plot_phylo #160

KatyBrown · 2024-02-22T11:55:59Z

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
EIC: @isabelizimm
Editor: @ctb
Reviewer 1: @ammaraziz
Reviewer 2: @jkanche
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.

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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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The text was updated successfully, but these errors were encountered:

isabelizimm · 2024-02-22T14:40:42Z

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 · 2024-02-27T23:46:14Z

Editor in Chief checks

Hi there! Thank you for submitting your package for pyOpenSci
review. Below are the basic checks that your package needs to pass
to begin our review. If some of these are missing, we will ask you
to work on them before the review process begins.

Please check our Python packaging guide for more information on the elements
below.

Initial onboarding survey was filled out
We appreciate each maintainer of the package filling out this survey individually. 🙌
Thank you authors in advance for setting aside five to ten minutes to do this. It truly helps our organization. 🙌

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 · 2024-03-01T00:15:56Z

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 · 2024-03-23T01:28:51Z

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 · 2024-03-26T15:01:10Z

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 · 2024-03-26T16:19:52Z

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 · 2024-04-06T17:28:58Z

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

KatyBrown · 2024-04-12T13:39:30Z

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 · 2024-04-12T21:02:19Z

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

ctb · 2024-05-01T20:49:33Z

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

KatyBrown · 2024-05-03T16:27:49Z

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

ctb · 2024-06-22T22:49:28Z

apologies for my long delay - have one reviewer locked in, reach out to some more today.

ctb · 2024-07-01T19:29:30Z

Editor response to review:

Editor comments

👋 Hi @ammaraziz and @jkanche! Thank you for volunteering to review
for pyOpenSci! Sorry it took me so long to post this, I blame ...umm, summer! Yeah, it's summer time! But seriously, thank you so much!!

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reviewer 1 survey completed (ammaraziz)
reviewer 2 survey completed (jkanche)

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Due date: July 22nd, 2024

jkanche · 2024-07-29T11:58:42Z

Apologies for the delay, I plan to finish my review this week.

ctb · 2024-07-29T12:02:01Z

Apologies for the delay, I plan to finish my review this week.

thanks for checking in! @ammaraziz, need anything from me?

jkanche · 2024-08-05T23:31:38Z

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

A statement of need clearly stating problems the software is designed to solve and its target audience in README.
Installation instructions: for the development version of the package and any non-standard dependencies in README.
Vignette(s) demonstrating major functionality that runs successfully locally.
Function Documentation: for all user-facing functions.
Examples for all user-facing functions.
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Readme file requirements
The package meets the readme requirements below:

Package has a README.md file in the root directory.

The README should include, from top to bottom:

The package name
Badges for:
- Continuous integration and test coverage,
- Docs building (if you have a documentation website),
- A repostatus.org badge,
- Python versions supported,
- Current package version (on PyPI / Conda).

NOTE: If the README has many more badges, you might want to consider using a table for badges: see this example. Such a table should be more wide than high. (Note that the a badge for pyOpenSci peer-review will be provided upon acceptance.)

Short description of package goals.
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Reviewers are encouraged to submit suggestions (or pull requests) that will improve the usability of the package as a whole.
Package structure should follow general community best-practices. In general please consider whether:

Package documentation is clear and easy to find and use.
The need for the package is clear
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The package is easy to install

Functionality

Review Comments

Cannot run tests following the instructions

I cloned the repo and installed it in edit mode:

⋊> ~/P/p/t/plot_phylo on main ◦ pytest --cov=plot_phylo                                   (reviews) 16:09:15
=========================================== test session starts ============================================
platform darwin -- Python 3.11.9, pytest-8.2.2, pluggy-1.5.0
rootdir: /Users/kancherj/Projects/public/trash/plot_phylo
configfile: pyproject.toml
plugins: cov-5.0.0
collected 0 items / 3 errors
/opt/homebrew/lib/python3.11/site-packages/coverage/control.py:888: CoverageWarning: No data was collected. (no-data-collected)
  self._warn("No data was collected.", slug="no-data-collected")

================================================== ERRORS ==================================================
______________________________ ERROR collecting tests/test_get_boxes_data.py _______________________________
ImportError while importing test module '/Users/kancherj/Projects/public/trash/plot_phylo/tests/test_get_boxes_data.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/homebrew/Cellar/python@3.11/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_get_boxes_data.py:2: in <module>
    import matplotlib.pyplot as plt
E   ModuleNotFoundError: No module named 'matplotlib'
________________________________ ERROR collecting tests/test_plot_phylo.py _________________________________
ImportError while importing test module '/Users/kancherj/Projects/public/trash/plot_phylo/tests/test_plot_phylo.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/homebrew/Cellar/python@3.11/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_plot_phylo.py:2: in <module>
    import matplotlib.pyplot as plt
E   ModuleNotFoundError: No module named 'matplotlib'
______________________________ ERROR collecting tests/test_plot_phylo_data.py ______________________________
ImportError while importing test module '/Users/kancherj/Projects/public/trash/plot_phylo/tests/test_plot_phylo_data.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/homebrew/Cellar/python@3.11/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_plot_phylo_data.py:2: in <module>
    import plot_phylo
E   ModuleNotFoundError: No module named 'plot_phylo'

