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[REVIEW]: PathFinder: A Matlab/Octave package for oscillatory integration #6902

Open editorialbot opened 5 months ago

editorialbot commented 5 months ago

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

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HTML: <a href="https://joss.theoj.org/papers/851d659a3a85536bfc6b86de45a1641d"><img src="https://joss.theoj.org/papers/851d659a3a85536bfc6b86de45a1641d/status.svg"></a>
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 commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago 
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 commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1044

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

editorialbot commented 5 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

YehorYudinIPP commented 4 months ago

Review checklist for @YehorYudinIPP

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

YehorYudinIPP commented 4 months ago

@editorialbot commands

editorialbot commented 4 months ago

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 commented 4 months ago

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 commented 4 months ago

@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 commented 4 months ago

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 commented 4 months ago

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 commented 4 months ago

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:

olexandr-konovalov commented 3 months ago

@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 commented 3 months ago

Review checklist for @fruzsinaagocs

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

olexandr-konovalov commented 1 month ago

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 commented 1 month ago

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

AndrewGibbs commented 1 month ago

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 commented 1 month ago

@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 commented 1 month ago

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.

fruzsinaagocs commented 1 week ago

The installation issues have now been resolved, so I'm continuing my review of the code. The paper already contains comparisons with other software performing oscillatory integrals, but the ones below might also be worth mentioning (without detailed comparisons):