chore: trigger release process #858
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Oct 17, 2024
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…li (#716) * feat: expose summary statistics qc to hydra cli * feat: expose locus breaker clumping step --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: Szymon Szyszkowski <[email protected]>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.2 → v0.5.5](astral-sh/ruff-pre-commit@v0.5.2...v0.5.5) - [github.com/pre-commit/mirrors-mypy: v1.10.1 → v1.11.0](pre-commit/mirrors-mypy@v1.10.1...v1.11.0) - [github.com/jsh9/pydoclint: 0.5.4 → 0.5.6](jsh9/pydoclint@0.5.4...0.5.6) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Bumps [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions) from 10.8.1 to 10.9. - [Release notes](https://github.com/facelessuser/pymdown-extensions/releases) - [Commits](facelessuser/pymdown-extensions@10.8.1...10.9) --- updated-dependencies: - dependency-name: pymdown-extensions 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: Szymon Szyszkowski <[email protected]>
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.17.0 to 0.18.0. - [Release notes](https://github.com/fpgmaas/deptry/releases) - [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md) - [Commits](fpgmaas/deptry@0.17.0...0.18.0) --- 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>
* feat: notebook for locus breaker and susie finemapping benchmark * fix: won't pass tests with matplotlib imported * feat: ukb_ppp_fm benchmark notebook * fix: check for nulls as well as nans * fix: removing matplotlib * fix: update notebooks * chore: re-run ukb ppp notebook * chore: rerun notebook
* fix: updating config paths and fine-mapping methods * Update ot_locus_to_gene_train.yaml
* docs: macos fix for some functions * docs: formatting
* build(deps-dev): bump ruff from 0.5.1 to 0.6.1 Bumps [ruff](https://github.com/astral-sh/ruff) from 0.5.1 to 0.6.1. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.5.1...0.6.1) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * fix: linting issues associated with ruff 0.6 * chore: fixing imports for notebooks * chore: removing old notebook --------- 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]> Co-authored-by: Daniel Considine <[email protected]>
* chore: pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.5 → v0.6.1](astral-sh/ruff-pre-commit@v0.5.5...v0.6.1) - [github.com/pre-commit/mirrors-mypy: v1.11.0 → v1.11.1](pre-commit/mirrors-mypy@v1.11.0...v1.11.1) * chore: pre-commit auto fixes [...] --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: David Ochoa <[email protected]>
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.18.0 to 0.19.1. - [Release notes](https://github.com/fpgmaas/deptry/releases) - [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md) - [Commits](fpgmaas/deptry@0.18.0...0.19.1) --- 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]>
Bumps [lxml](https://github.com/lxml/lxml) from 5.2.2 to 5.3.0. - [Release notes](https://github.com/lxml/lxml/releases) - [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt) - [Commits](lxml/lxml@lxml-5.2.2...lxml-5.3.0) --- updated-dependencies: - dependency-name: lxml 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>
* build(deps-dev): bump pre-commit from 3.7.1 to 3.8.0 Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 3.7.1 to 3.8.0. - [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@v3.7.1...v3.8.0) --- updated-dependencies: - dependency-name: pre-commit dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * fix: update lock --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: David Ochoa <[email protected]> Co-authored-by: David Ochoa <[email protected]>
* feat: update variant sources for variant idx and drop rsid mapping * chore: remove variant_index step from etl dag * chore: move gnomad annotation from dev to static assets * chore: change gentropy docker image * feat(convert_to_vcf): write data partitioned * feat: add vcf merging step * chore: assert merge is succesful * fix: remove non canonical variants from vcfs * chore: pass vcf types to merging rule * fix: match vep parser order of columns to variant index schema * fix: ditch `assign_variant_id` in favour of `hash_long_variant_ids` * chore: update `test_as_vcf_df_without_variant_id` * fix: correct test mock data * chore: pre-commit auto fixes [...] * chore: merge from dev * chore: pre-commit auto fixes [...] --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: Szymon Szyszkowski <[email protected]>
* feat: finngen r11 study index paths * feat: simplification of finngen susie finemapping ingestion * feat: efos in finngne study index * docs: updated docstring * fix: pass spark_session not gentropy session to step * fix: read uploaded file requires file:/// * fix: parallelize csv from url * fix: typo in docstring * chore: pre-commit auto fixes [...] --------- Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel Suveges <[email protected]>
* fix: adding carma_tau parameter to susie_finemapper * fix: changing default * fix: defaults
* refactor: generalised validation logic * refactor: generalised validation logic * fix(airflow): fine-tuning DAG for data validation * fix(validation): study locus uniqueness fixed * feat: add invalid/valid dataset generation in validation steps/dag (#734) * fix: does not belong in this PR * refactor: to be moved to orchestration repo * docs: respective docs pages for the steps * docs: ammend docstrings * revert: maintain dag for now but it should be removed eventually * feat: validate study_locus dataset to produce valid or invalid df * feat: adjust DAG to parametrise dataset validation * fix: duplicated row * feat: increase abstraction of Dataset validation of rows * docs: increase clarity of what the function does * fix: error message * revert: unintended change * test: testing dataset filtering by quality flag --------- Co-authored-by: DSuveges <[email protected]> * chore: pre-commit auto fixes [...] --------- Co-authored-by: David Ochoa <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <[email protected]>
