v2.0.1

What's Changed

🐛 Fix

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

♻️ Refactor

• drop version_engine (#940) @Szymon Szyszkowski

🏗 Build

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

🚀 Chore

• siplify the release CI conditions @project-defiant

v2.0.0

What's Changed

💥 Breaking

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

✨ Feature

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

🐛 Fix

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

v1.7.0

What's Changed

✨ Feature

• implement reading study locus paths from the manifest (#706) @Kirill Tsukanov

🏗 Build

• [deps-dev] bump mypy from 1.10.0 to 1.11.0 (#713) @dependabot[bot]
• [deps-dev] bump deptry from 0.16.1 to 0.17.0 (#714) @dependabot[bot]
• [deps-dev] bump pytest from 8.2.2 to 8.3.1 (#712) @dependabot[bot]

👷‍♂️ Ci

• [release] use github app token for tag push (#709) @Szymon Szyszkowski

v1.6.0

What's Changed

✨ Feature

• allow image push @Szymon Szyszkowski
• [docker] drom jq @Szymon Szyszkowski
• explode loci to extract variants + tests @Irene López

🐛 Fix

• [finemapping] typo in "elapsed_time" @Kirill Tsukanov
• typo in artifact file @Szymon Szyszkowski
• [docker] change JAVA_HOME env to /usr @Szymon Szyszkowski
• fix issue with gh commit not triggering artifact workflow @Szymon Szyszkowski

👷‍♂️ Ci

• authentication with github app @Szymon Szyszkowski

🚀 Chore

• pre-commit autoupdate @pre-commit-ci[bot]

v1.5.0

What's Changed

✨ Feature

• full orchestration of the variant index dag (#678) @Irene López Santiago
• [studyLocus validation] adding validation logic to studyLocus dataset (#686) @Daniel Suveges
• artifacts versionned by release (#692) @Szymon Szyszkowski

🐛 Fix

• moving hl.init (#687) @Daniel-Considine

👷‍♂️ Ci

• revert semantic-release update (#694) @Szymon Szyszkowski
• prevent user from rebasing in minimal way (#691) @Szymon Szyszkowski

🚀 Chore

• [study_index] improve study definition for the eQTL Catalogue and Finngen (#693) @Irene López Santiago

v1.4.0

What's Changed

✨ Feature

• [config] 24.06 data release fixes (#639) @Szymon Szyszkowski
• credible set quality filtering (#640) @Daniel-Considine
• enable interface with gcp secrets manager (#635) @Irene López
• adding locus-breaker clumping method (#634) @Daniel Suveges
• [spark-helpers] enforce schema of returned objects (#617) @Daniel Suveges
• [qtl] ingest credible sets from single cell derived QTLs (#630) @Irene López
• [data_release] preparation for 24.06 data release (#633) @Szymon Szyszkowski
• [config] extract gwas_significance parameter to step configuration (#628) @Szymon Szyszkowski
• [config] gnomAD steps configuration extraction and versioning (#620) @Szymon Szyszkowski
• fine-mapping simulations class (#618) @Yakov

🐛 Fix

• [L2GPrediction] schema validation (#642) @Szymon Szyszkowski
• [docs] fixed typo in l2g_prediciton schema page (#629) @Szymon Szyszkowski
• [SummaryStatistics] fix in sanity_filter (#623) @Yakov
• [susie_finemapper] fix in the fine-mapper in case of sum stat imputation is False (#627) @Yakov
• [susie_finemapper] correct syntax for saving the logs df (#625) @Kirill Tsukanov
• [ld] correct syntax for the static method (#624) @Kirill Tsukanov
• [docs] update roadmap.md (#622) @buniello
• [spark helpers] sorter function updated to avoid crash (#613) @Daniel Suveges

🏗 Build

• [deps-dev] bump dbldatagen from 0.3.5 to 0.4.0 (#637) @dependabot[bot]
• [deps] bump scikit-learn from 1.4.0 to 1.5.0 (#638) @dependabot[bot]
• [deps-dev] bump ipython from 8.24.0 to 8.25.0 (#636) @dependabot[bot]
• [deps] bump wandb from 0.16.2 to 0.17.0 (#606) @dependabot[bot]
• [deps-dev] bump pep8-naming from 0.13.3 to 0.14.1 (#616) @dependabot[bot]
• [deps] bump typing-extensions from 4.11.0 to 4.12.1 (#632) @dependabot[bot]
• [deps] use pandas[gcp, parquet] (#626) @Kirill Tsukanov

