Gentropy

What's Changed
* refactor: derive the _schema automatically by project-defiant in https://github.com/opentargets/gentropy/pull/941
* test: improve fixture definition by constraining dataset IDs by ireneisdoomed in https://github.com/opentargets/gentropy/pull/954
* fix: repair SusieFinemapperStep to work with new SL schema and fix lo… by Daniel-Considine in https://github.com/opentargets/gentropy/pull/957
* chore: update poetry to version 2 by ireneisdoomed in https://github.com/opentargets/gentropy/pull/969
* chore: clean documentation page about version engine by project-defiant in https://github.com/opentargets/gentropy/pull/960
* fix: updating info in finngen study index ingestion by Daniel-Considine in https://github.com/opentargets/gentropy/pull/972
* fix(`isProteinCoding`): get all overlapping genes from the variant index by ireneisdoomed in https://github.com/opentargets/gentropy/pull/948
* fix: skip leading 'v' in docker tag by project-defiant in https://github.com/opentargets/gentropy/pull/975
* refactor: remove gene_index step by vivienho in https://github.com/opentargets/gentropy/pull/946
* feat(qtls): flagging trans QTL credible sets by DSuveges in https://github.com/opentargets/gentropy/pull/973
* chore: multiple python version support with latest pyspark and hail by project-defiant in https://github.com/opentargets/gentropy/pull/974
* chore: bump pycln version by project-defiant in https://github.com/opentargets/gentropy/pull/978
* chore: pre-commit autoupdate by pre-commit-ci in https://github.com/opentargets/gentropy/pull/976
* chore: revert pre-commit update (a99ca8490ae6feab2494f9283f49b329d488116b) by ireneisdoomed in https://github.com/opentargets/gentropy/pull/980
* feat(l2gmodel): store features list metadata as instance attribute by ireneisdoomed in https://github.com/opentargets/gentropy/pull/979
* chore: removing symbols from QTL study identifiers by DSuveges in https://github.com/opentargets/gentropy/pull/971
* build(deps): update google-cloud-storage requirement from <2.15.0,>=2.14.0 to >=2.14.0,<3.1.0 by dependabot in https://github.com/opentargets/gentropy/pull/986
* fix: tweak spark session builder to fix type hints by Daniel-Considine in https://github.com/opentargets/gentropy/pull/982
* build(deps): update numpy requirement from <1.27.0,>=1.26.4 to >=1.26.4,<2.3.0 by dependabot in https://github.com/opentargets/gentropy/pull/985
* feat: labels for dataproc in dev mode by project-defiant in https://github.com/opentargets/gentropy/pull/987
* build(deps): update scipy requirement from <1.12.0,>=1.11.4 to >=1.11.4,<1.16.0 by dependabot in https://github.com/opentargets/gentropy/pull/983
* feat: FoldX predicted energies in variant annotation by DSuveges in https://github.com/opentargets/gentropy/pull/947
* fix: foldX normalisation to cover full range by DSuveges in https://github.com/opentargets/gentropy/pull/989
* feat: implement posterior prob filter for COLOC at small overlaps N<10 by xyg123 in https://github.com/opentargets/gentropy/pull/977
* chore: trigger release process by github-actions in https://github.com/opentargets/gentropy/pull/961


**Full Changelog**: https://github.com/opentargets/gentropy/compare/v2.0.1...v2.1.0

What's Changed



🐛 Fix

- release process runs twice [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- release process no longer triggers on skipped release [\project-defiant](mailto:szymonszyszkowskigmail.com)




♻️ Refactor

- drop version_engine (940) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)




🏗 Build

- \[**deps-dev**\] bump ipython from 8.29.0 to 8.30.0 [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump google-cloud-dataproc from 5.8.0 to 5.10.1 (951) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump lxml from 5.1.1 to 5.3.0 (950) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pytest-xdist from 3.5.0 to 3.6.1 (952) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipykernel from 6.28.0 to 6.29.5 (953) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- define dependency version constraints + other fixes (945) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)



🚀 Chore

- siplify the release CI conditions [\project-defiant](mailto:szymonszyszkowskigmail.com)

What's Changed

💥 Breaking

- \[**l2g!**\] implement new training strategy splitting between EFO/gene pairs and with cross validation (938) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**L2GFeatureMatrix!**\] streamline feature matrix management (745) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**Orchestration!**\] drop airflow orchestration layer from gentropy (758) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)


