Add ability to list pathogen repos available for setup

[victorlin]

Context

Currently, the only way to discover which pathogen repos are available for setup is to individually inspect nextstrain-pathogen.yaml files in pathogen repos.

Proposal

Design discussions happened in a Google Doc. Here is an example snippet:

$ nextstrain list

Runnable:

  measles
    measles@local {ingest, phylogenetic, nextclade}
    measles@main {ingest, phylogenetic, nextclade}

  zika
    zika@main (default) {ingest, phylogenetic}
    zika@local {ingest, phylogenetic, nextclade}

Available for setup:

  mumps@main {ingest, phylogenetic, nextclade}
    <https://github.com/nextstrain/mumps>

  ncov-ingest@master {manual-upload}
    <https://github.com/nextstrain/ncov-ingest>

  nipah@main {ingest, phylogenetic}
    <https://github.com/nextstrain/nipah>

Progress

• Add endpoint to list pathogen repos nextstrain.org#1307
• Add option to list run-compatible pathogen repos #503

[victorlin]

I chatted with Jover about this 1:1 a couple weeks ago. We concluded that, given the relatively low priority of rolling out nextstrain run support to more pathogen repos, making a command to list available repos is also low priority.

We can still consider a new command to list locally set up pathogen repos. I've created a new issue for that: #510