gentropy 2.4.0

v2.4.0

on Python PyPI

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-commit-ci[bot] in #118
• feat: first dag version in airflow by @d0choa in #121
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #123
• feat: Airflow managed workflow by @d0choa in #122
• feat: add StudyLocusOverlaps step to the project by @ireneisdoomed in #124
• Use Ruff as a linter + minor improvements by @ireneisdoomed in #126
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #127
• New LD annotator for GWASCatalog curated studies by @ireneisdoomed in #112
• Precompute LD sets for all possible variants by @ireneisdoomed in #110
• docs: fix incorrect reference by @d0choa in #129
• Docs build is now tested by @d0choa in #130
• Assign final studyLocusId to GWASCat data by @ireneisdoomed in #119
• Set Dataset as an abstract class by @ireneisdoomed in #115
• feat: update existing cluster for development by @ireneisdoomed in #120
• feat: rename credibleSet to locus by @d0choa in #131
• Pytest parallelisation using pytest-xdist by @d0choa in #132
• fix: missing dataset schemas do to wrong hook setup by @d0choa in #133
• Rename locus columns (no tags) by @d0choa in #134
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #137
• revert: remove airflow checkpoint by @ireneisdoomed in #139
• feat: ensure schema columns are camelcase by @d0choa in #135
• Window based clustering with carrying over locus around the semi indices by @DSuveges in #128
• Correct formula for PICS standard deviation by @ireneisdoomed in #113
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #145
• Correct formula for PICS standard deviation (duplicated) by @ireneisdoomed in #143
• fix: updating GWAS Catalog input files by @DSuveges in #142
• Externalise data sources by @d0choa in #141
• Generalizing population mapping by @DSuveges in #149
• Merge branch with main by @Daniel-Considine in #151
• feat: flexible window set up for locus collection by @DSuveges in #153
• Various refactors and bug fixes around ld annotation and pics by @d0choa in #152
• chore: unused dependency by @d0choa in #154
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #156
• fix: cleaning clumping by @DSuveges in #155
• merge with main by @Daniel-Considine in #158
• Some studies just don't have population data causing LD annotation fail by @DSuveges in #157
• Enhancements around credible set annotation by @d0choa in #159
• fix: Removing old gsutil cp command by @Daniel-Considine in #161
• fix: schema issues due to when condition by @d0choa in #160
• labelling tags with null posterior as false instead of null in annotate credible set by @d0choa in #162
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #165
• [Preprocess #1] Business logic for FinnGen summary stats ingestion by @tskir in #150
• Ds 3117 refactor clumping by @DSuveges in #169
• docs: several fixes in docstrings by @d0choa in #170
• Documentation structural changes and data source images by @d0choa in #172
• automatically PR to bump poetry packages by @d0choa in #174
• feat: changing the action by @d0choa in #175
• issue with docs images by @d0choa in #178
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #179
• Revert changes in main not to use actions by @d0choa in #176
• Github dependabot by @d0choa in #177
• chore(deps): bump actions/checkout from 2 to 4 by @dependabot[bot] in #182
• chore(deps): bump actions/setup-python from 2 to 4 by @dependabot[bot] in #181
• bumping dependency versions by @d0choa in #173
• build(deps-dev): bump apache-airflow-providers-google from 10.6.0 to 10.10.0 by @dependabot[bot] in #183
• chore(deps): bump actions/cache from 2 to 3 by @dependabot[bot] in #180
• Add missing columns in gene index by @ireneisdoomed in #189
• feat: run variant index step by @ireneisdoomed in #188
• fix(docs): schemas path for gene and study index by @ireneisdoomed in #192
• build(deps): bump pyspark from 3.3.0 to 3.3.3 by @dependabot[bot] in #195
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #198
• feat: run variant to gene step by @ireneisdoomed in #190
• build(deps-dev): bump mypy from 0.971 to 1.6.1 by @dependabot[bot] in #197
• build(deps-dev): bump mkdocs-autolinks-plugin from 0.6.0 to 0.7.1 by @dependabot[bot] in #196
• Added UKBB and open targets data source documentation by @hlnicholls in #191
• build(deps-dev): bump apache-airflow-providers-google from 10.10.0 to 10.10.1 by @dependabot[bot] in #194
• [Preprocess #2] Instructions for setting up Airflow by @tskir in #164
• [Preprocess #3] Refactor existing Airflow implementation by @tskir in #166
• feat: adapt session to extend the spark env configuration + consolidate testing env by @ireneisdoomed in #136
• Refactor step configuration by @tskir in #199
• Dependabot to monitor airflow docker by @d0choa in #202
• build(deps): bump apache/airflow from 2.7.1-python3.10 to 2.7.2-python3.10 in /src/airflow by @dependabot[bot] in #208
• feat: adding notebooks for finngen and ld matrix by @DSuveges in #209
• build(deps-dev): bump ruff from 0.0.287 to 0.1.3 by @dependabot[bot] in #206
• build(deps-dev): bump mkdocs-material from 9.4.6 to 9.4.7 by @dependabot[bot] in #204
• feat(session): start session inside step instance by @ireneisdoomed in #210
• Follow up changes to step configuration refactor by @tskir in #200
• feat: use pydoclint as a documentation linter by @ireneisdoomed in #212
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #211
• feat: display class name in docs and cleanup docs by @d0choa in #213
• build(deps-dev): bump mkdocs-minify-plugin from 0.5.0 to 0.7.1 by @dependabot[bot] in #205
• L2G progress based on Hydra branch by @ireneisdoomed in #67
• feat(airflow): change docker image to apache/airflow:slim-latest-python3.10 and minor changes by @ireneisdoomed in #214
• Streamline Airflow in Docker for GCP configuration by @d0choa in #201
• chore(dag): add l2g and overlaps steps to dag.yaml by @ireneisdoomed in #217
• Re-enable and fix the test_no_import_errors Airflow DAG test by @tskir in #218
• fix(airflow): job args are list of strings by @ireneisdoomed in #219
• A better way to fix DAG import test by @tskir in #220
• Implement Preprocess DAG following recent architecture updates by @tskir in #216
• feat(airflow): move variant_annotation and ldindex steps to preprocessing dag by @ireneisdoomed in #224
• build(deps-dev): bump pre-commit from 2.21.0 to 3.5.0 by @dependabot[bot] in #228
• chore: move L2GFeature to datasets by @d0choa in #215
• Airflow set up, part 1: Style updates for docs and DAG code by @tskir in #221
• build(deps-dev): bump apache-airflow from 2.7.2 to 2.7.3 by @dependabot[bot] in #230
• Airflow set up, part 2: Fixing issue with setting AIRFLOW_UID by @tskir in #222
• Enable autoscaling, tune cluster parameters, add docs by @tskir in #227
• build(deps): bump hail from 0.2.122 to 0.2.126 by @dependabot[bot] in #232
• gnomAD LD datasource with paths within class by @d0choa in #233
• GnomAD variants within class configuration by @d0choa in #234
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #235
• Small update in functionality to the GnomAD datasource toolset by @DSuveges in #236
• Type enhancements by @d0choa in #239
• Simplify configuration and remove config store by @tskir in #226
• fix: wrong python file uri in airflow by @d0choa in #242
• feat: hydra full error on dataproc by @d0choa in #241
• fix: extract config in root when we install deps on cluster by @ireneisdoomed in #243
• Access gnomad matrix slice with resolved variant identifiers by @DSuveges in #240
• feat(ld): minor improvements to gnomad matrix methods by @ireneisdoomed in #245
• fix(gwas_catalog): clump associations, remove hail and style fixes by @ireneisdoomed in #244
• build(deps-dev): bump mkdocs-material from 9.4.7 to 9.4.8 by @dependabot[bot] in #248
• build(deps-dev): bump pytest-xdist from 3.3.1 to 3.4.0 by @dependabot[bot] in #247
• fix(session): hail config was not set unless extended_spark_conf was provided by @ireneisdoomed in #237
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #251
• fix: coalesce variantid to assign a studylocusid by @ireneisdoomed in #253
• Adjust running parameters to increase stability by @tskir in #254
• fix: persist raw gwascat associations to return consistent results by @ireneisdoomed in #252
• build(deps): bump wandb from 0.13.11 to 0.16.0 by @dependabot[bot] in #250
• Enable local SSDs for worker nodes by @tskir in #256
• New PICS step by @d0choa in #259
• build(deps-dev): bump google-cloud-dataproc from 5.6.0 to 5.7.0 by @dependabot[bot] in #246
• Extra parametrisation on airflow common by @d0choa in #257
• build(deps-dev): bump apache-airflow-providers-google from 10.11.0 to 10.11.1 by @dependabot[bot] in #260
• build(deps-dev): bump mypy from 1.6.1 to 1.7.0 by @dependabot[bot] in #261
• build(deps-dev): bump mkdocs-material from 9.4.8 to 9.4.10 by @dependabot[bot] in #262
• build(deps-dev): bump mkdocstrings-python from 1.7.3 to 1.7.4 by @dependabot[bot] in #263
• feat: raise error in from_parquet when df is empty by @ireneisdoomed in #264
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #265
• Updating summary stats schema and ingtesion by @DSuveges in #266
• Ingest eQTL Catalogue by @tskir in #238
• Removing odds ratio, and confidence intervals from the schema by @DSuveges in #267
• fix: multiply standard error by zscore in calculate_confidence_interval by @ireneisdoomed in #268
