Changing References does nothing

Greetings, thanks for a great piece of software.

When I attempt to change the reference used (e.g., in order to use hg38 rather than hg19) according to the syntax specified in the example: igv.Reference(fasta_url=...), nothing happens. I must use camelCase for my parameter names instead: igv.Reference(fastaURL=...).

I feel that is a bug because at the very least, there should be some sort of warning when my attempt to update the reference failed. Instead, it silently and dutifully serves me hg19 coordinates.

I think this is due to some issue with the to_camel_case method potentially not working.

[jrobinso]

@a-slide I’ve started a major revision of this package. The new interface is much simpler, particularly if you are familiar with igv.js. Basically it mimics the igv.js API using python dictionaries where json-like config objects are specified in igv.js. The dictionaries are converted to JSON and passed to the front end as messages. I also added docstrings, but I’m not sure what you mean by “declaring the args”. Python is not my first or even second language, but have a look and feedback is welcome.

I have not pushed this to pypi yet.

[a-slide]

Hi @jrobinso, First, thanks a lot because I love the concept of having IGV running inside Jupyter. It is very handy to have a nice self-contained end to end analysis.

I would say that one of the main drawback is that the interface is not very pythonic, which makes everything hard to use in jupyter. Since the function/class args are not explicitly declared in the signatures, the only way to find them is to read the raw code. I understood that it gives more flexibility, but declaring the args + having a docstring for each functions would actually make the package usable without having to guess the arguments values. I have a few other suggestions but I suppose it would be best to open an issue for each !