[MRG] support loading of empty picklists

[ctb]

Support allow_empty=True on SignaturePicklist.load(...).

Also adds a test_picklist.py file and tests/test-data/picklist/ directory, for future picklist tests.

Fixes #2096

[codecov]

Codecov Report

Merging #2106 (685c1fd) into latest (50bc6dd) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           latest    #2106   +/-   ##
=======================================
  Coverage   84.32%   84.32%           
=======================================
  Files         130      130           
  Lines       15281    15283    +2     
  Branches     2170     2171    +1     
=======================================
+ Hits        12885    12887    +2     
  Misses       2098     2098           
  Partials      298      298           

Flag	Coverage Δ
python	91.78% <100.00%> (+<0.01%)	⬆️
rust	65.13% <ø> (ø)

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

Impacted Files	Coverage Δ
src/sourmash/picklist.py	91.50% <100.00%> (+0.11%)	⬆️

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[ctb]

Ready for review & merge @sourmash-bio/devs

[ctb]

Note: the rust checks that are failing have nothing to do with this PR. 🤷

[ccbaumler]

I notice one other warning about mamba in the dev_env.yml:

mamba
Mamba support is still experimental and can result in differently solved environments!

Is this at all a concern?
Would it be best to specify the version of Mamba to use in the yml instead of the latest?

[ctb]

I notice one other warning about mamba in the dev_env.yml:

mamba
Mamba support is still experimental and can result in differently solved environments!

Is this at all a concern? Would it be best to specify the version of Mamba to use in the yml instead of the latest?

I actually don't find any references anywhere to a dev_env.yml - where are you seeing this? :)

In any case, if it's not related to either the functionality being implemented for the PR, or the changed files, then it's not relevant to the PR & you should start a new issue with that as a question, I think!

[ccbaumler]

I created an issue like you suggested to investigate this warning further. See issue Mamba support is experimental 2109

The warning is located in any workflow that is under the Actions>Dev Env Instructions.

[ctb]

I created an issue like you suggested to investigate this warning further. See issue Mamba support is experimental 2109

The warning is located in any workflow that is under the Actions>Dev Env Instructions.

thx - yes, it was in dev_envs.yml under .github/workflows/, which was easier to find than dev_env.yml which does not exist :)

note you can refer to other issues in a few different ways:

• paste in the link https://github.com/sourmash-bio/sourmash/issues
• use a markdown link, like so: mamba support is experimental
• referring to issue number in a non-verbatim link with a pound sign, e.g. Mamba support is experimental #2109

all of these will reverse link that issue to here, which is nice!

[ccbaumler]

LGTM

[ctb]

thanks!