chore: trigger release process #565
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Apr 4, 2024
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chore(l2g): update inclusion features list with newer QTLs
…apping results (#518) * feat: dataflow decompress prototype (#501) * chore: commit susie results gist * feat(study_index): add `tissueFromSourceId` to schema and make `traitFromSource` nullable * fix: bug and linting fixes in new eqtl ingestion step * perf: config bugfixes and performance improvements * perf: remove data persistance to avoid executor failure * perf: load susie results for studies of interest only * perf: collect locus for leads only and optimise partitioning cols * feat: parametrise methods to include * feat: run full dag * test: add tests * fix: reorder test inputs * docs: update eqtl catalogue docs * fix: correct typos in tests docstrings * refactor: change mqtl_quantification_methods to mqtl_quantification_methods_blacklist * feat: studyId is based on measured trait and not on gene * feat: credible set lead is the variant with highest pip * feat(studies): change logic in _identify_study_type to extract qtl type based on quantization method * refactor: externalise reading logic to source classes * chore: add mqtl_quantification_methods_blacklist to yaml config * docs: update docs * fix(dag): pass bucket name to GCSDeleteBucketOperator * refactor(coloc): move get_logsum function to common utils * feat(studylocus): add calculate_credible_set_log10bf and use it for eqtlcat credible sets * fix: credible sets dataset is too large and cant be broadcasted * fix(dag): use GCSDeleteObjectsOperator instead of GCSDeleteBucketOperator * fix: correct typo * fix: correct typo
* chore: update ruff pre-commit and rules * refactor: to address None type and remove typeignore --------- Co-authored-by: Daniel Suveges <[email protected]>
* fix: pr labeler patterns * fix: change bug for fix * revert: as per reviewers will
* feat: include single snp overlaps in coloc calcs * chore: added unit test for coloc * feat: include single snp overlaps in coloc calcs * chore: added unit test for coloc * fix: check for differences in test results * fix: revert changes to single snp coloc tests for other pr * fix: revert single snp change * chore: restructure test folder * fix: compare differences in results rather than exact match * chore: test description * fix: allow for coloc when only one snp is overlapping * chore: include tests for h0 and h1/2 * fix: added pseudocount variable to coloc * fix: pseudocount as a Coloc attribute --------- Co-authored-by: David Ochoa <[email protected]>
chore: small updates to accomodate GWAS Catalog for feb release
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.2.0 to 0.3.2. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@v0.2.0...v0.3.2) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [mypy](https://github.com/python/mypy) from 1.8.0 to 1.9.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.8.0...1.9.0) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* feat(sumstat imputation): adding class for sumstat imputation * feat: added test * docs: update summary statistics imputation description * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * Update docs/python_api/methods/sumstat_imputation.md Co-authored-by: Irene López <[email protected]> * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * fix: changes according to comment * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * Update src/gentropy/method/sumstat_imputation.py Co-authored-by: Irene López <[email protected]> * fix: fixing tests --------- Co-authored-by: Irene López <[email protected]>
* feat: susie_finemapper_ss_gathered() * fix: docstring updates
* feat: add fm step with carma and sumstat imputation * fix: adding log * fix: fixing carma * fix: resolving conflict * fix: resolve conflicts with dev v2 * fix: siliencing FutureWarning in Carma
* feat: adding init to finemapping step * fix: removing some commented lines * chore: fixing indents * fix: schema * feat: changing output path to include studyLocusId mapped --------- Co-authored-by: Yakov <[email protected]>
Co-authored-by: David Ochoa <[email protected]>
* feat(sumstat qc): class for GWAS sumstat QC * feat: small fixes * feat: modifying sumarry_statistics class * feat: adding qc_pz_check * fix: test fix * feat: adding se_n check * chore: fixing functions * feat: adding gc lambda check * test: adding tests * fix: fixing tests * fix: fixing tests * fix: fixing tests and adding rounding * chore: pre-commit auto fixes [...] * feat(sumstat qc): adding new method class * test: fix tests * fix(sumstat qc): fixing tests * fix: remove number_of_snps from susmtat class * test: add multiple studyId test * docs: adding documentation for sumstat QC * fix: fixes according to comments --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ithin-study overlaps (#587) * feat: functionality added to StudyLocus.find_overlaps() for finding within-study overlaps * feat: removal of secondary credible sets at the same region as overlaps * fix: defining the join condition to make the code tidier
Co-authored-by: Irene López <[email protected]>
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.14.0 to 0.16.1. - [Release notes](https://github.com/fpgmaas/deptry/releases) - [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md) - [Commits](fpgmaas/deptry@0.14.0...0.16.1) --- updated-dependencies: - dependency-name: deptry dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: David Ochoa <[email protected]>
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@DSuveges, if we have time, let's aim to do a release with this Thursday's PR. There is no rush, so only if we find 15 min somewhere. |
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