…990)

* build(deps): update scipy requirementV

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: project-defiant <[email protected]>

* feat: add LOF curation ingestion step and config

* feat: add LOF annotations path to variant_index step

* feat: add parser for LOF data

* feat: add function to normalise LOF assessments

* feat: add function for creating LOF description

* feat: enable annotation of VariantIndex with the variantDescription field

* refactor: rename inSilicoPredictors to variantEffect

* refactor: rename inSilicoPredictors to variantEffect in merged files

* chore: consolidate variant annotation paths into list

* Update _ukb_ppp_eur.md

Original page hosted broken link for synapse and uninformative title for page

* chore: pre-commit auto fixes [...]

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* feat(prediction): add `model` as instance attribute

* feat: added `convert_map_type_to_columns` spark util

* feat(prediction): new method `explain` returns shapley values

* feat(prediction): `explain` returns predictions with shapley values

* chore: compute `shapleyValues` in the l2g step

* refactor: use pandas udf instead

* refactor: forget about udfs and get shaps single threaded

* chore: remove reference to chromatin interaction data in HF card

* fix(l2g_prediction): methods that return new instance preserve attribute

* feat(dataset): `filter` method preserves all instance attributes

* feat(l2gmodel): add features_list as model attribute and load it from the hub metadata

* fix: pass correct order of features to shapley explainer

* feat(l2g): predict mode to extract feature list from model, not from config

* feat(l2g): pass default features list if model is loaded from a path

* 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: remove `convert_map_type_to_columns`

* feat(l2gprediction): refactor feature annotation and change schema

* chore: pre-commit auto fixes [...]

* feat: report as log odds

* feat: calculate scaled probabilities

* chore(l2gprediction): remove shapBaseProbability

* chore: correct typo in add_features and make schemas non nullable

* fix: rename columns in pandas df after pivoting

* fix: add raw shap contributions

* fix(model): when saving create directory if not exists

* feat(l2g): bundle model and training data in hf

* feat(model): include data when loading model

* feat: final version of shap explanations

* fix: do not infer features_list from df

* fix: get_features_list_from_metadata returned cols that were not features

* refactor(model): read training data in the local filesystem w pandas

* chore: successful run, remove test

…3.0,>=2.12.6 to >=2.12.6,<2.24.0 (#994)

* build(deps): update google-cloud-secret-manager requirement

---
updated-dependencies:
- dependency-name: google-cloud-secret-manager
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>

* chore(uv): 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: Szymon Szyszkowski <[email protected]>

* chore: pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.7.4 → v0.9.6](astral-sh/ruff-pre-commit@v0.7.4...v0.9.6)
- [github.com/alessandrojcm/commitlint-pre-commit-hook: v9.18.0 → v9.21.0](alessandrojcm/commitlint-pre-commit-hook@v9.18.0...v9.21.0)
- [github.com/pre-commit/mirrors-mypy: v1.13.0 → v1.15.0](pre-commit/mirrors-mypy@v1.13.0...v1.15.0)
- [github.com/jsh9/pydoclint: 0.5.9 → 0.6.2](jsh9/pydoclint@0.5.9...0.6.2)
- [github.com/astral-sh/uv-pre-commit: 0.5.22 → 0.6.1](astral-sh/uv-pre-commit@0.5.22...0.6.1)

* chore: pre-commit auto fixes [...]

* chore(docstring): added assertion errors to the docstrings

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: Szymon Szyszkowski <[email protected]>

…ata filename (#997)

* fix(model): typo in filename when uploading training data to hub

* fix(l2g): direct model to hf repo when path is none

* fix: run_train to keep GS and geneId

* chore: pre-commit auto fixes [...]

---------

Co-authored-by: xyg123 <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ex (#1003)

* fix: remove certain methods from variantEffect struct generation

* fix: remove fields from vep output schema

* fix: bump gentropy base image

* fix: qemu version bump

* chore: dump version of github action runner to temp fix QEMU bug

* chore: revert base docker image update

* test: check gha no cache build

* fix: pin chemu build

* test: revert the change in CI pipeline for testing artifact workflow

---------

Co-authored-by: Szymon Szyszkowski <[email protected]>
Co-authored-by: Daniel Suveges <[email protected]>

* fix: change posterior filter

* fix: adjust test

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.6 → v0.9.9](astral-sh/ruff-pre-commit@v0.9.6...v0.9.9)
- [github.com/astral-sh/uv-pre-commit: 0.6.1 → 0.6.3](astral-sh/uv-pre-commit@0.6.1...0.6.3)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 3.4.0 to 3.6.0.
- [Release notes](https://github.com/docker/setup-qemu-action/releases)
- [Commits](docker/setup-qemu-action@v3.4.0...v3.6.0)

---
updated-dependencies:
- dependency-name: docker/setup-qemu-action
  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 [python-semantic-release/publish-action](https://github.com/python-semantic-release/publish-action) from 9.19.1 to 9.21.0.
- [Release notes](https://github.com/python-semantic-release/publish-action/releases)
- [Changelog](https://github.com/python-semantic-release/publish-action/blob/main/releaserc.toml)
- [Commits](python-semantic-release/publish-action@v9.19.1...v9.21.0)

---
updated-dependencies:
- dependency-name: python-semantic-release/publish-action
  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]>