chore: trigger release process#4

Open

github-actions[bot] wants to merge 387 commits intomainfrom dev

+38,941-17,338

This pull request is big! We're only showing the most recent 250 commits

Commits on Jun 11, 2024

feat: enable interface with gcp secrets manager (opentargets#635 )
ireneisdoomed
authored
feat: credible set quality filtering (opentargets#640 )
Daniel-Considine
authored

Commits on Jun 13, 2024

build(deps-dev): bump dbldatagen from 0.3.5 to 0.4.0 (opentargets#637 )
dependabot[bot]
authored
feat(config): 24.06 data release fixes (opentargets#639 )

project-defiant
and
Szymon Szyszkowski
authored

Commits on Jun 14, 2024

fix(L2GPrediction): schema validation (opentargets#642 )

project-defiant
and
Szymon Szyszkowski
authored

Commits on Jun 17, 2024

Commits on Jun 19, 2024

feat(stydyLocus): adding new locus collection using boundaries (opentargets#644 )

authored

Commits on Jun 24, 2024

Commits on Jun 25, 2024

Commits on Jun 28, 2024

Commits on Jun 30, 2024

feat(datasets): adding new variant index model (opentargets#641 )

DSuveges
and
pre-commit-ci[bot]
authored

Commits on Jul 4, 2024

feat: vep annotation (dockerised + google batch + airflow) (opentargets#608 )

authored

Commits on Jul 8, 2024

feat: locus_breaker_clumping (opentargets#655 )

Daniel-Considine
and
addramir
authored

Commits on Jul 11, 2024

Commits on Jul 12, 2024

build(deps-dev): bump ipython from 8.25.0 to 8.26.0 (opentargets#662 )

dependabot[bot]
and
d0choa
authored
ci: prevent user from rebasing in minimal way (opentargets#691 )

project-defiant
and
Szymon Szyszkowski
authored
feat: artifacts versionned by release (opentargets#692 )

project-defiant
and
Szymon Szyszkowski
authored
fix: moving hl.init (opentargets#687 )
Daniel-Considine
authored
chore(study_index): improve study definition for the eQTL Catalogue and Finngen (opentargets#693 )
ireneisdoomed
authored
feat(studyLocus validation): adding validation logic to studyLocus dataset (opentargets#686 )

DSuveges
and
d0choa
authored
ci: revert semantic-release update (opentargets#694 )

project-defiant
and
Szymon Szyszkowski
authored
feat: full orchestration of the variant index dag (opentargets#678 )

ireneisdoomed
and
DSuveges
authored

Commits on Jul 15, 2024

Commits on Jul 16, 2024

Commits on Jul 17, 2024

feat: implement reading study locus paths from the manifest (opentargets#706 )
tskir
authored

Commits on Jul 19, 2024

ci(release): use github app token for tag push (opentargets#709 )
project-defiant
authored

Commits on Jul 25, 2024

feat: expose summary statistics qc and locus breaker steps to hydra cli (opentargets#716 )

project-defiant
and
Szymon Szyszkowski
authored

Commits on Jul 29, 2024

fix: change config params to match new name (opentargets#721 )

project-defiant
and
Szymon Szyszkowski
authored

Commits on Jul 30, 2024

chore: pre-commit autoupdate (opentargets#715 )
pre-commit-ci[bot]
authored

Commits on Jul 31, 2024

build(deps-dev): bump pymdown-extensions from 10.8.1 to 10.9 (opentargets#720 )

dependabot[bot]
and
project-defiant
authored

Commits on Aug 15, 2024

docs: macos fix for some functions (opentargets#729 )
Daniel-Considine
authored

Commits on Aug 22, 2024

Commits on Aug 23, 2024

Commits on Aug 27, 2024

feat(variant_index): changes for a successful run (opentargets#735 )

authored

Commits on Aug 28, 2024

fix: update cluster creation command (opentargets#739 )

project-defiant
and
Szymon Szyszkowski
authored
fix: revert recursiveFileLookup to False (opentargets#738 )

project-defiant
and
Szymon Szyszkowski
authored

Commits on Aug 29, 2024

feat: Finngen r11 ingestion (opentargets#733 )

authored

Commits on Aug 30, 2024

fix: using h4 instead of log2(h4/h3) (opentargets#740 )
Daniel-Considine
authored

