feat(config): gnomAD steps configuration extraction and versioning #620
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added 9 commits
May 24, 2024 12:06
Signed-off-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
…nfigs 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.
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) * 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 <ss60@mib117351s.internal.sanger.ac.uk> Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
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✨ Context
The context is described in opentargets/issues#3324.
🛠 What does this PR implement
New functionalities
Configuration refactoring
use_version_from_inputset to True, in which case the version is inferred by the VersionEngine class and appended to the output catalog. By default this behaviour is set to False.Chores
make check.🙈 Missing
🚦 Before submitting
devbranch?make test)?poetry run pre-commit run --all-files)?