Inconsistent input/output argument order

[hyanwong]

Using the (undocumented) python API:

vcf2zarr.convert(input_vcfs, output_zarr)
vcf2zarr.explode(output_icf, input_vcfs)  # this has output path as first param, input as second?
vcf2zarr.encode(input_icf, output_zarr)

I think vcf2zarr.explode should probably reverse the order of the first 2 params? I guess since it's undocumented, it's possible to make changes like this without breaking the API at this stage?

[jeromekelleher]

Yes, well spotted. I've been debating with myself on what should be done here. It's not quite so obvious when you look at explode_init, explode_partition etc, where it makes sense for the "self" reference to be the first argument.

See #102 for a related problem that I've been dithering about

[jeromekelleher]

I wouldn't write any code using the Python API by the way, it will definitely change in breaking ways before being documented.

[hyanwong]

I wouldn't write any code using the Python API by the way, it will definitely change in breaking ways before being documented.

Thanks. I gathered that it's undocumented, so I'm expecting changes. The context is that I'm very roughly drafting some examples for teaching in a few months, so I'm happy to change any code as/when it is documented.

[jeromekelleher]

Would it not be easier to use the CLI? Bash cells in Jupyter notebooks work well.

[hyanwong]

Ah yes, probably sensible in this case. I'm not sure how they work in jupyterbook or pyodide formats, but that might not be needed in this case.

[jeromekelleher]

Doubt cyvcf2 will work in pyodide anyway.