• Fix local SSD attachment syntax by @tskir in #269
• gitignore env file by @d0choa in #273
• feat: ingestion supported for both new and old format of the harmonized GWAS Catalog Summary stats. by @DSuveges in #274
• fix: change definition of negative l2g evidence by @ireneisdoomed in #255
• build(deps): bump pyarrow from 11.0.0 to 14.0.1 by @dependabot[bot] in #275
• build(deps-dev): bump ipython from 8.17.2 to 8.18.1 by @dependabot[bot] in #280
• build(deps-dev): bump mkdocstrings-python from 1.7.4 to 1.7.5 by @dependabot[bot] in #279
• build(deps-dev): bump ruff from 0.1.3 to 0.1.6 by @dependabot[bot] in #276
• build(deps-dev): bump mypy from 1.7.0 to 1.7.1 by @dependabot[bot] in #278
• docs: minify plugin removed to prevent clash in local development by @d0choa in #284
• fix: proper parsing of gwas catalog study accession from filename by @DSuveges in #282
• fix: making standard_error column optional by @DSuveges in #286
• feat: add clump step by @ireneisdoomed in #288
• Il fix studies split by @ireneisdoomed in #289
• fix(clump): read input files recursively by @ireneisdoomed in #292
• build(deps-dev): bump mkdocs-material from 9.4.10 to 9.4.14 by @dependabot[bot] in #300
• build(deps): bump scipy from 1.11.3 to 1.11.4 by @dependabot[bot] in #299
• build(deps-dev): bump pymdown-extensions from 10.3.1 to 10.5 by @dependabot[bot] in #301
• build(deps-dev): bump mkdocs-git-committers-plugin-2 from 1.2.0 to 2.2.2 by @dependabot[bot] in #303
• build(deps-dev): bump apache-airflow-providers-google from 10.11.1 to 10.12.0 by @dependabot[bot] in #302
• feat: deptry added to handle unused, missing and transitive dependencies by @d0choa in #304
• feat: adding unpublished studies by @DSuveges in #290
• feat: add prettier as formatter (yaml, json, md, etc.) by @d0choa in #298
• chore(l2ggoldstandard): add studyId to schema by @ireneisdoomed in #305
• feat: Adding cohorts field to study index by @DSuveges in #309
• feat: add 'coalesce' and 'repartition' wrappers to 'Dataset' by @ireneisdoomed in #307
• chore(airflow): schedule_interval deprecation warning by @d0choa in #293
• feat: GWAS Catalog harmonisation prototype by @d0choa in #270
• test: failing doctest in different python version by @d0choa in #320
• build(deps): bump wandb from 0.16.0 to 0.16.1 by @dependabot[bot] in #315
• chore(deps): bump actions/setup-python from 4 to 5 by @dependabot[bot] in #319
• build(deps-dev): bump mkdocs-material from 9.4.14 to 9.5.2 by @dependabot[bot] in #324
• test: Improvements to test_dataset and test_clump_step by @ireneisdoomed in #312
• feat: Gnomad v4 based variant annotation by @d0choa in #311
• refactor: stop inheriting datasets in parsers by @d0choa in #313
• feat: add gwas_catalog_preprocess dag by @ireneisdoomed in #291
• build(deps-dev): bump pre-commit from 3.5.0 to 3.6.0 by @dependabot[bot] in #316
• build(deps): bump numpy from 1.26.1 to 1.26.2 by @dependabot[bot] in #314
• build(deps): bump typing-extensions from 4.8.0 to 4.9.0 by @dependabot[bot] in #317
• chore: add l2g_benchmark notebook to compare with production results by @ireneisdoomed in #323
• feat: finngen preprocess prototype by @d0choa in #272
• chore: create code of conduct by @d0choa in #327
• chore: review study locus and study index configs by @ireneisdoomed in #326
• feat: improve experiment tracking to W&B by @ireneisdoomed in #325
• chore: delete makefile_deprecated by @d0choa in #329
• feat: ruff as formatter by @d0choa in #322
• build(deps-dev): bump google-cloud-dataproc from 5.7.0 to 5.8.0 by @dependabot[bot] in #330
• build(deps-dev): bump ruff from 0.1.6 to 0.1.7 by @dependabot[bot] in #331
• feat: semantic release automation by @d0choa in #294
• feat: track feature missingness rates by @ireneisdoomed in #335
• feat: trigger on push by @d0choa in #337
• build(deps-dev): bump pytest-xdist from 3.4.0 to 3.5.0 by @dependabot[bot] in #333
• build(deps-dev): bump ipykernel from 6.26.0 to 6.27.1 by @dependabot[bot] in #332
• feat: yamllint to ensure yaml linting by @d0choa in #338
• fix: release actions fixes by @d0choa in #344
• docs: finngen description v1 by @addramir in #345
• chore: upgrade checkout by @d0choa in #346
• fix: github token by @d0choa in #348
• fix: several issues by @d0choa in #349
• feat: release branch by @d0choa in #350
• fix: unnecessary option by @d0choa in #351
• build(deps-dev): bump python-semantic-release from 8.3.0 to 8.5.1 by @dependabot[bot] in #343
• feat: activate release process by @d0choa in #352
• build(deps-dev): bump isort from 5.13.1 to 5.13.2 by @dependabot[bot] in #342
• build(deps-dev): bump ruff from 0.1.7 to 0.1.8 by @dependabot[bot] in #341
• feat: upload release by @d0choa in #353
• feat: semantic release gh action by @d0choa in #354
• revert: dispatch by @d0choa in #355
• build(deps): bump pyspark from 3.3.3 to 3.3.4 by @dependabot[bot] in #358
• chore(deps): bump python-semantic-release/python-semantic-release from 8.3.0 to 8.5.1 by @dependabot[bot] in #359
• feat: new changelog and release notes templates by @d0choa in #357
• fix(l2g): calculate_feature_missingness_rate counts features annotated with 0 as incomplete by @ireneisdoomed in #364
• docs: corrected and added documentation to datasource by @addramir in #362
• fix: incorrect parsing of app_name in makefile by @ireneisdoomed in #367
• ci: set codecov default branch to dev by @ireneisdoomed in #368
• feat: Finngen R10 harmonisation and preprocessing by @d0choa in #370
• feat(pics): remove variants from locus when PICS cannot be applied by @ireneisdoomed in #361
• chore(study_index): change numeric columns from long to integers by @ireneisdoomed in #371
• feat(l2g): add features based on predicted variant consequences by @ireneisdoomed in #360
• chore: set cluster delete TTL by @tskir in #379
• build(deps-dev): bump apache-airflow from 2.7.3 to 2.8.0 by @dependabot[bot] in #373
• build(deps-dev): bump mypy from 1.7.1 to 1.8.0 by @dependabot[bot] in #374
• chore(deps): bump python-semantic-release/python-semantic-release from 8.5.1 to 8.7.0 by @dependabot[bot] in #372
• build(deps-dev): bump python-semantic-release from 8.5.1 to 8.7.0 by @dependabot[bot] in #375
• build(deps-dev): bump mkdocs-git-revision-date-localized-plugin from 1.2.1 to 1.2.2 by @dependabot[bot] in #376
• build(deps-dev): bump ipython from 8.18.1 to 8.19.0 by @dependabot[bot] in #377
• feat(study_locus): remove statistics after conditioning from schema by @ireneisdoomed in #383
• feat: carma outlier detection method by @d0choa in #281
• chore: change picsed finngen outputh path by @ireneisdoomed in #385
• fix: release build using poetry by @d0choa in #387
• build(deps-dev): bump mkdocs-git-committers-plugin-2 from 2.2.2 to 2.2.3 by @dependabot[bot] in #393
• build(deps-dev): bump mkdocs-material from 9.5.2 to 9.5.3 by @dependabot[bot] in #391
• build(deps-dev): bump apache-airflow-providers-google from 10.12.0 to 10.13.1 by @dependabot[bot] in #392
• build(deps-dev): bump ipykernel from 6.27.1 to 6.28.0 by @dependabot[bot] in #389
• chore(deps): bump python-semantic-release/python-semantic-release from 8.7.0 to 8.7.2 by @dependabot[bot] in #388
• build(deps-dev): bump pymdown-extensions from 10.5 to 10.7 by @dependabot[bot] in #390
• feat(eqtl_catalogue): study index improvements by @ireneisdoomed in #369
• feat(colocalisation): new step runs ecaviar on credible sets by @ireneisdoomed in #396
• Do fixes semrelease by @d0choa in #399
• feat: adding logic to flag gwas catalog studies based on curation by @DSuveges in #347
• chore(studylocus): rename logABF statistics to logBF by @ireneisdoomed in #402
• fix: updating finngen sumstats ingestion by @DSuveges in #401
• feat(l2g): add coloc based features by @ireneisdoomed in #400
• feat: application configuration by @d0choa in #386
• test: generalise cli test for easier maintainance by @d0choa in #403
• feat: remove ukbiobank and overlaps steps by @d0choa in #404
• feat(l2g): limit l2g predictions to gwas-derived associations by @ireneisdoomed in #408
• test(study_locus): add semantic test for find_overlaps by @ireneisdoomed in #407
• build(deps-dev): bump mkdocstrings-python from 1.7.5 to 1.8.0 by @dependabot[bot] in #414
• feat: flex python version to make all 3.10 versions compatible by @d0choa in #406
• feat: not fail CI if codecov error by @d0choa in #416
• chore: update pre-commit hook versions by @d0choa in #411
• fix: release action by @d0choa in #417
• fix: some GWAS Catalog study curation logic fix - column names by @DSuveges in #418
• build(deps-dev): bump pytest from 7.4.3 to 7.4.4 by @dependabot[bot] in #415
• build(deps): bump wandb from 0.16.1 to 0.16.2 by @dependabot[bot] in #410
• build(deps): bump hail from 0.2.126 to 0.2.127 by @dependabot[bot] in #413
• build(deps-dev): bump lxml from 4.9.3 to 5.1.0 by @dependabot[bot] in #412
• ci: reorder commit types in release notes template by @ireneisdoomed in #419
• fix: deprecate version in init.py by @d0choa in #421
• refactor: rename otg to gentropy by @d0choa in #405
• refactor: rename genetics_etl_python to gentropy by @d0choa in #422
• ci: pypi and testpypi functionalities by @d0choa in #423
• fix: changelog template by @d0choa in #424
• chore: updaing configs to the propsed release folder structure by @DSuveges in #425
• ci: more complex setup with independent jobs by @d0choa in #427
