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 <ss60@mib117351s.internal.sanger.ac.uk>
Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
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] <support@github.com> 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] <support@github.com> * fix: linting issues associated with ruff 0.6 * chore: fixing imports for notebooks * chore: removing old notebook --------- 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 <dogcaesar@gmail.com> Co-authored-by: Daniel Considine <dc16@sanger.ac.uk>
* 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 <dogcaesar@gmail.com>
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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: David Ochoa <ochoa@ebi.ac.uk>
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] <support@github.com> 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] <support@github.com> * fix: update lock --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Co-authored-by: David Ochoa <dogcaesar@gmail.com> Co-authored-by: David Ochoa <ochoa@ebi.ac.uk>
* 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 <69353402+project-defiant@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
* 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 <ss60@mib117351s.internal.sanger.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>
* 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 <daniel.suveges@protonmail.com> * chore: pre-commit auto fixes [...] --------- 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: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
* 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 <69353402+project-defiant@users.noreply.github.com>
* 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 <45119610+ireneisdoomed@users.noreply.github.com> --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk> Co-authored-by: Irene López Santiago <45119610+ireneisdoomed@users.noreply.github.com>
* 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 <69353402+project-defiant@users.noreply.github.com>
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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
* fix: use mapping instead of enum values in valid_rows * fix: typos * fix: swap valid and invalid paths --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
* 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 <69353402+project-defiant@users.noreply.github.com> --------- Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
* 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
Co-authored-by: Yakov <yt4@sanger.ac.uk>
Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
…ital PICS) (#910) * feat: add OUT_OF_SAMPLE_LD QC flag to PICS credible sets * feat: change pics finemapping method to PICS * test: change pics to PICS in test data * fix: flag studies without sumstats without relying on hasSumstats column * fix: flag studies without sumstats without using update_quality_flag function
* feat(gold_standard): filter by protein coding genes * feat: arbitrary gold standards * feat: read model from gcs * feat: read model from gcs * feat: get untrusted types from blob * revert: changes to gene_index * fix: correct list of missing and unexpected fields * chore: addressing comments * fix: selective check on the schema issues --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
* feat: gzip evicence output to match existing format * docs: added info about compression to docstring --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
…st metric + other fixes (#913) * feat: mean to max * fix: remove protein coding * fix: adding protein coding * feat(l2g): neighbourhood features are a division between local and regional * feat(l2g): regional max for distance features only consider protein coding genes * fix(coloc_features): regional max for coloc features only consider protein coding genes * fix(vep_features): regional max for vep features only consider protein coding genes * feat(l2g): train and predict based on protein coding genes only * feat: set nbh feature to 1 if features are 0 in the region * feat: set nbh feature to 1 if features are 0 in the region * Revert "feat: set nbh feature to 1 if features are 0 in the region" This reverts commit da145ab. * fix: return nbh features only for protein coding genes + optimisation * test: change expected results based on changes * test: change expected results based on changes * fix: test --------- Co-authored-by: Yakov Tsepilov <yt4@sanger.ac.uk>
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action 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>
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 5.0.0 to 6.0.0. - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](pytest-dev/pytest-cov@v5.0.0...v6.0.0) --- updated-dependencies: - dependency-name: pytest-cov 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>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.1 → v0.7.3](astral-sh/ruff-pre-commit@v0.7.1...v0.7.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ences in transcripts (#914) * feat: extending the VEP schema * feat(vep parser): adding logic to build variant description based on VEP annotation * fix: remove commented lines * fix: improving consequence to so term mapping * fix: nullified variant descriptions * fix: assessment_flag_column_name type fix * chore: pre-commit auto fixes [...] * feat: adding formatting to distances in description * fix: formatting * fix: variant index schema * fix: conftest for variant index * feat(variant index): normalising assessments of in-silico predictors * feat: adding VEP predictor * fix: variant test config * fix: variant test config * fix: schema type * fix: dropping failing test * fix: variant annotatin * fix: gnomad variant index repartition --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* fix: r2 for lead varaint is always 1 * fix: removing not needed quality flag * test: removing unused condition * fix: type: ignore --------- Co-authored-by: DSuveges <daniel.suveges@protonmail.com>
* feat: reverting to 95% finngen credible sets * fix: updating tests and column names
* feat: changing studylocus validation to 95 percent credible sets * fix: updating comment in code to reflect 95% credset * fix: removing credset number of partitions * fix: flag name --------- Co-authored-by: Yakov Tsepilov <yt4@sanger.ac.uk>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.3 → v0.7.4](astral-sh/ruff-pre-commit@v0.7.3...v0.7.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…frequencies (#929) * fix: gnomad 4.1 frequencies * fix: removing in-silico extraction in gnomad * fix: removing in silico predictor ingestion from gnomad pre-process
* feat(gold_standard): add traitFromSourceMappedId to schema * chore: adapt tests * feat(feature_matrix): consider `traitFromSourceMappedId` a static column * feat(feature_matrix): consider `traitFromSourceMappedId` an optional column
Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
* chore: vep version bump * fix: bump version to most recent --------- Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
* feat: allow building package from tag * fix: indent --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
* feat: adding GERP conservation score to variant annotation * fix: typo --------- Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Bumps [ipython](https://github.com/ipython/ipython) from 8.29.0 to 8.30.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.29.0...8.30.0) --- 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>
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.7.1 to 0.8.1. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.7.1...0.8.1) --- updated-dependencies: - dependency-name: ruff 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>
… missing annotation (#925) * fix(prediction): do not annotate all features from matrix * fix(prediction): filter out features with 0 * chore: pre-commit auto fixes [...]
…e pairs and with cross validation (#938) * feat(gold_standard): add traitFromSourceMappedId to schema * chore: adapt tests * feat(feature_matrix): consider `traitFromSourceMappedId` a static column * feat(feature_matrix): consider `traitFromSourceMappedId` an optional column * feat: update l2g config with best hyperparams * feat(trainer): new train runs when cross_validate=False * chore(model): add default hyperparams based on best params * chore: debug sweep, one single run * feat(trainer): new train runs when cross_validate=True * feat(cross_validate): sweep runs are now together * chore: pre-commit auto fixes [...] * chore: improve error message
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