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* feat: e2g interval features for l2g * chore: pre-commit auto fixes [...] * feat: config for interval features * fix: splat columns in convert_from_long_to_wide * fix: interval start end to integers * feat: overlap intervals using bin candidates * fix: interval start end as integers * fix: binned interval join * fix: trainer _setup redundant parameter * chore: fix docstring in interval feature methods * chore: fix interval feature descriptions * chore: clarify caching strategy * fix: address comments and adjust tests accordingly --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Co-authored-by: project-defiant <szymonszyszkowski@gmail.com>
Co-authored-by: project-defiant <szymonszyszkowski@gmail.com>
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* fix: bug with allele matching in liftover * test: fixing tests and minor bugfix in code * fix: adding logic to ensure no unexpected contig ids --------- Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
* feat(dataset): universal reader * refactor(datasource): eqtl catalogue parser allow for parquet files * feat: updates to gentropy session * chore: update doctests --------- Co-authored-by: project-defiant <szymonszyszkowski@gmail.com>
Updates the requirements on [pre-commit](https://github.com/pre-commit/pre-commit) to permit the latest version. - [Release notes](https://github.com/pre-commit/pre-commit/releases) - [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md) - [Commits](pre-commit/pre-commit@v4.0.0...v4.5.0) --- updated-dependencies: - dependency-name: pre-commit dependency-version: 4.5.0 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Updates the requirements on [ipython](https://github.com/ipython/ipython) to permit the latest version. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.19.0...9.7.0) --- updated-dependencies: - dependency-name: ipython dependency-version: 9.7.0 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Updates the requirements on [ipykernel](https://github.com/ipython/ipykernel) to permit the latest version. - [Release notes](https://github.com/ipython/ipykernel/releases) - [Changelog](https://github.com/ipython/ipykernel/blob/main/CHANGELOG.md) - [Commits](ipython/ipykernel@v6.28.0...v7.2.0) --- updated-dependencies: - dependency-name: ipykernel dependency-version: 7.2.0 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Updates the requirements on [ruff](https://github.com/astral-sh/ruff) to permit the latest version. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.8.1...0.15.0) --- updated-dependencies: - dependency-name: ruff dependency-version: 0.15.0 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
* fix: add more tests using AI agent * fix: add more tests * fix: removing duplicates * fix: update AI-generated tests to reflect latest API changes and remove no-op tests (#1194) * Initial plan * fix: update tests to reflect latest changes and remove meaningless tests Co-authored-by: project-defiant <69353402+project-defiant@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: project-defiant <69353402+project-defiant@users.noreply.github.com> * chore: update tests --------- Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
* chore(deps): bump actions/upload-artifact from 5 to 6 Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 5 to 6. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v5...v6) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * ci: update artifact actions to v7 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Updates the requirements on [isort](https://github.com/PyCQA/isort) to permit the latest version. - [Release notes](https://github.com/PyCQA/isort/releases) - [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md) - [Commits](PyCQA/isort@5.13.2...7.0.0) --- updated-dependencies: - dependency-name: isort dependency-version: 7.0.0 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 6. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v6) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Updates the requirements on [wandb](https://github.com/wandb/wandb) to permit the latest version. - [Release notes](https://github.com/wandb/wandb/releases) - [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md) - [Commits](wandb/wandb@v0.19.4...v0.25.0) --- updated-dependencies: - dependency-name: wandb dependency-version: 0.25.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
* chore: pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.4 → v0.15.2](astral-sh/ruff-pre-commit@v0.14.4...v0.15.2) - [github.com/adrienverge/yamllint.git: v1.37.1 → v1.38.0](https://github.com/adrienverge/yamllint.git/compare/v1.37.1...v1.38.0) - [github.com/alessandrojcm/commitlint-pre-commit-hook: v9.23.0 → v9.24.0](alessandrojcm/commitlint-pre-commit-hook@v9.23.0...v9.24.0) - [github.com/pre-commit/mirrors-mypy: v1.18.2 → v1.19.1](pre-commit/mirrors-mypy@v1.18.2...v1.19.1) - [github.com/lovesegfault/beautysh: v6.4.1 → v6.4.2](lovesegfault/beautysh@v6.4.1...v6.4.2) - [github.com/jsh9/pydoclint: 0.8.1 → 0.8.3](jsh9/pydoclint@0.8.1...0.8.3) - [github.com/astral-sh/uv-pre-commit: 0.9.8 → 0.10.4](astral-sh/uv-pre-commit@0.9.8...0.10.4) * chore: pre-commit auto fixes [...] * chore: update ruff rules --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
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