• ci: remove unnecessary steps by @d0choa in #428
• docs: documentation link by @d0choa in #429
• docs: gentropy hero image by @d0choa in #430
• docs: update README.md by @d0choa in #431
• docs: release documentation preparation by @addramir in #432
• docs: several enhancements on docs including index and installation by @d0choa in #433
• chore: tidying up gwas catalog ingestion and process configuration by @DSuveges in #426
• docs: docs ammendments by @d0choa in #437
• docs: fix step name by @d0choa in #438
• chore: improvements to generate 2401 data release by @ireneisdoomed in #436
• docs: pypi badges by @d0choa in #439
• chore(deps): bump actions/cache from 3 to 4 by @dependabot[bot] in #446
• chore(deps): bump actions/download-artifact from 3 to 4 by @dependabot[bot] in #448
• chore(deps): bump actions/upload-artifact from 3 to 4 by @dependabot[bot] in #447
• build(deps-dev): bump ipython from 8.19.0 to 8.20.0 by @dependabot[bot] in #445
• build(deps): bump numpy from 1.26.2 to 1.26.3 by @dependabot[bot] in #441
• build(deps-dev): bump ipykernel from 6.28.0 to 6.29.0 by @dependabot[bot] in #442
• build(deps): bump pandas from 2.1.4 to 2.2.0 by @dependabot[bot] in #443
• build(deps): bump scikit-learn from 1.3.2 to 1.4.0 by @dependabot[bot] in #444
• chore: harmonizing finngen configuration by @DSuveges in #454
• chore(deps): bump codecov/codecov-action from 3 to 4 by @dependabot[bot] in #464
• ci: ignore patch versions in dependabot by @d0choa in #462
• build(deps-dev): bump ruff from 0.1.8 to 0.2.0 by @dependabot[bot] in #465
• build(deps-dev): bump ipython from 8.20.0 to 8.21.0 by @dependabot[bot] in #466
• build(deps-dev): bump pytest-sugar from 0.9.7 to 1.0.0 by @dependabot[bot] in #467
• build(deps-dev): bump google-cloud-dataproc from 5.8.0 to 5.9.0 by @dependabot[bot] in #468
• docs: add gentropy first steps guide by @ireneisdoomed in #449
• feat(LD): include leads with R2=1 in the ldSet when not found in LDIndex by @d0choa in #453
• docs(StudyLocusQualityCheck): update outdated attributes by @d0choa in #452
• chore: minor updates to gwas catalog pathnames by @ireneisdoomed in #440
• feat(dataset): add Dataset.filter to create a new dataset instance with filtered data by @ireneisdoomed in #470
• feat(finemapping): susie method by @Daniel-Considine in #398
• feat(finemapping): ingest finngen r10 finemapping w/ airflow by @xyg123 in #435
• chore: trigger release process by @d0choa in #472
• docs: susie inf method reloacated with the rest of the methods by @d0choa in #473
• ci(release): add action to open pr that triggers release weekly by @ireneisdoomed in #474
• fix: update github token variable by @ireneisdoomed in #476
• ci: exclude changelog.md from precommit by @d0choa in #479
• build(deps-dev): bump python-semantic-release from 8.7.0 to 9.0.3 by @dependabot[bot] in #482
• build(deps-dev): bump pytest from 7.4.4 to 8.0.1 by @dependabot[bot] in #493
• build(deps-dev): bump pydoclint from 0.3.8 to 0.4.1 by @dependabot[bot] in #497
• build(deps-dev): bump yamllint from 1.33.0 to 1.35.1 by @dependabot[bot] in #494
• build(deps-dev): bump python-semantic-release from 9.0.3 to 9.1.0 by @dependabot[bot] in #495
• build(deps-dev): bump apache-airflow-providers-google from 10.13.1 to 10.15.0 by @dependabot[bot] in #496
• ci: pre-commit updates by @d0choa in #499
• test: increase modularity of test directories by @d0choa in #502
• fix: pre-commit autoupdate message by @d0choa in #500
• fix(finemapping): finngen harmonisation (schema and orchestration) by @xyg123 in #489
• chore: trigger release process by @github-actions[bot] in #503
• build(deps-dev): bump ipython from 8.21.0 to 8.22.1 by @dependabot[bot] in #504
• build(deps): bump typing-extensions from 4.9.0 to 4.10.0 by @dependabot[bot] in #506
• build(deps-dev): bump mkdocs-git-committers-plugin-2 from 2.2.3 to 2.3.0 by @dependabot[bot] in #505
• test: Unit tests for coloc by @xyg123 in #509
• fix: variant annotation config by @RobinM-code in #510
• feat: extract credible sets and studies from eQTL Catalogue finemapping results by @ireneisdoomed in #514
• ci: pull request labeler by @d0choa in #519
• ci: pull request template by @d0choa in #517
• fix: pull-request labeler fixes by @d0choa in #520
• feat(CARMA): adding time limited CARMA by @addramir in #475
• feat: extract credible sets and studies from all eQTL Catalogue finemapping results by @ireneisdoomed in #518
• build(deps-dev): bump pytest from 8.0.1 to 8.1.0 by @dependabot[bot] in #516
• fix: make setup dev not to update pre-commits by @d0choa in #524
• chore: update ruff pre-commit and rules by @d0choa in #522
• fix: pr labeller patterns by @d0choa in #523
• ci: precommit checks for poetry TOML and lock by @d0choa in #526
• feat(coloc): single SNP case by @xyg123 in #511
• chore: trigger release process by @github-actions[bot] in #527
• chore(l2g): update inclusion features list with newer QTLs by @ireneisdoomed in #529
• chore: small updates to accomodate GWAS Catalog for feb release by @DSuveges in #507
• build(deps-dev): bump ruff from 0.2.0 to 0.3.2 by @dependabot[bot] in #531
• build(deps-dev): bump mypy from 1.8.0 to 1.9.0 by @dependabot[bot] in #532
• fix: pin version of commitlint by @louwenjjr in #533
• fix(datasource): read function for thurman data to include first line by @louwenjjr in #534
• feat(sumstat imputation): adding class for sumstat imputation by @addramir in #490
• ci: bugfix in PR labeller by @d0choa in #537
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #539
• feat(dag): add data transfer task group for release process by @DSuveges in #528
• build(deps-dev): bump deptry from 0.12.0 to 0.14.0 by @dependabot[bot] in #548
• build(deps-dev): bump mkdocstrings-python from 1.8.0 to 1.9.0 by @dependabot[bot] in #549
• chore(l2g): log annotated gold standards in w&b by @ireneisdoomed in #546
• perf(l2g): streamline feature generation by @ireneisdoomed in #544
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #550
• feat(l2g): distance features based on weighted score by @ireneisdoomed in #545
• perf(clump): refactored window based clumping by @d0choa in #492
• feat: notebook to run qc metrics each release by @xyg123 in #541
• fix: small fixes in susie defaults by @addramir in #552
• test(method): improved performance in coloc tests by @xyg123 in #536
• perf(l2g): optimise extraction of features from colocalisation results by @ireneisdoomed in #553
• fix(coloc): handle cases when the bayes factors are null by @ireneisdoomed in #556
• fix(sumstats): correct study id for dir of finngen studies by @louwenjjr in #551
• feat: add the step class for fine-mapping by @addramir in #554
• feat: LD index and block matrix extraction for a studyLocus by @Daniel-Considine in #463
• feat: the FineMapper function for one locus by @addramir in #564
• feat: susie_finemapper_ss_gathered() by @Daniel-Considine in #567
• feat: add FM step with carma and sumstat imputation by @addramir in #568
• fix: adding deduplication for GWAS in locus by @addramir in #573
• feat: add benchmarking for fine-mapping using Alzheimer as example by @addramir in #572
• fix: removing all duplicated variants in sumstats for finemapping functions by @Daniel-Considine in #574
• feat: adding notebook for mapping EFOs for the FinnGen study index by @addramir in #575
• feat: adding init to finemapping step by @Daniel-Considine in #577
• feat: dockerise gentropy python package by @ireneisdoomed in #579
• feat: updating step config file by @Daniel-Considine in #580
• fix: update error in config.py by @Daniel-Considine in #583
• feat: updating loci windows to locus radii by @Daniel-Considine in #582
• fix: minor updates and bug fixes by @DSuveges in #543
• fix: updating config.py argument for finemapper by @Daniel-Considine in #584
• feat(sumstat qc): adding methods for QC of summary statistics by @addramir in #455
• feat: susie_finemapper_one_studylocus_row_v3_dev_ss_gathered by @addramir in #586
• feat: functionality added to StudyLocus.find_overlaps() for finding within-study overlaps by @Daniel-Considine in #587
• feat: github action to upload docker image to artifact registry by @d0choa in #588
• fix: Java 11 in docker image and lighter image by @d0choa in #585
• fix: docker action fixes by @d0choa in #589
• fix: docker action fixes v2 by @d0choa in #590
• fix: docker action fixes v3 by @d0choa in #591
• build(deps-dev): bump deptry from 0.14.0 to 0.16.1 by @dependabot[bot] in #570
• build(deps-dev): bump lxml from 5.1.0 to 5.2.1 by @dependabot[bot] in #569
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #561
• build(deps-dev): bump pre-commit from 3.6.0 to 3.7.0 by @dependabot[bot] in #559
• build(deps-dev): bump pytest-cov from 4.1.0 to 5.0.0 by @dependabot[bot] in #560
• build(deps-dev): bump python-semantic-release from 9.1.0 to 9.4.1 by @dependabot[bot] in #571
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #593
• feat: add purity qc metrics to fine-mapping by @addramir in #592
• feat: check for if no overlapping variants in LD index by @Daniel-Considine in #594
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in #601
• build(deps-dev): bump pymdown-extensions from 10.7 to 10.8.1 by @dependabot[bot] in #600
• build(deps-dev): bump interrogate from 1.5.0 to 1.7.0 by @dependabot[bot] in #599
• build(deps-dev): bump pytest from 8.1.0 to 8.2.0 by @dependabot[bot] in #598
