[REVIEW]: RelativisticDynamics.jl: Relativistic Spin-Orbital 1 Dynamics in Julia

[editorialbot]

Submitting author: @tomkimpson (Tom Kimpson)
Repository: https://github.com/tomkimpson/RelativisticDynamics.jl
Branch with paper.md (empty if default branch):
Version: v0.1.2
Editor: @dfm
Reviewers: @langfzac, @tamasgal
Archive: 10.5281/zenodo.8412240

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/48d52c30fe45aea8ea04da814301448a"><img src="https://joss.theoj.org/papers/48d52c30fe45aea8ea04da814301448a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/48d52c30fe45aea8ea04da814301448a/status.svg)](https://joss.theoj.org/papers/48d52c30fe45aea8ea04da814301448a)

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

@farr & @duetosymmetry, 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 @dfm 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 @langfzac

📝 Checklist for @tamasgal

[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:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1142.6 files/s, 178939.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           18            619            121           1173
Markdown                         8            126              0            187
YAML                             6              5              7            141
TOML                             3             28              1            131
TeX                              1             12              0            130
Jupyter Notebook                 2              0           3206             64
-------------------------------------------------------------------------------
SUM:                            38            790           3335           1826
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1100

[editorialbot]

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

OK DOIs

- 10.1007/s10714-010-0939-y is OK
- 10.1098/rspa.1951.0200 is OK
- 10.1007/BF02734579 is OK
- 10.1093/mnras/stz389 is OK
- 10.1093/mnras/staa2103 is OK
- 10.1093/mnras/stz845 is OK
- 10.1051/0004-6361/202038561 is OK
- 10.1175/MWR-D-16-0228.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[dfm]

@farr, @duetosymmetry — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#4992 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 the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible!

[duetosymmetry]

Review checklist for @duetosymmetry

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/tomkimpson/RelativisticDynamics.jl?
• 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 (@tomkimpson) 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?

[farr]

Review checklist for @farr

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/tomkimpson/RelativisticDynamics.jl?
• 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 (@tomkimpson) 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?

[dfm]

@farr, @duetosymmetry, @tomkimpson — Happy new year! I'm writing to check in on the progress of this review, and to keep it on your radars. Please let me know if there are any major stoppers or if there's anything I can do to help move things along. Thanks!

[dfm]

@farr, @duetosymmetry, @tomkimpson — I'm checking in again to see what the status is on this review. Please let me know if you are running into any issues or if there's anything I can do to keep things rolling!

[duetosymmetry]

Hi all, sorry for being extremely slow... I've had a lot of responsibilities lately and let this one slide. Please forgive me! To avoid further delays let me just drop some initial thoughts here. Again sorry that this is not as thorough as it should be, but I thought that getting started with something is better than delaying.

First, I think the name RelativisticDynamics.jl is much too general for what is actually happening in this package. Lots of things could be relativistic dynamics. It could be fully nonlinear numerical relativity, or it could be simple post-Newtonian. This package is specifically for solving the MPD equations on the Kerr background, not more or less.

If the goal is for the package to become more flexible in the future — for example, solving the MPD equations on other exact spacetimes, or perturbatively away from Kerr — then it must be organized in such a way that a user could swap out the background metric with ease. That is impossible right now. All of the information for a background metric — code for computing contra- and covariant metric components, Christoffels, components of Riemann — should be collected together in a single piece of data.

The structure of metric.jl is rather messy (also, this is specific to Kerr, not any metric; and it's not just the metric, it's also connection coefficients and curvature). We have some functions whose names encode metric components, e.g. metric_g14. Then covariant_metric calls all of these. On the other hand, christoffel just computes all the Christoffel coefficients, without dispatching to anything like christoffel_111. Same thing for riemann. That is of course better. I don't know why there should be separate metric_gAB functions.

In some places in this code, there is reference to RelativisticDynamics.delta and RelativisticDynamics.sigma, while in other places it's just delta and sigma. I'm not sure why these are relegated to useful_functions.jl, or what determines why the functions in there ended up there. I would also recommend to use the relativists' naming to distinguish between the Levi-Civita symbol (which takes values either ±1 or 0) versus the Levi-Civita tensor (which transforms correctly under coordinate transformations).