✨ Feature

- adding GERP conservation score to variant annotation (933) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- allow building package from tag (930) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- coalesce l2g fm and predictions (934) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- coalescing the datasets (932) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**gold_standard**\] add traitFromSourceMappedId to schema (924) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- changing studylocus validation to 95 percent credible sets (921) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- reverting to using finngen 95% credible sets (922) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- \[**variant index**\] variant description to summarise variant consequences in transcripts (914) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- redefine neighbourhood features to represent similarity with best metric + other fixes (913) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- gzip evicence output to match existing format (915) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**gold_standard**\] arbitrary gold standards (912) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- changes to PICS credible sets (OUT_OF_SAMPLE_LD QC flag and capital PICS) (910) [\Vivien Ho](mailto:56025826+vivienhousers.noreply.github.com)
- extract pos and chromosome from variantid (909) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- improve partitioning of credible sets (900) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**feature_matrix**\] extract features for gwas associations only (901) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- adding l2g features to prediction table (899) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- \[**feature_matrix**\] impute values for gene attribute cols (895) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- deconvolute studies upon ingestion of GWAS Catalog datasets (887) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- add effect size direction to coloc output (854) [\Tobi Alegbe](mailto:alegbeebi.ac.uk)
- add step to generate association data (888) [\Vivien Ho](mailto:56025826+vivienhousers.noreply.github.com)
- \[**trainer**\] log model explanation with shap (886) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- flag and filter credible sets (879) [\Tobi Alegbe](mailto:alegbeebi.ac.uk)
- flagging duplicated entries while keeping one of the duplicates (876) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- making credset qc have an option to coalsce and deduplicate credible sets without ld pruning (877) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- l2g feature to indicate if gene is protein-coding or not (873) [\xyg123](mailto:33658607+xyg123users.noreply.github.com)
- \[**l2g**\] normalise distance features (878) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**l2g_feature_matrix**\] add `credibleSetConfidence` to L2G (875) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**variant_index**\] hash variants at the time of instance creation (874) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- step to export disease/target evidence (867) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- change betas to posterior mean from susie for Finngen credible sets (872) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- add gene count features to l2g (852) [\xyg123](mailto:33658607+xyg123users.noreply.github.com)
- adding desision tree to fine-mapper (860) [\Yakov](mailto:yt4sanger.ac.uk)
- gwas catalog top-hit + study step (808) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**l2g**\] extend colocalisation neighbourhood metrics to missing genes in the vicinity (851) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**susie_finemapper**\] allow for extraction of the log file from manifest (859) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**l2g**\] limit colocalisation neighbourhood to protein coding genes (847) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**coloc**\] step refactoring (845) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- adding new LD interface (759) [\Yakov](mailto:yt4sanger.ac.uk)
- enhance variant index partitioning (834) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**l2g**\] merge sQTL and tuQTL colocalisation features (824) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- decouple feature generation from L2G training step (823) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- change LD annotation for PICS fine-mapping to use major ancestry (821) [\Vivien Ho](mailto:56025826+vivienhousers.noreply.github.com)
- optimisation of qc step (813) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**l2g**\] implement variant consequence features from VEP (805) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- fix biosample study validation (810) [\Tobi Alegbe](mailto:obba2cam.ac.uk)
- add sumstat QC fields to schema (809) [\Yakov](mailto:yt4sanger.ac.uk)
- adding filtering to susie finemapper (796) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**validation**\] adding credible set confidence annotation at validation time (801) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- force reinstallation of the gentropy on the cluster (804) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- out sample LD qc reason (798) [\David Ochoa](mailto:ochoaebi.ac.uk)
- drop `v2g` and reimplement distance features (771) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- change `StudyLocusId` hashing method to md5 (and change `StudyLocusId` to string type) (783) [\Vivien Ho](mailto:56025826+vivienhousers.noreply.github.com)
- flag credible sets explained by SuSiE regions (780) [\David Ochoa](mailto:ochoaebi.ac.uk)
- 99% credible set validation during `study_locus_validation` (765) [\David Ochoa](mailto:ochoaebi.ac.uk)
- add biosample index (769) [\Tobi Alegbe](mailto:obba2cam.ac.uk)
- adding window based clumping to StudyLocus (779) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- add `studyType` to `StudyLocus` and `Colocalisation` (and `StudyLocusOverlap`) (782) [\Vivien Ho](mailto:56025826+vivienhousers.noreply.github.com)
- \[**dataproc**\] ability to version gentropy for dataproc cluster (774) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- flag PICS top hits in studies with credset sumstats (777) [\David Ochoa](mailto:ochoaebi.ac.uk)
- flag all top-hits from GWAS catalog curation (775) [\David Ochoa](mailto:ochoaebi.ac.uk)
- flag MHC credible sets based on lead (767) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**validation**\] adding credible set variant validation (757) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- ingest FinnGen UKB meta-analysis data (756) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)
- adding finemapping method to studylocusid hash (744) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- \[**variant index**\] improved data structure (710) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- logic and airflow pipeline for validation (730) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- Finngen r11 ingestion (733) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**variant_index**\] changes for a successful run (735) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- notebook for locus breaker and susie finemapping benchmark (717) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- expose summary statistics qc and locus breaker steps to hydra cli (716) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)


