What's Changed

• fix: ensure Omegaconf list can be passed to deprecated_project_ids by @project-defiant in #1177
• chore: trigger release process by @github-actions[bot] in #1179

Full Changelog: v3.1.0...v3.1.1

What's Changed

What's Changed

• Add part of to biosample index relationships by @Tobi1kenobi in #1164
• feat(step): allow for deprecating project during study validation by @project-defiant in #1173
• fix: fixing the docstring in _harmonise_beta by @Daniel-Considine in #1175
• chore: trigger release process by @github-actions[bot] in #1176

Full Changelog: v3.0.0...v3.1.0

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

What's Changed

📖 Documentation

• fix typo @Szymon Szyszkowski
• update release badge and xgboost instructions @project-defiant

What's Changed

What's Changed

• improve join conditions and better hash function by @mkarmona in #1
• Do_lintchanges by @d0choa in #3
• Do black action by @d0choa in #2
• pre-commit replaces GitHub actions for all code quality checks by @d0choa in #6
• Managing build and dependencies using poetry + makefile by @d0choa in #4
• generalising project by @d0choa in #7
• Do setupenvironment by @d0choa in #8
• feat: Adding parsers for intervals dataset. by @DSuveges in #9
• The main interval script is added to the repo by @DSuveges in #10
• feat: modular hydra configs and other enhancements by @d0choa in #12
• Variant annot by @DSuveges in #13
• GWAS Catalog Association Ingest by @DSuveges in #14
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #17
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #18
• Intervals from target by @d0choa in #20
• Support to ensure schemas by @d0choa in #21
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #22
• Adding more stuff to GWAS Catalog ingest by @DSuveges in #15
• docs: schema functions description by @d0choa in #23
• feat: docs support by @d0choa in #25
• Do docs by @d0choa in #27
• Ingesting GWAS Catalog study table by @DSuveges in #26
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #28
• Support for doctests implemented by @d0choa in #29
• feat: codecov integration by @d0choa in #30
• feat: token added to codecov by @d0choa in #31
• feat: ipython support by @d0choa in #32
• Fixing bug in pvalue -> z-score calculation by @DSuveges in #34
• Modification of the variant annotation schema by @ireneisdoomed in #24
• Do_removepandas by @d0choa in #37
• pvalue to zscore refactor by @d0choa in #35
• docs: removing old docs by @d0choa in #36
• Adding variant pipeline docs by @DSuveges in #38
• Add variant index generation module by @ireneisdoomed in #33
• codecov coverage target by @d0choa in #39
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #40
• Amend and separate the script for dependency installation by @tskir in #47
• Minor improvements to the variant datasets generation by @ireneisdoomed in #45
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #42
• Add gnomad3VariantId to variant annotation schema by @ireneisdoomed in #48
• feat: plugin not to automatically handle required pages by @d0choa in #50
• feat: ignore docstrings from private functions in documentation by @d0choa in #51
• Extract V2G evidence from functional predictions by @ireneisdoomed in #41
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #52
• Reorganisation of the coloc logic by @ireneisdoomed in #53
• Update package to Python 3.8.15 by @ireneisdoomed in #55
• Update the coloc pipeline to the newer credible sets and study datasets by @ireneisdoomed in #54
• Integrate eCAVIAR colocalization by @ireneisdoomed in #58
• Do pics by @DSuveges in #57
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #56
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #63
• Extract V2G evidence from a variant distance to a gene TSS by @ireneisdoomed in #46
• Clumping refactor by @DSuveges in #64
• Summary statistics dataset by @DSuveges in #68
• Do hydra by @d0choa in #66
• Validate schemas overlooking the nullability fields by @ireneisdoomed in #71
• test: is in credset function by @d0choa in #72
• Test session streamline by @d0choa in #75
• Do va slim by @d0choa in #73
• Improved validation of nested structures by @ireneisdoomed in #76
• Redefinition of credible set annotation by @ireneisdoomed in #77
• FinnGen ingestion by @tskir in #59
• docs: missing docs for finngen step added by @d0choa in #80
• Implement version aware code deployment by @tskir in #82
• docs: update documentation by @buniello in #84
• Update roadmap.md by @buniello in #85
• Debugging GWAS Catalog pipeline by @ireneisdoomed in #83
• Python and Spark upgrade + fixes in fine mapping by @ireneisdoomed in #79
• Create a contributing checklist for the genetics repository by @tskir in #87
• Update roadmap.md by @buniello in #89
• Update roadmap.md by @buniello in #90
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #91
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #93
• UKBiobank ingestion by @hlnicholls in #86
• feat: add create-dev-cluster rule to makefile by @ireneisdoomed in #94
• Fix GWASCatalog data issues by @ireneisdoomed in #92
• Migrate to FinnGen R9 by @tskir in #88
• Amend and reorganise troubleshooting section by @tskir in #96
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #95
• chore: suggestions on structure by @d0choa in #99
• fix: stacking avatars in docs by @d0choa in #98
• feat: fix ldclumping, tests, and docs by @ireneisdoomed in #101
• fix: pValueMantissa as float in summary stats by @d0choa in #100
• fix: avoid empty credible set (#3016) by @ireneisdoomed in #102
• feat: add get_study_locus_id by @ireneisdoomed in #103
• Add test__finemap by @ireneisdoomed in #104
• Finding loci via a distance based clumping by @DSuveges in #97
• Remove ambiguous variants from LDIndex by @ireneisdoomed in #105
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #107
• refactor: some minor issues sorted out around summary statistics by @DSuveges in #106
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #111
• Fixes to the annotate_ld function by @ireneisdoomed in #108
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #114
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #116
• Small new features for Dataset by @ireneisdoomed in #117
• [pre-commit.ci] pre-commit autoupdate by @pre-commi...

