[REVIEW]: PhyloX: A Python package for complete phylogenetic network workflows

[editorialbot]

Submitting author: @RemieJanssen (Remie Janssen)
Repository: https://github.com/RemieJanssen/phylox
Branch with paper.md (empty if default branch):
Version: v1.0.3
Editor: @fboehm
Reviewers: @abhishektiwari, @bgyori
Archive: Pending

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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @abhishektiwari

📝 Checklist for @bgyori

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (1707.9 files/s, 110963.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          68           1092           3159           6262
reStructuredText               128           1455            742            291
Markdown                         6             95              0            213
YAML                             4             17             27            104
TeX                              1              8              0             85
TOML                             1              4              0             35
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           210           2683           3936           7025
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 785

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/btp163 is OK

MISSING DOIs

- 10.1186/1471-2105-13-209 may be a valid DOI for title: Bio. Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython
- 10.1093/bioinformatics/btq228 may be a valid DOI for title: DendroPy: a Python library for phylogenetic computing
- 10.1007/978-3-030-42266-0_8 may be a valid DOI for title: Linear time algorithm for tree-child network containment
- 10.1093/molbev/msx307 may be a valid DOI for title: Bayesian inference of species networks from multilocus sequence data
- 10.1007/978-3-030-42266-0_7 may be a valid DOI for title: Combining networks using cherry picking sequences

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[abhishektiwari]

Review checklist for @abhishektiwari

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/RemieJanssen/phylox?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@RemieJanssen) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[abhishektiwari]

@RemieJanssen Please see my initial comments.

Example code on documentation landing page did not run for me. Otherwise I was able run test scripts and create my own scripts without any issues.

A few minor typos in paper reported here. I also think first line of paper's Summary section as well other places describing PhyloX will read just fine without with tools, i.e. "PhyloX is a Python package for generating, manipulating, and analyzing phylogenetic networks."

[fboehm]

@bgyori - I hope that everything's ok. please feel free to create your review checklist. Please let me know if you have questions.

[fboehm]

@RemieJanssen - do you have any questions about the comments from & suggestions from @abhishektiwari ?

[bgyori]

Review checklist for @bgyori

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/RemieJanssen/phylox?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@RemieJanssen) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[fboehm]

@bgyori - just wanted to check to see how the review is going; do you have any questions or need assistance as you look over things? Thank you!

[fboehm]

@RemieJanssen - did you have a chance to update the software in response to the comments from @abhishektiwari ? Please let us know if you need any clarifications. Thank you!

[bgyori]

I have now completed my initial review, see checklist above. Below, I provide further context for checkboxes that I didn't check.

General checks

• Substantial scholarly effort: following the review guidelines at https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort, here are my observations on this: the code was written by a single author over a limited period of time. There are no external stars/watchers/forks/issue submitters for the project so usage has not yet been demonstrated. Despite this, the quantitative metrics over the code (i.e., number of lines) and my own review of the code show that the work put into the implementation is not trivial. If these characteristics are consistent with a JOSS publication, I can check this box - guidance from @fboehm would be helpful.

• Reproducibility: across the entire repository, documentation and paper, there
  is a single piece of example code demonstrating the software, however, this
  does not work as expected. One or more demonstration notebooks of the utility of the
  software on some example use cases would improve the package and the paper.

Functionality

• Functionality: The functionality of the software is not clearly described.
  Across the repository's README, the documentation, and the paper there isn't a
  single place where a clear and well structured summary exists of the software's
  functionalities. This should be improved for clarity and usability.

Documentation

• Example usage: There is only one piece of example code at
  https://phylox.readthedocs.io/en/latest/index.html but it is not working as
  expected: Example code is not working RemieJanssen/PhyloX#42.
• Functionality documentation: The documentation is not complete. It should
  provide a better way to navigate the software modules from the documentation landing page. When reviewing the code
  I found many of the classes and functions in different modules were missing
  docstrings, e.g., https://github.com/RemieJanssen/PhyloX/blob/main/src/phylox/generators/heath/heath.py - these then don't show up in the documentation.
• Community guidelines: The repository provides a CONTRIBUTING.md description at https://github.com/RemieJanssen/PhyloX/blob/main/CONTRIBUTING.md. However, the description of Pull requests is not perfect: it assumes a contributor can
  git clone git@github.com:RemieJanssen/PhyloX.git and then push to origin. This will generally not work for outside contributors. The contribution guidelines should therfore mention forking the project to contribute.

Software paper

• Summary: the current description is not clear, especially for a non-specialist audience. It could be improved by a clearer description of the basic concepts the package uses (e.g., phylogenetic network vs tree, what is "cherry-picking", etc.). Obviously one can't expect to go into details so this would have to be succinct and to the point. Perhaps approaching this by more clearly stating the kinds of analysis the package enables could also help.

• Quality of writing: Currently more than half of the paper is discussing other related tools. This should be rebalanced by focusing on PhyloX and giving a proper description of it. I also found some typos and language issues that I submitted a PR to improve.

[RemieJanssen]

**fboehm ** commented Mar 23, 2024

@fboehm I have updated the software to fix the main example in the documentation. It's still only in the main branch, so it's not released yet. I'll do that once I have updated the paper, and possibly the documentation, if that is required as well.