v1.3.0

What's Changed

✨ Feature

• [airflow] include COLOC as a node in the DAG (#530) @Irene López
• check for if no overlapping variants in LD index (#594) @Daniel-Considine
• add purity qc metrics to fine-mapping (#592) @Yakov
• lighter dockerfile (#585) @David Ochoa
• github action to upload docker image to registry (#588) @David Ochoa
• functionality added to StudyLocus.find_overlaps() for finding within-study overlaps (#587) @Daniel-Considine
• susie_finemapper_one_studylocus_row_v3_dev_ss_gathered (#586) @Yakov
• [sumstat qc] adding methods for QC of summary statistics (#455) @Yakov
• changing locus window to locus radius to be consistent with other functions (#582) @Daniel-Considine
• updating step config file (#580) @Daniel-Considine
• dockerise gentropy python package (#579) @Irene López
• adding init to finemapping step (#577) @Daniel-Considine
• adding notebook for mapping EFOs for the FinnGen study index (#575) @Yakov
• add benchmarking for fine-mapping using Alzheimer as example (#572) @Yakov
• add FM step with carma and sumstat imputation (#568) @Yakov
• susie_finemapper_ss_gathered() (#567) @Daniel-Considine
• the FineMapper function for one locus (#564) @Yakov
• LD index and block matrix extraction for a studyLocus (#463) @Daniel-Considine
• add the step class for fine-mapping (#554) @Yakov
• notebook to run qc metrics each release (#541) @xyg123
• [l2g] distance features based on weighted score (#545) @Irene López
• [sumstat imputation] adding class for sumstat imputation (#490) @Yakov
• [coloc] single SNP case (#511) @xyg123
• extract credible sets and studies from all eQTL Catalogue finemapping results (#518) @Irene López

🐛 Fix

• fix python-semantic-release version (again) @David Ochoa
• fix python-semantic-release version @David Ochoa
• docker action fixes v3 (#591) @David Ochoa
• docker action fixes (#590) @David Ochoa
• docker action fixes (#589) @David Ochoa
• updating config.py argument for finemapper (#584) @Daniel-Considine
• minor updates and bug fixes (#543) @Daniel Suveges
• update error in config.py (#583) @Daniel-Considine
• removing all duplicated variants in sumstats for finemapping functions (#574) @Daniel-Considine
• adding deduplication for GWAS in locus (#573) @Yakov
• [sumstats] correct study id for dir of finngen studies (#551) @Joris Louwen
• [coloc] handle cases when the bayes factors are null (#556) @Irene López
• small fixes in susie defaults (#552) @Yakov
• read function for thurman data to include first line (#534) @Joris Louwen
• pin version of commitlint (#533) @Joris Louwen
• pr labeller patterns (#523) @David Ochoa

♻️ Refactor

• moving all variant coordinates to GnomAD (#566) @Daniel Suveges

⚡️ Performance

• [l2g] optimise extraction of features from colocalisation results (#553) @Irene López
• [clump] refactored window based clumping (#492) @David Ochoa
• [l2g] streamline feature generation (#544) @Irene López

✅ Test

• [method] improved performance in coloc tests (#536) @xyg123

🏗 Build

• [deps-dev] bump mypy from 1.9.0 to 1.10.0 (#604) @dependabot[bot]
• [deps-dev] bump ipython from 8.22.1 to 8.24.0 (#603) @dependabot[bot]
• [deps] bump typing-extensions from 4.10.0 to 4.11.0 (#602) @dependabot[bot]
• [deps-dev] bump ruff from 0.3.2 to 0.4.3 (#596) @dependabot[bot]
• [deps-dev] bump pytest-xdist from 3.5.0 to 3.6.1 (#597) @dependabot[bot]
• [deps-dev] bump pytest from 8.1.0 to 8.2.0 (#598) @dependabot[bot]
• [deps-dev] bump interrogate from 1.5.0 to 1.7.0 (#599) @dependabot[bot]
• [deps-dev] bump pymdown-extensions from 10.7 to 10.8.1 (#600) @dependabot[bot]
• [deps-dev] bump python-semantic-release from 9.1.0 to 9.4.1 (#571) @dependabot[bot]
• [deps-dev] bump pytest-cov from 4.1.0 to 5.0.0 (#560) @dependabot[bot]
• [deps-dev] bump pre-commit from 3.6.0 to 3.7.0 (#559) @dependabot[bot]
• [deps-dev] bump lxml from 5.1.0 to 5.2.1 (#569) @dependabot[bot]
• [deps-dev] bump deptry from 0.14.0 to 0.16.1 (#570) @dependabot[bot]
• [deps-dev] bump mkdocstrings-python from 1.8.0 to 1.9.0 (#549) @dependabot[bot]
• [deps-dev] bump deptry from 0.12.0 to 0.14.0 (#548) @dependabot[bot]
• [deps-dev] bump mypy from 1.8.0 to 1.9.0 (#532) @dependabot[bot]
• [deps-dev] bump ruff from 0.2.0 to 0.3.2 (#531) @dependabot[bot]

