chore: trigger release process #688
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Jul 11, 2024
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* feat(SusieFineMapperStep): add new fucntion that takes boundaries as input * fix: typo in function
* refactor: remove ot_pics * refactor: gwas_catalog_sumstat_preprocess config removed * refactor: ot_finngen_studies removed * refactor: ot_finngen_studies removed * refactor: window_based_clumping cleanup
* feat(ld_annotator): apply r2 threshold * feat(ld_annotator): apply r2 threshold * chore(ldannotator): change threshold to 0.5
* feat(stydyLocus): adding new locus collection using boundaries * fix: fix in test * Update tests/gentropy/dataset/test_study_locus.py Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> * chore: pre-commit auto fixes [...] --------- Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Sometimes it is very useful to be able to spin up a Jupyter notebook on a Dataproc cluster which has access to Gentropy and all its configured environment. Previously, I already added the “enable_component_gateway” option; however, it doesn't really take any effect unless you also specify the list of components to enable, which is what I'm doing in this PR.
* chore: checkpoint * chore: checkpoint * chore: deprecate spark evaluator * chore: checkpoint * chore: resolve conflicts with dev * chore: resolve conflicts with dev * chore(model): add parameters class property * feat: add module to export model to hub * refactor: make model agnostic of features list * chore: add wandb to gitignore * feat: download model from hub * chore(model): adapt predict method * feat(trainer): add hyperparameter tuning * chore: deprecate trainer tests * refactor: modularise step * feat: download model from hub by default * fix: convert omegaconfig defaults to python objects * fix: write serialised model to disk and then upload to gcs * fix(matrix): drop goldStandardSet when in predict mode * chore: pass token to access private model * chore: pass token to access private model * fix: pass right schema * chore: pre-commit auto fixes [...] * chore: fix mypy issues * build: remove xgboost * chore: merge * chore: pre-commit auto fixes [...] * chore: address comments
* feat: implement UKB PPP (EUR) ingestion & harmonisation * fix: correct module name for docs * fix: definitely correct module name for docs * test: update output of neglog_pvalue_to_mantissa_and_exponent * fix: test syntax with <BLANKLINE> * Update src/gentropy/datasource/ukb_ppp_eur/summary_stats.py Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> * fix: code review updates for docs and version * fix: syntax for concat_ws * style: list harmonisation steps in the docstring * style: rename freq to MAF * style: use concat_ws * style: use two distinct parameters for study index and summary stats output paths --------- Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Code inspection shows that it is not used anymore.
Bumps [python-semantic-release/python-semantic-release](https://github.com/python-semantic-release/python-semantic-release) from 9.6.0 to 9.8.3. - [Release notes](https://github.com/python-semantic-release/python-semantic-release/releases) - [Changelog](https://github.com/python-semantic-release/python-semantic-release/blob/master/CHANGELOG.md) - [Commits](python-semantic-release/python-semantic-release@v9.6.0...v9.8.3) --- updated-dependencies: - dependency-name: python-semantic-release/python-semantic-release 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> Co-authored-by: Kirill Tsukanov <tskir@users.noreply.github.com>
Bumps [pydoclint](https://github.com/jsh9/pydoclint) from 0.4.1 to 0.5.1. - [Release notes](https://github.com/jsh9/pydoclint/releases) - [Changelog](https://github.com/jsh9/pydoclint/blob/main/CHANGELOG.md) - [Commits](jsh9/pydoclint@0.4.1...0.5.1) --- updated-dependencies: - dependency-name: pydoclint 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>
* fix: remove check merge conflict * fix: remove line for now
* feat(variant annotation): new variant annotation schema + logic to extract from VEP * fix: typehints in function * refactor(variant annotation): migrating methods to the new schema * chore: pre-commit auto fixes [...] * refactor(variant index): sorting out new variant index dataset * chore: pre-commit auto fixes [...] * feature(vep): adding predictors to vep transcript object * fix(schema): fixing schema missing fields * fix(schema): fixing schema missing fields * fix(schema): fixing schema missing fields * fix(schema): fixing schema missing fields * chore: pre-commit auto fixes [...] * fix(annotation): array union under condition * fix: merging dbxref objects * feat(variants): updating variants to make more robust * feat: migrating methods to new variant index * adjusting variant index methods * some updates * rename v2g to variant to gene * chore: pre-commit auto fixes [...] * adding test * chore: pre-commit auto fixes [...] * fix(precommit): json file needed to rename to jsonl * fix(precommit): removing steps depending on old data model * fix(coftest): fixing variant index mock generation * fix: typo in package import * fix: sorting out conftest * refactor(gwas ingest): Updating GnomAD handling * refactor(gnomad): variant annotation removed, changed to variant index, steps updated * refactor: shuffling around gnomad logic * fix: references in tests * refactor: sorting out gnomad variant dag * refactor: cleaning configs and tests * docs(vep): adding datasource description * test(vep): adding more test to the vep parser * test(vep): tests are now running * fix: removing version suffix from pyproject and airflow config * fix: reverting DAGs - removing temporary modifications I added for testing * fix: addressing reviewer comments * refactor: fiddling with variant index annotation logic * chore: addressing comments * fix: variant cross-ref snake case * fix: correcting join strategy --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* fix: typo in cs_lbf_thr parameter name * fix: removing two parameters --------- Co-authored-by: Yakov Tsepilov <yt4@sanger.ac.uk>
As it is, when the susie_finemapper step is triggered, nothing happens because the configuration class is not linked via _target_ to the step class. This commit addresses the problem
* feat: custom dockerfile to run ensembl vep * ci: automate vep image build and artifact registry * chore: update airflow google operators (not required) * feat: working version of google batch airflow vep job * feat: working version of google batch airflow vep job * feat(VEP): adding CADD plugin * feat: local loftee file * feat: working with input bucket full of input files * feat: prevent writing html * fix: minor adjustments to retry strategy * feat(airflow): separating mounting points for input/output and cache * fix: typo in airflow dag * fix: pre-commit pain * chore: rename airflow dag file --------- Co-authored-by: DSuveges <daniel.suveges@protonmail.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
* feat: locus_breaker_clumping * fix: dosctring * feat: _process_locus_breaker function * feat: locus breaker clumping step * fix: tidying parameters * feat: option to remove MHC region * fix: description for LocusBreakerClumpingStep * fix: removing division of distance * fix: adding new parameters for wbc distance separate from large_loci_size * fix: resolving comments * refactor: refactored code in process_locus_breaker_output * fix: removing superfluous variable * fix: persisting sumstats parquet to improve analysis plan --------- Co-authored-by: Yakov <yt4@sanger.ac.uk>
* feat: add qc step * fix: remove .df * fix: fix in name * fix: fix v3 * Update src/gentropy/sumstat_qc_step.py Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * Update src/gentropy/sumstat_qc_step.py Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com> * fix: optimisation of code --------- Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>
* feat: adding sanity filter to GWASCatalogSumstatsPreprocessStep * fix: adding description
* fix: improving locus_breaker_step logic * fix: updating susie_finemapper.py to deal with new I/O logic * chore: removing unused log output path
Two values were recently removed from the step. This brings config in alignment with these changes.
