chore: trigger release process #527
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Mar 7, 2024
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Bumps [ipython](https://github.com/ipython/ipython) from 8.21.0 to 8.22.1. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.21.0...8.22.1) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
build(deps-dev): bump ipython from 8.21.0 to 8.22.1
Bumps [typing-extensions](https://github.com/python/typing_extensions) from 4.9.0 to 4.10.0. - [Release notes](https://github.com/python/typing_extensions/releases) - [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md) - [Commits](https://github.com/python/typing_extensions/commits) --- updated-dependencies: - dependency-name: typing-extensions dependency-type: direct:production 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>
…3.0 (#505) Bumps [mkdocs-git-committers-plugin-2](https://github.com/ojacques/mkdocs-git-committers-plugin-2) from 2.2.3 to 2.3.0. - [Release notes](https://github.com/ojacques/mkdocs-git-committers-plugin-2/releases) - [Commits](ojacques/mkdocs-git-committers-plugin-2@2.2.3...2.3.0) --- updated-dependencies: - dependency-name: mkdocs-git-committers-plugin-2 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: 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
…ng results (#514) * 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 * fix: correct typos in tests docstrings * test: fix * revert: revert unwanted change in studyId definition * test: final fix --------- Co-authored-by: David Ochoa <[email protected]>
* ci: pull request labeler * fix: adjust capitalisation * refactor: add size to make clear what the letters are about * feat: trigger on issues * revert: mergeable does not seem to work
* ci: pull request template * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * chore: pre-commit auto fixes [...] * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * Update .github/pull_request_template.md Co-authored-by: Irene López <[email protected]> * refactor: il-suggestion --------- Co-authored-by: Irene López <[email protected]>
* fix: adding missing gentropy * fix: allowing for scope to be there * feat: step label added
* feat(CARMA): adding time limited CARMA * feat: correct the function * feat(CARMA): added tests * chore: small fix of varaible types * chore: fix of test descriptions
…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
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.0.1 to 8.1.0. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@8.0.1...8.1.0) --- updated-dependencies: - dependency-name: pytest 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]>
* 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
* ci: precommit poetry checks for toml and lock * test: add poetry lock to ensure this is working * fix: specify python version in pre-commit config * fix: skip poetry lock in remote
* 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]>
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