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[WIP] revise documentation structure; add internals page.

1

This PR rearranges the docs to according to the https://diataxis.fr/ structure, per https://github.com/sourmash-bio/sourmash/issues/2054. New pages: * [A heavily revised index page](https://sourmash--2184.org.readthedocs.build/en/2184/new.html) * [A guide to the internals of sourmash](https://sourmash--2184.org.readthedocs.build/en/2184/sourmash-internals.html) ---...

ctb

[WIP] fix tax argument parsing

1

Fixes #2213 - [x] add `action= 'extend'` to appropriate args - [ ] add some tests to make sure args are passed in appropriately

bluegenes

we have a lot of "breaking" issues that are waiting for v5 - see the ["5.0" tag](https://github.com/sourmash-bio/sourmash/labels/5.0). it will probably take a few weeks, or even a month or two,...

ctb

github moved its default branch name to `main`, away from `master` (see [article](https://www.theserverside.com/feature/Why-GitHub-renamed-its-master-branch-to-main) for background) but made it configurable on repos first. We (for whatever reason ;) standardized on `latest`,...

ctb

[WIP] fix containment direction for ANI calculation

2

Fixes https://github.com/sourmash-bio/sourmash/issues/2193 Fixes https://github.com/sourmash-bio/sourmash/issues/2194 This PR fixes the direction of containment for the ANI calculation, per #2193. TODO: - [ ] rename `containment_ani` to `contained_by_as_ani` - [ ] write more...

ctb

Properly document/warning users about ANI b/t translated sequences and protein.

1

tl;dr Yay ANI! https://github.com/sourmash-bio/sourmash/pull/1967 Boo ANI on translated sequences unless max_containment used :(. Longer backstory: For translated DNA x protein, we will have many spurious proteins (unless we use orpheum...

ctb

[MRG] use stderr for test output printing

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Sets `sys.stdout=sys.stderr`, per https://github.com/sourmash-bio/sourmash/pull/2138#issuecomment-1216779696. Suggested as a solution to `pytest-xdist` not printing test output here: https://github.com/pytest-dev/pytest-xdist/issues/354#issuecomment-430502446 restores test output printing @ctb is this a desired solution? Or did you find...

bluegenes

how should we adjust output when using 6-frame-translated signatures?

2

in charcoal we are trying out 6-frame translations to do decontamination: https://github.com/dib-lab/charcoal/pull/120. The gather output that is reported is pretty lousy because it doesn't adjust for the (large) number of...

ctb

6-frame translated sketches are useful for searching protein databases, but also come with a few complications. - translated signatures should not be compared to each other (containment, jaccard, ANI will...

bluegenes

Interpreting Sourmash Gather Results

5

Hi, I am getting some funky results from the sourmash gather command. I am plotting the results of the csv that gather outputs, but when I sort the values by...

krastegar