[REVIEW]: Taxonomy Resolver: A Python package for building and filtering taxonomy trees

[editorialbot]

Submitting author: @biomadeira (Fabio Madeira)
Repository: https://github.com/ebi-jdispatcher/taxonomy-resolver
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @csoneson
Reviewers: @ryneches, @tbrittoborges
Archive: Pending

Status

Status badge code:

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@ryneches & @tbrittoborges, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @csoneson know.

✨ 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 @ryneches

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.1093/database/baaa062 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.1111/2041-210X.12628 is OK
- 10.5281/zenodo.13819579 is OK
- 10.1093/sysbio/syz013 is OK
- 10.1016/j.tree.2023.08.004 is OK
- 10.1016/B978-155860920-4/50005-2 is OK
- 10.1093/nar/gkae241 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Entrez Direct: E-utilities on the Unix Command Lin...
- No DOI given, and none found for title: Anytree: Python tree data library
- No DOI given, and none found for title: BigTree: Tree Implementation and Methods for Pytho...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.02 s (1025.1 files/s, 137987.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           6            179            199           1096
Text                             6              0              0            628
reStructuredText                 3            180            112            277
TeX                              1             11              0            158
YAML                             4              6             27             91
Markdown                         1             16              0             60
TOML                             1              4              0             37
JSON                             1              0              0             15
-------------------------------------------------------------------------------
SUM:                            23            396            338           2362
-------------------------------------------------------------------------------

Commit count by author:

   204	Fábio Madeira
     1	Fábio Madeira

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 993

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

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

[csoneson]

👋🏼 @biomadeira, @ryneches, @tbrittoborges - this is the review thread for the submission. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread. These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks (of course, we are also aware that many people will be off for the next few weeks). Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

[ryneches]

Review checklist for @ryneches

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/ebi-jdispatcher/taxonomy-resolver?
• 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 (@biomadeira) 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?

[biomadeira]

@editorialbot generate pdf

[editorialbot]

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

[ryneches]

A few minor issues :

• Fix typo in CLI docs
• Bring test data up to date

Some things that would be nice to have :

• Automatically update the test data with a CI integration
• Report progress of downloads or large traversals (e.g., tqdm)
• An example that arrives at an end point with a concrete meaning for the audience (biologists). For example, using @SimonGreenhill's Treemaker to produce an up-to-date NEWICK tree of taxa in an interesting clade, or a FASTA file of marker genes for members of an interesting clade.

[biomadeira]

@ryneches Thanks! I am going through those and will report back.