v2.4.0
·
94 commits
to dev
since this release
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
gnomad3VariantIdto 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_idby @ireneisdoomed in #103 - Add
test__finemapby @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_ldfunction 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
StudyLocusOverlapsstep 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
studyLocusIdto GWASCat data by @ireneisdoomed in #119 - Set
Datasetas 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
pydoclintas 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-python3.10and 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.yamlby @ireneisdoomed in #217 - Re-enable and fix the
test_no_import_errorsAirflow 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_annotationandldindexsteps 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_UIDby @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_parquetwhen 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_intervalby @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
clumpstep 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_datasetandtest_clump_stepby @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_benchmarknotebook 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_ratecounts 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_namein 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
locuswhen 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.filterto 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_matrixstatic 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_thrparameter 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
studyTypetoStudyLocusandColocalisation(andStudyLocusOverlap) 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_validationby @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
StudyLocusIdhashing method to md5 (and changeStudyLocusIdto string type) by @vivienho in https://github.com/opentargets/gentropy/pull/783 - feat: drop
v2gand 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
qualityControlscolumn 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
studyLocusIdbefore 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_rsidsby @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
numberColocalisingVariantsfield 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
credibleSetConfidenceto 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
isProteinCodingby @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_messagetoLocusToGeneStepby @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):
filtermaintains 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 invariantEffectstruct 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
qualityControlsandanalysisFlagscolumns are always added whencuration_tableis 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_featuresparam 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