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* test: refactor test_gnomad_ld * build(deps-dev): bump mkdocs-material from 9.4.7 to 9.4.8 Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.4.7 to 9.4.8. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.4.7...9.4.8) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps-dev): bump pytest-xdist from 3.3.1 to 3.4.0 Bumps [pytest-xdist](https://github.com/pytest-dev/pytest-xdist) from 3.3.1 to 3.4.0. - [Changelog](https://github.com/pytest-dev/pytest-xdist/blob/master/CHANGELOG.rst) - [Commits](pytest-dev/pytest-xdist@v3.3.1...v3.4.0) --- updated-dependencies: - dependency-name: pytest-xdist dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * fix: revert testing changes * fix: gnomad paths are not necessary after #233 * build(deps): bump wandb from 0.13.11 to 0.16.0 Bumps [wandb](https://github.com/wandb/wandb) from 0.13.11 to 0.16.0. - [Release notes](https://github.com/wandb/wandb/releases) - [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md) - [Commits](wandb/wandb@v0.13.11...v0.16.0) --- updated-dependencies: - dependency-name: wandb dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.4 → v0.1.5](astral-sh/ruff-pre-commit@v0.1.4...v0.1.5) - [github.com/psf/black: 23.10.1 → 23.11.0](psf/black@23.10.1...23.11.0) - [github.com/alessandrojcm/commitlint-pre-commit-hook: v9.7.0 → v9.8.0](alessandrojcm/commitlint-pre-commit-hook@v9.7.0...v9.8.0) - [github.com/pre-commit/mirrors-mypy: v1.6.1 → v1.7.0](pre-commit/mirrors-mypy@v1.6.1...v1.7.0) * fix: persist raw gwascat associations to return consistent results * fix: coalesce variantid to assign a studylocusid closes #3151 * chore: use a higher RAM master machine * chore: use gs:// prefix for FinnGen input data * chore: use more partitions for FinnGen * chore: always error if the output data exists * feat: add eQTL ingestion to the list of steps in DAG * docs: update running instructions * docs: update contributing checklist * docs: add automatically generated docs * chore: add configuration * chore: unify FinnGen config with eQTL Catalogue * feat: eQTL Catalogue main ingestion script * feat: implement study index ingestion * feat: implement summary stats ingestion * refactor: update eQTL study index import * refactor: reorganise study index ingestion for readability * style: docstring for eQTL Catalogue summary stats ingestion * feat: construct study ID based on all appropriate columns * feat: map partial and full study IDs * feat: join dataframes to add the full study ID information * feat: populate geneId column * refactor: move gene ID joining into the study index class * fix: do not partition by chromosome for QTL studies * fix: update class names * chore: add __init__.py for eQTL Catalogue * fix: eqtl_catalogue path in docs * fix: name of EqtlCatalogueStep class * chore: replace attributes with static methods for eQTL study index * chore: replace attributes with static methods for eQTL summary stats * fix: do not initialise session in the main class * test: add conftests for eQTL Catalogue * fix: include header when reading the study index * fix: populating publicationDate * fix: cast nSamples as long * fix: manually specify schema for eQTL Catalogue summary stats * fix: typo in position field name * test: add sample eQTL Catalogue studies * test: add sample eQTL Catalogue summary stats * test: add test for eQTL Catalogue study index * test: add test for eQTL Catalogue summary stats * chore: partition output data by chromosome * chore: read input data from Google Storage * fix: studies sample filename * chore: repartition data before processing * revert: repartition call * revert: repartition call * build(deps-dev): bump google-cloud-dataproc from 5.6.0 to 5.7.0 Bumps [google-cloud-dataproc](https://github.com/googleapis/google-cloud-python) from 5.6.0 to 5.7.0. - [Release notes](https://github.com/googleapis/google-cloud-python/releases) - [Changelog](https://github.com/googleapis/google-cloud-python/blob/main/CHANGELOG.md) - [Commits](googleapis/google-cloud-python@google-cloud-dataproc-v5.6.0...google-cloud-dataproc-v5.7.0) --- updated-dependencies: - dependency-name: google-cloud-dataproc dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * fix: change definition of negative l2g evidence * refactor: modularise logic for gold standards * refactor: move hardcoded