What's Changed

• fix: addressing #3800 and #3799 by @DSuveges in #1017
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1018
• Fix: Ensure qualityControls and analysisFlags columns are always added when curation_table is None by @ffrnz in #1020
• refactor(l2g): make wandb logging optional by @ireneisdoomed in #1019
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1022
• chore: offline check uv lock by @project-defiant in #1024
• chore: skip uv-lock on pre-commit ci by @project-defiant in #1027
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1028
• build(deps): update shap requirement by @dependabot[bot] in #1016
• feat: (coloc) parameterise the small overlaps filtering criteria so they can be specified in orchestration by @Daniel-Considine in #1030
• feat: slimmer docker image by @ffrnz in #1023
• chore(deps): bump actions/create-github-app-token from 1 to 2 by @dependabot[bot] in #1033
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1031
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1036
• fix: remove trans molQTLs from FM by @addramir in #1038
• docs: remove roadmap section by @d0choa in #1042
• chore(VEP): Update Ensembl to 144 by @DSuveges in #1043
• refactor(summary_statistics_qc): Summary Statistics QC dataset by @project-defiant in #1040
• fix: correction of the code for calculating log10BF for credible sets by @Daniel-Considine in #1041
• fix: ensure the coloc method name is not added to the output by @project-defiant in #1044
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1037
• chore(deps): bump astral-sh/setup-uv from 5 to 6 by @dependabot[bot] in #1035
• chore: remove vep image and artifact build by @project-defiant in #1045
• fix: fix isProteincoding by @addramir in #1046
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #1047
• fix(changelog): ensure the changelog template is reused by @project-defiant in #1048
• fix(l2g): half of the feature matrix have distance features larger than 1 by @ireneisdoomed in #1053
• feat: pass partition number to the step by @project-defiant in #1054
• feat(sumstat): rescue standard error from p-value and beta by @project-defiant in #1059
• feat: standard error from ci by @project-defiant in #1061
• fix: spark plan optimisation by @DSuveges in #1055
• fix: neglog func fix by @addramir in #1062
• chore: adding pubmed identifier to evidence by @DSuveges in #1068
• fix: adding rsids to GnomAD variants by @DSuveges in #1060
• feat: adding pmid to finngen studies by @DSuveges in #1069
• chore: trigger release process by @github-actions[bot] in #1021

New Contributors

• @ffrnz made their first contribution in #1020

Full Changelog: v2.2.0...v2.3.0

What's Changed

• fix(study_locus_valiation): ensure the transQtlColumn is overwritten when reading from parquet @project-defiant in #990
• feat: new Loss-of-Function variant data from OTAR2075 by @vivienho in #991
• chore(docs): update _ukb_ppp_eur.md by @buniello in #995
• fix(dataset): filter maintains instance attributes by @ireneisdoomed in #996
• feat(l2gprediction): add score explanation based on features by @ireneisdoomed in #939
• build(deps): update google-cloud-secret-manager requirement from <2.13.0,>=2.12.6 to >=2.12.6,<2.24.0 by @dependabot in #994
• chore: pre-commit autoupdate by @pre-commit-ci in #988
• fix(l2g): direct model path to hf repo when none and align training data filename by @ireneisdoomed in #997
• chore(shap): sample background dataset to make explanation faster by @ireneisdoomed in #998
• feat: local dataproc cluster settings udpate by @project-defiant in #999
• fix: dev release process by @project-defiant in #992
• fix: foldx column name fix by @DSuveges in #1005
• chore(trainer): sample train set to base model importances on by @ireneisdoomed in #1001
• fix: solve NULLs found in variantEffect struct of the variant index by @vivienho in #1003
• fix: qemu libc segfault during docker build action by @project-defiant in #1004
• fix: change posterior filter by @xyg123 in #1006
• chore: pre-commit autoupdate by @pre-commit-ci in #1002
• chore(deps): bump docker/setup-qemu-action from 3.4.0 to 3.6.0 by @dependabot in #1011
• chore(deps): bump python-semantic-release/publish-action from 9.19.1 to 9.21.0 by @dependabot in #1010
• build(deps): update google-cloud-storage requirement from <3.1.0,>=2.14.0 to >=2.14.0,<3.2.0 by @dependabot in #1009
• chore(l2g): make shap optional by @ireneisdoomed in #1012
• feat(l2g): update params after fine tuning for the new training data by @ireneisdoomed in #1014
• feat(l2g): download specific model version from hub by @ireneisdoomed in #1015
• chore: trigger release process by @github-actions in #993

