modify pytaxonkit.py to handle taxonkit's fuzzy matching

[DavidBSauer]

Hi,
I've made a modification to name2taxid to support taxonkit's fuzzymatching (available since 0.17.0).

ps: Please let me know how I can improve. This is my first attempt at a pull request. Aside from modifying the code, I am unfamiliar with the contribution/merge process.

Best wishes,
David

[DavidBSauer]

Also, I've added an additional function to validate the number of fuzzy returns (validate_n) based on the existing validate_threads.

Two thoughts

• These could be combined in principle, as they are both testing for valid integers >0. But need a way to record which variable has the problem if there is an error.
• As-is, I think these functions have a problem. They're meant to throw a warning and cause taxonkit to use its default value. However, these functions return a None. This cannot be converted to a string, so it will instead cause an error.

[standage]

Hi @DavidBSauer! Thanks for your interest and your contribution. Your code looks pretty good after a brief first glance, but I'll want to do a bit of testing before I can make any conclusive comments. It may be a couple of days before I can get to this. Thanks for your patience, and stand by!

[standage]

In the meantime, I just merged a minor update to fix a test that started failing recently due to an update to the NCBI taxonomy database. I'll go ahead and approve the test suite to run for this PR, but it will likely fail until you rebase.

[standage]

Welp, it looks like the CI is failing on a style check before even running the test suite. If you run make format in your dev environment it will autoformat the code for you.

[DavidBSauer]

Hi @standage think I've got it reformatted with "make format". Please try this version

[standage]

I'm not sure how running make format ended up making so many changes, including to files it typically doesn't touch. But I was able to reset to the version of your code at e4068ea and run make format to fix the very small style issues. I also merged the latest updates to the master branch into this branch. Evaluation of the substance of this PR is still pending!

[standage]

I tested the feature on the example provided in shenwei356/taxonkit#88 when the feature was first implemented in TaxonKit. Looks good to me! I went ahead and codified this example as a test in the automated test suite.

Thanks for this contribution @DavidBSauer!