values to constants * refactor: turn `OpenTargetsL2GGoldStandard` into class methods * refactor(gold_standard): move logic to refine gold standards to `L2GGoldStandard` * chore: remove the num_local_ssds arg which has no effect * chore: align default values with docstring * feat: add ability to attach local SSDs * chore: make local SSDs a default * test: add `test_parse_positive_curation` * test: fix and test logic in `expand_gold_standard_with_negatives` * test: add `test_expand_gold_standard_with_negatives_same_positives` * test: testing for `process_gene_interactions` * feat: parametrise autoscaling policy * feat: finetune spark job: taskid, trigger rule, other args * feat: new PICS step * feat: configuration for PICS step * docs: pics step * feat: datasets config * Revert "feat: datasets config" This reverts commit a07c7c4. * feat: gcp dataset config * fix: wrong lines removed * feat: raise error in `from_parquet` when df is empty * chore: add `variantId` to gold standards schema * chore: change `sources` in gold standards schema to a nullable * test: add `test_filter_unique_associations` * Update src/otg/pics.py Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update src/otg/pics.py Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update src/otg/pics.py Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update src/otg/pics.py Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * feat(overlaps): add and test method to transform the overlaps as a square matrix * chore(overlaps): chromosome and statistics are not mandatory fields in the schema * feat(l2g_gold_standard): change `filter_unique_associations` logic * test(l2g_gold_standard): add `test_remove_false_negatives` * fix(l2g_gold_standard): fix logic in `remove_false_negatives` * chore(gold_standards): define gs labels as `L2GGoldStandard` attributes * build(deps-dev): bump apache-airflow-providers-google Bumps [apache-airflow-providers-google](https://github.com/apache/airflow) from 10.11.0 to 10.11.1. - [Release notes](https://github.com/apache/airflow/releases) - [Changelog](https://github.com/apache/airflow/blob/main/RELEASE_NOTES.rst) - [Commits](apache/airflow@providers-google/10.11.0...providers-google/10.11.1) --- updated-dependencies: - dependency-name: apache-airflow-providers-google dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps-dev): bump mypy from 1.6.1 to 1.7.0 Bumps [mypy](https://github.com/python/mypy) from 1.6.1 to 1.7.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.6.1...v1.7.0) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps-dev): bump mkdocs-material from 9.4.8 to 9.4.10 Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.4.8 to 9.4.10. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.4.8...9.4.10) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps-dev): bump mkdocstrings-python from 1.7.3 to 1.7.4 Bumps [mkdocstrings-python](https://github.com/mkdocstrings/python) from 1.7.3 to 1.7.4. - [Release notes](https://github.com/mkdocstrings/python/releases) - [Changelog](https://github.com/mkdocstrings/python/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/python@1.7.3...1.7.4) --- updated-dependencies: - dependency-name: mkdocstrings-python dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * chore: pre-commit autoupdate * feat: updating summary stats schema and ingtesion * chore: remove beta value interval calculation * refactor: removing odds ratio, and confidence intervals from the schema * fix: multiply standard error by zscore in `calculate_confidence_interval` * chore: remove reference to confidence intervals * fix: local SSD initialisation * feat: gitignore .venv file * feat: ingestion supported for both new and old format of the harmonized GWAS Catalog Summary stats. (#274) * feat: converting gwas catalog ingestion to the new format * feat: generalizing GWAS catalog sumstas ingestion both format supported * fix: sample file must follow the convention of the real files * fix: woopsie, the sample file is not added * test: adding trst for old gwas format * feat: updating gwas summary stats ingestion step to the new way of getting data * fix: casting types to make schema explicit * build(deps): bump pyarrow from 11.0.0 to 14.0.1 Bumps [pyarrow](https://github.com/apache/arrow) from 11.0.0 to 14.0.1. - [Commits](apache/arrow@go/v11.0.0...go/v14.0.1) --- updated-dependencies: - dependency-name: pyarrow dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * chore: rename study_locus to credible_set for l2g * build(deps-dev): bump ipython from 8.17.2 to 8.18.1 (#280) Bumps [ipython](https://github.com/ipython/ipython) from 8.17.2 to 8.18.1. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.17.2...8.18.1) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump mkdocstrings-python from 1.7.4 to 1.7.5 (#279) Bumps [mkdocstrings-python](https://github.com/mkdocstrings/python) from 1.7.4 to 1.7.5. - [Release notes](https://github.com/mkdocstrings/python/releases) - [Changelog](https://github.com/mkdocstrings/python/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/python@1.7.4...1.7.5) --- updated-dependencies: - dependency-name: mkdocstrings-python dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump ruff from 0.1.3 to 0.1.6 (#276) Bumps [ruff](https://github.com/astral-sh/ruff) from 0.1.3 to 0.1.6. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@v0.1.3...v0.1.6) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump mypy from 1.7.0 to 1.7.1 (#278) Bumps [mypy](https://github.com/python/mypy) from 1.7.0 to 1.7.1. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.7.0...v1.7.1) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * docs: minify plugin removed to prevent clash in local development (#284) * fix: proper parsing of gwas catalog study accession from filename (#282) * fix: proper parsing of gwas catalog study accession from filename * fix: interestingly, I had to add an extra line to pass doctest on VSCode * feat: bumping mypy version --------- Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> * fix: making standard_error column optional (#286) * fix: making standard-error column optional * feat: add `clump` step (#288) * feat: join clump methods into step canonical * refactor: keep clump step minimal * docs: add clump step docs page * fix: add clump config * revert(pre-commit): downgrade mypy version to 1.7.0 * feat(clump): add attribute to collect locus in window-based clumping * refactor(clump): make study and ld indices non mandatory * test: add test for clumpstep when input is ss * test: rename test_clump_py to avoid clashes * refactor: remove data variable in clumpstep * fix: correct and test study splitter when subStudyDescription is the same (#289) * fix(clump): read input files recursively (#292) * build(deps-dev): bump mkdocs-material from 9.4.10 to 9.4.14 (#300) Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.4.10 to 9.4.14. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.4.10...9.4.14) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump scipy from 1.11.3 to 1.11.4 (#299) Bumps [scipy](https://github.com/scipy/scipy) from 1.11.3 to 1.11.4. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.11.3...v1.11.4) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump pymdown-extensions from 10.3.1 to 10.5 (#301) Bumps [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions) from 10.3.1 to 10.5. - [Release notes](https://github.com/facelessuser/pymdown-extensions/releases) - [Commits](facelessuser/pymdown-extensions@10.3.1...10.5) --- updated-dependencies: - dependency-name: pymdown-extensions dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump mkdocs-git-committers-plugin-2 from 1.2.0 to 2.2.2 (#303) Bumps [mkdocs-git-committers-plugin-2](https://github.com/ojacques/mkdocs-git-committers-plugin-2) from 1.2.0 to 2.2.2. - [Release notes](https://github.com/ojacques/mkdocs-git-committers-plugin-2/releases) - [Commits](ojacques/mkdocs-git-committers-plugin-2@1.2.0...2.2.2) --- updated-dependencies: - dependency-name: mkdocs-git-committers-plugin-2 dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump apache-airflow-providers-google (#302) Bumps [apache-airflow-providers-google](https://github.com/apache/airflow) from 10.11.1 to 10.12.0. - [Release notes](https://github.com/apache/airflow/releases) - [Changelog](https://github.com/apache/airflow/blob/main/RELEASE_NOTES.rst) - [Commits](apache/airflow@providers-google/10.11.1...providers-google/10.12.0) --- updated-dependencies: - dependency-name: apache-airflow-providers-google dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat: deptry added to handle unused, missing and transitive dependencies (#304) * feat: add deptry to the project * feat: deptry as pre-commit and associated changes * feat: deptry as pre-commit and associated changes * fix: exclude deptry from pre-commit.ci * ci: check deptry when testing * fix: poetry lock with no update * feat: adding unpublished studies (#290) * feat: adding unpublished studies * feat: updating all gwas catalog sources * feat: generalizing study ingestion to accept list of files * fix: removing unused configuration * feat: adding unpublished ancestries as well * fix: updating ancestry config name * Apply suggestions from code review Co-authored-by: Kirill Tsukanov <tskir@users.noreply.github.com> --------- Co-authored-by: Kirill Tsukanov <tskir@users.noreply.github.com> * feat: add prettier as formatter (yaml, json, md, etc.) (#298) * feat: prettier added to the project and precommit * feat: recommend vscode extension * fix: adjusted prettier * fix: all files reformated by prettier * fix: unnecessary comment * chore(l2ggoldstandard): add studyId to schema (#305) * chore(l2ggoldstandard): add studyId to schema * fix: add `studyId` to gold standards testing fixtures --------- Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> * feat: Adding cohorts field to study index (#309) * feat: ingesting cohort information for GWAS Catalog * feat: adding cohort to finngen study index * feat: add 'coalesce' and 'repartition' wrappers to 'Dataset' (#307) * feat(dataset): add `coalesce` * feat(clump): coalesce summary stats to 1000 partitions * feat(dataset): change coalesce to setPartitions * test(dataset): added `TestSetPartitions` * refactor(dataset): split set_partitions into repartition and coalesce * chore(clump): decrease number of sumstats partitions to 400 * chore: change number of partitions to window clumping to 4000 Number estimate on the basis of 60 workers x 16 cores x 4 partitions Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> --------- Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> * chore(airflow): schedule_interval deprecation warning (#293) Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * feat: GWAS Catalog harmonisation prototype (#270) * chore: merge main * feat: partitioning GWAS Catalog dataset to 20 equally-sized partitions * fix: missing config * feat: dag with gwas catalog harmonisation * feat: adding more primary workers to help with the task * refactor: changed autoscaling policy * feat: allow to specify number of preeptible workers * fix: bugs on to_do_list * revert: version number * fix: gwas_catalog_sumstat_preprocess no longer needs study_id * fix: unnecessary config causes issues * fix: improved regexp * refactor: generalising the config * fix: rename cluster to prevent clashes with other dags * Update src/airflow/dags/gwas_catalog_harmonisation.py Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> --------- Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * test: failing doctest in different python version (#320) * test: issue on test with different python version * refactor: value error instead of assertion * build(deps): bump wandb from 0.16.0 to 0.16.1 (#315) Bumps [wandb](https://github.com/wandb/wandb) from 0.16.0 to 0.16.1. - [Release notes](https://github.com/wandb/wandb/releases) - [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md) - [Commits](wandb/wandb@v0.16.0...v0.16.1) --- updated-dependencies: - dependency-name: wandb dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * chore(deps): bump actions/setup-python from 4 to 5 (#319) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * build(deps-dev): bump mkdocs-material from 9.4.14 to 9.5.2 (#324) Bumps [mkdocs-material](https://github.com/squidfunk/mkdocs-material) from 9.4.14 to 9.5.2. - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.4.14...9.5.2) --- updated-dependencies: - dependency-name: mkdocs-material dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * test: Improvements to `test_dataset` and `test_clump_step` (#312) * test: rename TestDataset to MockDataset * test: output test_clumpstep_summary_stats results to temp dir * feat: Gnomad v4 based variant annotation (#311) * feat: gnomad4 parser and changes in schema * fix: variant annotation schema * feat: required changes in variant index * test: fix schema * test: adjust testing to absence of sift and polyphen * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix: typo in schema * fix: preventing skewed