Full Changelog: v2.1.0...v2.2.0

What's Changed

• refactor: derive the _schema automatically by @project-defiant in #941
• test: improve fixture definition by constraining dataset IDs by @ireneisdoomed in #954
• fix: repair SusieFinemapperStep to work with new SL schema and fix lo… by @Daniel-Considine in #957
• chore: update poetry to version 2 by @ireneisdoomed in #969
• chore: clean documentation page about version engine by @project-defiant in #960
• fix: updating info in finngen study index ingestion by @Daniel-Considine in #972
• fix(isProteinCoding): get all overlapping genes from the variant index by @ireneisdoomed in #948
• fix: skip leading 'v' in docker tag by @project-defiant in #975
• refactor: remove gene_index step by @vivienho in #946
• feat(qtls): flagging trans QTL credible sets by @DSuveges in #973
• chore: multiple python version support with latest pyspark and hail by @project-defiant in #974
• chore: bump pycln version by @project-defiant in #978
• chore: pre-commit autoupdate by @pre-commit-ci in #976
• chore: revert pre-commit update (a99ca84) by @ireneisdoomed in #980
• feat(l2gmodel): store features list metadata as instance attribute by @ireneisdoomed in #979
• chore: removing symbols from QTL study identifiers by @DSuveges in #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 #986
• fix: tweak spark session builder to fix type hints by @Daniel-Considine in #982
• build(deps): update numpy requirement from <1.27.0,>=1.26.4 to >=1.26.4,<2.3.0 by @dependabot in #985
• feat: labels for dataproc in dev mode by @project-defiant in #987
• build(deps): update scipy requirement from <1.12.0,>=1.11.4 to >=1.11.4,<1.16.0 by @dependabot in #983
• feat: FoldX predicted energies in variant annotation by @DSuveges in #947
• fix: foldX normalisation to cover full range by @DSuveges in #989
• feat: implement posterior prob filter for COLOC at small overlaps N<10 by @xyg123 in #977
• chore: trigger release process by @github-actions in #961

Full Changelog: v2.0.1...v2.1.0

What's Changed

🐛 Fix

• release process runs twice @Szymon Szyszkowski
• release process no longer triggers on skipped release @project-defiant

♻️ Refactor

• drop version_engine (#940) @Szymon Szyszkowski

🏗 Build

• [deps-dev] bump ipython from 8.29.0 to 8.30.0 @dependabot[bot]
• [deps-dev] bump google-cloud-dataproc from 5.8.0 to 5.10.1 (#951) @dependabot[bot]
• [deps-dev] bump lxml from 5.1.1 to 5.3.0 (#950) @dependabot[bot]
• [deps-dev] bump pytest-xdist from 3.5.0 to 3.6.1 (#952) @dependabot[bot]
• [deps-dev] bump ipykernel from 6.28.0 to 6.29.5 (#953) @dependabot[bot]
• define dependency version constraints + other fixes (#945) @Irene López Santiago

🚀 Chore

• siplify the release CI conditions @project-defiant

What's Changed

💥 Breaking

• [l2g!] implement new training strategy splitting between EFO/gene pairs and with cross validation (#938) @Irene López Santiago
• [L2GFeatureMatrix!] streamline feature matrix management (#745) @Irene López Santiago
• [Orchestration!] drop airflow orchestration layer from gentropy (#758) @Szymon Szyszkowski

✨ Feature

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

🐛 Fix

• [l2g_predictions] annotate based on list of features + filter out missing annotation (#925) @Irene López Santiago
• swap the ref parse (#935) @Szymon Szyszkowski
• r2 for lead variant is always 1 (#919) @Yakov
• using the 99% PIP cs column, (#904) @Daniel-Considine
• reclassify eqtl catalogue sc datasets (#894) @Tobi Alegbe
• do not impute ...