[REVIEW]: Special relativity in R: the lorentz package

[whedon]

Submitting author: @RobinHankin (Robin Hankin)
Repository: https://github.com/RobinHankin/lorentz
Branch with paper.md (empty if default branch):
Version: 1.1-0
Editor: @arm61
Reviewers: @HaoZeke, @IanHawke
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://jose.theoj.org/papers/316a824a674ee61d79bd0bdb07d07ba1/status.svg)](https://jose.theoj.org/papers/316a824a674ee61d79bd0bdb07d07ba1)

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

@HaoZeke & @IanHawke, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/jose-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arm61 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 ✨

Review checklist for @HaoZeke

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (1.1-0)?
• Authorship: Has the submitting author (@RobinHankin) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
• 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 the need for this software 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?
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Tests: Are there automated tests or manual steps described so that the function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state the need for this software and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @IanHawke

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (1.1-0)?
• Authorship: Has the submitting author (@RobinHankin) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
• 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 the need for this software 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?
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Tests: Are there automated tests or manual steps described so that the function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state the need for this software and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @HaoZeke, @IanHawke it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

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@whedon commands

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

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[whedon]

Wordcount for paper.md is 765

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.31 s (93.4 files/s, 18529.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              1              1           2693
R                               14            310             76           1210
Markdown                         3             72              0            419
TeX                              5             49              0            414
Rmd                              4            122            243            108
YAML                             1              6              1             16
make                             1              2              0              8
-------------------------------------------------------------------------------
SUM:                            29            562            321           4868
-------------------------------------------------------------------------------


Statistical information for the repository 'c6ded0290f69d2c7bee4b4ea' was
gathered on 2023/02/22.
No commited files with the specified extensions were found.

[whedon]

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

[arm61]

Okay, we are ready to roll!

@HaoZeke and @IanHawke thanks for agreeing to review this interesting work! If you work through the checklist and if there is any problems/comments about the material, I would recommend opening an issue on the material repository and the authors can sort them out. More information about the review guidelines can be found on the Open Journals documentation pages: https://openjournals.readthedocs.io/en/jose/reviewer_guidelines.html

If anyone has any questions just ping me on here!

[whedon]

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

OK DOIs

- 10.48550/ARXIV.2012.15149 is OK
- 10.48550/ARXIV.2212.07005 is OK
- 10.48550/ARXIV.1812.11589 is OK
- 10.21105/jose.00091 is OK

MISSING DOIs

- 10.1007/bf02550347 may be a valid DOI for title: Thomas precession: its underlying gyrogroup axioms and their use in hyperbolic geometry and relativistic physics
- 10.1063/1.168517 may be a valid DOI for title: Teaching special relativity with a computer
- 10.1119/1.4938057 may be a valid DOI for title: Visualizing relativity: the OpenRelativity project
- 10.1002/andp.19053220607 may be a valid DOI for title: Über einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt
- 10.1007/978-94-015-3445-1_5 may be a valid DOI for title: Electromagnetic phenomena in a system moving with any velocity smaller than that of light
- 10.1007/978-3-663-19510-8_9 may be a valid DOI for title: Kosmologische Betrachtungen zur allgemeinen Relativitätstheorie

INVALID DOIs

- None

[arm61]

@RobinHankin it looks like there some DOIs missing from the paper, it would be great if you can fill them in when you have a chance.

[RobinHankin]

OK thanks for this, will investigate the DOI issue over at

RobinHankin/lorentz#43

• Robin

[RobinHankin]

Missing DOI issue fixed in bd03475

• Robin

[arm61]

@whedon generate pdf

[whedon]

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

[arm61]

@whedon check references

[whedon]

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

OK DOIs

- 10.1007/bf02550347 is OK
- 10.1063/1.168517 is OK
- 10.1119/1.4938057 is OK
- 10.48550/ARXIV.2012.15149 is OK
- 10.48550/ARXIV.2212.07005 is OK
- 10.1002/andp.19053220607 is OK
- 10.1007/978-94-015-3445-1_5 is OK
- 10.1007/978-3-663-19510-8_9 is OK
- 10.48550/ARXIV.1812.11589 is OK
- 10.21105/jose.00091 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arm61]

Perfect, thanks @RobinHankin

[whedon]

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

[whedon]

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

[arm61]

Hey @HaoZeke and @IanHawke, thought I would check in to see how the reviews are going?