* feat(variant index): upating schema and logic * feat(variant index): vep transcript annotation improved with consequence score + transcript index * refactor: removed hardcoded schema definition from parser * fix(test): fixing mock variant index * fix: schema extraction fixed * fix: doctest issue resolved * fix: updating vep command in the DAG * fix: removing un-used sequence ontology terms * fix: adding example to sorter method + changing variable names --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
* fix(finngen_r11): preserve all studyIds Preserve all studyIds, even if EFO mapping is missing, so mapping between studyIndex and StudyLocus is by studyId column is accurate. * fix: typo in docstring Co-authored-by: Irene López Santiago <[email protected]> --------- Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: Irene López Santiago <[email protected]>
* feat: adding finemapping method to studylocusid hash * chore: updating function in needed files * test: update doc test * fix: mistakes * fix: tidying logic * chore: adding studyLocusId recalculation to pics finemapping method --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
Bumps [ipython](https://github.com/ipython/ipython) from 8.26.0 to 8.27.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.26.0...8.27.0) --- updated-dependencies: - dependency-name: ipython 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: Szymon Szyszkowski <[email protected]>
Bumps [deptry](https://github.com/fpgmaas/deptry) from 0.19.1 to 0.20.0. - [Release notes](https://github.com/fpgmaas/deptry/releases) - [Changelog](https://github.com/fpgmaas/deptry/blob/main/CHANGELOG.md) - [Commits](fpgmaas/deptry@0.19.1...0.20.0) --- 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: Szymon Szyszkowski <[email protected]>
* fix: use mapping instead of enum values in valid_rows * fix: typos * fix: swap valid and invalid paths --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: Szymon Szyszkowski <[email protected]>
* refactor: move VA preparation logic into a separate module * refactor: generalise per-chromosome summary stats ingestion * Update src/gentropy/common/per_chromosome.py Co-authored-by: Szymon Szyszkowski <[email protected]> --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
* refactor: move harmonisation into a separate module * refactor: make column names configurable * feat: make INFO and A1FREQ columns optional * docs: expand comments on tmp_variant_annotation_path and variant types
* chore: add chromosome validation * test: chromosome validation --------- Co-authored-by: DSuveges <[email protected]>
* feat: add gene count features to l2g * fix: add genecount to pytest * fix: use alias in gene count * fix: use alias in gene count * fix: pytest now works * chore: pre-commit auto fixes [...] * fix: type hint * feat(coloc): step refactoring (#845) * feat: prior fix * refactor: coloc step * fix: subclasss colocalisation methods on interface * fix: failing coloc step * chore(coloc): step tests * chore: restore old script --------- Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: project-defiant <[email protected]> * test: skip `fetch_coordinates_from_rsids` (#850) * fix(eqtl): deduplicating credible set loci (#849) * fix(eqtl): deduplicating credible set loci * fix: removing * chore: adding logging even when no CS in locus (#848) * chore: adding logging even when no CS in locus * fix: addin CS count to log * fix: type hints * added test_l2g_feature tests * fix: remove print statements from tests * feat: add genecount features to FM + config * feat: add to l2g config * chore: pre-commit auto fixes [...] --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: project-defiant <[email protected]> Co-authored-by: Irene López Santiago <[email protected]> Co-authored-by: Daniel Suveges <[email protected]> Co-authored-by: Yakov <[email protected]>
…sets (#872) * feat: using mean instead of univariate beta * fix: missing f-string * fix: typo * fix: beta column in locus * feat: populating locusStart and locusEnd from region column * fix: locusStart/End cast to integer --------- Co-authored-by: Yakov <[email protected]>
* feature(l2g): step to export disease/target evidence * fix: sorting out typo in function docstring * fix: evidence is written as json * fix: addressing reviewer comments * docs: adding step documentation * chore: pre-commit auto fixes [...] * fix: removing default value from step definition --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…874) * fix(variant_index): pass config threshold after joining with gnomad * feat(dataset): ability to pass class params to `from_parquet` * feat(variant_index): hash variants after initialising class * test: ensure hashing happens and params are correcly separated * fix: add threshold in `test_extract_variant_index_from_vep` * feat(variant_index): make hash threshold inclusive
* feat(feature_matrix): add `credibleSetConfidence` * feat: add feature to l2g * test: add semantic and minor fixes * test: fix * test: fix
* feat(l2g): normalise distance features * feat(l2g): normalise distance features * chore: fix tests