partitions * fix: remove sift and polyphen predictions from v2g * feat: rename gnomad3VariantId to gnomadVariantId name * refactor: stop inheriting datasets in parsers (#313) * refactor: stop inheriting datasets in parsers * fix: typing issue * refactor: include datasets in datasources * test: fix incorrect import * test: doctest function calls fixed * test: doctest function calls fixed in studyindex --------- Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * feat: add gwas_catalog_preprocess dag (#291) * feat: gwas_catalog step stops at ingestion * feat: gwas_catalog step stops at ingestion * feat: add gwas_catalog_preprocess dag * fix: change step_id to task_id as task_id * feat: group gwas_catalog_preprocess tasks into sumstats and curation groups * fix: add all dependencies when ld clumping * fix: update gwas catalog docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * refactor(dag): extract releasebucket and sumstats paths as constants * refactor: streamline study locus paths * build(deps-dev): bump pre-commit from 3.5.0 to 3.6.0 (#316) Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 3.5.0 to 3.6.0. - [Release notes](https://github.com/pre-commit/pre-commit/releases) - [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md) - [Commits](pre-commit/pre-commit@v3.5.0...v3.6.0) --- updated-dependencies: - dependency-name: pre-commit dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump numpy from 1.26.1 to 1.26.2 (#314) Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.2. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v1.26.1...v1.26.2) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump typing-extensions from 4.8.0 to 4.9.0 (#317) Bumps [typing-extensions](https://github.com/python/typing_extensions) from 4.8.0 to 4.9.0. - [Release notes](https://github.com/python/typing_extensions/releases) - [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md) - [Commits](python/typing_extensions@4.8.0...4.9.0) --- updated-dependencies: - dependency-name: typing-extensions dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * chore: add `l2g_benchmark` notebook to compare with production results (#323) * feat: finngen preprocess prototype (#272) All steps associated with the preprocessing of Finngen studies (PICS-road) included in a DAG: - summary stats harmonisation - window-based clumping - LD-based clumping - PICS Several enhancements might follow in different PRs. --------- Co-authored-by: Irene López <irene.lopezs@protonmail.com> * chore: create code of conduct (#327) * Create CODE_OF_CONDUCT.md * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * chore: review study locus and study index configs (#326) * chore: make studylocus and study indices configs clearer * chore: temporarily turn off removal of redundancies due to perf * refactor: read studyindex and studylocus recursively * feat: track training data and feature importance (#325) * chore: delete makefile_deprecated (#329) Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * feat: ruff as formatter (#322) * ruff formatter instead of black * refactor: ruff reformatted files * feat: more complete ruff adjustments * refactor: all codebase to comply with ruff rules * chore: update lock * feat: more stringent docstring rules * revert: remove isort and black from Makefile * build(deps-dev): bump google-cloud-dataproc from 5.7.0 to 5.8.0 (#330) Bumps [google-cloud-dataproc](https://github.com/googleapis/google-cloud-python) from 5.7.0 to 5.8.0. - [Release notes](https://github.com/googleapis/google-cloud-python/releases) - [Changelog](https://github.com/googleapis/google-cloud-python/blob/main/packages/google-cloud-documentai/CHANGELOG.md) - [Commits](googleapis/google-cloud-python@google-cloud-dataproc-v5.7.0...google-cloud-dataproc-v5.8.0) --- updated-dependencies: - dependency-name: google-cloud-dataproc dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump ruff from 0.1.6 to 0.1.7 (#331) Bumps [ruff](https://github.com/astral-sh/ruff) from 0.1.6 to 0.1.7. