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chore: trigger release process#565

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Commits on Feb 27, 2024

• chore: small updates to accomodate GWAS Catalog for feb release

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Commits on Feb 28, 2024

• fix: updating cohort parser to new GWAS Catalog format

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Commits on Mar 4, 2024

• fix: updating study index generation from gwas flat files

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Commits on Mar 6, 2024

• Merge branch 'dev' into ds_gwas_update

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Commits on Mar 7, 2024

• chore: resolve merge commit

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• chore: bumping for 24.03 release

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• fix: reverting some changes

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Commits on Mar 8, 2024

• chore: add tuqtl features to L2Gfeaturematrix schema

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• chore: add sqtl, tuqtl, pqtl features to l2g inclusion list

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• Merge pull request #529 from opentargets/il-l2g-config-changes

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• feat: extract credible sets and studies from all eQTL Catalogue finemapping results (#518)

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• fix: fixing merge conflict

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• revert: make setup dev not to update pre-commits (#524)

  

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• chore: update ruff pre-commit and rules (#522)

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• fix: pr labeller patterns (#523)

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• fix: fixing merge conflict

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• feat(coloc): single SNP case (#511)

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• fix: sorting out merge conflicts

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• fix: removing fsspec from dependencies

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• Merge branch 'dev' into ds_gwas_update

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• fix: fixing lock file

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• fix: updating gwas catalog test files following schema changes

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• Merge pull request #507 from opentargets/ds_gwas_update

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Commits on Mar 11, 2024

• build(deps-dev): bump ruff from 0.2.0 to 0.3.2 (#531)

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• build(deps-dev): bump mypy from 1.8.0 to 1.9.0 (#532)

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• fix: pin version of commitlint (#533)

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• Merge branch 'dev' into ds_3238_update_ETL_DAG

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Commits on Mar 12, 2024

• fix: read function for thurman data to include first line (#534)

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• feat(sumstat imputation): adding class for sumstat imputation (#490)

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• Merge branch 'dev' into ds_3238_update_ETL_DAG

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Commits on Mar 13, 2024

• chore: apply suggestions from code review

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• refactor: tidying up the ETL DAG

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• ci: bugfix in PR labeller (#537)

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• chore: pre-commit autoupdate (#539)

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• Merge branch 'dev' into ds_3238_update_ETL_DAG

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Commits on Mar 14, 2024

• fix(dag): sorting out the checks for the existence of GCP folders

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• Merge branch 'ds_3238_update_ETL_DAG' of https://github.com/opentargets/gentropy into ds_3238_update_ETL_DAG

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• Merge pull request #528 from opentargets/ds_3238_update_ETL_DAG

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Commits on Mar 18, 2024

• build(deps-dev): bump deptry from 0.12.0 to 0.14.0 (#548)

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• build(deps-dev): bump mkdocstrings-python from 1.8.0 to 1.9.0 (#549)

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• chore(l2g): log annotated gold standards in w&b (#546)

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• perf(l2g): streamline feature generation (#544)

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Commits on Mar 19, 2024

• chore: pre-commit autoupdate (#550)

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• feat(l2g): distance features based on weighted score (#545)

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Commits on Mar 20, 2024

• perf(clump): refactored window based clumping (#492)

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• feat: notebook to run qc metrics each release (#541)

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Commits on Mar 21, 2024

• fix: small fixes in susie defaults (#552)

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• test(method): improved performance in coloc tests (#536)

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Commits on Mar 22, 2024

• perf(l2g): optimise extraction of features from colocalisation results (#553)

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• fix(coloc): handle cases when the bayes factors are null (#556)

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Commits on Mar 26, 2024

• fix(sumstats): correct study id for dir of finngen studies (#551)

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Commits on Apr 2, 2024

• feat: add the step class for fine-mapping (#554)

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Commits on Apr 3, 2024

• feat: LD index and block matrix extraction for a studyLocus (#463)

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Commits on Apr 5, 2024

• feat: the FineMapper function for one locus (#564)

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• feat: susie_finemapper_ss_gathered() (#567)

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Commits on Apr 9, 2024

• feat: add FM step with carma and sumstat imputation (#568)

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Commits on Apr 10, 2024

• fix: adding deduplication for GWAS in locus (#573)

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• feat: add benchmarking for fine-mapping using Alzheimer as example (#572)

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• fix: removing all duplicated variants in sumstats for finemapping functions (#574)

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Commits on Apr 14, 2024

• feat: adding notebook for mapping EFOs for the FinnGen study index (#575)

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Commits on Apr 23, 2024

• feat: adding init to finemapping step (#577)

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• feat: dockerise gentropy python package (#579)

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• feat: updating step config file (#580)

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• fix: update error in config.py (#583)

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• feat: changing locus window to locus radius to be consistent with other functions (#582)

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Commits on Apr 24, 2024

• fix: minor updates and bug fixes (#543)

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• fix: updating config.py argument for finemapper (#584)

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• feat(sumstat qc): adding methods for QC of summary statistics (#455)

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Commits on Apr 25, 2024

• feat: susie_finemapper_one_studylocus_row_v3_dev_ss_gathered (#586)

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Commits on Apr 26, 2024

• feat: functionality added to StudyLocus.find_overlaps() for finding within-study overlaps (#587)

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• feat: github action to upload docker image to registry (#588)

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• feat: lighter dockerfile (#585)

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• fix: docker action fixes (#589)

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• fix: docker action fixes (#590)

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• fix: docker action fixes v3 (#591)

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Commits on Apr 29, 2024

• build(deps-dev): bump deptry from 0.14.0 to 0.16.1 (#570)

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