Various docs improvements

[corneliusroemer]

Resolves #259

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[corneliusroemer]

Since this has come up for the second time now, do you @ivan-aksamentov think we should write a few lines about downloading datasets behind a proxy? Downloading the files manually using wget or curl after getting the link from the index.json?

See #552 #726

[ivan-aksamentov]

We should write a few lines about downloading datasets behind a proxy? Downloading the files manually using wget or curl after getting the link from the index.json?

@corneliusroemer I don't think it should be in the official docs. Or perhaps as a little note, with a link to GitHub issue, but definitely no official recommendations, especially that we cannot guarantee stability of the data GitHub repo, or even its existence, as well as stability of the index file format.

I think we are also might be about to break the format soon (according to Richard's plans).

[corneliusroemer]

@ivan-aksamentov yes was thinking the same, maybe a small note with link. But then it's not that common a use case so if the question comes up again, we can just link to the existing issues with up to date info on what the best workaround is right now.

[ivan-aksamentov]

@corneliusroemer I find that some of the changes are overly focused on SARS-CoV-2.

This is still the primary target right now, but we should consider a more generic approach to documenting things in the future. Or at least when you are taking about specific mutations, labels, clades etc., to mention that you are talking about a particular virus (I'd imagine language like "For example, in SARS-CoV-2", "In case of SARS-CoV-2", etc.).

But right now it's not a big deal. Users are expected to have some understanding about the current situation in the field, so they should be able to recognize the virus.

[corneliusroemer]

You're right, once SC2 is less preeminent, I'm happy to go through it and put any SC2 specifics in a box to separate from general parts.

[corneliusroemer]

I've created an issue to separate out the SC2 specifics from the more generally valid parts: #729