• build(deps-dev): bump pytest-xdist from 3.5.0 to 3.6.1 by @dependabot[bot] in #597
• build(deps-dev): bump ruff from 0.3.2 to 0.4.3 by @dependabot[bot] in #596
• feat(airflow): include COLOC as a node in the DAG by @ireneisdoomed in #530
• build(deps): bump typing-extensions from 4.10.0 to 4.11.0 by @dependabot[bot] in #602
• build(deps-dev): bump ipython from 8.22.1 to 8.24.0 by @dependabot[bot] in #603
• build(deps-dev): bump mypy from 1.9.0 to 1.10.0 by @dependabot[bot] in #604
• refactor: moving all variant coordinates to GnomAD by @DSuveges in #566
• chore: trigger release process by @github-actions[bot] in #595
• fix: fix python-semantic-release version by @d0choa in #609
• chore: trigger release process by @github-actions[bot] in #610
• fix: fix python-semantic-release version (again) by @d0choa in #611
• chore: trigger release process by @github-actions[bot] in #612
• fix(spark helpers): sorter function updated to avoid crash by @DSuveges in #613
• feat: fine-mapping simulations class by @addramir in #618
• feat(config): gnomAD steps configuration extraction and versioning by @project-defiant in #620
• fix(docs): update roadmap.md by @buniello in #622
• fix(ld): correct syntax for the get_numpy_matrix static method by @tskir in #624
• fix(susie_finemapper): correct syntax for saving the logs df by @tskir in https://github.com/opentargets/gentropy/pull/625
• fix(susie_finemapper): fix in the fine-mapper in case of sum stat imputation is False by @addramir in https://github.com/opentargets/gentropy/pull/627
• fix(SummaryStatistics): fix in sanity_filter by @addramir in https://github.com/opentargets/gentropy/pull/623
• build(deps): add [gcp] and [parquet] extras to enable saving Pandas dataframes to Google Storage by @tskir in https://github.com/opentargets/gentropy/pull/626
• fix(docs): fixed typo in l2g_prediciton schema page by @project-defiant in https://github.com/opentargets/gentropy/pull/629
• feat(config): extract gwas_significance parameter to step configuration by @project-defiant in https://github.com/opentargets/gentropy/pull/628
• feat(data_release): preparation for 24.06 data release by @project-defiant in https://github.com/opentargets/gentropy/pull/633
• build(deps): bump typing-extensions from 4.11.0 to 4.12.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/632
• build(deps-dev): bump pep8-naming from 0.13.3 to 0.14.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/616
• feat(qtl): ingest credible sets from single cell derived QTLs by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/630
• feat(spark-helpers): enforce schema of returned objects by @DSuveges in https://github.com/opentargets/gentropy/pull/617
• feat: adding locus-breaker clumping method by @DSuveges in https://github.com/opentargets/gentropy/pull/634
• build(deps): bump wandb from 0.16.2 to 0.17.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/606
• build(deps-dev): bump ipython from 8.24.0 to 8.25.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/636
• build(deps): bump scikit-learn from 1.4.0 to 1.5.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/638
• feat: enable interface with gcp secrets manager by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/635
• feat: credible set quality filtering by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/640
• build(deps-dev): bump dbldatagen from 0.3.5 to 0.4.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/637
• feat(config): 24.06 data release fixes by @project-defiant in https://github.com/opentargets/gentropy/pull/639
• fix(L2GPrediction): schema validation by @project-defiant in https://github.com/opentargets/gentropy/pull/642
• feat(SusieFineMapperStep): add new function with boundaries by @addramir in https://github.com/opentargets/gentropy/pull/645
• feat: exclude region for StudyLocus object by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/646
• refactor: delete unnecessary config files by @d0choa in https://github.com/opentargets/gentropy/pull/647
• build: remove python-semantic-release as project dependency by @d0choa in https://github.com/opentargets/gentropy/pull/650
• feat(ld_annotator): optional r2 threshold by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/648
• feat(stydyLocus): adding new locus collection using boundaries by @addramir in https://github.com/opentargets/gentropy/pull/644
• chore: enable Jupyter Notebook gateway for the Dataproc cluster by @tskir in https://github.com/opentargets/gentropy/pull/651
• feat(l2g): better l2g training, evaluation, and integration by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/576
• feat: implement UKB PPP (EUR) ingestion & harmonisation by @tskir in https://github.com/opentargets/gentropy/pull/652
• chore(SusieFineMapperStep): remove the locus_radius parameter by @tskir in https://github.com/opentargets/gentropy/pull/659
• chore(deps): bump python-semantic-release/python-semantic-release from 9.6.0 to 9.8.3 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/656
• build(deps-dev): bump pydoclint from 0.4.1 to 0.5.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/658
• ci: pre-commit update with pydoclint adjustments by @d0choa in https://github.com/opentargets/gentropy/pull/660
• fix: remove check merge conflict from pre-commit by @d0choa in https://github.com/opentargets/gentropy/pull/661
• fix(SusieFineMapperStep): adding filtering of NANs in LD by @addramir in https://github.com/opentargets/gentropy/pull/654
• feat(datasets): adding new variant annotation model by @DSuveges in https://github.com/opentargets/gentropy/pull/641
• fix: typo in cs_lbf_thr parameter name by @tskir in https://github.com/opentargets/gentropy/pull/667
• fix: make extended_spark_conf an empty dict instead of None by @tskir in https://github.com/opentargets/gentropy/pull/668
• fix(SusieFineMapperStep): link configuration and step classes by @tskir in https://github.com/opentargets/gentropy/pull/669
• feat: vep annotation (dockerised + google batch + airflow) by @d0choa in https://github.com/opentargets/gentropy/pull/608
• feat: locus_breaker_clumping by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/655
• feat: add qc step by @addramir in https://github.com/opentargets/gentropy/pull/675
• feat: adding sanity filter to GWASCatalogSumstatsPreprocessStep by @addramir in https://github.com/opentargets/gentropy/pull/677
• fix: leave only five ancestries in LD by @addramir in https://github.com/opentargets/gentropy/pull/680
• fix: improving locus_breaker_step logic by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/679
• fix(finemapping): reconcile changes in the finemapping step with config by @tskir in https://github.com/opentargets/gentropy/pull/682
• feat: credible set quality control step by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/681
• feat(docker): image update for new orchestration by @project-defiant in https://github.com/opentargets/gentropy/pull/683
• feat(StudyIndex): validation for study type, disease, target etc by @DSuveges in https://github.com/opentargets/gentropy/pull/672
• build(deps-dev): bump ruff from 0.4.10 to 0.5.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/674
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/676
• fix: fixed selection of major ancestry for finemapper by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/685
• build(deps): bump skops from 0.9.0 to 0.10.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/673
• build(deps-dev): bump google-cloud-dataproc from 5.9.3 to 5.10.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/684
• feat(variant index): calculate hash as variant id for long variants by @DSuveges in https://github.com/opentargets/gentropy/pull/665
• build(deps-dev): bump ipython from 8.25.0 to 8.26.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/662
• Main 3 by @project-defiant in https://github.com/opentargets/gentropy/pull/690
• ci: prevent user from rebasing in minimal way by @project-defiant in https://github.com/opentargets/gentropy/pull/691
• ci: artifacts versionned by release by @project-defiant in https://github.com/opentargets/gentropy/pull/692
• fix: moving hl.init by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/687
• chore(study_index): improve study definition for the eQTL Catalogue and Finngen by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/693
• feat(studyLocus validation): adding validation logic to studyLocus dataset by @DSuveges in https://github.com/opentargets/gentropy/pull/686
• chore: trigger release process by @github-actions[bot] in https://github.com/opentargets/gentropy/pull/688
• ci: revert semantic-release update by @project-defiant in https://github.com/opentargets/gentropy/pull/694
• feat: full orchestration of the variant index dag by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/678
• chore: trigger release process by @github-actions[bot] in https://github.com/opentargets/gentropy/pull/695
• fix(variants): explode loci to generate list of variants + tests by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/698
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/699
• ci: Refactoring of the docker release process for gentropy by @project-defiant in https://github.com/opentargets/gentropy/pull/700
• fix(finemapping): typo in "elapsed_time" by @tskir in https://github.com/opentargets/gentropy/pull/701
