feat(config): move from hydra to pydantic models - #1221
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- Create config/ package with SessionDefaults (Pydantic frozen model) - Move all legacy step config dataclasses to config/defaults.py - Rewrite test_config.py for Pydantic SessionDefaults model - All 15 existing step config dataclasses remain importable from gentropy.config Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
- Add BiosampleIndexDefaults Pydantic model (all fields required) - Update BiosampleIndexStep constructor to accept (config, session) - Rewrite test to construct config and validate step initialization - Add config validation test Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
- Add ColocalisationDefaults Pydantic model with 3 required + 3 optional fields - Update ColocalisationStep constructor to accept (config, session) - Add config validation tests and update existing tests to use config Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Migrate the following steps from dataclass StepConfig to Pydantic config models: credible_set_qc, decode_ingestion (4 configs), intervals (2 configs), study_locus_validation, study_validation, sumstat_qc_step, variant_index (2 configs). Fix duplicate class definition bugs caused by sequential Write tool operations in 4 files: sumstat_qc_step, study_validation, variant_index, intervals. Update all corresponding test files to use (config=Defaults(...), session=...) pattern and add config validation tests. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Add co-located Pydantic config models and update step classes to accept (config, session) parameters for: - eqtl_catalogue, finngen_finemapping_ingestion, finngen_studies, finngen_sumstat_preprocess, finngen_ukb_mvp_meta, foldx_ingestion - gnomad_ingestion - gwas_catalog_study_curation, gwas_catalog_study_index, gwas_catalog_sumstat_preprocess, gwas_catalog_top_hits - l2g (4 configs: evidence, associations, feature_matrix, model) - ld_based_clumping, locus_breaker_clumping - lof_curation_ingestion, molecular_complex, pics, pqtl_study - ukb_ppp_eur_sumstat_preprocess, window_based_clumping All files pass ruff check, ruff format, and mypy. 8 test failures are pre-existing (unrelated to these changes). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
…ation_method - Replace mutable list[] defaults with Field(default_factory=list) in: - study_validation.py (StudyValidationDefaults.invalid_qc_reasons) - study_locus_validation.py (StudyLocusValidationDefaults.invalid_qc_reasons) - intervals.py (IntervalE2GDefaults.invalid_qc_reasons) - intervals.py (IntervalEpiractionDefaults.invalid_qc_reasons) - Add field_validator for colocalisation_method in colocalisation.py to reject invalid values at config validation time (case-insensitive) - Simplify step body normalization code since fields are now always list[str] Agent-Logs-Url: https://github.com/project-defiant/gentropy/sessions/25062353-a56a-4286-a077-a67a6c204c94 Co-authored-by: project-defiant <69353402+project-defiant@users.noreply.github.com>
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