[REVIEW]: X-PSI: A Python package for neutron star X-ray Pulse Simulation and Inference #4977

editorialbot · 2022-11-28T13:27:17Z

Submitting author: @drannawatts (Anna Watts)
Repository: https://github.com/xpsi-group/xpsi
Branch with paper.md (empty if default branch):
Version: v1.2.2
Editor: @adonath
Reviewers: @JohannesBuchner, @matteobachetti
Archive: 10.5281/zenodo.7632629

Status

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Markdown: [![status](https://joss.theoj.org/papers/273bb2617b21963c43bd58b279760721/status.svg)](https://joss.theoj.org/papers/273bb2617b21963c43bd58b279760721)

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Checklists

📝 Checklist for @matteobachetti

📝 Checklist for @JohannesBuchner

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-11-28T13:27:18Z

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editorialbot · 2022-11-28T13:27:32Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.94 s (189.5 files/s, 66540.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          54           3942           5541          11524
Cython                          58           2414           1606           7986
Jupyter Notebook                12              0          17877           5569
reStructuredText                41           1334           1612           2089
TeX                              1             35              0            456
YAML                             5             10             12            304
Markdown                         2             22              0            139
make                             1              4              6             10
C                                2              0              0              2
C/C++ Header                     2              0              0              2
-------------------------------------------------------------------------------
SUM:                           178           7761          26654          28081
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-11-28T13:27:34Z

Wordcount for paper.md is 925

editorialbot · 2022-11-28T13:28:30Z

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

OK DOIs

- 10.3847/2041-8213/ac0a81 is OK
- 10.3847/2041-8213/ab481c is OK
- 10.5281/zenodo.4697625 is OK
- 10.5281/zenodo.3386449 is OK
- 10.3847/2041-8213/ab451a is OK
- 10.3847/2041-8213/ab53e7 is OK
- 10.1063/1.5117798 is OK
- 10.1051/0004-6361/201630261 is OK
- 10.3847/1538-4357/aacea0 is OK
- 10.21105/joss.00849 is OK
- 10.1093/mnras/sty3090 is OK
- 10.1214/17-BA1075 is OK
- 10.21105/joss.00916 is OK
- 10.1051/0004-6361/201322971 is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1109/MCSE.2007.53 is OK
- 10.5281/zenodo.1202077 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.jpdc.2007.09.005 is OK
- 10.1109/MCSE.2010.118 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/MCSE.2007.58 is OK
- 10.1117/12.2231304 is OK
- 10.1086/670067 is OK

MISSING DOIs

- 10.1109/99.660313 may be a valid DOI for title: OpenMP: an industry standard API for shared-memory programming

INVALID DOIs

- None

editorialbot · 2022-11-28T13:28:44Z

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

JohannesBuchner · 2022-11-28T13:40:52Z

Besides the linked "LICENSE.rst" license file link being broken in https://github.com/xpsi-group/xpsi#copyright-and-licensing , I want to point out that it's not really possible to release a project under MIT license if it depends on GPL libraries. One of your named dependencies is GSL. see https://www.gnu.org/software/gsl/#licensing

Also MultiNest is not open source, so if the project depends on it, you need to add a GPL with exception to allow redistributing as a package. That is what PyMultiNest does as well, so you could adopt the licence from there. You can circumvent this requirement if your project has an interface which allows multiple inference engines (e.g., allow the user to switch in UltraNest instead of MultiNest), and thus is not reliant on running/building with MultiNest.

adonath · 2022-11-28T14:55:43Z

Thanks a lot @JohannesBuchner, for pointing out the issue with the license!

@drannawatts I'd propose to resolve this first, before we proceed with a more detailed review. Do you see any issue in re-licensing your project to fulfill the compatibility with the GSL dependency?

matteobachetti · 2022-11-28T15:39:00Z

Review checklist for @matteobachetti

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/xpsi-group/xpsi?
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 (@drannawatts) 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?

