[REVIEW]: PyPO: a Python package for Physical Optics

[editorialbot]

Submitting author: @arend95 (Arend Moerman)
Repository: https://github.com/PyPO-dev/PyPO
Branch with paper.md (empty if default branch):
Version: v1.0.1
Editor: @danielskatz
Reviewers: @MikeHughesKent, @brandondube
Archive: 10.5281/zenodo.8241427

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/baa668ad384488715dbfb1a540fb67fd/status.svg)](https://joss.theoj.org/papers/baa668ad384488715dbfb1a540fb67fd)

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

@MikeHughesKent & @brandondube, 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 @danielskatz 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 @brandondube

📝 Checklist for @MikeHughesKent

[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 1.88  T=0.18 s (455.6 files/s, 125353.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          53           2605           2635           8141
C/C++ Header                    15            781           1422           2738
CUDA                             2            411            701           1240
C++                              4            246            661            776
Markdown                         5             23              0            154
CSS                              1              7              3            119
TeX                              1              7              0             93
CMake                            1             16              1             33
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            83           4097           5427          13312
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 630

[editorialbot]

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

OK DOIs

- 10.1007/s10909-022-02888-5 is OK
- 10.1117/12.551391 is OK
- 10.1117/12.925230 is OK
- 10.21105/joss.01352 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[danielskatz]

@MikeHughesKent and @brandondube - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#5478 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 reviews to be completed within about 2-4 weeks. Please let me know if either 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 (@danielskatz) if you have any questions/concerns.

[brandondube]

Review checklist for @brandondube

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/PyPO-dev/PyPO?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@arend95) 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?

[arendMoerman]

Hi @brandondube, thank you very much for your feedback. We will start working on the raised issues as soon as possible!

[danielskatz]

@arend95 - Can you report on your progress? I see some issues have been closed, but some are still open.

[danielskatz]

👋 @MikeHughesKent - can you please generate your checklist as instructed above and evaluate and check off the COI item, just to be sure there are no problems with the system? (any further progress after that would also be welcome 🙂)

[arendMoerman]

@danielskatz - We have worked on all the raised issues and are now awaiting @brandondube his responses for the remaining open issues.

[danielskatz]

@brandondube - please respond in the issues when you get a chance

[bdube-jpl]

The last time I interacted with one of the issues was only 2 days ago, please be patient with volunteer peer reviewers

[danielskatz]

@bdube-jpl - ok, sorry. I've been on vacation and was trying to catch up and might have compressed some things.

[danielskatz]

👋 @MikeHughesKent - can you please generate your checklist as instructed above and evaluate and check off the COI item, just to be sure there are no problems with the system? (any further progress after that would also be welcome 🙂)

[brandondube]

My (lengthy!) review is now complete, cheers

[danielskatz]

thanks @brandondube!

[arendMoerman]

@editorialbot generate pdf

[editorialbot]

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

[arendMoerman]

@danielskatz - Sorry again for this final mess: it seems all ok again.

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1007/s10909-022-02888-5 is OK
- 10.1117/12.551391 is OK
- 10.1117/12.925230 is OK
- 10.21105/joss.01352 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4479, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@arend95 - please change "Github" in the Availability section to "GitHub".

[arendMoerman]

@danielskatz - done!

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1007/s10909-022-02888-5 is OK
- 10.1117/12.551391 is OK
- 10.1117/12.925230 is OK
- 10.21105/joss.01352 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4480, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@arend95 - a few more small changes in the bib that I missed before - sorry this is taking so many iterations...

PyPO-dev/PyPO#166

[arendMoerman]

@danielskatz - no problem, just merged the PR!

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1007/s10909-022-02888-5 is OK
- 10.1117/12.551391 is OK
- 10.1117/12.925230 is OK
- 10.21105/joss.01352 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4481, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Moerman
  given-names: Arend
  orcid: "https://orcid.org/0000-0002-0475-6134"
- family-names: Gafaji
  given-names: Maikel H.
- family-names: Karatsu
  given-names: Kenichi
  orcid: "https://orcid.org/0000-0003-4562-5584"
- family-names: Endo
  given-names: Akira
  orcid: "https://orcid.org/0000-0003-0379-2341"
contact:
- family-names: Moerman
  given-names: Arend
  orcid: "https://orcid.org/0000-0002-0475-6134"
doi: 10.5281/zenodo.8241427
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Moerman
    given-names: Arend
    orcid: "https://orcid.org/0000-0002-0475-6134"
  - family-names: Gafaji
    given-names: Maikel H.
  - family-names: Karatsu
    given-names: Kenichi
    orcid: "https://orcid.org/0000-0003-4562-5584"
  - family-names: Endo
    given-names: Akira
    orcid: "https://orcid.org/0000-0003-0379-2341"
  date-published: 2023-08-12
  doi: 10.21105/joss.05478
  issn: 2475-9066
  issue: 88
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5478
  title: "PyPO: a Python package for Physical Optics"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05478"
  volume: 8
title: "PyPO: a Python package for Physical Optics"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05478 joss-papers#4482
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05478
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulation to @arend95 (Arend Moerman) and co-authors on your publication!!

And thanks to @MikeHughesKent and @brandondube for reviewing!
JOSS is volunteer-run and depends on your time and effort

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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reStructuredText:
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