Storage in Rtensor is extremely wasteful. There are only 10 independent quantities, but Rtensor allocates 256. This can be avoided be everywhere rewriting Riemann in terms of its electric/magnetic decomposition, both of these STF tensors having only 5 independent components (though needing to store 6, or more likely 9; still a huge improvement). This is not really a big point, since we're integrating an ODE, not solving a PDE. But still, I thought I should bring up these kind of design decisions.

I don't know why there is a separate schwarzchild_covariant_riemann function — and why does it have the spin, a, as an argument, when Schwarzschild is non-spinning? I would have thought that to make it obviously correct, one should just dispatch to riemann but with a=0, and lower the first index with the metric.

The documentation in orbit.jl refers to a file parameters.jl but there is no such file.

In universal_constants.jl, the speed of light should not be 3e8. It is defined to be exactly 299792458 m/s in SI units. In that same file: a capital G should probably be used for Newton's G. However, G is only measured to a level of 2*10^{-5}, and the mass of the Sun is similarly uncertain. However the product GM_☉ is known to a level of about 10^{-10}. It should be clear how to rewrite things so that you only ever use the product GM_☉ instead of either G or M_☉ by themselves (as is done in the pulsar timing and GR communities).

There are really many more issues about the clarity and organization of the code along these same lines, so I will not try to enumerate any more. In general, I think the code should organized better.

Turning to the documentation and article: I think the issue of spin supplementary conditions needs to be discussed much, much more. The SSCs are the main point of confusion when it comes to the MPD equations. Some statements you make in the code / documentation are only true for one particular SSC. It's fine to stick to one, as long as you make it clear that no others are allowed, and point out which statements are specific to the SSC you chose. It would be helpful to point to a specialist article about different SSCs.

Going back to the big picture: If the point of a specialized package like this one is for spinning bodies just in the Kerr spacetime, and you want to have high precision over very long times, then it would be better to use an action-angle formulation (see e.g. Vojtech Witzany's papers). That is only appropriate for the first order in spin, but as the article rightly mentions, the multipole expansion of the small body has already been truncated to dipole order — so the MPD equations are already an expansion. Of course the AA formulation is specific to Kerr. It would still be relevant spacetimes close to Kerr, perturbation theory. On the other hand to make it totally general, for any background spacetime, you can't use AA variables. I think it would be appropriate, in the Statement of Need, to discuss why this has been formulated as a generic ODE integration problem, rather than specializing to AA variables.

Sorry again that I waited so long to say anything. I hope this gives some useful directions for improvement of both the code and documentation. We can continue to discuss.

[tomkimpson]

Thanks @duetosymmetry for the thorough comments. No worries re the delay - I understand you're busy and appreciate you taking the time to review. I'll open a PR and start working through your comments and ping for any further discussion. Cheers!

[dfm]

Thanks to @duetosymmetry for these comments and suggestion, and to @tomkimpson for starting to work through them!

I want to also ping @farr to keep this on the radar. Please try to start going through the checklist ASAP to see if you have some comments to add to what @duetosymmetry has so far. Many thanks!!

[tomkimpson]

Thanks all for the help with this. Just giving this issue a bump - the comments have all been addressed on my side

[duetosymmetry]

Ping @farr for any review.

Question for @dfm: Should we be reviewing the PR tomkimpson/RelativisticDynamics.jl#41, or should @tomkimpson merge it in if he sees fit, and we do another round of refereeing back here? (Tangentially related, are the Julia docs also being generated from the PR branch? I can't find those separately).

[dfm]

Thanks for checking in @tomkimpson and @duetosymmetry! I'll email @farr to remind him as well.

Should we be reviewing the PR tomkimpson/RelativisticDynamics.jl#41, or should @tomkimpson merge it in if he sees fit, and we do another round of refereeing back here? (Tangentially related, are the Julia docs also being generated from the PR branch? I can't find those separately).

Good question! These reviews can progress either way. It's actually recommended to do as much of the iteration as you can on PRs and issues in the parent repository, rather than directly in this thread. So it certainly could be a good approach to go through that PR directly, but we're flexible, so please use whichever approach works best for you!

