chore: trigger release process #1
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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] <support@github.com>
…ython-8.22.1 build(deps-dev): bump ipython from 8.21.0 to 8.22.1
…#506) 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…3.0 (opentargets#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] <support@github.com> 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 (opentargets#514) * feat: dataflow decompress prototype (opentargets#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 <ochoa@ebi.ac.uk>
* 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 <45119610+ireneisdoomed@users.noreply.github.com> * Update .github/pull_request_template.md Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update .github/pull_request_template.md Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update .github/pull_request_template.md Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update .github/pull_request_template.md Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update .github/pull_request_template.md Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update .github/pull_request_template.md Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * chore: pre-commit auto fixes [...] * Update .github/pull_request_template.md Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update .github/pull_request_template.md Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * Update .github/pull_request_template.md Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> * refactor: il-suggestion --------- Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com>
* 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 (opentargets#518) * feat: dataflow decompress prototype (opentargets#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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: David Ochoa <ochoa@ebi.ac.uk>
* chore: update ruff pre-commit and rules * refactor: to address None type and remove typeignore --------- Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>
* 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 <ochoa@ebi.ac.uk>
…nges chore(l2g): update inclusion features list with newer QTLs
…apping results (opentargets#518) * feat: dataflow decompress prototype (opentargets#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
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…ts/gentropy into ds_3238_update_ETL_DAG
…L_DAG feat(dag): add data transfer task group for release process
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.12.0 to 0.14.0. - [Release notes](https://github.com/fpgmaas/deptry/releases) - [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md) - [Commits](fpgmaas/deptry@0.12.0...0.14.0) --- updated-dependencies: - dependency-name: deptry 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>
…rgets#549) Bumps [mkdocstrings-python](https://github.com/mkdocstrings/python) from 1.8.0 to 1.9.0. - [Release notes](https://github.com/mkdocstrings/python/releases) - [Changelog](https://github.com/mkdocstrings/python/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/python@1.8.0...1.9.0) --- updated-dependencies: - dependency-name: mkdocstrings-python 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>
* refactor(l2g): select features of interest in data outside trainer * chore(l2g): log annotated gold standards in w&b * fix: update test_train
* refactor(l2g): streamline coloc feature factory * perf(l2g): make joins in _get_vep_features lighter * fix(l2g): use weighted scores for _get_vep_features * refactor(l2g): minor improvements * perf(l2g): adapt session to set partition number for shuffling to 800 --------- Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>
* chore: pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.2 → v0.3.3](astral-sh/ruff-pre-commit@v0.3.2...v0.3.3) - [github.com/python-poetry/poetry: 1.8.2 → 1.8.0](python-poetry/poetry@1.8.2...1.8.0) * fix: poetry lock adjustments --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: David Ochoa <dogcaesar@gmail.com>
* refactor(l2g): streamline coloc feature factory * perf(l2g): make joins in _get_vep_features lighter * fix(l2g): use weighted scores for _get_vep_features * refactor(l2g): minor improvements * perf(l2g): adapt session to set partition number for shuffling to 800 * feat(l2g): distance features based on weighted score * docs: update docs * refactor(l2g): select features of interest in data outside trainer * chore(l2g): log annotated gold standards in w&b * fix: update test_train * fix(l2g): typo in _get_tss_distance_features with no consequences
* perf: refactored window based clumping * fix: gwas catalog clump step adjusted * fix: broadcast logic * revert: coalesce instruction * fix: add alias * docs: enhance docs * test: accidentally removed test * test: rescue missing test * chore: remove unused step * refactor: increased modularisation * feat: restructure data model * test: structural test for annotate function * fix: prevent locus column could be duplicated * chore: up-to-date with pre-commit
* feat: notebook to run qc metrics each release * feat: added additional checks as discussed * feat: additional checks * fix: remove matplotlib from dependencies * fix: address comments
* fix: pytest for coloc unit tests * fix: removed unused coloc tests * test(coloc): add coloc semantic test (opentargets#538) * test(coloc): define fixtures and parametrise coloc tests * test(coloc): compare dfs with assert_frame_equal * fix: remove unused threshold variable --------- Co-authored-by: Irene López <45119610+ireneisdoomed@users.noreply.github.com> Co-authored-by: David Ochoa <ochoa@ebi.ac.uk>
opentargets#553) * perf(l2g): rewrite ColocalisationFactory._get_max_coloc_per_credible_set * perf(l2g): more elegant rewrite ColocalisationFactory._get_max_coloc_per_credible_set * chore: adapt tests to changes * refactor: import colocalisation attributes
…#556) * fix(coloc): fillna doesnt fill nested data * test(coloc): added test_coloc_no_logbf (semantic) * revert(ecaviar): revert accidental changes
* feat: add the step class for fine-mapping * test: adding test for susie to studylocus converter * chore: fix the class description * chore: answering comments --------- Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>
…ets#463) * test: adding test for pairwiseLD * feat: adding ld matrix extraction * chore: merge from dev * feat: index and block matrix extraction for studyLocus * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * chore: updating some test files to gentropy * chore: updating tests * chore: updating pairwise_ld_schema for tests * chore: updating pairwise_ld tests * chore: fix ld_pairwise tests * chore: fix pairwise_ld tests * chore: fix tests * chore: fix tests * chore: fixing typing for tests * chore: fixing tests * chore: fixing ld tests * Update src/gentropy/dataset/study_index.py Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * feat: moving functions to their appropriate locations and improving logic * fix: optimise conversion of BM to NumPy * feat: updating get_locus_index to allow for just chromosome and position inputs * fix: suggested changes * Update study_index.py * fix: changes to datasource/gnomad/ld.py * feat: updated method for ld_index extraction * fix: sorting idx in hail --------- Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* test: adding test for pairwiseLD * feat: adding ld matrix extraction * chore: merge from dev * feat: index and block matrix extraction for studyLocus * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * chore: updating some test files to gentropy * chore: updating tests * chore: updating pairwise_ld_schema for tests * chore: updating pairwise_ld tests * chore: fix ld_pairwise tests * chore: fix pairwise_ld tests * chore: fix tests * chore: fix tests * chore: fixing typing for tests * chore: fixing tests * chore: fixing ld tests * Update src/gentropy/dataset/study_index.py Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * feat: moving functions to their appropriate locations and improving logic * fix: optimise conversion of BM to NumPy * feat: updating get_locus_index to allow for just chromosome and position inputs * fix: suggested changes * Update study_index.py * fix: changes to datasource/gnomad/ld.py * feat: add the draft of finemapper fucntion * feat: updated method for ld_index extraction * fix: changing input * fix: adding fillter by studyId * fix: sorting idx in hail * feat: add fine-mapping of one study_locus_row * fix: small fix in majpop * fix: small fixes in function * fix: using more spark before converting to pandas * fix: fix in test --------- Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> Co-authored-by: Daniel Considine <dc16@sanger.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel-Considine <113430683+Daniel-Considine@users.noreply.github.com>
* 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
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