Commits on Sep 4, 2024

fix(finngen_r11): preserve all studyIds (opentargets#747 )

authored

Commits on Sep 9, 2024

Commits on Sep 10, 2024

build(deps-dev): bump deptry from 0.19.1 to 0.20.0 (opentargets#742 )

dependabot[bot]
and
project-defiant
authored
fix: validation name mapping (opentargets#753 )

project-defiant
and
Szymon Szyszkowski
authored

Commits on Sep 12, 2024

feat(validation): adding credible set variant validation (opentargets#757 )
DSuveges
authored
feat: drop airflow orchestration layer from gentropy (opentargets#758 )

project-defiant
and
Szymon Szyszkowski
authored

Commits on Sep 13, 2024

Commits on Sep 17, 2024

Commits on Sep 19, 2024

perf: quickly build a Docker image for every branch (opentargets#773 )
tskir
authored

Commits on Sep 24, 2024

Commits on Sep 25, 2024

fix: clean unused study_locus step parameter (opentargets#786 )
d0choa
authored

Commits on Sep 26, 2024

Commits on Sep 27, 2024

fix(safe_array_union): allow for sorting nested structs (opentargets#793 )

project-defiant
and
Szymon Szyszkowski
authored
fix: fix bag in neglog_pvalue_to_mantissa_and_exponent (opentargets#795 )
addramir
authored

Commits on Oct 1, 2024

feat: drop v2g and reimplement distance features (opentargets#771 )
ireneisdoomed
authored
feat: out sample LD qc reason (opentargets#798 )

d0choa
and
DSuveges
authored
chore: drop redundant parameter (opentargets#802 )

project-defiant
and
Szymon Szyszkowski
authored
fix: align the schema of study_index for ukb ppp eur (opentargets#803 )

project-defiant
and
Szymon Szyszkowski
authored
feat: force reinstallation of the gentropy on the cluster (opentargets#804 )

project-defiant
and
Szymon Szyszkowski
authored
feat(validation): adding credible set confidence annotation at validation time (opentargets#801 )
DSuveges
authored

Commits on Oct 2, 2024

Commits on Oct 7, 2024

fix: biosample id duplication (opentargets#822 )
Tobi1kenobi
authored

Commits on Oct 8, 2024

Commits on Oct 10, 2024

Commits on Oct 12, 2024

feat: enhance variant index partitioning (opentargets#834 )
d0choa
authored

Commits on Oct 14, 2024

Commits on Oct 16, 2024

fix: updating the susie_finemapper init (opentargets#846 )

Daniel-Considine
and
addramir
authored

Commits on Oct 17, 2024

Commits on Oct 21, 2024

Commits on Oct 22, 2024

Commits on Oct 23, 2024

Commits on Oct 25, 2024

Commits on Oct 26, 2024

feat: flagging duplicated entries while keeping one of the duplicates (opentargets#876 )

DSuveges
and
addramir
authored

Commits on Nov 6, 2024

Commits on Nov 7, 2024

Commits on Nov 8, 2024

refactor: finemapping method enum (opentargets#897 )

d0choa
and
addramir
authored

Commits on Nov 11, 2024

Commits on Nov 12, 2024

feat: changes to PICS credible sets (OUT_OF_SAMPLE_LD QC flag and capital PICS) (opentargets#910 )
vivienho
authored

Commits on Nov 14, 2024

feat(gold_standard): arbitrary gold standards (opentargets#912 )

project-defiant
and
Szymon Szyszkowski
authored

Commits on Nov 15, 2024

Commits on Nov 19, 2024

feat(variant index): variant description to summarise variant consequences in transcripts (opentargets#914 )

DSuveges
and
pre-commit-ci[bot]
authored

Commits on Nov 20, 2024

fix: r2 for lead variant is always 1 (opentargets#919 )

addramir
and
DSuveges
authored

Commits on Nov 21, 2024

Commits on Nov 22, 2024

chore: pre-commit autoupdate (opentargets#918 )
pre-commit-ci[bot]
authored

Commits on Nov 26, 2024

chore(gnomad): updating GnomAD version to 4.1 from 4.0 + using joint frequencies (opentargets#929 )
DSuveges
authored

Commits on Nov 27, 2024

feat(gold_standard): add traitFromSourceMappedId to schema (opentargets#924 )
ireneisdoomed
authored
feat: coalescing the datasets (opentargets#932 )

project-defiant
and
Szymon Szyszkowski
authored