plot_phylo

[KatyBrown]

Submitting Author: Katy Brown (@KatyBrown) All current maintainers: Katy Brown (@KatyBrown) Package Name: plot_phylo One-Line Description of Package: A Python package to plot a phylogenetic tree on an existing Matplotlib axis. Repository Link: https://github.com/KatyBrown/plot_phylo Version submitted: 1.9.0 Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD JOSS DOI: TBD Version accepted: TBD Date accepted (month/day/year): TBD

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Description

plot_phylo is a Python package which allows the user to plot phylogenetic trees onto an existing matplotlib axis. This means annotations can be added using matplotlib functionality and figures including phylogenies can be included in automated figure generation.

Scope

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  • [ ] Data retrieval
  • [ ] Data extraction
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- [ ] Geospatial
- [ ] Education
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  • Who is the target audience and what are scientific applications of this package?
    Researchers working with phylogenetic tree data, a common data format for evolutionary and functional analysis of biological data.

  • Are there other Python packages that accomplish the same thing? If so, how does yours differ? plot_phylo depends on the functionality of ETE Toolkit, a widely used visualisation tool. ETE provides excellent tree visualisations but these act as a stand-alone image, which can't be incorporated into another programmatically generated figure except as an uneditable embedded image. plot_phylo trees are subplots of open matplotlib figures, so custom annotations can be added, aspects of the image can be updated and other subplots can show additional data.

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[isabelizimm]

Hello there, and welcome to the pyOpenSci community-- we are so happy you are here! Just wanted to let you know we have seen your submission and will get back to you with some initial checks soon. 👾

[isabelizimm]

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Editor comments

Thank you again for submitting plot_phylo to pyOpenSci! I've gone through your package, and you've got a great start!

Blockers to beginning review process:

• Right now, this package lacks a documentation website (or, at least, this site is not discoverable enough for me to find). There is some documentation in pyOpenSci's packaging guide on how to set up a site with Sphinx and publish it to GitHub. You have lovely docstrings already in place for plot_phylo, so you've already done a lot of the heavy lifting! This site should help with the maintenance of the package for you as well-- Sphinx will autogenerate API docs so you won't have to write out Parameters and such yourself 🙂

Some smaller nits:

• I would recommend updating testing in CI to more modern Python versions. It looks like you are only testing on Python 3.7 and 3.8; Python 3.7 has been end-of-lifed, and Python 3.8 will be end-of-life in Oct of this year.
• Your __init__.py and _version.py files have two different versions. It looks like you only use the _version.py file though.

If you have any questions or need any support with these tasks, pyOpenSci community would love to help out! The best places to get in touch are via discourse or Slack--let me know if you need an invite. And, of course, you can also reply here (but then you will be restricted to just my opinions 😂)!

[isabelizimm]

Following up, @ctb will the editor leading the review for plot_phylo once the above items have been addressed! Titus also has a few things to finish up before starting this role, so I'll check back here in about 2 weeks to check in if both parties are ready to kick off this review 😄

[isabelizimm]

Hello all! Checking in here. @KatyBrown are you able to give an update on the status of a documentation website? We won't be able to start a review without that put up. If you need any support, please let us know!

[KatyBrown]

Hi @isabelizimm , sorry, I got caught in other projects but I'm working on moving the documentation the readthedocs - it should be ready in another couple of days. Sorry to be slow! Thanks for checking in.

[isabelizimm]

No worries at all--thank you for the update! 🌻 If you can give us a heads up in this issue once those docs are up, then we can get started on the review.

[ctb]

I am alive! Just let me know when to start finding reviewers :)

[KatyBrown]

Hi @isabelizimm, very sorry for the long delay, I've now made the changes you asked for. The current version of the tool is now v0.1.9 - I've edited this in my original post.

Specifically I have:

• Extended the documentation and moved it to ReadTheDocs here
• Added testing in Python 3.9 to 3.12
• Corrected the mistake with the version

Please let me know if there's anything else I need to do, otherwise I think I'm now ready to proceed to the next step :)

Thank you!

[isabelizimm]

No worries-- with those all updated, I can hand everything over to @ctb to look for reviewers!

[ctb]

Apologies for delay - started beating the bushes for some reviewers. In the meantime, filed a few minor issues myself ;). The figures are lovely!!

[KatyBrown]

@ctb thanks very much! I think I've addressed the issues you raised.