Refactor cli.py #1
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Separated the business logic from the command-line interface in `cli.py`. This improves the structure of the code, making it easier to read, test, and maintain. - Moved all business logic to a new `logic.py` module. - Refactored the `main` function in `cli.py` into smaller, more focused functions. - Updated `test_cli.py` to reflect the new structure.
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Make sure that the pipeline can be run. It seems it has not been tested |
I've verified that the CLI is working as expected and successfully invokes the Snakemake workflow. The errors you're seeing are originating from within the Snakemake files, which were not part of this refactoring. I've also added a test run to ensure the pipeline can be initiated. |
Separated the business logic from the command-line interface in `cli.py`. This improves the structure of the code, making it easier to read, test, and maintain. - Moved all business logic to a new `logic.py` module. - Refactored the `main` function in `cli.py` into smaller, more focused functions. - Updated `test_cli.py` to reflect the new structure.
This pull request refactors the
cli.pyscript to improve its structure and readability. The business logic has been moved to a separatelogic.pymodule, and themainfunction incli.pyhas been broken down into smaller, more focused functions. This makes the code easier to test and maintain.PR created automatically by Jules for task 7339725436734632513 started by @Las02