This PR, while incomplete WRT to simulating reads, activates testing for the huge API change inside harpy
The changes:
Modules return the snakemake command that main() will process at the workflow
this reduces the code redundancy for each module to have to generate conda deps, run the workflow
deprecated fetch_file() in favor of building the scripts and rules with the harpy package, meaning the files will live alongside the harpy python installation (managed by pip) and the files can be called by importlib_resources.files(), which is much MUCH less brittle than before.
This PR, while incomplete WRT to simulating reads, activates testing for the huge API change inside harpy
The changes:
main()will process at the workflowfetch_file()in favor of building the scripts and rules with the harpy package, meaning the files will live alongside the harpy python installation (managed by pip) and the files can be called byimportlib_resources.files(), which is much MUCH less brittle than before.