🐛 Fix

- \[**l2g_predictions**\] annotate based on list of features + filter out missing annotation (925) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- swap the ref parse (935) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- r2 for lead variant is always 1 (919) [\Yakov](mailto:yt4sanger.ac.uk)
- using the 99% PIP cs column, (904) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- reclassify eqtl catalogue sc datasets (894) [\Tobi Alegbe](mailto:alegbeebi.ac.uk)
- do not impute `isProteinCoding` (902) [\Yakov](mailto:yt4sanger.ac.uk)
- ensure the CHROM is not quoted (896) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**`credibleSetConfidence`**\] inner join between study locus and variant index to avoid null genes (890) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- revert distinct for associations input file (871) [\Vivien Ho](mailto:56025826+vivienhousers.noreply.github.com)
- \[**distance_features**\] correct mean distance equation and correct rows with negative values (889) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- fix in calculate_credible_set_log10bf (868) [\Yakov](mailto:yt4sanger.ac.uk)
- logging of finemamper (870) [\Yakov](mailto:yt4sanger.ac.uk)
- add scQTLs into coloc features (833) [\Yakov](mailto:yt4sanger.ac.uk)
- biosample index add efo cell types (853) [\Tobi Alegbe](mailto:obba2cam.ac.uk)
- adding beta for lead variant (863) [\Yakov](mailto:yt4sanger.ac.uk)
- susie credible sets with unknown confidence (862) [\David Ochoa](mailto:ochoaebi.ac.uk)
- filter nan in CSs (855) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**eqtl**\] deduplicating credible set loci (849) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- updating the susie_finemapper init (846) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- l2g fixes (844) [\David Ochoa](mailto:ochoaebi.ac.uk)
- fix ukbppp studindex (839) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**l2g**\] remove custom session params + other fixes (841) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**trainer**\] drop `studyLocusId` from training sets (837) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- \[**find_overlap**\] missing right study type in output (828) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- adding single point statistics to pics loci (832) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- write mode added to validation steps (826) [\David Ochoa](mailto:ochoaebi.ac.uk)
- empty inSilicoPredictors object in GnomAD variant index (807) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- mhc flag incorrect (825) [\David Ochoa](mailto:ochoaebi.ac.uk)
- biosample id duplication (822) [\Tobi Alegbe](mailto:obba2cam.ac.uk)
- adding studId to FM log (816) [\Yakov](mailto:yt4sanger.ac.uk)
- fix of type error in schema checking (817) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**validation**\] add `qualityControls` column if missing in StudyLocus dataset when perfroming validation (814) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- align the schema of study_index for ukb ppp eur (803) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- adding data specific p-value filters (788) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**schema**\] recursive validation of arbitrarily deep nested structure (790) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- fix bag in neglog_pvalue_to_mantissa_and_exponent (795) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**safe_array_union**\] allow for sorting nested structs (793) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- remove study_index_path from coloc step (791) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**vep_parser**\] use nested schema for insilico predictors (789) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- clean unused study_locus step parameter (786) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**finngen_study_index**\] improved tests for finngen study index (776) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- remove n_eff check from qc_step (785) [\Yakov](mailto:yt4sanger.ac.uk)
- small qc flag fixes (784) [\Yakov](mailto:yt4sanger.ac.uk)
- \[**ld clumping**\] a revised logic allows a more accurate clumping (772) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- \[**effect harmonisation**\] addressing beta harmonisation bug (762) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- add condition to eQTL study index and schema (770) [\Vivien Ho](mailto:56025826+vivienhousers.noreply.github.com)
- prevent multiple credible filters to override spark plan (766) [\David Ochoa](mailto:ochoaebi.ac.uk)
- multiple fixes after debugging and test runs (760) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)
- removing old functions (752) [\Yakov](mailto:yt4sanger.ac.uk)
- validation name mapping (753) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**finngen_r11**\] preserve all studyIds (747) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- remove finngen prefix from credible set (746) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- adding carma_tau parameter to susie_finemapper (743) [\Yakov](mailto:yt4sanger.ac.uk)
- using h4 instead of log2(h4/h3) (740) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- revert recursiveFileLookup to False (738) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- update cluster creation command (739) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- updating config paths and fine-mapping methods (725) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)
- change config params to match new name (721) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)