• feat: allow image push by @project-defiant in https://github.com/opentargets/gentropy/pull/702
• chore: trigger release process by @github-actions[bot] in https://github.com/opentargets/gentropy/pull/703
• feat: implement reading study locus paths from the manifest by @tskir in https://github.com/opentargets/gentropy/pull/706
• ci(release): use github app token for tag push by @project-defiant in https://github.com/opentargets/gentropy/pull/709
• build(deps-dev): bump pytest from 8.2.2 to 8.3.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/712
• build(deps-dev): bump deptry from 0.16.1 to 0.17.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/714
• build(deps-dev): bump mypy from 1.10.0 to 1.11.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/713
• chore: trigger release process by @github-actions[bot] in https://github.com/opentargets/gentropy/pull/708
• feat: expose summary statistics qc and locus breaker steps to hydra cli by @project-defiant in https://github.com/opentargets/gentropy/pull/716
• fix: change config params to match new name by @project-defiant in https://github.com/opentargets/gentropy/pull/721
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/715
• build(deps-dev): bump pymdown-extensions from 10.8.1 to 10.9 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/720
• build(deps-dev): bump deptry from 0.17.0 to 0.18.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/723
• feat: notebook for locus breaker and susie finemapping benchmark by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/717
• fix: updating config paths and fine-mapping methods by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/725
• docs: macos fix for some functions by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/729
• build(deps-dev): bump ruff from 0.5.1 to 0.6.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/732
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/724
• build(deps-dev): bump deptry from 0.18.0 to 0.19.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/728
• build(deps-dev): bump lxml from 5.2.2 to 5.3.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/727
• build(deps-dev): bump pre-commit from 3.7.1 to 3.8.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/719
• feat(variant_index): changes for a successful run by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/735
• fix: update cluster creation command by @project-defiant in https://github.com/opentargets/gentropy/pull/739
• fix: revert recursiveFileLookup to False in Session.load_data by @project-defiant in https://github.com/opentargets/gentropy/pull/738
• feat: Finngen r11 ingestion by @project-defiant in https://github.com/opentargets/gentropy/pull/733
• fix: using h4 instead of log2(h4/h3) by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/740
• fix: adding carma_tau parameter to susie_finemapper by @addramir in https://github.com/opentargets/gentropy/pull/743
• feat: logic and airflow pipeline for validation by @DSuveges in https://github.com/opentargets/gentropy/pull/730
• feat(variant index): improved data structure by @DSuveges in https://github.com/opentargets/gentropy/pull/710
• fix: remove finngen prefix from credible set by @project-defiant in https://github.com/opentargets/gentropy/pull/746
• fix(finngen_r11): preserve all studyIds by @project-defiant in https://github.com/opentargets/gentropy/pull/747
• feat: adding finemapping method to studylocusid hash by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/744
• build(deps-dev): bump ipython from 8.26.0 to 8.27.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/741
• build(deps-dev): bump deptry from 0.19.1 to 0.20.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/742
• fix: validation name mapping by @project-defiant in https://github.com/opentargets/gentropy/pull/753
• chore: removing old susie_finemapper functions by @addramir in https://github.com/opentargets/gentropy/pull/752
• refactor: generalise per-chromosome processing by @tskir in https://github.com/opentargets/gentropy/pull/754
• refactor: generalise the harmonisation pipeline by @tskir in https://github.com/opentargets/gentropy/pull/755
• feat: ingest FinnGen UKB meta-analysis data by @tskir in https://github.com/opentargets/gentropy/pull/756
• feat(validation): adding credible set variant validation by @DSuveges in https://github.com/opentargets/gentropy/pull/757
• feat: drop airflow orchestration layer from gentropy by @project-defiant in https://github.com/opentargets/gentropy/pull/758
• fix(FinngenUkbMetaIngestionStep): multiple fixes after debugging and test runs by @tskir in https://github.com/opentargets/gentropy/pull/760
• build(deps-dev): bump mkdocstrings-python from 1.10.5 to 1.11.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/749
• build(deps): bump wandb from 0.17.2 to 0.18.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/763
• fix: prevent multiple credible filters to override spark plan by @d0choa in https://github.com/opentargets/gentropy/pull/766
• feat: flag MHC credible sets based on lead by @d0choa in https://github.com/opentargets/gentropy/pull/767
• feat: add condition to eQTL study index and schema by @vivienho in https://github.com/opentargets/gentropy/pull/770
• fix(effect harmonisation): addressing beta harmonisation bug by @DSuveges in https://github.com/opentargets/gentropy/pull/762
• perf: quickly build a Docker image for every branch by @tskir in https://github.com/opentargets/gentropy/pull/773
• feat: flag all top-hits from GWAS catalog curation by @d0choa in https://github.com/opentargets/gentropy/pull/775
• docs: update broken refs by @d0choa in https://github.com/opentargets/gentropy/pull/768
• feat: flag PICS top hits in studies with PICS from sumstats by @d0choa in https://github.com/opentargets/gentropy/pull/777
• fix(ld clumping): a revised logic allows a more accurate clumping by @DSuveges in https://github.com/opentargets/gentropy/pull/772
• refactor(L2GFeatureMatrix)!: streamline feature matrix management by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/745
• feat(dataproc): ability to version gentropy for dataproc cluster by @project-defiant in https://github.com/opentargets/gentropy/pull/774
• feat: add studyType to StudyLocus and Colocalisation (and StudyLocusOverlap) by @vivienho in https://github.com/opentargets/gentropy/pull/782
• feat: adding window based clumping to StudyLocus by @DSuveges in https://github.com/opentargets/gentropy/pull/779
• fix: small qc flag fixes by @addramir in https://github.com/opentargets/gentropy/pull/784
• feat: add biosample index by @Tobi1kenobi in https://github.com/opentargets/gentropy/pull/769
• feat: 99% credible set validation during study_locus_validation by @d0choa in https://github.com/opentargets/gentropy/pull/765
• feat: flag credible sets explained by SuSiE regions by @d0choa in https://github.com/opentargets/gentropy/pull/780
• fix: remove n_eff check from qc_step by @addramir in https://github.com/opentargets/gentropy/pull/785
• build(deps-dev): bump pymdown-extensions from 10.9 to 10.10.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/781
• build: updated precommits including adjustments to docstrings by @d0choa in https://github.com/opentargets/gentropy/pull/787
• fix(finngen_study_index): improved tests for finngen study index by @project-defiant in https://github.com/opentargets/gentropy/pull/776
• fix: clean unused study_locus_validation step parameter by @d0choa in https://github.com/opentargets/gentropy/pull/786
• fix(vep_parser): use nested schema for insilico predictors by @project-defiant in https://github.com/opentargets/gentropy/pull/789
• fix: remove study_index_path from coloc step by @project-defiant in https://github.com/opentargets/gentropy/pull/791
• fix(safe_array_union): allow for sorting nested structs by @project-defiant in https://github.com/opentargets/gentropy/pull/793
• fix: bug in neglog_pvalue_to_mantissa_and_exponent by @addramir in https://github.com/opentargets/gentropy/pull/795
• fix(schema): recursive validation of arbitrarily deep nested structure by @DSuveges in https://github.com/opentargets/gentropy/pull/790
• fix: adding data specific p-value filters by @addramir in https://github.com/opentargets/gentropy/pull/788
• feat: change StudyLocusId hashing method to md5 (and change StudyLocusId to string type) by @vivienho in https://github.com/opentargets/gentropy/pull/783
• feat: drop v2g and reimplement distance features by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/771
• feat: out sample LD qc reason by @d0choa in https://github.com/opentargets/gentropy/pull/798
• chore: drop redundant parameter from sumstat qc step by @project-defiant in https://github.com/opentargets/gentropy/pull/802
• fix: align the schema of study_index for ukb ppp eur by @project-defiant in https://github.com/opentargets/gentropy/pull/803
• feat: force reinstallation of the gentropy on the cluster by @project-defiant in https://github.com/opentargets/gentropy/pull/804
• feat(validation): adding credible set confidence annotation at validation time by @DSuveges in https://github.com/opentargets/gentropy/pull/801
• chore: make the lb clumping ingest the partitionned data by @project-defiant in https://github.com/opentargets/gentropy/pull/806
