[REVIEW]: ParticlePhaseSpace: A python package for streamlined import, analysis, and export of particle phase space data

[editorialbot]

Submitting author: @bwheelz36 (Brendan Whelan)
Repository: https://github.com/bwheelz36/ParticlePhaseSpace
Branch with paper.md (empty if default branch): paper
Version: v0.5.5
Editor: @matthewfeickert
Reviewers: @benjaminbolling, @ax3l
Archive: 10.5281/zenodo.8299964

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/94f4a820f1296ec3af83273e45b61e47"><img src="https://joss.theoj.org/papers/94f4a820f1296ec3af83273e45b61e47/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/94f4a820f1296ec3af83273e45b61e47/status.svg)](https://joss.theoj.org/papers/94f4a820f1296ec3af83273e45b61e47)

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

@benjaminbolling & @ProfLeao, 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 @matthewfeickert 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 @benjaminbolling

📝 Checklist for @ProfLeao

📝 Checklist for @ax3l

[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=0.03 s (1045.1 files/s, 98384.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            240            390           1184
Jupyter Notebook                 3              0            800            136
TeX                              1             11              0            134
YAML                             4             16             10            107
Markdown                         5             37              0            101
DOS Batch                        1             11              1             32
reStructuredText                 3             15             19             21
make                             1              5              9             10
JSON                             3              0              0              3
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            35            335           1229           1731
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 735

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1088/1361-6587/ac2e3e is OK
- 10.1007/978-3-319-18317-6_8 is OK
- 10.1118/1.3397455 is OK

MISSING DOIs

- 10.1002/mp.15887 may be a valid DOI for title: Bayesian optimization to design a novel x-ray shaping device

INVALID DOIs

- None

[matthewfeickert]

@benjaminbolling, @ProfLeao, @ax3l 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 (and if you leave notes on each item that's even better). There are also links to the JOSS reviewer guidelines. I find it particularly helpful to also use the JOSS review criteria and review checklist docs as supplement/guides to the reviewer checklist @editorialbot will make for you.

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#5375 so that a link is created to this Issue 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 4 weeks. Please let me know if either of you require some more time (that's perfectly okay). We can also use @editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@matthewfeickert) if you have any questions/concerns.

[ProfLeao]

Review checklist for @ProfLeao

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/bwheelz36/ParticlePhaseSpace?
• 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 (@bwheelz36) 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?

[benjaminbolling]

Review checklist for @benjaminbolling

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/bwheelz36/ParticlePhaseSpace?
• 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 (@bwheelz36) 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?

[matthewfeickert]

@editorialbot add @ax3l as reviewer

[editorialbot]

@ax3l added to the reviewers list!

[matthewfeickert]

@bwheelz36 As I mentioned over on #5356 (comment) we have a few other people who were interested in being reviewers, so we now have 3 reviewers with the addition of @ax3l!

@ax3l please check out #5375 (comment) and as this is your first JOSS review (welcome!) please feel free to ask me if you have any questions. 👍

[ax3l]

Review checklist for @ax3l

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/bwheelz36/ParticlePhaseSpace?
• 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 (@bwheelz36) 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?
  • Minor doc fix Doc: Fix PyPI Package bwheelz36/ParticlePhaseSpace#160 at one location.
• 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?

[matthewfeickert]

👋 @bwheelz36, @benjaminbolling, @ProfLeao, @ax3l Just checking in on things. It seems that the review is ongoing, which is good. 👍

As the review has been going for 2 weeks at this point I'll have @editorialbot give us reminders in 3 weeks to follow up on anything outstanding.

[matthewfeickert]

@editorialbot remind @benjaminbolling in 3 weeks

[editorialbot]

Reminder set for @benjaminbolling in 3 weeks

[matthewfeickert]

@editorialbot remind @ProfLeao in 3 weeks

[editorialbot]

Reminder set for @ProfLeao in 3 weeks

[matthewfeickert]

@editorialbot remind @ax3l in 3 weeks

[editorialbot]

Reminder set for @ax3l in 3 weeks

[benjaminbolling]

Initial review completed, very nice package and paper.

Issues reported and to be solved, from my point of view:

• Paper comments in pull request bwheelz36/ParticlePhaseSpace#146
• Fix description of README.md in examples/ bwheelz36/ParticlePhaseSpace#147
• pytest package missing bwheelz36/ParticlePhaseSpace#148
• Automated test bwheelz36/ParticlePhaseSpace#149
• Paper comment: Acknowledgements bwheelz36/ParticlePhaseSpace#150
• Paper: State of the field bwheelz36/ParticlePhaseSpace#151

[bwheelz36]

Thankyou @benjaminbolling - I've started responding to all your points inside each issue thread :-)

[editorialbot]

👋 @benjaminbolling, please update us on how your review is going (this is an automated reminder).