📖 Documentation

- fix broken refs (768) [\David Ochoa](mailto:ochoaebi.ac.uk)
- macos fix for some functions (729) [\Daniel-Considine](mailto:113430683+Daniel-Considineusers.noreply.github.com)



♻️ Refactor

- finemapping method enum (897) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**convert to vcf**\] allow multiple input sources (891) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- \[**vep_parser**\] store consequence to impact score as a project config (811) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- generalise the harmonisation pipeline (755) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)
- generalise per-chromosome processing (754) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)


⚡️ Performance

- quickly build a Docker image for every branch (773) [\Kirill Tsukanov](mailto:tskirusers.noreply.github.com)


✅ Test

- skip `fetch_coordinates_from_rsids` (850) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)


🏗 Build

- \[**deps-dev**\] bump ruff from 0.7.1 to 0.8.1 (936) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipython from 8.29.0 to 8.30.0 (937) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pytest-cov from 5.0.0 to 6.0.0 (893) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mypy from 1.12.1 to 1.13.0 (884) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipython from 8.28.0 to 8.29.0 (883) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ruff from 0.6.1 to 0.7.0 (864) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mypy from 1.11.0 to 1.12.1 (865) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mkdocstrings-python from 1.11.1 to 1.12.1 (842) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pyparsing from 3.1.2 to 3.2.0 (836) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mkdocs-git-committers-plugin-2 from 2.3.0 to 2.4.1 (818) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pymdown-extensions from 10.10.1 to 10.11.2 (815) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pre-commit from 3.8.0 to 4.0.0 (820) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipython from 8.27.0 to 8.28.0 (819) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- updated precommits including adjustments to docstrings (787) [\David Ochoa](mailto:ochoaebi.ac.uk)
- \[**deps-dev**\] bump pymdown-extensions from 10.9 to 10.10.1 (781) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps**\] bump wandb from 0.17.2 to 0.18.0 (763) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump mkdocstrings-python from 1.10.5 to 1.11.1 (749) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump deptry from 0.19.1 to 0.20.0 (742) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ipython from 8.26.0 to 8.27.0 (741) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pre-commit from 3.7.1 to 3.8.0 (719) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump lxml from 5.2.2 to 5.3.0 (727) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump deptry from 0.18.0 to 0.19.1 (728) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump ruff from 0.5.1 to 0.6.1 (732) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump deptry from 0.17.0 to 0.18.0 (723) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- \[**deps-dev**\] bump pymdown-extensions from 10.8.1 to 10.9 (720) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)


👷‍♂️ Ci

- configure java v8 (840) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)


🚀 Chore

- \[**vep**\] Ensembl version update (931) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- \[**gnomad**\] updating GnomAD version to 4.1 from 4.0 + using joint frequencies (929) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- pre-commit autoupdate (918) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- pre-commit autoupdate (898) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- \[**deps**\] bump codecov/codecov-action from 4 to 5 (916) [\dependabot[bot]](mailto:49699333+dependabot[bot]users.noreply.github.com)
- validate chromosome (906) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- \[**l2g**\] parametrise score threshold when writing predictions (907) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- add `hf_model_commit_message` to `LocusToGeneStep` (905) [\Irene López Santiago](mailto:45119610+ireneisdoomedusers.noreply.github.com)
- pre-commit autoupdate (885) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- add chromosome validation (869) [\Yakov](mailto:yt4sanger.ac.uk)
- pre-commit autoupdate (866) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- \[**coloc**\] changing the content of `numberColocalisingVariants` field (857) [\Daniel Suveges](mailto:daniel.suvegesprotonmail.com)
- adding logging even when no CS in locus (848) [\Yakov](mailto:yt4sanger.ac.uk)
- remove h4/h3 ratio (829) [\Yakov](mailto:yt4sanger.ac.uk)
- adding priors to coloc step (830) [\Yakov](mailto:yt4sanger.ac.uk)
- make the lb clumping ingest the partitionned data (806) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- drop redundant parameter (802) [\Szymon Szyszkowski](mailto:69353402+project-defiantusers.noreply.github.com)
- pre-commit autoupdate (724) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)
- pre-commit autoupdate (715) [\pre-commit-ci[bot]](mailto:66853113+pre-commit-ci[bot]users.noreply.github.com)

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)