• feat: adding filtering to susie finemapper by @addramir in https://github.com/opentargets/gentropy/pull/796
• feat: add sumstat QC fields to schema by @addramir in https://github.com/opentargets/gentropy/pull/809
• feat: fix biosample study validation by @Tobi1kenobi in https://github.com/opentargets/gentropy/pull/810
• refactor(vep_parser): store consequence to impact score as a project config by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/811
• feat(l2g): implement variant consequence features from VEP by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/805
• feat: optimisation of qc step by @addramir in https://github.com/opentargets/gentropy/pull/813
• fix(validation): add qualityControls column if missing in StudyLocus dataset when perfroming validation by @project-defiant in https://github.com/opentargets/gentropy/pull/814
• fix: fix of type error in schema checking by @addramir in https://github.com/opentargets/gentropy/pull/817
• fix: adding studId to FM log by @addramir in https://github.com/opentargets/gentropy/pull/816
• fix: biosample id duplication by @Tobi1kenobi in https://github.com/opentargets/gentropy/pull/822
• feat: change LD annotation for PICS fine-mapping to use major ancestry by @vivienho in https://github.com/opentargets/gentropy/pull/821
• build(deps-dev): bump ipython from 8.27.0 to 8.28.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/819
• build(deps-dev): bump pre-commit from 3.8.0 to 4.0.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/820
• feat: decouple feature generation from L2G training step by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/823
• fix: mhc flag incorrect by @d0choa in https://github.com/opentargets/gentropy/pull/825
• revert: no longer rescuing variants not in LD matrix when overlapping with SuSiE by @d0choa in https://github.com/opentargets/gentropy/pull/827
• fix: empty inSilicoPredictors object in GnomAD variant index by @DSuveges in https://github.com/opentargets/gentropy/pull/807
• fix: write mode added to validation steps by @d0choa in https://github.com/opentargets/gentropy/pull/826
• feat(l2g): merge sQTL and tuQTL colocalisation features by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/824
• fix: adding single point statistics to pics loci by @DSuveges in https://github.com/opentargets/gentropy/pull/832
• fix(find_overlap): missing right study type in output by @DSuveges in https://github.com/opentargets/gentropy/pull/828
• feat: enhance variant index partitioning by @d0choa in https://github.com/opentargets/gentropy/pull/834
• feat: adding new LD interface by @addramir in https://github.com/opentargets/gentropy/pull/759
• ci: configure java v8 by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/840
• fix(trainer): drop studyLocusId before creating training sets by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/837
• fix(l2g): remove custom session params + other fixes by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/841
• build(deps-dev): bump pymdown-extensions from 10.10.1 to 10.11.2 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/815
• build(deps-dev): bump mkdocs-git-committers-plugin-2 from 2.3.0 to 2.4.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/818
• build(deps-dev): bump pyparsing from 3.1.2 to 3.2.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/836
• build(deps-dev): bump mkdocstrings-python from 1.11.1 to 1.12.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/842
• chore: adding priors to coloc step by @addramir in https://github.com/opentargets/gentropy/pull/830
• fix: fix ukbppp studindex by @addramir in https://github.com/opentargets/gentropy/pull/839
• fix: l2g fixes by @d0choa in https://github.com/opentargets/gentropy/pull/844
• chore: remove h4/h3 ratio by @addramir in https://github.com/opentargets/gentropy/pull/829
• fix: updating the susie_finemapper init by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/846
• feat(coloc): step refactoring by @project-defiant in https://github.com/opentargets/gentropy/pull/845
• test: skip fetch_coordinates_from_rsids by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/850
• fix(eqtl): deduplicating credible set loci by @DSuveges in https://github.com/opentargets/gentropy/pull/849
• chore: adding logging even when no CS in locus by @addramir in https://github.com/opentargets/gentropy/pull/848
• feat(l2g): limit colocalisation neighbourhood to protein coding genes by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/847
• fix: filter nan in CSs by @addramir in https://github.com/opentargets/gentropy/pull/855
• revert(finngen): restore the studyId prefix in finngen cs and si by @project-defiant in https://github.com/opentargets/gentropy/pull/856
• feat(susie_finemapper): allow for extraction of the log file from manifest by @project-defiant in https://github.com/opentargets/gentropy/pull/859
• chore(coloc): changing the content of numberColocalisingVariants field by @DSuveges in https://github.com/opentargets/gentropy/pull/857
• fix: susie credible sets with unknown confidence by @d0choa in https://github.com/opentargets/gentropy/pull/862
• fix: adding beta for lead variant by @addramir in https://github.com/opentargets/gentropy/pull/863
• fix: biosample index add efo cell types by @Tobi1kenobi in https://github.com/opentargets/gentropy/pull/853
• feat(l2g): extend colocalisation neighbourhood metrics to missing genes in the vicinity by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/851
• fix: add scQTLs into coloc features by @addramir in https://github.com/opentargets/gentropy/pull/833
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/866
• feat: gwas catalog top-hit + study step by @d0choa in https://github.com/opentargets/gentropy/pull/808
• build(deps-dev): bump mypy from 1.11.0 to 1.12.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/865
• feat: adding desision tree to fine-mapper by @addramir in https://github.com/opentargets/gentropy/pull/860
• build(deps-dev): bump ruff from 0.6.1 to 0.7.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/864
• fix: logging of finemamper by @addramir in https://github.com/opentargets/gentropy/pull/870
• chore: add chromosome validation by @addramir in https://github.com/opentargets/gentropy/pull/869
• feat: add gene count features to l2g by @xyg123 in https://github.com/opentargets/gentropy/pull/852
• feat: change betas to posterior mean from susie for Finngen credible sets by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/872
• feat: step to export disease/target evidence by @DSuveges in https://github.com/opentargets/gentropy/pull/867
• feat(variant_index): hash variants at the time of instance creation by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/874
• fix: fix in calculate_credible_set_log10bf by @addramir in https://github.com/opentargets/gentropy/pull/868
• feat(l2g_feature_matrix): add credibleSetConfidence to L2G by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/875
• feat(l2g): normalise distance features by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/878
• feat: l2g feature to indicate if gene is protein-coding or not by @xyg123 in https://github.com/opentargets/gentropy/pull/873
• feat: making credset qc have an option to coalsce and deduplicate credible sets without ld pruning by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/877
• test(study_locus) credible_set_qc step integration test by @project-defiant in https://github.com/opentargets/gentropy/pull/880
• feat: flagging duplicated entries while keeping one of the duplicates by @DSuveges in https://github.com/opentargets/gentropy/pull/876
• feat: flag and filter credible sets by @Tobi1kenobi in https://github.com/opentargets/gentropy/pull/879
• build(deps-dev): bump ipython from 8.28.0 to 8.29.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/883
• build(deps-dev): bump mypy from 1.12.1 to 1.13.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/884
• feat(trainer): log model explanation with shap by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/886
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/885
• fix(distance_features): correct mean distance equation and correct rows with negative values by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/889
• feat: add step to generate association data by @vivienho in https://github.com/opentargets/gentropy/pull/888
• fix: revert distinct for associations input file by @vivienho in https://github.com/opentargets/gentropy/pull/871
• feat: add effect size direction to coloc output by @Tobi1kenobi in https://github.com/opentargets/gentropy/pull/854
• refactor(convert to vcf): allow multiple input sources by @project-defiant in https://github.com/opentargets/gentropy/pull/891
• feat: deconvolute studies upon ingestion of GWAS Catalog datasets by @DSuveges in https://github.com/opentargets/gentropy/pull/887
• fix(credibleSetConfidence): avoid null geneId in feature matrix by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/890
• feat(feature_matrix): impute values for gene attribute cols by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/895
• feat: adding l2g features to prediction table by @DSuveges in https://github.com/opentargets/gentropy/pull/899
• fix: ensure the #CHROM is not quoted by @project-defiant in https://github.com/opentargets/gentropy/pull/896