@bgyori Thank you for the explanation of the non-checked items. I will go through those and respond and fix what I can.

@fboehm What is generally the way forward in this phase? I'm quite used to the clearly delineated phases of a more conventional review process, this seems somewhat more fluid.

I'm sorry I'm taking so long, I unfortunately do not have as much time to work on this as I would want to.

[abhishektiwari]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[abhishektiwari]

@RemieJanssen

Please see more feedback

Quality of writing

Some parts need rewriting like related packages (State of the field). It can be more crisp, bit shorter (as suggested by other reviewer), and objective. I will avoid using weasel phrases like fit that bill to a certain extent, and be more specific. I felt comparison on the documentation page did a better job by calling out the specific differences between PhyloX and alternatives.

Unlike other packages like Biopython and DendroPy, PhyloX is designed to work with phylogenetic networks, rather than phylogenetic trees.

I also suggest highlighting some of the key features/functionalities of the PhyloX software in paper. Again, I think documentation page does a better job describing key features of PhyloX.

Example usage

Thanks for fixing the example. I would love to see one or two Jupyter notebook based example use cases. But this is not a blocker from my side.

API documentation

Module functions for the health generator are missing please fix RST tree.

[fboehm]

@RemieJanssen - do you have questions about next steps? Thanks again!

[fboehm]

@RemieJanssen - do you have questions about next steps? Thanks again!

Sorry that I missed your earlier messsge. Yes, compared to some review processes, that of Joss may feel different. It is essentially an iterative process between you and the reviewers. Once they are able to check all boxes, their roles are complete. As author, you just need to respond to their suggestions. If you disagree with a suggestion, please discuss it in this thread.

[bgyori]

I'm just checking back again, @RemieJanssen have you had a chance to look into the paper improvements / documentation improvements that @abhishektiwari and I suggested? I don't see any recent changes since my PR was merged with some typo fixes, though I might have missed something.

[RemieJanssen]

@RemieJanssen - do you have questions about next steps? Thanks again!

Sorry that I missed your earlier messsge. Yes, compared to some review processes, that of Joss may feel different. It is essentially an iterative process between you and the reviewers. Once they are able to check all boxes, their roles are complete. As author, you just need to respond to their suggestions. If you disagree with a suggestion, please discuss it in this thread.

Ah! That does answer my question, thank you :) I finally have some time again, so I'll try to get as far as possible responding to all the comments this week.

[RemieJanssen]

I have now completed my initial review, see checklist above. Below, I provide further context for checkboxes that I didn't check.

General checks

* **Substantial scholarly effort**: following the review guidelines at https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort, here are my observations on this: the code was written by a single author over a limited period of time. There are no external stars/watchers/forks/issue submitters for the project so usage has not yet been demonstrated. Despite this, the quantitative metrics over the code (i.e., number of lines) and my own review of the code show that the work put into the implementation is not trivial. If these characteristics are consistent with a JOSS publication, I can check this box - guidance from @fboehm would be helpful.

I don't think I can really argue with you here, most of the package was written by me, and compiled over a short period of time. However, it's not really true that it was written over a limited period. The package is a compilation of most code was written during the 4 years of my PhD and the few years after (and not even all by me, but also by co-authors). This package is an attempt to not let all that effort go to waste because of our unFAIR code practices.

[fboehm]

I have now completed my initial review, see checklist above. Below, I provide further context for checkboxes that I didn't check.
General checks

* **Substantial scholarly effort**: following the review guidelines at https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort, here are my observations on this: the code was written by a single author over a limited period of time. There are no external stars/watchers/forks/issue submitters for the project so usage has not yet been demonstrated. Despite this, the quantitative metrics over the code (i.e., number of lines) and my own review of the code show that the work put into the implementation is not trivial. If these characteristics are consistent with a JOSS publication, I can check this box - guidance from @fboehm would be helpful.

I don't think I can really argue with you here, most of the package was written by me, and compiled over a short period of time. However, it's not really true that it was written over a limited period. The package is a compilation of most code was written during the 4 years of my PhD and the few years after (and not even all by me, but also by co-authors). This package is an attempt to not let all that effort go to waste because of our unFAIR code practices.

@RemieJanssen @bgyori - can you elaborate on this point? Why does it appear to @bgyori that things were written over a short period while @RemieJanssen says otherwise? Is @bgyori relying on git commit times, while @RemieJanssen and co-workers perhaps didn't use git while writing?

[bgyori]

I have now completed my initial review, see checklist above. Below, I provide further context for checkboxes that I didn't check.
General checks

* **Substantial scholarly effort**: following the review guidelines at https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort, here are my observations on this: the code was written by a single author over a limited period of time. There are no external stars/watchers/forks/issue submitters for the project so usage has not yet been demonstrated. Despite this, the quantitative metrics over the code (i.e., number of lines) and my own review of the code show that the work put into the implementation is not trivial. If these characteristics are consistent with a JOSS publication, I can check this box - guidance from @fboehm would be helpful.

