chore: trigger release process #4
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Nov 28, 2024
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* feat: enable interface with gcp secrets manager * chore: add google-cloud-secret-manager * chore: merge
* feat: credible set quality filtering * fix: purity threshold
Bumps [dbldatagen](https://github.com/databrickslabs/data-generator) from 0.3.5 to 0.4.0. - [Release notes](https://github.com/databrickslabs/data-generator/releases) - [Changelog](https://github.com/databrickslabs/dbldatagen/blob/master/CHANGELOG.md) - [Commits](databrickslabs/dbldatagen@release/v0.3.5...release/v0.4.0) --- updated-dependencies: - dependency-name: dbldatagen 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(config): typos fix * fix(config): moved ld_index dataset to static assets --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
* feat(dataset): schema mismatch issue * feat(L2GPrediction): schema unification * fix: swapped data types --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
…ets#645) * 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
…argets#644) * 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 <[email protected]> * 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>
…targets#651) 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.
…ets#576) * 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 <[email protected]> * 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 <[email protected]>
Code inspection shows that it is not used anymore.
…entargets#656) 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] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Kirill Tsukanov <[email protected]>
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] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: David Ochoa <[email protected]>
* 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 <[email protected]>
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
…ts#608) * 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 <[email protected]> Co-authored-by: Szymon Szyszkowski <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]> * Update src/gentropy/sumstat_qc_step.py Co-authored-by: Daniel Suveges <[email protected]> * fix: optimisation of code --------- Co-authored-by: Daniel Suveges <[email protected]>
…targets#677) * 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
…ant index to avoid null genes (opentargets#890)
…ets#895) * 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
* fix: tweak sc vs bulk eqtl catalogue logic * fix: update tests * fix: correct coloc calling of method * fix: address PR comments * fix: change string to col * fix: change eqtl catalogue path to specific commit * chore: fix method description
* feat: changing to 99 credible sets * fix: change summary schema * fix: adding purity metrics * fix: updating test data samples * fix: updating test data samples * Update finemapping.py
Co-authored-by: Yakov <[email protected]>
Co-authored-by: Szymon Szyszkowski <[email protected]>
…ital PICS) (opentargets#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 <[email protected]>
* feat: gzip evicence output to match existing format * docs: added info about compression to docstring --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
…st metric + other fixes (opentargets#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 <[email protected]>
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] <[email protected]> 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] <[email protected]> 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 (opentargets#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 <[email protected]>
* feat: reverting to 95% finngen credible sets * fix: updating tests and column names
…ntargets#921) * 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 <[email protected]>
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 (opentargets#929) * fix: gnomad 4.1 frequencies * fix: removing in-silico extraction in gnomad * fix: removing in silico predictor ingestion from gnomad pre-process
…ts#924) * 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 <[email protected]>
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