• feat(feature_matrix): extract features for gwas associations only by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/901
• fix: do not impute isProteinCoding by @addramir in https://github.com/opentargets/gentropy/pull/902
• fix: reclassify eqtl catalogue sc datasets by @Tobi1kenobi in https://github.com/opentargets/gentropy/pull/894
• feat: improve partitioning of credible sets by @d0choa in https://github.com/opentargets/gentropy/pull/900
• fix: using the 99% PIP cs column, by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/904
• chore: add hf_model_commit_message to LocusToGeneStep by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/905
• refactor: finemapping method enum by @d0choa in https://github.com/opentargets/gentropy/pull/897
• chore(l2g): parametrise score threshold when writing predictions by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/907
• chore: validate chromosome by @DSuveges in https://github.com/opentargets/gentropy/pull/906
• feat: extract pos and chromosome from variantid by @project-defiant in https://github.com/opentargets/gentropy/pull/909
• feat: changes to PICS credible sets (OUT_OF_SAMPLE_LD QC flag and capital PICS) by @vivienho in https://github.com/opentargets/gentropy/pull/910
• feat(gold_standard): arbitrary gold standards by @project-defiant in https://github.com/opentargets/gentropy/pull/912
• feat: gzip evicence output to match existing format by @project-defiant in https://github.com/opentargets/gentropy/pull/915
• feat: redefine neighbourhood features to represent similarity with best metric + other fixes by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/913
• chore(deps): bump codecov/codecov-action from 4 to 5 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/916
• build(deps-dev): bump pytest-cov from 5.0.0 to 6.0.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/893
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/898
• feat(variant index): variant description to summarise variant consequences in transcripts by @DSuveges in https://github.com/opentargets/gentropy/pull/914
• fix: r2 for lead variant is always 1 by @addramir in https://github.com/opentargets/gentropy/pull/919
• feat: reverting to using finngen 95% credible sets by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/922
• feat: changing studylocus validation to 95 percent credible sets by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/921
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/918
• chore(gnomad): updating GnomAD version to 4.1 from 4.0 + using joint frequencies by @DSuveges in https://github.com/opentargets/gentropy/pull/929
• feat(gold_standard): add traitFromSourceMappedId to schema by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/924
• feat: coalescing the datasets by @project-defiant in https://github.com/opentargets/gentropy/pull/932
• chore(vep): Ensembl version update by @DSuveges in https://github.com/opentargets/gentropy/pull/931
• feat: coalesce l2g fm and predictions by @project-defiant in https://github.com/opentargets/gentropy/pull/934
• feat: allow building package from tag by @project-defiant in https://github.com/opentargets/gentropy/pull/930
• feat: adding GERP conservation score to variant annotation by @DSuveges in https://github.com/opentargets/gentropy/pull/933
• fix: swap the ref parse by @project-defiant in https://github.com/opentargets/gentropy/pull/935
• build(deps-dev): bump ipython from 8.29.0 to 8.30.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/937
• build(deps-dev): bump ruff from 0.7.1 to 0.8.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/936
• fix(l2g_predictions): annotate based on list of features + filter out missing annotation by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/925
• feat(l2g): implement new training strategy splitting between EFO/gene pairs and with cross validation by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/938
• chore: trigger release process by @github-actions[bot] in https://github.com/opentargets/gentropy/pull/858
• build: define dependency version constraints + other fixes by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/945
• build(deps-dev): bump ipykernel from 6.28.0 to 6.29.5 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/953
• build(deps-dev): bump pytest-xdist from 3.5.0 to 3.6.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/952
• build(deps-dev): bump lxml from 5.1.1 to 5.3.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/950
• build(deps-dev): bump google-cloud-dataproc from 5.8.0 to 5.10.1 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/951
• refactor: drop version_engine by @project-defiant in https://github.com/opentargets/gentropy/pull/940
• build(deps-dev): bump ipython from 8.29.0 to 8.30.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/949
• chore: trigger release process by @github-actions[bot] in https://github.com/opentargets/gentropy/pull/959
• 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[bot] in https://github.com/opentargets/gentropy/pull/976
• chore: revert pre-commit update (a99ca84) 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[bot] 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[bot] 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[bot] 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[bot] in https://github.com/opentargets/gentropy/pull/961
• fix(study_locus_valiation): ensure the the transQtlColumn is missing by @project-defiant in https://github.com/opentargets/gentropy/pull/990
• feat: new Loss-of-Function variant data from OTAR2075 by @vivienho in https://github.com/opentargets/gentropy/pull/991
• chore(docs): update _ukb_ppp_eur.md by @buniello in https://github.com/opentargets/gentropy/pull/995
• fix(dataset): filter maintains instance attributes by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/996
• feat(l2gprediction): add score explanation based on features by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/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[bot] in https://github.com/opentargets/gentropy/pull/994
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/988
• fix(l2g): direct model path to hf repo when none and align training data filename by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/997
• chore(shap): sample background dataset to make explanation faster by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/998
• feat: local dataproc cluster settings udpate by @project-defiant in https://github.com/opentargets/gentropy/pull/999
• fix: dev release process by @project-defiant in https://github.com/opentargets/gentropy/pull/992
• fix: foldx column name fix by @DSuveges in https://github.com/opentargets/gentropy/pull/1005
• chore(trainer): sample train set to base model importances on by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1001
• fix: solve NULLs found in variantEffect struct of the variant index by @vivienho in https://github.com/opentargets/gentropy/pull/1003
• fix: qemu libc segfault during docker build action by @project-defiant in https://github.com/opentargets/gentropy/pull/1004
• fix: change posterior filter by @xyg123 in https://github.com/opentargets/gentropy/pull/1006
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1002
• chore(deps): bump docker/setup-qemu-action from 3.4.0 to 3.6.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1011
• chore(deps): bump python-semantic-release/publish-action from 9.19.1 to 9.21.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1010
• build(deps): update google-cloud-storage requirement from <3.1.0,>=2.14.0 to >=2.14.0,<3.2.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1009
• chore(l2g): make shap optional by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1012
• feat(l2g): update params after fine tuning for the new training data by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1014
• feat(l2g): download specific model version from hub by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1015
• chore: trigger release process by @github-actions[bot] in https://github.com/opentargets/gentropy/pull/993
• fix: addressing #3800 and #3799 by @DSuveges in https://github.com/opentargets/gentropy/pull/1017
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1018
• Fix: Ensure qualityControls and analysisFlags columns are always added when curation_table is None by @ffrnz in https://github.com/opentargets/gentropy/pull/1020
• refactor(l2g): make wandb logging optional by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1019
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1022
• chore: offline check uv lock by @project-defiant in https://github.com/opentargets/gentropy/pull/1024
• chore: skip uv-lock on pre-commit ci by @project-defiant in https://github.com/opentargets/gentropy/pull/1027
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1028
• build(deps): update shap requirement by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1016
• feat: (coloc) parameterise the small overlaps filtering criteria so they can be specified in orchestration by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/1030
• feat: slimmer docker image by @ffrnz in https://github.com/opentargets/gentropy/pull/1023
• chore(deps): bump actions/create-github-app-token from 1 to 2 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1033
