[REVIEW]: PathFinder: A Matlab/Octave package for oscillatory integration

[editorialbot]

Submitting author: @AndrewGibbs (Andrew Gibbs)
Repository: https://github.com/AndrewGibbs/PathFinder
Branch with paper.md (empty if default branch):
Version: v1.1.0
Editor: @olexandr-konovalov
Reviewers: @YehorYudinIPP, @fruzsinaagocs
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/851d659a3a85536bfc6b86de45a1641d/status.svg)](https://joss.theoj.org/papers/851d659a3a85536bfc6b86de45a1641d)

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

@YehorYudinIPP & @fruzsinaagocs, 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 @olexandr-konovalov 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 @YehorYudinIPP

📝 Checklist for @fruzsinaagocs

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1666.4 files/s, 130325.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                          76            616           1048           2872
C/C++ Header                     3            152            416           1014
Markdown                         3            132              0            286
C                                4             79             86            278
TeX                              1             12              0            146
YAML                             4              1              4             52
Jupyter Notebook                 1              0              1              0
-------------------------------------------------------------------------------
SUM:                            92            992           1555           4648
-------------------------------------------------------------------------------

Commit count by author:

   160	Andrew Gibbs
    34	Unknown
     6	DaveHewett
     1	Daan Huybrechs

[editorialbot]

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

OK DOIs

- 10.1016/j.wavemoti.2023.103257 is OK
- 10.1016/j.jcp.2024.112787 is OK
- 10.1137/050636814 is OK
- 10.1137/18M1221138 is OK
- 10.1016/j.wavemoti.2018.09.015 is OK
- 10.1016/S0010-4655(00)00126-0 is OK

MISSING DOIs

- No DOI given, and none found for title: NIST Digital Library of Mathematical Functions
- No DOI given, and none found for title: Mathematica NIntegrate Integration Rules - LevinRu...
- No DOI given, and none found for title: Dijkstra Algorithm
- No DOI given, and none found for title: Computing Highly Oscillatory Integrals
- No DOI given, and none found for title: The problem of whispering gallery waves in a neigh...
- No DOI given, and none found for title: The structure of an electromagnetic field in the n...
- No DOI given, and none found for title: Lagrangian manifolds with singularities, asymptoti...

INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1044

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[YehorYudinIPP]

Review checklist for @YehorYudinIPP

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/AndrewGibbs/PathFinder?
• 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 (@AndrewGibbs) 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?

[YehorYudinIPP]

@editorialbot commands

[editorialbot]

Hello @YehorYudinIPP, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[YehorYudinIPP]

Dear @olexandr-konovalov ,

in principle, I went through the checklist as well as explored and tried out the package, checked some of the references etc.

However, before checking in some of the list points, I would like to raise some questions. Should I simply openly create a repository issue for each of the points I have?

Best,
Yehor

[olexandr-konovalov]

@fruzsinaagocs could you please generate your checklist, as explained above? Seeing it partially checked helps us to better understand the state of the review process. Thanks!

[olexandr-konovalov]

Many thanks, @YehorYudinIPP! Yes, we encourage you to submit issues to https://github.com/AndrewGibbs/PathFinder/issues - see https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. I've just noticed that you have already submitted some - if they have to be resolved before checking the remaining tickboxes, please add cross-references to link those issues to this reviews.

[AndrewGibbs]

Thank you for your excellent suggestions on the issues page, @YehorYudinIPP; they are much appreciated. I should inform you that I will be off work until September, and I will address these changes then.
Best wishes,
Andrew

[YehorYudin]

Many thanks, @YehorYudinIPP! Yes, we encourage you to submit issues to https://github.com/AndrewGibbs/PathFinder/issues - see https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. I've just noticed that you have already submitted some - if they have to be resolved before checking the remaining tickboxes, please add cross-references to link those issues to this reviews.

Here is a summary of current suggestions from my side:

• Stating dependencies list or preparing an installation script: LAPACKE dependency AndrewGibbs/PathFinder#16
• Checking Octave plotting functionality and performance: LAPACKE dependency AndrewGibbs/PathFinder#16
• Checking the JOSS paper citation and adding information from the references: Comments on the paper AndrewGibbs/PathFinder#18
• Reporistory community guide and API documentation: Repository suggestions AndrewGibbs/PathFinder#19

[olexandr-konovalov]

@fruzsinaagocs how are you getting on with this review? If you are still happy to review this paper for JOSS, could you please generate your checklist, as explained above, and start filling it in, to help us to see at which stage you're with the review? Please let me know if you have any questions about the process!

[fruzsinaagocs]

Review checklist for @fruzsinaagocs

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/AndrewGibbs/PathFinder?
• 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 (@AndrewGibbs) 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?

[olexandr-konovalov]

Thanks @fruzsinaagocs, for starting the review - how are you getting on with the rest of the checks?

In the meantime, I see that some issues by @YehorYudin are still open - apparently they are needed to complete @YehorYudin's review. @AndrewGibbs are you going to respond to them, or are you waiting to hear from @fruzsinaagocs first?

[fruzsinaagocs]

Hi @olexandr-konovalov, thank you for the reminder -- I should be able to finish this review this week or next.

[AndrewGibbs]

Hi all, thank you for the time you are putting into this. I will wait for @fruzsinaagocs to finish their review before I begin making changes.

[fruzsinaagocs]

@olexandr-konovalov @AndrewGibbs I'm facing installation issues, I posted an issue about it. It could be macOS-specific problem, but I don't currently have access to any other system.

[AndrewGibbs]

Oh dear! A colleague had an issue with his Mac installation but we decided it was a more general MEX-OSX issue. I will look into this next week and get back to you.