chore: trigger release process #653
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Jun 20, 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]>
* 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]>
* 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 <[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>
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 <[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.
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
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