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1031
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1036
• fix: remove trans molQTLs from FM by @addramir in https://github.com/opentargets/gentropy/pull/1038
• docs: remove roadmap section by @d0choa in https://github.com/opentargets/gentropy/pull/1042
• chore(VEP): Update Ensembl to 144 by @DSuveges in https://github.com/opentargets/gentropy/pull/1043
• refactor(summary_statistics_qc): Summary Statistics QC dataset by @project-defiant in https://github.com/opentargets/gentropy/pull/1040
• fix: correction of the code for calculating log10BF for credible sets by @Daniel-Considine in https://github.com/opentargets/gentropy/pull/1041
• fix: ensure the coloc method name is not added to the output by @project-defiant in https://github.com/opentargets/gentropy/pull/1044
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1037
• chore(deps): bump astral-sh/setup-uv from 5 to 6 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1035
• chore: remove vep image and artifact build by @project-defiant in https://github.com/opentargets/gentropy/pull/1045
• fix: fix isProteincoding by @addramir in https://github.com/opentargets/gentropy/pull/1046
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1047
• fix(changelog): ensure the changelog template is reused by @project-defiant in https://github.com/opentargets/gentropy/pull/1048
• fix(l2g): half of the feature matrix have distance features larger than 1 by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1053
• feat: pass partition number to the step by @project-defiant in https://github.com/opentargets/gentropy/pull/1054
• feat(sumstat): rescue standard error from p-value and beta by @project-defiant in https://github.com/opentargets/gentropy/pull/1059
• feat: standard error from ci by @project-defiant in https://github.com/opentargets/gentropy/pull/1061
• fix: spark plan optimisation by @DSuveges in https://github.com/opentargets/gentropy/pull/1055
• fix: neglog func fix by @addramir in https://github.com/opentargets/gentropy/pull/1062
• chore: adding pubmed identifier to evidence by @DSuveges in https://github.com/opentargets/gentropy/pull/1068
• fix: adding rsids to GnomAD variants by @DSuveges in https://github.com/opentargets/gentropy/pull/1060
• feat: adding pmid to finngen studies by @DSuveges in https://github.com/opentargets/gentropy/pull/1069
• chore: trigger release process by @github-actions[bot] in https://github.com/opentargets/gentropy/pull/1021
• fix: add pyarrow for pyspark pandas_udf api by @project-defiant in https://github.com/opentargets/gentropy/pull/1071
• build(deps): update pandas[gcp,parquet] requirement from <2.3.0,>=2.2.3 to >=2.2.3,<2.4.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1056
• chore(deps): bump python-semantic-release/publish-action from 9.21.0 to 10.2.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1067
• build(deps): update wandb requirement from <0.20.0,>=0.19.4 to >=0.19.4,<0.22.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1070
• feat: implement Germline Methods team compatibility changes by @Germline-Methods in https://github.com/opentargets/gentropy/pull/1072
• build(deps): update google-cloud-storage requirement from <3.2.0,>=2.14.0 to >=2.14.0,<3.3.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1075
• build(deps): update shap requirement from <0.48,>=0.46 to >=0.46,<0.49 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1066
• build(deps): update google-cloud-secret-manager requirement from <2.24.0,>=2.12.6 to >=2.12.6,<2.25.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1058
• build(deps): update scikit-learn requirement from <1.7.0,>=1.6.1 to >=1.6.1,<1.8.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1065
• build(deps): update mkdocs-git-committers-plugin-2 requirement from <2.5.0,>=2.2.3 to >=2.2.3,<2.6.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1083
• fix(l2g): move append_null_features param to feature matrix step by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1078
• chore(deps): bump python-semantic-release/publish-action from 10.2.0 to 10.3.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1084
• build(deps): update pytest-xdist requirement from <3.7.0,>=3.5.0 to >=3.5.0,<3.9.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1081
• build(deps): update ruff requirement from <0.9.0,>=0.8.1 to >=0.8.1,<0.13.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1080
• build(deps): update lxml requirement from <5.4.0,>=5.1.0 to >=5.1.0,<6.1.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1082
• build(deps): update ipython requirement from <8.31.0,>=8.19.0 to >=8.19.0,<8.38.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1085
• build(deps): update google-cloud-storage requirement from <3.2.0,>=2.14.0 to >=2.14.0,<3.3.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1079
• build(deps): update ipykernel requirement from <6.30.0,>=6.28.0 to >=6.28.0,<6.31.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1093
• build(deps): update pydoclint requirement from <0.6.0,>=0.3.8 to >=0.3.8,<0.7.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1092
• build(deps): update typing-extensions requirement from <4.13.0,>=4.12.2 to >=4.12.2,<4.15.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1095
• build(deps): update mkdocstrings-python requirement from <1.13.0,>=1.12.2 to >=1.12.2,<1.17.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1094
• build(deps): update pymdown-extensions requirement from <10.13,>=10.7 to >=10.7,<10.17 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1088
• feat(l2g): hierarchical splitting by gene by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1076
• feat(l2g): log train and test sets into hugging face by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1086
• feat(l2g): migrate to xgboost classifier and set best params by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1077
• build(deps): update pep8-naming requirement from <0.15.0,>=0.14.1 to >=0.14.1,<0.16.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1089
• build(deps): update mkdocs-git-revision-date-localized-plugin requirement from <1.4.0,>=1.2.2 to >=1.2.2,<1.5.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1090
• chore(deps): bump actions/download-artifact from 4 to 5 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1091
• build(deps): update pre-commit requirement from <4.1.0,>=4.0.0 to >=4.0.0,<4.4.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1096
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1052
• chore(l2g): set random seed to 777 🧘‍♀️ by @ireneisdoomed in https://github.com/opentargets/gentropy/pull/1097
• build(docker,xgboost): update docker build by @project-defiant in https://github.com/opentargets/gentropy/pull/1108
• build(deps): update mkdocstrings-python requirement from <1.17.0,>=1.12.2 to >=1.12.2,<1.18.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1104
• build(deps): update yamllint requirement from <1.36.0,>=1.33.0 to >=1.33.0,<1.38.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1112
• chore(deps): bump docker/build-push-action from 5 to 6 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1111
• chore(deps): bump google-github-actions/auth from 2 to 3 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1110
• chore(deps): bump actions/attest-build-provenance from 1 to 3 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1109
• chore(deps): bump actions/setup-java from 4 to 5 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1105
• build(deps): update skops requirement from <0.12.0,>=0.11.0 to >=0.11.0,<0.14.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1103
• build(deps): update mypy requirement from <1.14,>=1.13 to >=1.13,<1.18 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1102
• build(deps): update isort requirement from <5.14.0,>=5.13.2 to >=5.13.2,<6.1.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1101
• build(deps): update google-cloud-storage requirement from <3.3.0,>=2.14.0 to >=2.14.0,<3.4.0 by @dependabot[bot] in https://github.com/opentargets/gentropy/pull/1100
• chore: pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/opentargets/gentropy/pull/1099
• chore: trigger release process by @github-actions[bot] in https://github.com/opentargets/gentropy/pull/1107

New Contributors

• @mkarmona made their first contribution in #1
• @pre-commit-ci[bot] made their first contribution in #17
• @tskir made their first contribution in #47
• @buniello made their first contribution in #84
• @hlnicholls made their first contribution in #86
• @dependabot[bot] made their first contribution in #182
• @addramir made their first contribution in #345
• @RobinM-code made their first contribution in #510
• @louwenjjr made their first contribution in #533
• @vivienho made their first contribution in https://github.com/opentargets/gentropy/pull/770
• @Tobi1kenobi made their first contribution in https://github.com/opentargets/gentropy/pull/769
• @ffrnz made their first contribution in https://github.com/opentargets/gentropy/pull/1020
• @Germline-Methods made their first contribution in https://github.com/opentargets/gentropy/pull/1072

Full Changelog: https://github.com/opentargets/gentropy/commits/v2.4.0