---------- coverage: platform darwin, python 3.11.9-final-0 ----------
Name                       Stmts   Miss  Cover   Missing
--------------------------------------------------------
plot_phylo/plot_phylo.py     144    144     0%   2-586
--------------------------------------------------------
TOTAL                        144    144     0%

========================================= short test summary info ==========================================
ERROR tests/test_get_boxes_data.py
ERROR tests/test_plot_phylo.py
ERROR tests/test_plot_phylo_data.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 3 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Add a short description and link to docs for the repository metadata. Helps users quickly understand the scope and link to the documentation (right side bar on the repository page):
Publishing seems to be manual right now and don't understand how that is setup? I usually use pyscaffold and it makes it easier for some routine package maintenance tasks.
code quality (linting) is not included in the CI/CD tests.
As I was reviewing the package, I thought a couple of features may be super helpful:
- Highlight paths/features of interest
- Ability to choose or specify branch widths

Overall, the package provides an intuitive and easy way to integrate phylogeny visualizations with matplotlib based workflows. Let me know if you have any questions.

ammaraziz · 2024-08-06T05:20:40Z

Hi @ctb and @KatyBrown, please accept my apologies. I've been stretched thin over the last few months.

I will make time for reviewing this week if that is acceptable?

ctb · 2024-08-06T14:29:51Z

Hi @ctb and @KatyBrown, please accept my apologies. I've been stretched thin over the last few months.

as have we all! no worries and I really appreciate your willingness to review!

I will make time for reviewing this week if that is acceptable?

please and thank you!

ammaraziz · 2024-08-12T12:50:52Z

Package Review

As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

A statement of need clearly stating problems the software is designed to solve and its target audience in README.
Installation instructions: for the development version of the package and any non-standard dependencies in README.
Vignette(s) demonstrating major functionality that runs successfully locally.
Function Documentation: for all user-facing functions.
Examples for all user-facing functions.
Community guidelines including contribution guidelines in the README or CONTRIBUTING.
Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements
The package meets the readme requirements below:

Package has a README.md file in the root directory.

The README should include, from top to bottom:

The package name
Badges for:
- Continuous integration and test coverage,
- Docs building (if you have a documentation website),
- A repostatus.org badge,
- Python versions supported,
- Current package version (on PyPI / Conda).

NOTE: If the README has many more badges, you might want to consider using a table for badges: see this example. Such a table should be more wide than high. (Note that the a badge for pyOpenSci peer-review will be provided upon acceptance.)

Short description of package goals.
Package installation instructions
Any additional setup required to use the package (authentication tokens, etc.)
Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
- X ] Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
Link to your documentation website.
If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
Citation information

Usability

Reviewers are encouraged to submit suggestions (or pull requests) that will improve the usability of the package as a whole.
Package structure should follow general community best-practices. In general please consider whether:

Package documentation is clear and easy to find and use.
The need for the package is clear
All functions have documentation and associated examples for use
The package is easy to install

Functionality

For packages also submitting to JOSS

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Final approval (post-review)

The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing:

Review Comments

Great package, works nicely and the provided example is a great start. The power of matplotlib means it's possible to make great plots.

Similar to the previous review, when testing the package I get errors. However, the documentation states:

Run unit tests in the root directoy as pytest --cov=plot_phylo and ensure that they pass and that coverage is 100%.

But I get an error:

pytest: error: unrecognized arguments: --cov=plot_phylo

Testing works if you run just pytest in the root dir:

============================== test session starts ===============================
platform darwin -- Python 3.9.19, pytest-8.3.2, pluggy-1.5.0
rootdir: ~Desktop/plot_phylo
configfile: pyproject.toml
collected 138 items

tests/test_plot_phylo.py ................................................. [ 35%]
.......................................................................... [ 89%]
...............                                                            [100%]

================================ warnings summary ================================
tests/test_plot_phylo.py:23
  /Users/aaziz/Desktop/plot_phylo/tests/test_plot_phylo.py:23: MatplotlibDeprecationWarning: Auto-close()ing of figures upon backend switching is deprecated since 3.8 and will be removed in 3.10.  To suppress this warning, explicitly call plt.close('all') first.
    matplotlib.use('Agg')

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=================== 138 passed, 1 warning in 62.46s (0:01:02) ====================

Consider adding some basic usage docs to the readme to get people started.
Provide example of how to color internal nodes and branches.
Consider using github actions for testing and publishing.
Add a section on how to cite your work, even if it's just the github repo, for example:

# Cite
KatyBrown - plot_phylo https://github.com/KatyBrown/plot_phylo

Good job on the great package.

ctb · 2024-08-12T16:09:36Z

thanks @ammaraziz and @jkanche!!

@KatyBrown please take a detailed look at the above, and I will do the same!

ctb · 2024-08-12T16:10:15Z

@jkanche https://pyscaffold.org/en/stable/ looks fascinating!

ctb · 2024-08-27T16:35:56Z

@jkanche and @ammaraziz, thank you so much for your reviews!!

