chore: trigger release process #3
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Nov 7, 2024
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…utation is False (opentargets#627) * fix(susie_finemapper): fix in the FMer in case ss_imp=False * fix: small fix in docs
* fix(SummaryStatistics): fix in sanity_filter * fix: adding prune of inf values * fix(dataset): removal of inf values from beta and stderr * fix: fix in test and sanity filter --------- Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: Yakov <[email protected]>
Co-authored-by: Szymon Szyszkowski <[email protected]>
…on (opentargets#628) * feat(clumping): lower p-value significance threshold for clumping step * feat(config): extract gwas_significance to config * feat(config): synced p-value in association parsing --------- Co-authored-by: Szymon Szyszkowski <[email protected]> Co-authored-by: Yakov <[email protected]>
* feat(airflow): drop finngen PICS results from etl * feat(l2g): allow to publish feature matrix * fix(types): typo in types * chore(data_release): bumped release date --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
…s#632) Bumps [typing-extensions](https://github.com/python/typing_extensions) from 4.11.0 to 4.12.1. - [Release notes](https://github.com/python/typing_extensions/releases) - [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md) - [Commits](python/typing_extensions@4.11.0...4.12.1) --- updated-dependencies: - dependency-name: typing-extensions 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: Szymon Szyszkowski <[email protected]>
) Bumps [pep8-naming](https://github.com/PyCQA/pep8-naming) from 0.13.3 to 0.14.1. - [Release notes](https://github.com/PyCQA/pep8-naming/releases) - [Changelog](https://github.com/PyCQA/pep8-naming/blob/main/CHANGELOG.rst) - [Commits](PyCQA/pep8-naming@0.13.3...0.14.1) --- updated-dependencies: - dependency-name: pep8-naming 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>
…rgets#630) * chore: prototype ingestion of sceqtls * chore: use credible sets from ftp * feat(study_index): rename tissuefromsourceid to biosamplefromsourceid to accommodate cell type ids * chore: update output paths to final destination
) * feat(spark-helpers): enforce schema of returned objects by other function * fix: fixing docstring * test: adding test for array sorter * chore: pre-commit auto fixes [...] * fix: addressing a typo * chore: pre-commit auto fixes [...] * fix: removing duplicated rows * fix: addressing review comments * fix: adding StructType hint --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* feat(schema): adding locus start/end position to the study locus schema * feat(clumping) adding clumping logic + docs * test(clumpin): adding tests for locus breaker method * test(clumping): adding semantic tests for locus breaker clumping * fix(config): reverting gwas significance threshold
Bumps [wandb](https://github.com/wandb/wandb) from 0.16.2 to 0.17.0. - [Release notes](https://github.com/wandb/wandb/releases) - [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md) - [Commits](wandb/wandb@v0.16.2...v0.17.0) --- updated-dependencies: - dependency-name: wandb dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [ipython](https://github.com/ipython/ipython) from 8.24.0 to 8.25.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.24.0...8.25.0) --- 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>
Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.4.0 to 1.5.0. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@1.4.0...1.5.0) --- updated-dependencies: - dependency-name: scikit-learn 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>
* 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]>
) * 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]>
…opentargets#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 (opentargets#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]>
…entargets#887) * 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 (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
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