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chore: trigger release process#858

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project-defiant merged 188 commits intomainopentargets/gentropy:mainfrom devopentargets/gentropy:devCopy head branch name to clipboardDec 10, 2024

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Commits on Jul 25, 2024

• feat: expose summary statistics qc and locus breaker steps to hydra cli (#716)

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Commits on Jul 29, 2024

• fix: change config params to match new name (#721)

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Commits on Jul 30, 2024

• chore: pre-commit autoupdate (#715)

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Commits on Jul 31, 2024

• build(deps-dev): bump pymdown-extensions from 10.8.1 to 10.9 (#720)

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Commits on Aug 8, 2024

• build(deps-dev): bump deptry from 0.17.0 to 0.18.0 (#723)

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• feat: notebook for locus breaker and susie finemapping benchmark (#717)

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• fix: updating config paths and fine-mapping methods (#725)

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Commits on Aug 15, 2024

• docs: macos fix for some functions (#729)

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Commits on Aug 22, 2024

• build(deps-dev): bump ruff from 0.5.1 to 0.6.1 (#732)

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• chore: pre-commit autoupdate (#724)

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• build(deps-dev): bump deptry from 0.18.0 to 0.19.1 (#728)

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Commits on Aug 23, 2024

• build(deps-dev): bump lxml from 5.2.2 to 5.3.0 (#727)

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• build(deps-dev): bump pre-commit from 3.7.1 to 3.8.0 (#719)

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Commits on Aug 27, 2024

• feat(variant_index): changes for a successful run (#735)

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Commits on Aug 28, 2024

• fix: update cluster creation command (#739)

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• fix: revert recursiveFileLookup to False (#738)

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Commits on Aug 29, 2024

• feat: Finngen r11 ingestion (#733)

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Commits on Aug 30, 2024

• fix: using h4 instead of log2(h4/h3) (#740)

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Commits on Sep 3, 2024

• fix: adding carma_tau parameter to susie_finemapper (#743)

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• feat: logic and airflow pipeline for validation (#730)

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• feat(variant index): improved data structure (#710)

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• fix: remove finngen prefix from credible set (#746)

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Commits on Sep 4, 2024

• fix(finngen_r11): preserve all studyIds (#747)

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Commits on Sep 9, 2024

• feat: adding finemapping method to studylocusid hash (#744)

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• build(deps-dev): bump ipython from 8.26.0 to 8.27.0 (#741)

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Commits on Sep 10, 2024

• build(deps-dev): bump deptry from 0.19.1 to 0.20.0 (#742)

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• fix: validation name mapping (#753)

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Commits on Sep 11, 2024

• fix: removing old functions (#752)

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• refactor: generalise per-chromosome processing (#754)

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• refactor: generalise the harmonisation pipeline (#755)

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• feat: ingest FinnGen UKB meta-analysis data (#756)

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Commits on Sep 12, 2024

• feat(validation): adding credible set variant validation (#757)

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• feat: drop airflow orchestration layer from gentropy (#758)

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Commits on Sep 13, 2024

• fix: multiple fixes after debugging and test runs (#760)

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• build(deps-dev): bump mkdocstrings-python from 1.10.5 to 1.11.1 (#749)

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Commits on Sep 17, 2024

• build(deps): bump wandb from 0.17.2 to 0.18.0 (#763)

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• fix: prevent multiple credible filters to override spark plan (#766)

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Commits on Sep 18, 2024

• feat: flag MHC credible sets based on lead (#767)

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• fix: add condition to eQTL study index and schema (#770)

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• fix(effect harmonisation): addressing beta harmonisation bug (#762)

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Commits on Sep 19, 2024

• perf: quickly build a Docker image for every branch (#773)

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Commits on Sep 20, 2024

• feat: flag all top-hits from GWAS catalog curation (#775)

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• docs: fix broken refs (#768)

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• feat: flag PICS top hits in studies with credset sumstats (#777)

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Commits on Sep 23, 2024

• fix(ld clumping): a revised logic allows a more accurate clumping (#772)

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• refactor(L2GFeatureMatrix)!: streamline feature matrix management (#745)

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• feat(dataproc): ability to version gentropy for dataproc cluster (#774)

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Commits on Sep 24, 2024

• feat: add studyType to StudyLocus and Colocalisation (and StudyLocusOverlap) (#782)

