feat(train and test sets): expose the paths to save train and test sets during L2G training#1217
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feat(train and test sets): expose the paths to save train and test sets during L2G training#1217project-defiant wants to merge 9 commits into
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Pull request overview
This PR extends the L2G (locus-to-gene) training step configuration so callers can optionally persist the generated train/test splits as parquet outputs during model training.
Changes:
- Added
training_setandtest_setoutput-path fields toLocusToGeneConfig. - Wired
training_set/test_setthroughLocusToGeneStepand implemented pandas-based parquet persistence after training. - Added a config test asserting the new config fields exist.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
src/gentropy/config.py |
Adds training_set and test_set fields to LocusToGeneConfig so they can be provided via structured config. |
src/gentropy/l2g.py |
Passes through new config params and writes train/test split pandas DataFrames to parquet when paths are provided. |
tests/gentropy/test_config.py |
Adds a unit test to ensure the new config fields are exposed on LocusToGeneConfig. |
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✨ Context
This PR adds the option to save the train and test sets from L2G training step.
🛠 What does this PR implement
training_setandtest_setparameters to L2G Step configuration🙈 Missing
🚦 Before submitting
devbranch?make test)?uv run pre-commit run --all-files)?