[dfm]

Just an update that I'm not getting anything from @farr even over email so I'm working on finding another reviewer to replace him.

In the meantime, I wanted to check in with @tomkimpson and @duetosymmetry to see where things stand with the currently open discussion points. Please let me know if there are any issues or major stoppers, and if you have a sense of the timeline for both of you working through the rest of the review. Thanks!

[tomkimpson]

Thanks @dfm. All of @duetosymmetry comments were address in tomkimpson/RelativisticDynamics.jl#41 . I have been leaving this PR open for more comments, but if @duetosymmetry is happy I will close it while we wait for the new reviewer.

One question for @dfm : it was recommended to change the package name to be less general. This is obviously straightforward but are there any issue on the JOSS side if I update the github repo name?

[dfm]

@editorialbot generate pdf

[dfm]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/s10714-010-0939-y is OK
- 10.1098/rspa.1951.0200 is OK
- 10.1007/BF02734579 is OK
- 10.1093/mnras/stz389 is OK
- 10.1093/mnras/staa2103 is OK
- 10.1093/mnras/stz845 is OK
- 10.1051/0004-6361/202038561 is OK
- 10.1175/MWR-D-16-0228.1 is OK
- 10.48550/arXiv.2203.11952 is OK
- 10.21105/joss.03703 is OK
- 10.1103/PhysRevD.45.1840 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[tomkimpson]

Thanks! (As I mentioned above ☝️) Can you update the Zenodo metadata (title and authors) to exactly match the JOSS paper? You should have an "Edit" button at the top right of the record page if you're logged in.

@dfm This is now done 👍

[dfm]

@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/s10714-010-0939-y is OK
- 10.1098/rspa.1951.0200 is OK
- 10.1007/BF02734579 is OK
- 10.1093/mnras/stz389 is OK
- 10.1093/mnras/staa2103 is OK
- 10.1093/mnras/stz845 is OK
- 10.1051/0004-6361/202038561 is OK
- 10.1175/MWR-D-16-0228.1 is OK
- 10.48550/arXiv.2203.11952 is OK
- 10.21105/joss.03703 is OK
- 10.1103/PhysRevD.45.1840 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

ID figU003Aexample already defined

[dfm]

@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/s10714-010-0939-y is OK
- 10.1098/rspa.1951.0200 is OK
- 10.1007/BF02734579 is OK
- 10.1093/mnras/stz389 is OK
- 10.1093/mnras/staa2103 is OK
- 10.1093/mnras/stz845 is OK
- 10.1051/0004-6361/202038561 is OK
- 10.1175/MWR-D-16-0228.1 is OK
- 10.48550/arXiv.2203.11952 is OK
- 10.21105/joss.03703 is OK
- 10.1103/PhysRevD.45.1840 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/aass-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#4675, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[dfm]

@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: Kimpson
  given-names: Tom
doi: 10.5281/zenodo.8412240
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Kimpson
    given-names: Tom
  date-published: 2023-10-10
  doi: 10.21105/joss.04992
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4992
  title: "RelativisticDynamics.jl: Relativistic Spin-Orbital Dynamics in
    Julia"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04992"
  volume: 8
title: "RelativisticDynamics.jl: Relativistic Spin-Orbital Dynamics in
  Julia"

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.04992 joss-papers#4677
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04992
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...

[dfm]

@langfzac, @tamasgal — Many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@tomkimpson — Your paper is now accepted and published in JOSS! ⚡🚀💥

Note: The PDF doesn't seem to be rendering properly on the publication page. Don't worry, this happens frequently and it's caused by a caching issue when the DOI link is clicked on too soon. It should be fixed within a few hours, but we can check back later to make sure!

[editorialbot]

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.04992/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.04992

This is how it will look in your documentation:

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[tamasgal]

My sincere congratulations on your paper and Julia package, nice work!

[tomkimpson]

Thanks @dfm @tamasgal @langfzac ! Really appreciate your time and feedback.

[tomkimpson]

@editorialbot generate preprint

[editorialbot]

📄 Preprint file created: Find it here in the Artifacts list 📄