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@v0.1.6...v0.1.7) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat: semantic release automation (#294) Feature needs to be fully tested * feat: track feature missingness rates (#335) * feat(L2GFeatureMatrix): add `features_list` as attribute * fix: log wandb table * feat(L2GFeatureMatrix): track missingness rate for each feature * feat(L2GFeatureMatrix): track missingness rate for each feature * chore(LocusToGeneModel): remove evaluation outside experiment tracking * feat: trigger on push (#337) * build(deps-dev): bump pytest-xdist from 3.4.0 to 3.5.0 (#333) * build(deps-dev): bump ipykernel from 6.26.0 to 6.27.1 (#332) * feat: yamllint to ensure yaml linting (#338) * feat: yamllint support * feat: updates yamllint rules * fix: release actions fixes (#344) * feat: metadata on toml * feat: several fixes * refactor: linting * refactor: externalise python version * fix: single quotes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * docs: finngen description v1 (#345) * chore: upgrade checkout (#346) * fix: github token (#348) * fix: several issues (#349) * feat: release branch (#350) * fix: unnecessary option (#351) * build(deps-dev): bump python-semantic-release from 8.3.0 to 8.5.1 (#343) Bumps [python-semantic-release](https://github.com/python-semantic-release/python-semantic-release) from 8.3.0 to 8.5.1. - [Release notes](https://github.com/python-semantic-release/python-semantic-release/releases) - [Changelog](https://github.com/python-semantic-release/python-semantic-release/blob/master/CHANGELOG.md) - [Commits](python-semantic-release/python-semantic-release@v8.3.0...v8.5.1) --- updated-dependencies: - dependency-name: python-semantic-release dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> * feat: activate release process (#352) * feat: serious release * revert: no tests within release workflow * build(deps-dev): bump isort from 5.13.1 to 5.13.2 (#342) Bumps [isort](https://github.com/pycqa/isort) from 5.13.1 to 5.13.2. - [Release notes](https://github.com/pycqa/isort/releases) - [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md) - [Commits](PyCQA/isort@5.13.1...5.13.2) --- updated-dependencies: - dependency-name: isort dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump ruff from 0.1.7 to 0.1.8 (#341) Bumps [ruff](https://github.com/astral-sh/ruff) from 0.1.7 to 0.1.8. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@v0.1.7...v0.1.8) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat: upload release (#353) * feat: semantic release gh action (#354) * revert: dispatch (#355) * build(deps): bump pyspark from 3.3.3 to 3.3.4 (#358) Bumps [pyspark](https://github.com/apache/spark) from 3.3.3 to 3.3.4. - [Commits](apache/spark@v3.3.3...v3.3.4) --- updated-dependencies: - dependency-name: pyspark dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * chore(deps): bump python-semantic-release/python-semantic-release (#359) Bumps [python-semantic-release/python-semantic-release](https://github.com/python-semantic-release/python-semantic-release) from 8.3.0 to 8.5.1. - [Release notes](https://github.com/python-semantic-release/python-semantic-release/releases) - [Changelog](https://github.com/python-semantic-release/python-semantic-release/blob/master/CHANGELOG.md) - [Commits](python-semantic-release/python-semantic-release@v8.3.0...v8.5.1) --- updated-dependencies: - dependency-name: python-semantic-release/python-semantic-release dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * ci: new changelog and release notes templates (#357) Templates for CHANGELOG and release notes. To be fully tested on the next release. * fix(l2g): `calculate_feature_missingness_rate` counts features annotated with 0 as incomplete (#364) * chore: import wandb classes explicitly * fix: count feature annotation with 0 as incomplete * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docs: corrected and added documentation to datasource (#362) * docs: corrected and added documentation to datasource * docs: corrected documentation to datasource - answering comments v1 * docs: corrections in datasource documentation * fix: incorrect parsing of `app_name` in makefile (#367) * fix: correct app_name in makefile * chore: remove redundant dist cleaning * chore: streamline make rules dependencies * ci: set codecov default branch to dev (#368) * feat: Finngen R10 harmonisation and preprocessing (#370) * chore: remove unnecessary file * fix: several fixes on finngen harmonisation and preprocess * docs: update docs * fix: test * fix: uncomment line Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> --------- Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * feat(pics): remove