Added method to retrieve the raw spectrum from any USI

[douweschulte]

This is a new PR with fixed history (squashed all my earlier commits into one). See #14 for the previous discussion.

[douweschulte]

I fixed the CURIE problem by having the PROXI acession be either a CURIE or a string in that way all metadata comes over and all logic still works with the drawback of the structure being slightly more complex. With this all my tests are positive and I made all these tests also run in the github action. With that I am ready for merging, let me know if there are other things you want to have fixed before merging.

[mobiusklein]

Stylistically I'm tempted to ask this be renamed to something more succinct but "proxi" is meaningless to many new users and I've no better ideas.

[douweschulte]

I fully agree, but also did not find a better name yet. Maybe 'retrieve'/'fetch'/'load' with or without the 'spectrum' part?

[douweschulte]

pytoemics calls the function 'proxi()' so we might get away with 'proxi_blocking()' and 'proxi_async' especially if we link to that in the main documentation for USI.

[mobiusklein]

Since I wrote the pyteomics implementation, I was partial to that here too. PROXI was still being worked on in recent memory way back then too. The mzSpecLib project has taken all the attention away from PROXI since then, and it's on the "todo" list to switch the PROXI JSON format to mirror the mzSpecLib JSON format.

[douweschulte]

Reading a bit more into the PROXI standard I do agree that calling it .proxi is not the best name, if only for the fact that proxi allows many more types of calls to the server. Keeping it on get_spectrum seems fine to me, that is also roughly the name of the proxi 'function' that is called in the function. Although the 'get' part could be swapped out to indicate the network request a bit more, something like 'download_spectrum' might be more clear to anyone reading that it does network requests.

[douweschulte]

While using this implementation in the annotator I found a small bug with parsing the signal continuity. Otherwise it works like a charm. I renamed the function to download_spectrum_blocking/async which I think clearly states the point of the function: "you will get the spectrum, downloaded over the internet". The last factor, downloading, was not clear enough with the previous name and I think making it obvious in this way would flag more clearly to users that the internet is involved.

With that I am ready for merging, do you have any questions/comments left?