chore: trigger release process #961
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
![github-actions[bot]](https://avatars.githubusercontent.com/in/15368?s=60&v=4){kind=small}
github-actions
bot
commented
Dec 19, 2024
github-actions
bot
commented
…ally refactor: derive the _schema automatically
* feat(study_index): add `StudyIndex.VALID_TYPES` enum * test: mock data have more stringent ID definition + other improvements * refactor: set ID specification in fixtures with expression to avoid changing nullability status * refactor: set ID specification in fixtures with expression to avoid changing nullability status * chore: fix issues
#957) * fix: repair SusieFinemapperStep to work with new SL schema and fix locus missing the lead variantID * fix: changing schema --------- Co-authored-by: Szymon Szyszkowski <[email protected]>
* fix: `poetry shell` is deprecated * chore: update versionin precommit hook * chore: update versionin precommit hook * chore: migrate toml * chore: update version in dockerfile * chore: pre-commit auto fixes [...] * chore: do not use typing deprecated classes according to ruff * build: update `deptry` * build: update `deptry`
Co-authored-by: project-defiant <[email protected]>
github-actions
bot
added
the
documentation
…dex (#948) * feat: rewrite `is_protein_coding_feature_logic` to take info from the variant index * chore: correct genomic_window definition * test: adapt `TestCommonProteinCodingFeatureLogic` * test: adapt `test_build_feature_matrix` * test: adapt `test_build_feature_matrix` * test: adapt `test_build_feature_matrix`
* fix: skip leading 'v' in docker tag * fix: approach with bash * feat: infer version with two steps * chore: comments * revert: tag regex * fix: tag regex * fix: whitespace * chore: pre-commit auto fixes [...] --------- Co-authored-by: project-defiant <[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>
* refactor: rename all gene_index related files to target_index * refactor: rename gene_index to target_index in various files * refactor: rename gene_index to target_index in tests * refactor: rename fields to be compatible with new target_index * refactor: replace examples that use gene_index * refactor: delete gene_index step files * refactor: remove gene_index step from config * feat: replace the gene_index schema with the target_index schema * refactor: modify mock_target_index * fix: remove mock_target_index from test_validate_schema_missing_field * refactor: delete target.md * fix: fix study index validation tests * fix: fix l2g feature tests * chore: pre-commit auto fixes [...] * revert: revert column name after merging from dev --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel Suveges <[email protected]>
* test: adding tests for trans qtl flagging * fix: failing tests due to changing schema * chore: updating code for TargetIndex * chore: addressing review comments
…974) * chore(pyspark): update to 3.5.X * chore: fix doctest syntax * chore: bump temurin version to 11 * feat: allow multiple python versions * feat: python matrix for gha * chore: pre-commit auto fixes [...] * chore: typos * chore: fix python version in setup dev script * fix: attempt to fix the 3.11 tests * fix: set the session correctly in variant_index_config * Revert "chore: fix doctest syntax" This reverts commit 630c0c9. * chore: update dependencies * Revert "Revert "chore: fix doctest syntax"" This reverts commit 18c66b1. * chore: bump image to 2.2 * chore: update lock files * build: poetry cleanup * build: uv checks droped * chore: fix dockerfile and install test deps * build(uv): add all dependencies to run tests * chore: fix test issue with rounding error * chore: fix dependency version lower bounds * chore: add .python-version file to ignored * build: new setup * build: new setup * build: new setup * build: new setup * build: new setup * revert: bring back initialization actions * chore: align variable name * chore: update pre-commit python version * chore: docs update * feat: more complex uv installation * feat: notify to source shellrc file when installing uv * fix: checks * chore: debug gha * chore: debug gha * feat: debug gha * feat: debug gha * feat: debug gha * feat: force user shell * feat: gha debug * feat: gha debug * feat: gha debug * feat: gha debug --------- Co-authored-by: project-defiant <[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>
Co-authored-by: Szymon Szyszkowski <[email protected]>
* chore: pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.4 → v0.9.3](astral-sh/ruff-pre-commit@v0.7.4...v0.9.3) - [github.com/hadialqattan/pycln: v2.4.0 → v2.5.0](hadialqattan/pycln@v2.4.0...v2.5.0) - [github.com/alessandrojcm/commitlint-pre-commit-hook: v9.18.0 → v9.20.0](alessandrojcm/commitlint-pre-commit-hook@v9.18.0...v9.20.0) - [github.com/pre-commit/mirrors-mypy: v1.13.0 → v1.14.1](pre-commit/mirrors-mypy@v1.13.0...v1.14.1) - [github.com/jsh9/pydoclint: 0.5.9 → 0.6.0](jsh9/pydoclint@0.5.9...0.6.0) - [github.com/python-poetry/poetry: 2.0.0 → 2.0.1](python-poetry/poetry@2.0.0...2.0.1) * chore: pre-commit auto fixes [...]
) * feat(l2gmodel): add features_list as model attribute and load it from the hub metadata * feat(l2g): predict mode to extract feature list from model, not from config * feat(l2gprediction): add `model` as attribute * feat(l2gmodel): add features_list as model attribute and load it from the hub metadata * feat(l2g): predict mode to extract feature list from model, not from config * feat(l2gprediction): add `model` as attribute * chore: fix typo
* chore: adding logic to sanitize QTL study identifiers * fix: instead using urllib.parser.quote, just use regexrepace * refactor: moving sanitizing logic to qtl ingestion
….14.0 to >=2.14.0,<3.1.0 (#986) * build(deps): update google-cloud-storage requirement Updates the requirements on [google-cloud-storage](https://github.com/googleapis/python-storage) to permit the latest version. - [Release notes](https://github.com/googleapis/python-storage/releases) - [Changelog](https://github.com/googleapis/python-storage/blob/main/CHANGELOG.md) - [Commits](googleapis/python-storage@v2.14.0...v3.0.0) --- updated-dependencies: - dependency-name: google-cloud-storage dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * chore: update uv.lock --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: project-defiant <[email protected]>
Co-authored-by: Szymon Szyszkowski <[email protected]>
….4,<2.3.0 (#985) * build(deps): update numpy requirement Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v1.26.4...v2.2.2) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * chore: update uv.lock --------- 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]> Co-authored-by: project-defiant <[email protected]>
Co-authored-by: project-defiant <[email protected]>
….4,<1.16.0 (#983) * build(deps): update scipy requirement Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.11.4...v1.15.1) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * chore: update uv.lock --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: project-defiant <[email protected]> Co-authored-by: Szymon Szyszkowski <[email protected]>
* feat: ingest OTAR2082 FoldX data * feat: adding FoldX ddG scaling * feat: adding foldx ingestion step * feat: adding amio acid annotation to ingestion * fix: explode funcion repaced with explode_outer * fix: changing ddG scaling logic * chore: pre-commit auto fixes [...] * fix: making fold-x threshold less permissive --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.