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• feat: adding window based clumping to StudyLocus (#779)

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• fix: small qc flag fixes (#784)

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• feat: add biosample index (#769)

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• feat: 99% credible set validation during study_locus_validation (#765)

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• feat: flag credible sets explained by SuSiE regions (#780)

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• fix: remove n_eff check from qc_step (#785)

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• build(deps-dev): bump pymdown-extensions from 10.9 to 10.10.1 (#781)

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• build: updated precommits including adjustments to docstrings (#787)

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• fix(finngen_study_index): improved tests for finngen study index (#776)

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Commits on Sep 25, 2024

• fix: clean unused study_locus step parameter (#786)

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Commits on Sep 26, 2024

• fix(vep_parser): use nested schema for insilico predictors (#789)

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• fix: remove study_index_path from coloc step (#791)

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Commits on Sep 27, 2024

• fix(safe_array_union): allow for sorting nested structs (#793)

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• fix: fix bag in neglog_pvalue_to_mantissa_and_exponent (#795)

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Commits on Sep 30, 2024

• fix(schema): recursive validation of arbitrarily deep nested structure (#790)

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• fix: adding data specific p-value filters (#788)

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• feat: change StudyLocusId hashing method to md5 (and change StudyLocusId to string type) (#783)

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Commits on Oct 1, 2024

• feat: drop v2g and reimplement distance features (#771)

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• feat: out sample LD qc reason (#798)

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• chore: drop redundant parameter (#802)

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• fix: align the schema of study_index for ukb ppp eur (#803)

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• feat: force reinstallation of the gentropy on the cluster (#804)

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• feat(validation): adding credible set confidence annotation at validation time (#801)

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Commits on Oct 2, 2024

• chore: make the lb clumping ingest the partitionned data (#806)

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• feat: adding filtering to susie finemapper (#796)

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• feat: add sumstat QC fields to schema (#809)

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Commits on Oct 3, 2024

• feat: fix biosample study validation (#810)

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• refactor(vep_parser): store consequence to impact score as a project config (#811)

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• feat(l2g): implement variant consequence features from VEP (#805)

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• feat: optimisation of qc step (#813)

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Commits on Oct 4, 2024

• fix(validation): add qualityControls column if missing in StudyLocus dataset when perfroming validation (#814)

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• fix: fix of type error in schema checking (#817)

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• fix: adding studId to FM log (#816)

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Commits on Oct 7, 2024

• fix: biosample id duplication (#822)

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Commits on Oct 8, 2024

• feat: change LD annotation for PICS fine-mapping to use major ancestry (#821)

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• build(deps-dev): bump ipython from 8.27.0 to 8.28.0 (#819)

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Commits on Oct 9, 2024

• build(deps-dev): bump pre-commit from 3.8.0 to 4.0.0 (#820)

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• feat: decouple feature generation from L2G training step (#823)

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• fix: mhc flag incorrect (#825)

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Commits on Oct 10, 2024

• revert: no longer rescuing variants not in LD matrix when overlapping with SuSiE (#827)

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• fix: empty inSilicoPredictors object in GnomAD variant index (#807)

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Commits on Oct 11, 2024

• fix: write mode added to validation steps (#826)

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• feat(l2g): merge sQTL and tuQTL colocalisation features (#824)

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• fix: adding single point statistics to pics loci (#832)

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• fix(find_overlap): missing right study type in output (#828)

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Commits on Oct 12, 2024

• feat: enhance variant index partitioning (#834)

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Commits on Oct 14, 2024

• feat: adding new LD interface (#759)

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• ci: configure java v8 (#840)

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• fix(trainer): drop studyLocusId from training sets (#837)

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• fix(l2g): remove custom session params + other fixes (#841)

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• build(deps-dev): bump pymdown-extensions from 10.10.1 to 10.11.2 (#815)

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• build(deps-dev): bump mkdocs-git-committers-plugin-2 from 2.3.0 to 2.4.1 (#818)

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• build(deps-dev): bump pyparsing from 3.1.2 to 3.2.0 (#836)

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• build(deps-dev): bump mkdocstrings-python from 1.11.1 to 1.12.1 (#842)

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Commits on Oct 15, 2024

• chore: adding priors to coloc step (#830)

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• fix: fix ukbppp studindex (#839)

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• fix: l2g fixes (#844)

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• chore: remove h4/h3 ratio (#829)

