Release v2.4.0 · opentargets/gentropy

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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

v2.4.0

Choose a tag to compare

Sorry, something went wrong.

Sorry, something went wrong.

Uh oh!

No results found

What's Changed

What's Changed

New Contributors

Contributors

Uh oh!