I don't think I can really argue with you here, most of the package was written by me, and compiled over a short period of time. However, it's not really true that it was written over a limited period. The package is a compilation of most code was written during the 4 years of my PhD and the few years after (and not even all by me, but also by co-authors). This package is an attempt to not let all that effort go to waste because of our unFAIR code practices.

@RemieJanssen @bgyori - can you elaborate on this point? Why does it appear to @bgyori that things were written over a short period while @RemieJanssen says otherwise? Is @bgyori relying on git commit times, while @RemieJanssen and co-workers perhaps didn't use git while writing?

Based on @RemieJanssen's comments, I understand that the code was written over a several years but was consolidated into this integrated repository later, over a shorter period of time. This makes sense to me, and I definitely see the value in turning fragmented code into an integrated and reusable package.

[RemieJanssen]

I have now completed my initial review, see checklist above. Below, I provide further context for checkboxes that I didn't check.
General checks

* **Substantial scholarly effort**: following the review guidelines at https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort, here are my observations on this: the code was written by a single author over a limited period of time. There are no external stars/watchers/forks/issue submitters for the project so usage has not yet been demonstrated. Despite this, the quantitative metrics over the code (i.e., number of lines) and my own review of the code show that the work put into the implementation is not trivial. If these characteristics are consistent with a JOSS publication, I can check this box - guidance from @fboehm would be helpful.

I don't think I can really argue with you here, most of the package was written by me, and compiled over a short period of time. However, it's not really true that it was written over a limited period. The package is a compilation of most code was written during the 4 years of my PhD and the few years after (and not even all by me, but also by co-authors). This package is an attempt to not let all that effort go to waste because of our unFAIR code practices.

@RemieJanssen @bgyori - can you elaborate on this point? Why does it appear to @bgyori that things were written over a short period while @RemieJanssen says otherwise? Is @bgyori relying on git commit times, while @RemieJanssen and co-workers perhaps didn't use git while writing?

Based on @RemieJanssen's comments, I understand that the code was written over a several years but was consolidated into this integrated repository later, over a shorter period of time. This makes sense to me, and I definitely see the value in turning fragmented code into an integrated and reusable package.

That is correct. If you want to see proof of this, take a look at the second commit: RemieJanssen/PhyloX@2b412c8
This is where I started PhyloX by simply dumping all scripts I could find in one git repo.

[RemieJanssen]

I tried to re-balance the paper as @bgyori suggested, in this PR: RemieJanssen/PhyloX#52
Please let me know if this is the direction you were thinking of. If it is, I will go through the paper again to clean up the text (language and structure), but I'd first like to know if these additions are wanted/necessary/appreciated.

[RemieJanssen]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[RemieJanssen]

@bgyori
Your comment on the Community guidelines is handled in RemieJanssen/PhyloX#50

About the Functionality documentation. Did you have any problems navigating the docs besides the issue of missing docstrings?
The missing docstrings will be fixed in

• Update _autosummary RST to include missing health generator module RemieJanssen/PhyloX#46
• Missing docstrings in phylox.generators.lgt.base RemieJanssen/PhyloX#51
• Missing docstring for from_cherry_picking_sequence RemieJanssen/PhyloX#53

I think that is all of them (except some helper functions for API methods), please let me know if you find any more

[fboehm]

@bgyori - do you have any feedback for @RemieJanssen in response to the latest changes?

[bgyori]

As far as I understand, @RemieJanssen is working on some documentation updates still (is that right?), I will reassess everything once that is wrapped up.

[RemieJanssen]

@bgyori I have filled in the missing docstrings wherever I could find them, and I have improved (hopefully) the navigability of the docs: https://phylox.readthedocs.io/en/latest/

If you find anything else, please let me know :)

[fboehm]

@abhishektiwari @bgyori @RemieJanssen - how are the reviews going? Has @RemieJanssen addressed your concerns? Or is there more revision needed?

[abhishektiwari]

@fboehm I have marked my review completed. Thanks authors for updating documentation and paper.

[fboehm]

Thank you for the helpful review, @abhishektiwari !

[fboehm]

@bgyori - have you had a chance to review the latest revisions from @RemieJanssen ?

[fboehm]

@bgyori - I hope that things are going ok. Have you had a chance to review changes from @RemieJanssen ? DO you have any questions on how to proceed?

[bgyori]

I will aim to finish my review before the end of this week.

[bgyori]

Thanks @RemieJanssen, I think all aspects of the software and paper have been improved substantially and I checked all the review boxes. I submitted a PR with a couple of small typo fixes to the paper.

[fboehm]

Thanks, @bgyori ! @RemieJanssen - please let me know when you've addressed the PR from @bgyori . Thanks again!

[RemieJanssen]

Thanks @bgyori and @abhishektiwari for the helpful reviews, and @fboehm for the smooth process!
I have addressed the last PR from bgyori and fixed a few typos myself as well.
This must mean that we can finish up this phase, is that correct?

The last thing I'd like to fix is some metadata.
I see the version is still 1.0.3 at the top of this thread.
The version the paper corresponds to should be updated I think, is that still possible, and how do I do that?

[fboehm]

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[fboehm]

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