* feat: l2g feature to indicate if gene is protein-coding or not * chore: pre-commit auto fixes [...] * fix: remove print from tests * fix: remove print from tests * fix: correct window size for gene annotation * fix: test error with MkDocs * fix: rename feature to remove range --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…dible sets without ld pruning (#877) * feat: making credset qc have an option to coalsce and deduplicate credible sets without ld pruning * fix: adding recursiveFileLookup for reading credible sets * Update src/gentropy/credible_set_qc.py Co-authored-by: Szymon Szyszkowski <[email protected]> * Update src/gentropy/method/susie_inf.py Co-authored-by: Szymon Szyszkowski <[email protected]> * Update src/gentropy/method/susie_inf.py Co-authored-by: Szymon Szyszkowski <[email protected]> * chore: pre-commit auto fixes [...] * fix: few typos from review * fix: if statement tweaks --------- Co-authored-by: Yakov <[email protected]> Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* test(credible_set_qc_step): added main functionality test * chore: moved default values to step config * chore: ensure to save with study locus schema * chore: enhanced docs * docs(credible_set_qc_ste): docs page * chore: typo --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
…#876) * feat: flagging duplicated entries while keeping one of the duplicates * feat: turning validation on for validation step * fix: test for duplication flagging * fix: test for duplication flagging --------- Co-authored-by: Yakov <[email protected]>
* feat(flag_and_filter_credible_sets): add code for identifying abnormal credible sets * feat(flag_and_filter_credible_sets): restructure tests * chore(flag_and_filter_credible_sets): update schema for spark loading * feat(flag_and_filter_credible_sets): first comple draft filtering abnormal pips code * fix(flag_and_filter_credible_sets): tweak broken code and unresolved merge * fix(flag_and_filter_credible_sets): amend test logic * fix(flag_and_filter_credible_sets): modify logic to simplify and account for floating point errors * chore(flag_and_filter_credible_sets): simplify logic to boolean
Bumps [ipython](https://github.com/ipython/ipython) from 8.28.0 to 8.29.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.28.0...8.29.0) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [mypy](https://github.com/python/mypy) from 1.12.1 to 1.13.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.12.1...v1.13.0) --- 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>
* build: add `shap` * feat(l2g): log feature contributions with shap * chore: update lock file * fix: ignore installed packages in `install_dependencies_on_cluster.sh` (problem with llvm) * build: add `matplotlib` * fix: pin `matplotlib` version to avoid mplDeprecation issue * fix(trainer): set default features_list + minor bugs * chore: pre-commit auto fixes [...]
updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.0 → v0.7.1](astral-sh/ruff-pre-commit@v0.7.0...v0.7.1) - [github.com/pre-commit/mirrors-mypy: v1.12.1 → v1.13.0](pre-commit/mirrors-mypy@v1.12.1...v1.13.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ws with negative values (#889) * fix(distance_features): hack to set to null negative values * fix(distance_features): correct mean distance equation
* feat: add step to generate association data * fix: evidence input file is json * feat: changed maximum theoretical harmonic sum formula * test: add test for calculate_harmonic_sum function * chore: move calculate_harmonic_sum function to spark_helpers.py * chore: update import statement
* fix: revert distinct for associations input file * refactor: rename the temporary studyLocusId to rowId * refactor: rename the temporary studyLocusId to rowId in test * revert: add back assign_study_locus_id in window_baased_clumping as required for SummaryStatistics --------- Co-authored-by: Daniel Suveges <[email protected]>
* feat(coloc effect sizes): add calculate beta ratio method * feat(coloc effect sizes): update schema and coloc code * fix(coloc effect sizes): tweak beta ratio return * chore: tweak colocalisation schema * feat(coloc_effect_sizes): add simple test * fix(coloc_effect_sizes): change variable to camel case * fix: test broken * feat: remove zero betas too * chore: stylistic changes --------- Co-authored-by: Daniel Suveges <[email protected]>
* refactor(convert to vcf step): parse variants from multiple data sources * chore(config): align config * fix: pass write mode from session * feat: allow for 2 columns to create partitions --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
* feat: adding logic to deconvolute studies with the same id * fix: import type * fix: import again * fix: flagging condition * feat: adding flag to gwas catalog studies to indicate no summary statistics * feat: adding flags for gwas catalog hop hit ingestion * feat: remove not curated flag if no sumstats available * fix: removing test for duplicated study locus * fix: changing flag name to clarify meaning * fix: flagging condition
…ant index to avoid null genes (#890)
* feat(feature_matrix): impute values for gene attribute cols + semantic test * fix: change window * chore: fill na in the feature matrix generation step
* feat: adding l2g features to prediction table * fix: renaming method for better name * fix: remove show statement * fix: dropping locusToGeneFeatures if already exist * feat: dropping features with null values from the map
Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: Daniel Suveges <[email protected]>
* fix: fix col names for imputation * fix: fix v1 * fix: test
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