[editorialbot]

👋 @ProfLeao, please update us on how your review is going (this is an automated reminder).

[matthewfeickert]

@editorialbot generate pdf

[editorialbot]

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

[matthewfeickert]

@editorialbot set v0.5.4 as version

[editorialbot]

Done! version is now v0.5.4

[matthewfeickert]

@bwheelz36 all that's left to do now before publication is to ensure that there is a long term public archive of the code that was reviewed, in this case ParticlePhaseSpace v0.5.4.

We'd suggest depositing the code either with Zenodo or with figshare to get an archive with a DOI. If you use Zenodo there is an (optional) GitHub integration that can create a Zenodo archive for you anytime you make a GitHub release of your code.

Once you have a DOI for the archive please just report it here and I'll have @editorialbot add the archive (and update the version in the review if a new releases was created — not required to be clear).

Let me know if you have any questions. 👍

[bwheelz36]

Great, done:
https://zenodo.org/record/8299964

[matthewfeickert]

@editorialbot set v0.5.5 as version

[editorialbot]

Done! version is now v0.5.5

[matthewfeickert]

Great, done: https://zenodo.org/record/8299964

@bwheelz36 Excellent. Can you also revise the Zenodo archive metadata through the website to have the authors be the authors listed on the paper (this is a minor thing that we ask for all JOSS papers)? After that I'll recommend the EiC trigger publication.

[matthewfeickert]

@editorialbot set 10.5281/zenodo.8299964 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8299964

[matthewfeickert]

Can you also revise the Zenodo archive metadata through the website to have the authors be the authors listed on the paper (this is a minor thing that we ask for all JOSS papers)?

@bwheelz36 It is already Friday evening in Australia and so I don't expect that you will have time to get to this before the next week (totally reasonable). I'll go ahead and still recommend publication to the Editor in Chief so that this can get put on their radar to look at once the author metadata for the archive gets updated. 👍

[matthewfeickert]

@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

- 10.1118/1.4941309 is OK
- 10.1088/1361-6587/ac2e3e is OK
- 10.1007/978-3-319-18317-6_8 is OK
- 10.1118/1.3397455 is OK
- 10.1002/mp.15887 is OK
- 10.5281/zenodo.591699 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#4523, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[bwheelz36]

Great, done: https://zenodo.org/record/8299964

@bwheelz36 Excellent. Can you also revise the Zenodo archive metadata through the website to have the authors be the authors listed on the paper (this is a minor thing that we ask for all JOSS papers)? After that I'll recommend the EiC trigger publication.

done :-)

[matthewfeickert]

@openjournals/pe-eics, just wanted to send a reminder ping this submission is ready for EiC checks and acceptance. The recommend-accept notice was sent on a Friday during a long weekend for the US, so this is just a ping to make sure it doesn't get burried in the notification landslide that usually hits everyone at the start of the week. :)

[kyleniemeyer]

@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: Whelan
  given-names: Brendan
  orcid: "https://orcid.org/0000-0002-2326-0927"
- family-names: Esnault
  given-names: Leo
  orcid: "https://orcid.org/0000-0002-0795-9957"
doi: 10.5281/zenodo.8299964
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Whelan
    given-names: Brendan
    orcid: "https://orcid.org/0000-0002-2326-0927"
  - family-names: Esnault
    given-names: Leo
    orcid: "https://orcid.org/0000-0002-0795-9957"
  date-published: 2023-09-11
  doi: 10.21105/joss.05375
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5375
  title: "ParticlePhaseSpace: A python package for streamlined import,
    analysis, and export of particle phase space data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05375"
  volume: 8
title: "ParticlePhaseSpace: A python package for streamlined import,
  analysis, and export of particle phase space data"

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.05375 joss-papers#4552
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05375
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...

[kyleniemeyer]

Congratulations @bwheelz36 on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @benjaminbolling and @ax3l for reviewing this, and @matthewfeickert for editing.

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05375/status.svg)](https://doi.org/10.21105/joss.05375)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05375">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05375/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05375/status.svg
   :target: https://doi.org/10.21105/joss.05375

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[matthewfeickert]

Congratulations @bwheelz36 on a very nice publication, as well as your patience at the final stages! Thank you for excellent detailed reviews, @benjaminbolling and @ax3l.