* feat: credible set quality control step * feat: credible_set_qc.py step * chore: updating genotropy/config.py to include CredibleSetQCConfig() * chore: updated LocusBreakerClumpingConfig(StepConfig) * fix: changing default configs in code
* feat: added jq to the docker image dependencies * feat: added gsutil to gentropy image * fix: added missing env vars --------- Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
* chore: snapshot * feat(StudyIndex): adding valiation methods * feat(studyIdex): adding disease validation * fix: typo in test * fix: moving import under the type checking condition * fix: some columns might need to be dropped * fix(study index): preventing [null] arrays in the cohorts object * fix(study index): more context is provided for disease normalisation
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.4.10 to 0.5.1. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@v0.4.10...0.5.1) --- 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> Co-authored-by: David Ochoa <ochoa@ebi.ac.uk>
* chore: pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.5.1](astral-sh/ruff-pre-commit@v0.4.3...v0.5.1) - [github.com/pre-commit/mirrors-mypy: v1.10.0 → v1.10.1](pre-commit/mirrors-mypy@v1.10.0...v1.10.1) - [github.com/jsh9/pydoclint: 0.4.1 → 0.5.3](jsh9/pydoclint@0.4.1...0.5.3) * chore: update lock --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> Co-authored-by: David Ochoa <dogcaesar@gmail.com>
* build(deps): bump skops from 0.9.0 to 0.10.0 Bumps [skops](https://github.com/skops-dev/skops) from 0.9.0 to 0.10.0. - [Release notes](https://github.com/skops-dev/skops/releases) - [Changelog](https://github.com/skops-dev/skops/blob/main/docs/changes.rst) - [Commits](skops-dev/skops@v0.9.0...v0.10) --- updated-dependencies: - dependency-name: skops dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * fix: update `trusted` in load to avoid typeerror --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Irene López <irene.lopezs@protonmail.com>
Bumps [google-cloud-dataproc](https://github.com/googleapis/google-cloud-python) from 5.9.3 to 5.10.1. - [Release notes](https://github.com/googleapis/google-cloud-python/releases) - [Changelog](https://github.com/googleapis/google-cloud-python/blob/main/packages/google-cloud-documentai/CHANGELOG.md) - [Commits](googleapis/google-cloud-python@google-cloud-dataproc-v5.9.3...google-cloud-dataproc-v5.10.1) --- updated-dependencies: - dependency-name: google-cloud-dataproc dependency-type: direct:development update-type: version-update:semver-minor ...
…665) * feat(variant index): calculate hash as variant id for variants with long alleles * fix: adjusting hashing method * fix: painful iteration to get gnomad running with the new schema + fine tune with variant index * chore: fixing variant index step * fix: reverting changes * fix: minor updates * feat(variant index): null values of array columns are enforced to be replaced with empty arrays * fix: array union vs coalese fix * fix(variant index): annotation logic made more robust * fix: addressing review comments * fix: renaming helper function for better readability * fix(liftover): fixing docstring
Bumps [ipython](https://github.com/ipython/ipython) from 8.25.0 to 8.26.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.25.0...8.26.0) --- 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: David Ochoa <ochoa@ebi.ac.uk> Co-authored-by: David Ochoa <dogcaesar@gmail.com>
Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
github-actions
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added tags to the artifact github actions triggers, so the images produced by gentropy will be versionned by tag name Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
* fix: moving hl.init * fix: missed a hl.init * fix: removing the hl.init from notebooks
…nd Finngen (#693) * chore: remove finngen prefix from studyIds * feat(eqtl_catalogue): changes from #3357 * fix: update study table * fix: update _identify_study_type example
…taset (#686) * feat(studyLocus validation): adding validation logic to studyLocus dataset * feat: making QC more granular * Update src/gentropy/dataset/study_locus.py Co-authored-by: David Ochoa <ochoa@ebi.ac.uk> --------- Co-authored-by: David Ochoa <ochoa@ebi.ac.uk>
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