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Commits on Oct 16, 2024

• fix: updating the susie_finemapper init (#846)

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Commits on Oct 17, 2024

• feat(coloc): step refactoring (#845)

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• test: skip fetch_coordinates_from_rsids (#850)

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• fix(eqtl): deduplicating credible set loci (#849)

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• chore: adding logging even when no CS in locus (#848)

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• feat(l2g): limit colocalisation neighbourhood to protein coding genes (#847)

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• fix: filter nan in CSs (#855)

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• revert(finngen): restore the studyId prefix in finngen cs and si (#856)

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Commits on Oct 18, 2024

• feat(susie_finemapper): allow for extraction of the log file from manifest (#859)

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• chore(coloc): changing the content of numberColocalisingVariants field (#857)

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• fix: susie credible sets with unknown confidence (#862)

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Commits on Oct 21, 2024

• fix: adding beta for lead variant (#863)

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• fix: biosample index add efo cell types (#853)

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• feat(l2g): extend colocalisation neighbourhood metrics to missing genes in the vicinity (#851)

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Commits on Oct 22, 2024

• fix: add scQTLs into coloc features (#833)

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• chore: pre-commit autoupdate (#866)

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• feat: gwas catalog top-hit + study step (#808)

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  5 peopleauthored
  df220e9

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• build(deps-dev): bump mypy from 1.11.0 to 1.12.1 (#865)

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• feat: adding desision tree to fine-mapper (#860)

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  addramir

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  project-defiant

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• build(deps-dev): bump ruff from 0.6.1 to 0.7.0 (#864)

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Commits on Oct 23, 2024

• fix: logging of finemamper (#870)

  addramir

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• chore: add chromosome validation (#869)

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  addramir

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  DSuveges

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Commits on Oct 24, 2024

• feat: add gene count features to l2g (#852)

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  8 peopleauthored
  9fe77ca

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• feat: change betas to posterior mean from susie for Finngen credible sets (#872)

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  Daniel-Considine

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• feat: step to export disease/target evidence (#867)

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  DSuveges

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  pre-commit-ci[bot]

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• feat(variant_index): hash variants at the time of instance creation (#874)

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  ireneisdoomed

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• fix: fix in calculate_credible_set_log10bf (#868)

  addramir

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Commits on Oct 25, 2024

• feat(l2g_feature_matrix): add credibleSetConfidence to L2G (#875)

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  ireneisdoomed

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• feat(l2g): normalise distance features (#878)

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• feat: l2g feature to indicate if gene is protein-coding or not (#873)

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• feat: making credset qc have an option to coalsce and deduplicate credible sets without ld pruning (#877)

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  4 peopleauthored
  85be796

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• test(study_locus) credible_set_qc step integration test (#880)

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  project-defiant

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  Szymon Szyszkowski

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  5d9d7cb

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Commits on Oct 26, 2024

• feat: flagging duplicated entries while keeping one of the duplicates (#876)

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  DSuveges

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Commits on Oct 28, 2024

• feat: flag and filter credible sets (#879)

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• build(deps-dev): bump ipython from 8.28.0 to 8.29.0 (#883)

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• build(deps-dev): bump mypy from 1.12.1 to 1.13.0 (#884)

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Commits on Oct 31, 2024

• feat(trainer): log model explanation with shap (#886)

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  ireneisdoomed

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• chore: pre-commit autoupdate (#885)

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• fix(distance_features): correct mean distance equation and correct rows with negative values (#889)

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  ireneisdoomed

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Commits on Nov 1, 2024

• feat: add step to generate association data (#888)

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  vivienho

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  b812f67

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• fix: revert distinct for associations input file (#871)

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  vivienho

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  DSuveges

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• feat: add effect size direction to coloc output (#854)

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  Tobi1kenobi

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  DSuveges

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  9295d58

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Commits on Nov 4, 2024

• refactor(convert to vcf): allow multiple input sources (#891)

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  project-defiant

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  Szymon Szyszkowski

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  9237d73

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• feat: deconvolute studies upon ingestion of GWAS Catalog datasets (#887)

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  DSuveges

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  e0304fc

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• fix(credibleSetConfidence): inner join between study locus and variant index to avoid null genes (#890)

  ireneisdoomed

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  3639b23

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Commits on Nov 5, 2024

• feat(feature_matrix): impute values for gene attribute cols (#895)

