[MRG] a 2022 update - fix many misc things!

[ctb]

Fix many issues. Also -

• merges 00_getting_started into index (they were already identical) and puts index in the TOC;

• rewrites things to use mamba instead of conda in most places.

• [x] This should fix #42 by pinning python to 3.8 but we need to verify that.

• [x] This should fix #43 by switching to gather but we should also update the output (and maybe the database used - switch to GTDB?)

• [x] This should fix #44 and #46 by switching sourmash compute to sourmash sketch, but the command needs to be verified

Fixes https://github.com/dib-lab/dib_rotation/issues/34 Fixes https://github.com/dib-lab/dib_rotation/issues/41 Fixes https://github.com/dib-lab/dib_rotation/issues/42 Fixes https://github.com/dib-lab/dib_rotation/issues/43 Fixes https://github.com/dib-lab/dib_rotation/issues/44 Fixes https://github.com/dib-lab/dib_rotation/issues/45 by installing mamba up front Fixes https://github.com/dib-lab/dib_rotation/issues/46

Note that early attempts to pin the dib_rotation conda environment to python=3.8 ran afoul of this problem where conda installs a very old version of mamba when python=3.8! So I ended up installing mamba in base.

cc @ccbaumler

[ctb]

we need to manually update the mkdocs site, right @bluegenes ?

[bluegenes]

we need to manually update the mkdocs site, right @bluegenes ?

No, I think the GitHub actions should automatically deploy the site, as long as the markdown syntax is good!

If you're adding pages, then yes, we need to manually add those refs to mkdocs.yml

[ctb]

If you're adding pages, then yes, we need to manually add those refs to mkdocs.yml

no added pages!

[ctb]

@ccbaumler have you taken a look at these changes? any comments or concerns?

[ccbaumler]

Hi @ctb,

I am not noticing anything glaring but if you would like I can work through the entire website again this week to find any remaining typos or possible areas of improvement.

Respectfully, Colton