👷‍♂️ Ci

• bugfix in PR labeller (#537) @David Ochoa

🚀 Chore

• pre-commit autoupdate (#601) @pre-commit-ci[bot]
• pre-commit autoupdate (#593) @pre-commit-ci[bot]
• pre-commit autoupdate (#561) @pre-commit-ci[bot]
• pre-commit autoupdate (#550) @pre-commit-ci[bot]
• [l2g] log annotated gold standards in w&b (#546) @Irene López
• pre-commit autoupdate (#539) @pre-commit-ci[bot]
• update ruff pre-commit and rules (#522) @David Ochoa
• add sqtl, tuqtl, pqtl features to l2g inclusion list @Irene López
• add tuqtl features to L2Gfeaturematrix schema @Irene López

v1.2.0

What's Changed

✨ Feature

• [coloc] single SNP case (#511) @xyg123
• extract credible sets and studies from all eQTL Catalogue finemapping results (#518) @Irene López
• [CARMA] adding time limited CARMA (#475) @Yakov
• extract credible sets and studies from eQTL Catalogue finemapping results (#514) @Irene López

🐛 Fix

• pr labeller patterns (#523) @David Ochoa
• pull-request labeler fixes (#520) @David Ochoa

🏗 Build

• [deps-dev] bump pytest from 8.0.1 to 8.1.0 (#516) @dependabot[bot]
• [deps-dev] bump mkdocs-git-committers-plugin-2 from 2.2.3 to 2.3.0 (#505) @dependabot[bot]
• [deps] bump typing-extensions from 4.9.0 to 4.10.0 (#506) @dependabot[bot]
• [deps-dev] bump ipython from 8.21.0 to 8.22.1 @dependabot[bot]

👷‍♂️ Ci

• precommit checks for poetry TOML and lock (#526) @David Ochoa
• pull request template (#517) @David Ochoa
• pull request labeler (#519) @David Ochoa

🚀 Chore

• update ruff pre-commit and rules (#522) @David Ochoa
• Unit tests for coloc (#509) @xyg123

v1.1.1

What's Changed

🐛 Fix

• [finemapping] finngen harmonisation (schema and orchestration) (#489) @xyg123
• update github token variable (#476) @Irene López

📖 Documentation

• susie inf method reloacated with the rest of the methods @David Ochoa

✅ Test

• increase modularity of test directories (#502) @David Ochoa

🏗 Build

• [deps-dev] bump apache-airflow-providers-google (#496) @dependabot[bot]
• [deps-dev] bump python-semantic-release from 9.0.3 to 9.1.0 (#495) @dependabot[bot]
• [deps-dev] bump yamllint from 1.33.0 to 1.35.1 (#494) @dependabot[bot]
• [deps-dev] bump pydoclint from 0.3.8 to 0.4.1 (#497) @dependabot[bot]
• [deps-dev] bump pytest from 7.4.4 to 8.0.1 (#493) @dependabot[bot]
• [deps-dev] bump python-semantic-release from 8.7.0 to 9.0.3 @dependabot[bot]

👷‍♂️ Ci

• pre-commit autoupdate message (#500) @David Ochoa
• pre-commit updates (#499) @David Ochoa
• exclude changelog.md from precommit (#479) @David Ochoa
• [release] add action to open pr that triggers release weekly (#474) @Irene López

v1.1.0

What's Changed

✨ Feature

• [finemapping] ingest finngen r10 finemapping w/ airflow (#435) @xyg123
• [finemapping] susie method (#398) @Daniel-Considine
• [dataset] add Dataset.filter to create a new dataset instance with filtered data (#470) @Irene López
• [LD] include leads with R2=1 in the ldSet when not found in LDIndex (#453) @David Ochoa

📖 Documentation

• [StudyLocusQualityCheck] update outdated attributes (#452) @David Ochoa
• add gentropy first steps guide (#449) @Irene López
• pypi badges (#439) @David Ochoa

🏗 Build

• [deps-dev] bump google-cloud-dataproc from 5.8.0 to 5.9.0 (#468) @dependabot[bot]
• [deps-dev] bump pytest-sugar from 0.9.7 to 1.0.0 (#467) @dependabot[bot]
• [deps-dev] bump ipython from 8.20.0 to 8.21.0 (#466) @dependabot[bot]
• [deps-dev] bump ruff from 0.1.8 to 0.2.0 (#465) @dependabot[bot]
• [deps] bump scikit-learn from 1.3.2 to 1.4.0 (#444) @dependabot[bot]
• [deps] bump pandas from 2.1.4 to 2.2.0 (#443) @dependabot[bot]
• [deps-dev] bump ipykernel from 6.28.0 to 6.29.0 (#442) @dependabot[bot]
• [deps] bump numpy from 1.26.2 to 1.26.3 (#441) @dependabot[bot]
• [deps-dev] bump ipython from 8.19.0 to 8.20.0 (#445) @dependabot[bot]

👷‍♂️ Ci

• ignore patch versions in dependabot (#462) @David Ochoa

🚀 Chore

• merge dev @David Ochoa
• minor updates to gwas catalog pathnames (#440) @Irene López
• [deps] bump codecov/codecov-action from 3 to 4 (#464) @dependabot[bot]
• harmonizing finngen configuration (#454) @Daniel Suveges
• [deps] bump actions/upload-artifact from 3 to 4 (#447) @dependabot[bot]
• [deps] bump actions/download-artifact from 3 to 4 (#448) @dependabot[bot]
• [deps] bump actions/cache from 3 to 4 (#446) @dependabot[bot]