@KatyBrown, I've extracted the unchecked bits of the reviews below -- please see bottom for my thoughts!

pyopensci -- summary of reviews by CTB

Package review by @jkanche:

Documentation

The package includes all the following forms of documentation:

Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

The README should include, from top to bottom:

The package name
Badges for:
- Continuous integration and test coverage,
- Docs building (if you have a documentation website),
- A repostatus.org badge,
- Python versions supported,
- Current package version (on PyPI / Conda).
If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
Citation information

Usability

In general please consider whether:

The need for the package is clear

Functionality

Automated tests:
- All tests pass on the reviewer's local machine for the package version submitted by the author. Ideally this should be a tagged version making it easy for reviewers to install.
Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines.

Review Comments

Cannot run tests following the instructions

I cloned the repo and installed it in edit mode:

(errors elided)

Add a short description and link to docs for the repository metadata. Helps users quickly understand the scope and link to the documentation (right side bar on the repository page):
Publishing seems to be manual right now and don't understand how that is setup? I usually use pyscaffold and it makes it easier for some routine package maintenance tasks.
code quality (linting) is not included in the CI/CD tests.
As I was reviewing the package, I thought a couple of features may be super helpful:
- Highlight paths/features of interest
- Ability to choose or specify branch widths

CTB comment: you could put these in the issue tracker, if you didn't want to implement them now :)

Overall, the package provides an intuitive and easy way to integrate phylogeny visualizations with matplotlib based workflows. Let me know if you have any questions.

Package Review by @ammaraziz

Documentation

The README should include, from top to bottom:

Badges for:
- Continuous integration and test coverage,
- Docs building (if you have a documentation website),
- A repostatus.org badge,
- Python versions supported,
- Current package version (on PyPI / Conda).
Any additional setup required to use the package (authentication tokens, etc.)
If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
Citation information

Functionality

Performance: Any performance claims of the software been confirmed.
Automated tests:
- All tests pass on the reviewer's local machine for the package version submitted by the author. Ideally this should be a tagged version making it easy for reviewers to install.
- Tests cover essential functions of the package and a reasonable range of inputs and conditions.
Continuous Integration: Has continuous integration setup (We suggest using Github actions but any CI platform is acceptable for review)

Review Comments

Great package, works nicely and the provided example is a great start. The power of matplotlib means it's possible to make great plots.

Similar to the previous review, when testing the package I get errors. However, the documentation states:

Run unit tests in the root directoy as pytest --cov=plot_phylo and ensure that they pass and that coverage is 100%.

But I get an error:

pytest: error: unrecognized arguments: --cov=plot_phylo

Testing works if you run just pytest in the root dir:

(elided)

Consider adding some basic usage docs to the readme to get people started.
Provide example of how to color internal nodes and branches.
Consider using github actions for testing and publishing.
Add a section on how to cite your work, even if it's just the github repo, for example:

# Cite
KatyBrown - plot_phylo https://github.com/KatyBrown/plot_phylo

Good job on the great package.

Editor comments from CTB

The three major suggestions from the reviews that stand out are -

a few more usage docs are suggested/would be welcome!
test the instructions for running the tests, and/or improve the documentation;
suggest using GitHub CI - lmk if you need some pointers to quickstarts! I have some projects that do basically what you need, I think. Note that putting CI in place will help with the test running & documentation, above, too!

The rest all seem like fairly quick add-this/adjust-that changes.

Please let me know if you have thoughts or questions!

KatyBrown · 2024-08-30T17:49:00Z

Hi @ctb @jkanche @ammaraziz thanks so much for looking at this and sorry for my slow response. I will look at your comments over the next few days.

One quick thing, I do have CI testing which runs my test suite - the workflow is here https://github.com/KatyBrown/plot_phylo/actions/workflows/main.yml. I'm not sure if they are not showing up somehow.

Thanks again and I'll address everything else asap.

KatyBrown added 0/pre-review-checks New Submission! labels Feb 22, 2024

isabelizimm removed the New Submission! label Feb 28, 2024

isabelizimm added 1/editor-assigned and removed 0/pre-review-checks labels Mar 1, 2024

lwasser assigned ctb Mar 27, 2024

ctb added 2/seeking-reviewers 3/reviewers-assigned labels Jul 1, 2024

cmarmo removed 2/seeking-reviewers 1/editor-assigned labels Jul 17, 2024

ctb added 4/reviews-in-awaiting-changes and removed 3/reviewers-assigned labels Aug 27, 2024

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edited by cmarmo

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KatyBrown commented Aug 30, 2024

plot_phylo #160

plot_phylo #160

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KatyBrown commented Feb 22, 2024 • edited by cmarmo Loading

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pyopensci -- summary of reviews by CTB

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KatyBrown commented Aug 30, 2024

KatyBrown commented Feb 22, 2024 •

edited by cmarmo

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jkanche commented Aug 5, 2024 •

edited

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