[MRG] Document sourmash.figusage and behavior

[ctb]

Add a notebook showcasing sourmash.fig for matrix/dendrogram plotting, and link the notebook into the documentation. Provide code examples for customizing the dendrogram.

• view new notebook, Building plots from sourmash compare output
• run notebook in binder, off of this branch

Note that the binder environment loads correctly and the paths are set up properly, but until the next conda release this notebook won't work. Not 100% sure how to deal with that but it does render on the documentation site properly ;).

Fixes #501
Fixes #220
Fixes #1023
Fixes #311

• Is it mergeable?
• make test Did it pass the tests?
• make coverage Is the new code covered?
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Was a spellchecker run on the source code and documentation after
  changes were made?

[codecov]

Codecov Report

Merging #859 into master will increase coverage by 9.16%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #859      +/-   ##
==========================================
+ Coverage   83.87%   93.04%   +9.16%     
==========================================
  Files          98       74      -24     
  Lines        9112     5810    -3302     
==========================================
- Hits         7643     5406    -2237     
+ Misses       1469      404    -1065     

Flag	Coverage Δ
#rusttests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
sourmash/cli/plot.py	100.00% <100.00%> (ø)
sourmash/commands.py	87.00% <100.00%> (+0.22%)	⬆️
sourmash/fig.py	89.13% <100.00%> (+0.24%)	⬆️
src/core/src/index/linear.rs
src/core/src/index/bigsi.rs
src/core/src/index/sbt/mhbt.rs
src/core/src/index/mod.rs
src/core/src/ffi/mod.rs
src/core/src/ffi/utils.rs
src/core/src/lib.rs
... and 17 more

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[sonarcloud]

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities (and 0 Security Hotspots to review)
1 Code Smell

No Coverage information
0.0% Duplication

[ctb]

Ready for review! @taylorreiter @bluegenes

[ctb]

anyone? Bueller? ...Bueller?

:)

[taylorreiter]

Should the binder work now?

This cell:

f, reordered_labels, reordered_matrix = fig.plot_composite_matrix(matrix, labels)

Gives me:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-5-4d0f52de32a5> in <module>
----> 1 f, reordered_labels, reordered_matrix = fig.plot_composite_matrix(matrix, labels)

TypeError: cannot unpack non-iterable Figure object

[ctb]

On Wed, Jul 22, 2020 at 07:46:38AM -0700, Taylor Reiter wrote: Should the binder work now?

alas, it will not, until this is merged into master and released.

[taylorreiter]

Then LGTM!

[ctb]

thanks!