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  ireneisdoomed

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  04b1e22

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• feat: adding l2g features to prediction table (#899)

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  DSuveges

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• fix: ensure the #CHROM is not quoted (#896)

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  3 peopleauthored
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• feat(feature_matrix): extract features for gwas associations only (#901)

  ireneisdoomed

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• fix: do not impute isProteinCoding (#902)

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  addramir

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Commits on Nov 6, 2024

• fix: reclassify eqtl catalogue sc datasets (#894)

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  Tobi1kenobi

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• feat: improve partitioning of credible sets (#900)

  d0choa

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Commits on Nov 7, 2024

• fix: using the 99% PIP cs column, (#904)

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  Daniel-Considine

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• chore: add hf_model_commit_message to LocusToGeneStep (#905)

  ireneisdoomed

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Commits on Nov 8, 2024

• refactor: finemapping method enum (#897)

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Commits on Nov 11, 2024

• chore(l2g): parametrise score threshold when writing predictions (#907)

  ireneisdoomed

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  0e7e815

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• chore: validate chromosome (#906)

  DSuveges

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• feat: extract pos and chromosome from variantid (#909)

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  project-defiant

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  Szymon Szyszkowski

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  10b4be0

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Commits on Nov 12, 2024

• feat: changes to PICS credible sets (OUT_OF_SAMPLE_LD QC flag and capital PICS) (#910)

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  e5b3c9e

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Commits on Nov 14, 2024

• feat(gold_standard): arbitrary gold standards (#912)

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  project-defiant

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  Szymon Szyszkowski

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  253fe31

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Commits on Nov 15, 2024

• feat: gzip evicence output to match existing format (#915)

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  project-defiant

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  Szymon Szyszkowski

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  c46480b

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• feat: redefine neighbourhood features to represent similarity with best metric + other fixes (#913)

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  ireneisdoomed

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  40ca215

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Commits on Nov 18, 2024

• chore(deps): bump codecov/codecov-action from 4 to 5 (#916)

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• build(deps-dev): bump pytest-cov from 5.0.0 to 6.0.0 (#893)

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• chore: pre-commit autoupdate (#898)

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Commits on Nov 19, 2024

• feat(variant index): variant description to summarise variant consequences in transcripts (#914)

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  DSuveges

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Commits on Nov 20, 2024

• fix: r2 for lead variant is always 1 (#919)

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  addramir

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  a858662

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Commits on Nov 21, 2024

• feat: reverting to using finngen 95% credible sets (#922)

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  Daniel-Considine

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  b6303d5

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• feat: changing studylocus validation to 95 percent credible sets (#921)

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  Daniel-Considine

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  05e47a3

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Commits on Nov 22, 2024

• chore: pre-commit autoupdate (#918)

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Commits on Nov 26, 2024

• chore(gnomad): updating GnomAD version to 4.1 from 4.0 + using joint frequencies (#929)

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  DSuveges

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  008aa38

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Commits on Nov 27, 2024

• feat(gold_standard): add traitFromSourceMappedId to schema (#924)

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  ireneisdoomed

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  4837a4b

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• feat: coalescing the datasets (#932)

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  project-defiant

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  Szymon Szyszkowski

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  7b3bfad

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• chore(vep): Ensembl version update (#931)

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  DSuveges

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  project-defiant

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• feat: coalesce l2g fm and predictions (#934)

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  project-defiant

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  Szymon Szyszkowski

  authored
  9a9fb7b

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• feat: allow building package from tag (#930)

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  project-defiant

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  Szymon Szyszkowski

  authored
  8595e5b

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• feat: adding GERP conservation score to variant annotation (#933)

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  DSuveges

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  project-defiant

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  19219dd

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Commits on Nov 28, 2024

• fix: swap the ref parse (#935)

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  project-defiant

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  Szymon Szyszkowski

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  ff35db4

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Commits on Dec 3, 2024

• build(deps-dev): bump ipython from 8.29.0 to 8.30.0 (#937)

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• build(deps-dev): bump ruff from 0.7.1 to 0.8.1 (#936)

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Commits on Dec 5, 2024

• fix(l2g_predictions): annotate based on list of features + filter out missing annotation (#925)

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  ireneisdoomed

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Commits on Dec 9, 2024

• feat(l2g)!: implement new training strategy splitting between EFO/gene pairs and with cross validation (#938)

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