[IanHawke]

Apologies for being slow about this - March was heavier than I expected. Will be back on this in about 10 days time. In my general look-through so far it has looked good, but I want to think about the examples and the role of Thomas precession (eg) in the docs a bit more.

[arm61]

@HaoZeke and @IanHawke just checking in to see how the reviews are going?

[arm61]

Hey all (@HaoZeke and @IanHawke), how are the reviews going?

[arm61]

I have followed up with both reviewers via email as many months have now passed without changes to the review status. I will keep you updated.

[arm61]

Checking in one last time with @IanHawke and @HaoZeke and if there is no reply I will find alternative reviewers. My apologies for the delay.

[HaoZeke]

Apologies @arm61 and @RobinHankin. I've started opening issues for the review, though it looks very good :)

I've opened issues with the specific concerns. Some small things left to finish (docs, apidocs, build systems, ci, contributing docs etc.), otherwise its all good. I didn't consider the celerity portions because they are marked as experimental.

[arm61]

@RobinHankin please respond to the issues that @HaoZeke has opened when you have some time.

[RobinHankin]

Hi there, thanks for this, I will attend to these (perfectly reasonable) points shortly.
Best wishes - Robin

[arm61]

@HaoZeke I see that @RobinHankin has closed most of the issues you opened are you able to now complete the review?

@IanHawke have you had a chance to progress this at all?

[HaoZeke]

@HaoZeke I see that @RobinHankin has closed most of the issues you opened are you able to now complete the review?

I'm not sure. @RobinHankin would it be possible to wrap up that issue sometime soon? If not, I would still recommend acceptance (since the code is relatively simple, and there are tests), but it would be nicer to have it finished :)

[RobinHankin]

Hi there, sorry for the delay [I have had some family and personal issues to deal with recently]. I've sorted out all the comments apart from the workflow comments and the code coverage comments. I spent a massive amount of time trying to sort out the automatic code coverage and the travis checking, to no avail. You can see from commits such as RobinHankin/lorentz@dae66c1 that this was a frustrating and ultimately unsuccessful task. As you say, the code is relatively simple and indeed passes local tests [for me this is "R CMD check"] and the test coverage is almost complete. If Rohit recommends acceptance then this would be a great relief from my mind. With best wishes Robin

…

-- Robin K. S. Hankin Associate Professor, computational statistics

On Tue, Nov 14, 2023 at 9:30 AM Rohit Goswami ***@***.***> wrote: @HaoZeke <https://github.com/HaoZeke> I see that @RobinHankin <https://github.com/RobinHankin> has closed most of the issues you opened are you able to now complete the review? I'm not sure. @RobinHankin <https://github.com/RobinHankin> would it be possible to wrap up that issue sometime soon? If not, I would still recommend acceptance (since the code is relatively simple, and there are tests), but it would be nicer to have it finished :) — Reply to this email directly, view it on GitHub <#196 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADFFZUVJDFJSIUQ5BFQYPQ3YEJ7PJAVCNFSM6AAAAAAVEMARMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBZGA2DCNJQHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[HaoZeke]

sorry for the delay [I have had some family and personal issues
to deal with recently].

No worries, I'm sorry to hear that, hope things are looking up.

@arm61 I completed my review checklist and am happy to recommend this for publication :)
Thanks for responding in a timely manner @RobinHankin !

[RobinHankin]

@whedon generate pdf

[editorialbot]

My name is now @editorialbot

[RobinHankin]

@editorialbotbot generate pdf

[RobinHankin]

@editorialbot generate pdf

[editorialbot]

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

[RobinHankin]

@editorialbot generate pdf

[editorialbot]

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

[arm61]

I am no longer getting responses from @IanHawke, therefore I will start to look for a new reviewer.

[arm61]

@hughshanahan, @jwagemann, or @dpshelio would any of you be interested in reviewing this JOSE paper?