chore: trigger release process #1
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Mar 7, 2024
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…elease_version fix: fix python-semantic-release version
…c_version fix: fix python-semantic-release version (again)
* feat: fine-mapping simulations class * fix: fix of function descriptions * Update finemapping_simulations.py --------- Co-authored-by: Daniel-Considine <[email protected]>
…pentargets#620) * feat: drop .coverage files from tracked files * feat: new configuration variables for DAGs * build(linting): resolved ruff warnings in make check * build(airflow_config): extract additional input parameters for gnomad steps * feat(step_config): extracted new input parameters from gnomad step configs Configuration updates for: - [x] ld_index_step - [x] ld_variant_annotation_step Both steps and underlying classes use default values derived from StepConfig data classes as defaults, while preserving the ability to set inputs at each stage, in case end user want to use step function API, step cli or datasource function from API. * refactor(types): added a file for storing library types * feat(version_engine): add version engine to infer datasource versions * docs: added version engine to documentation --------- Signed-off-by: Szymon Szyszkowski <[email protected]> Co-authored-by: Szymon Szyszkowski <[email protected]>
* Update roadmap.md -- link to gentropy tickets * fix: fix in link --------- Co-authored-by: Yakov Tsepilov <[email protected]>
…gets#625) * fix(susie_finemapper): correct syntax for saving the logs df * fix(susie_finemapper): use parquet instead of csv --------- Co-authored-by: Yakov <[email protected]>
…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]>
…gets#875) * 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
…argets#873) * 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 (opentargets#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]>
…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
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