumstat imputation**\] adding class for sumstat imputation (490) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**coloc**\] single SNP case (511) [\xyg123](mailto:33658607+xyg123users.noreply.github.com)
- extract credible sets and studies from all eQTL Catalogue finemapping results (518) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)


🐛 Fix

- fix python-semantic-release version (again) [\David Ochoa](mailto:dogcaesargmail.com)
- fix python-semantic-release version [\David Ochoa](mailto:dogcaesargmail.com)
- docker action fixes v3 (591) [\David Ochoa](mailto:ochoaebi.ac.uk)
- docker action fixes (590) [\David Ochoa](mailto:ochoaebi.ac.uk)
- docker action fixes (589) [\David Ochoa](mailto:ochoaebi.ac.uk)
- updating config.py argument for finemapper (584) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- minor updates and bug fixes (543) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- update error in config.py (583) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- removing all duplicated variants in sumstats for finemapping functions (574) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- adding deduplication for GWAS in locus (573) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**sumstats**\] correct study id for dir of finngen studies (551) [\Joris Louwen](mailto:62542407+louwenjjrusers.noreply.github.com)
- \[**coloc**\] handle cases when the bayes factors are null (556) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- small fixes in susie defaults (552) [\Yakov](mailto:yt4sanger.ac.uk)
- read function for thurman data to include first line (534) [\Joris Louwen](mailto:62542407+louwenjjrusers.noreply.github.com)
- pin version of commitlint (533) [\Joris Louwen](mailto:62542407+louwenjjrusers.noreply.github.com)
- pr labeller patterns (523) [\David Ochoa](mailto:ochoaebi.ac.uk)




♻️ Refactor

- moving all variant coordinates to GnomAD (566) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)

⚡️ Performance

- \[**l2g**\] optimise extraction of features from colocalisation results (553) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**clump**\] refactored window based clumping (492) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**l2g**\] streamline feature generation (544) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)


✅ Test

- \[**method**\] improved performance in coloc tests (536) [\xyg123](mailto:33658607+xyg123users.noreply.github.com)


🏗 Build

- \[**deps-dev**\] bump mypy from 1.9.0 to 1.10.0 (604) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipython from 8.22.1 to 8.24.0 (603) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] bump typing-extensions from 4.10.0 to 4.11.0 (602) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ruff from 0.3.2 to 0.4.3 (596) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pytest-xdist from 3.5.0 to 3.6.1 (597) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pytest from 8.1.0 to 8.2.0 (598) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump interrogate from 1.5.0 to 1.7.0 (599) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pymdown-extensions from 10.7 to 10.8.1 (600) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump python-semantic-release from 9.1.0 to 9.4.1 (571) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pytest-cov from 4.1.0 to 5.0.0 (560) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pre-commit from 3.6.0 to 3.7.0 (559) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump lxml from 5.1.0 to 5.2.1 (569) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump deptry from 0.14.0 to 0.16.1 (570) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mkdocstrings-python from 1.8.0 to 1.9.0 (549) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump deptry from 0.12.0 to 0.14.0 (548) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mypy from 1.8.0 to 1.9.0 (532) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ruff from 0.2.0 to 0.3.2 (531) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)


👷‍♂️ Ci

- bugfix in PR labeller (537) [\David Ochoa](mailto:ochoaebi.ac.uk)


🚀 Chore

- pre-commit autoupdate (601) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- pre-commit autoupdate (593) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- pre-commit autoupdate (561) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- pre-commit autoupdate (550) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- \[**l2g**\] log annotated gold standards in w&b (546) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- pre-commit autoupdate (539) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- update ruff pre-commit and rules (522) [\David Ochoa](mailto:ochoaebi.ac.uk)
- add sqtl, tuqtl, pqtl features to l2g inclusion list [\Irene López](mailto:irene.lopezsprotonmail.com)
- add tuqtl features to L2Gfeaturematrix schema [\Irene López](mailto:irene.lopezsprotonmail.com)

What's Changed


✨ Feature

- \[**coloc**\] single SNP case (511) [\xyg123](mailto:33658607+xyg123users.noreply.github.com)
- extract credible sets and studies from all eQTL Catalogue finemapping results (518) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**CARMA**\] adding time limited CARMA (475) [\Yakov](mailto:yt4sanger.ac.uk)
- extract credible sets and studies from eQTL Catalogue finemapping results (514) [\Irene López](mailto:45119610+ireneisdoomedusers.noreply.github.com)


🐛 Fix

- pr labeller patterns (523) [\David Ochoa](mailto:ochoaebi.ac.uk)
- pull-request labeler fixes (520) [\David Ochoa](mailto:ochoaebi.ac.uk)







🏗 Build

- \[**deps-dev**\] bump pytest from 8.0.1 to 8.1.0 (516) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mkdocs-git-committers-plugin-2 from 2.2.3 to 2.3.0 (505) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] bump typing-extensions from 4.9.0 to 4.10.0 (506) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipython from 8.21.0 to 8.22.1 [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)


👷‍♂️ Ci

- precommit checks for poetry TOML and lock (526) [\David Ochoa](mailto:ochoaebi.ac.uk)
- pull request template (517) [\David Ochoa](mailto:ochoaebi.ac.uk)
- pull request labeler (519) [\David Ochoa](mailto:ochoaebi.ac.uk)


🚀 Chore

- update ruff pre-commit and rules (522) [\David Ochoa](mailto:ochoaebi.ac.uk)
- Unit tests for coloc (509) [\xyg123](mailto:33658607+xyg123users.noreply.github.com)