[REVIEW]: Pydre: A Python package for driving simulation data reduction

[editorialbot]

Submitting author: @tkerwin (Thomas Kerwin)
Repository: https://github.com/OSUDSL/pydre
Branch with paper.md (empty if default branch): joss
Version: v24.0.2
Editor: @arfon
Reviewers: @fredshone, @xoolive, @fxjung
Archive: Pending

Status

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Reviewers and authors:

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Reviewer instructions & questions

@fredshone & @xoolive & @fxjung, 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 @arfon 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 @xoolive

📝 Checklist for @fxjung

📝 Checklist for @fredshone

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.4271/2014-01-0452 is OK
- 10.1016/j.trf.2024.05.021 is OK
- 10.1201/b10836-21 is OK
- 10.1109/SoutheastCon44009.2020.9249691 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.04 s (2262.1 files/s, 154096.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            512            983           2102
JSON                            29             45              0           1063
TOML                            32            181              1            654
CSV                              6              0              0            444
Markdown                        11            176              0            330
Text                             1             23              0             96
YAML                             2              7              4             62
TeX                              1              3              0             47
CSS                              1              3              0              8
-------------------------------------------------------------------------------
SUM:                            99            950            988           4806
-------------------------------------------------------------------------------

Commit count by author:

   266	BuildTools
   168	Thomas Kerwin
    78	Craig Fouts
    41	Allison Broccolo
    29	yu.2479
    16	Tiya Chhajed
    14	Kevin Smearsoll
    12	Josh
    11	Karthick Sivasubramanian
    11	karthicksiva
    10	Aashka Baruah
     9	Allyson Boone
     9	Peter Yu
     7	Cameron Wrabel
     7	abbyatchleyy
     7	tiyachhajed
     6	LAPTOP-6SCSKCBVouts
     5	Saana
     5	Shreyas Chaudhari
     4	Will Blanton
     4	unknown
     3	Kendra Harder
     2	Casey Schomer
     2	Maggie Wilson
     2	Margaret Wilson
     2	Viren Gadkari
     2	maggieowilson
     1	DrIMBA
     1	JWHI7830
     1	Zachary Ritter

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1001

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[arfon]

@fredshone, @xoolive, @fxjung – many thanks for agreeing to review this submission for JOSS! This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also 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 and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/7870 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[editorialbot]

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

[xoolive]

Review checklist for @xoolive

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/OSUDSL/pydre?
• 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 (@tkerwin) 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?

[fxjung]

Review checklist for @fxjung

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/OSUDSL/pydre?
• 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 (@tkerwin) 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?

[fredshone]

Review checklist for @fredshone

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/OSUDSL/pydre?
• 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 (@tkerwin) 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?

[fredshone]

@tkerwin nice project and paper!

Some pretty minor changes please:

• Add installation instructions (ideally including venv for example) - suggest aim these at someone new to python.
• Your dev install instructions are incomplete (I think). After install (with uv) i have to use uv run python -m src.pydre.run... for example, tried on UNIX and Windows 11, basically pydre isn't executable? Perhaps this works with release installs?
• Please add docs for running tests and a bit more for community guidelines, eg.
• You have broken tests i think...
• Please add test coverage report, for example add pytest-cov to install and I suggest setting a fail under, eg.

Minor thoughts:

• Your dev install docs use Rye but i think this is intended to be replaced by uv now?
• Your example usage in docs is a bit clunky to run (i had to work out the paths).

Otherwise really nice project! very clear use case and paper.

[tkerwin]

A general comment: I released a new version (25.0) two days ago. That version (hopefully) has fewer bugs and better documentation.

@fredshone Thank you very much for your comments.

I am working on installation instructions, docs for running tests and contribution guidelines currently. Thank you for the link to the excellent example for contribution guidelines. I expect to push those documentation updates soon and will update here when that it done. I can add a test coverage report as well, although we not yet close to full coverage

Although uv is recommended for new projects, rye is still being actively maintained, so I don't think there's a need to shift off of it for now. However, the published package should work correctly with uv. I just ran the following steps on my machine with the expected results:

mkdir pydre-test
cd pydre-test
uv init
uv add pydre
uv sync
uv run python -m pydre.run

If you get an error with those steps, can you please make an issue? I haven't tried running pydre from the working development directory with uv, so maybe that's the use case you are getting the error in?

If you can also give me a little more detail about the broken tests, I would greatly appreciate it.

Thanks again for your review.

[fredshone]

Sounds good.

re coverage - no need to go for 100% - but just need to check there is a reasonable amount. I completely appreciate getting coverage for data pipelines is painful. So no stress.

re rye versus uv, fine by me (I'm not familiar with either in any case), those uv steps are close to what I did - I will await your updated docs.

re tests: issue here, but might simply be my install.