Move filtering/subsampling docs into a separate file

[victorlin]

Description of proposed changes

This makes it possible to use in the Nextstrain docs project.

Related issue(s)

• Follow-up to filter: Expand subsampling docs #1425
• Used by Add guide on filtering and subsampling docs.nextstrain.org#192

Checklist

• Preview still looks good
• Checks pass
• If making user-facing changes, add a message in CHANGES.md summarizing the changes in this PR no user-facing changes

[joverlee521]

Nice, I forgot about the include directive!

Not asking for a change, but just curious, what prompted you to make this a separate page that can be included in the Nextstrain docs project rather than just a direct link to the Augur project?

(I might have answered my own question, this is a nice flow in the Nextstrain docs project)

[victorlin]

what prompted you to make this a separate page that can be included in the Nextstrain docs project rather than just a direct link to the Augur project?

(I might have answered my own question, this is a nice flow in the Nextstrain docs project)

Yes, I thought this guide should be shown in a context above Augur docs, where one can see other higher-level guides in the same sidebar. The docs fetching is meant to be a temporary solution but it seems to be working well.

[tsibley]

…but it seems to be working well.

😬 It's full of pitfalls (both technical and human), and I'd prefer to continue to excise it rather than expand it.

[victorlin]

The goal here was to show the subsampling guide contents both on the main docs project (because it's a commonly ask) and also directly on the augur filter doc page (so users can easily cross-reference the options) . Maybe that's not the best idea. An alternative:

Store filter-and-subsampling.rst in the main docs project and simply link to that from the augur filter docs page. If each option on the augur filter doc page (e.g. --group-by) can be made link-able, having those links from a subsampling guide housed in the main docs project should suffice.

[tsibley]

Nod. I like the idea of keeping the augur filter page as a reference page and the making the guide separate, but cross-linking the two. This also keeps with our documentation organization model. The individual command-line options for augur filter can be made linkable, for sure. There's Sphinx support for it, and I've done it for Nextstrain CLI command reference pages. Implementation may be a little different for Augur since that's generating the reference pages another way.