chore: trigger release process #619
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May 23, 2024
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* feat: fine-mapping simulations class * fix: fix of function descriptions * Update finemapping_simulations.py --------- Co-authored-by: Daniel-Considine <[email protected]>
) * 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]>
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* Update roadmap.md -- link to gentropy tickets * fix: fix in link --------- Co-authored-by: Yakov Tsepilov <[email protected]>
* 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 (#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 (#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]>
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>
* 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]>
This was referenced Jul 12, 2024
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