variants from `locus` when PICS cannot be applied (#361) * feat(pics): variants not in locus when if pips cant be calculated * feat(pics): add empty_locus qc flag * chore(pics): add to finemappingMethod column * refactor(pics): change definition of non picsable based on ldset * Update src/otg/dataset/study_locus.py Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> * Update src/otg/method/pics.py Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> * Update tests/method/test_pics.py Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> --------- Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * chore(study_index): change numeric columns from long to integers (#371) * chore(study_index): change numeric columns to integers * chore(study_index): accommodate parsers to schema changes * feat(l2g): add features based on predicted variant consequences (#360) * chore: import wandb classes explicitly * feat(l2g): add studylocusfeaturefactory._get_vep_features * chore: accommodate project to newer features * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * feat(l2g): include averaged features * chore: set cluster delete TTL (#379) * build(deps-dev): bump apache-airflow from 2.7.3 to 2.8.0 (#373) Bumps [apache-airflow](https://github.com/apache/airflow) from 2.7.3 to 2.8.0. - [Release notes](https://github.com/apache/airflow/releases) - [Changelog](https://github.com/apache/airflow/blob/main/RELEASE_NOTES.rst) - [Commits](apache/airflow@2.7.3...2.8.0) --- updated-dependencies: - dependency-name: apache-airflow dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Kirill Tsukanov <tskir@users.noreply.github.com> * build(deps-dev): bump mypy from 1.7.1 to 1.8.0 (#374) Bumps [mypy](https://github.com/python/mypy) from 1.7.1 to 1.8.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.7.1...v1.8.0) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * chore(deps): bump python-semantic-release/python-semantic-release (#372) Bumps [python-semantic-release/python-semantic-release](https://github.com/python-semantic-release/python-semantic-release) from 8.5.1 to 8.7.0. - [Release notes](https://github.com/python-semantic-release/python-semantic-release/releases) - [Changelog](https://github.com/python-semantic-release/python-semantic-release/blob/master/CHANGELOG.md) - [Commits](python-semantic-release/python-semantic-release@v8.5.1...v8.7.0) --- updated-dependencies: - dependency-name: python-semantic-release/python-semantic-release dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Kirill Tsukanov <tskir@users.noreply.github.com> * build(deps-dev): bump python-semantic-release from 8.5.1 to 8.7.0 (#375) Bumps [python-semantic-release](https://github.com/python-semantic-release/python-semantic-release) from 8.5.1 to 8.7.0. - [Release notes](https://github.com/python-semantic-release/python-semantic-release/releases) - [Changelog](https://github.com/python-semantic-release/python-semantic-release/blob/master/CHANGELOG.md) - [Commits](python-semantic-release/python-semantic-release@v8.5.1...v8.7.0) --- updated-dependencies: - dependency-name: python-semantic-release dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Kirill Tsukanov <tskir@users.noreply.github.com> * build(deps-dev): bump mkdocs-git-revision-date-localized-plugin (#376) Bumps [mkdocs-git-revision-date-localized-plugin](https://github.com/timvink/mkdocs-git-revision-date-localized-plugin) from 1.2.1 to 1.2.2. - [Release notes](https://github.com/timvink/mkdocs-git-revision-date-localized-plugin/releases) - [Commits](timvink/mkdocs-git-revision-date-localized-plugin@v1.2.1...v1.2.2) --- updated-dependencies: - dependency-name: mkdocs-git-revision-date-localized-plugin dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump ipython from 8.18.1 to 8.19.0 (#377) Bumps [ipython](https://github.com/ipython/ipython) from 8.18.1 to 8.19.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.18.1...8.19.0) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Irene López <irene.lopezs@protonmail.com> Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> Co-authored-by: Kirill Tsukanov <tskir@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Kirill Tsukanov <tsukanoffkirill@gmail.com> Co-authored-by: David Ochoa <dogcaesar@gmail.com> Co-authored-by: Yakov <yt4@sanger.ac.uk>
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