JohannesBuchner · 2022-11-28T15:40:32Z

Review checklist for @JohannesBuchner

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/xpsi-group/xpsi?
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 (@drannawatts) 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?

matteobachetti · 2022-11-28T15:43:59Z

Re-licensing under the GPL potentially limits its future usage (as this exchange shows), so I would be wary of going that path.
Not a lawyer, but I seem to understand that people typically use more permissive licenses (MIT, BSD), so that other people can use them freely and decide whether to release their code under the GPL or not.
If I'm not mistaken, the problem here is just that the authors are linking to the GSL in compiled code, right? If it just were an external dependency of a python script, this restriction would not apply?

JohannesBuchner · 2022-11-28T15:55:24Z

see https://softwareengineering.stackexchange.com/questions/87446/using-a-gplv3-python-module-will-my-entire-project-have-to-be-gplv3-licensed

In any case, cython is compiled here.

An alternative is to rewrite the package without GPL dependencies.

adonath · 2022-11-28T17:30:42Z

Thanks @matteobachetti for joining so quickly!

If I'm not mistaken, the problem here is just that the authors are linking to the GSL in compiled code, right? If it just were an external dependency of a python script, this restriction would not apply?

This is my understanding too.

An alternative is to rewrite the package without GPL dependencies.

From what I can tell, this seems not a real option now. The GSL routines are used in many, many places for integration and interpolation. This seems like a major refactoring for the project which recently tagged v1.0. However I agree that the code readability and accessibility would actually benefit from relying on e.g. Scipy functionality.

To me it seems the short term option is re-licensing and then including larger refactoring in a roadmap for v2.0.

JohannesBuchner · 2022-11-28T19:48:53Z

I agree that re-licensing is the easiest and safest option. Here are the two files you need:

https://github.com/JohannesBuchner/PyMultiNest/blob/master/LICENSE (adjust the first line, and take note of the last paragraph)
and
https://github.com/JohannesBuchner/PyMultiNest/blob/master/COPYING

adonath · 2022-11-28T20:39:49Z

I also asked the JOSS editorial team for advice and there was the proposal to maybe choose a dual license here. Here is the quote:

If they envision possibly replacing GSL, they can say the code is dual licensed (so if you build it with GSL, then you need to comply with GPL, but if you copy out a function that doesn't use GSL, you would only need to comply with a more permissive license).

This would allow complying with GSL, while maximizing the reuse of other parts of the software which might not depend on GSL. The downside is probably just that it's a rare thing to do and might need a more complex license description...

drannawatts · 2022-11-28T23:30:45Z

Thank you for all of your input on this!! I think re-licensing is probably the only way to go for now - I'll discuss properly with the rest of the team tomorrow just in case I've missed anything and then get this fixed ASAP. Will update here once it's done!

drannawatts · 2022-12-05T10:55:40Z

License files and links are now updated, thanks again!

matteobachetti · 2022-12-09T13:15:48Z

@drannawatts (and also @JohannesBuchner ) I tried to install it following the instructions at https://xpsi-group.github.io/xpsi/install.html
When I execute one of the simple example scripts, I get errors like:

ERROR:   Could not load MultiNest library "libmultinest.so"
ERROR:   You have to build it first,
ERROR:   and point the LD_LIBRARY_PATH environment variable to it!
ERROR:   manual: https://johannesbuchner.github.io/PyMultiNest/install.html

It seems that pymultinest does not find the compiled Multinest library. Maybe there needs to be some addition to LD_LIBRARY_PATH?

thjsal · 2022-12-09T14:08:03Z

Hi Matteo. The solution is indeed to export the following path (or something similar depending on where MultiNest was installed):
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/multinest/MultiNest_v3.12_CMake/multinest/lib/
Seems that this instruction is currently only on the HPC installation page, but it sure should be mentioned on the main installation page as well (we can add it there).

matteobachetti · 2022-12-09T14:20:39Z

@thjsal yes, it would be good to add this step to the instructions please

drannawatts · 2022-12-09T14:59:47Z

@matteobachetti @JohannesBuchner we are creating GitHub issues tagged 'jossreview' for all of the things that you raise in review. We'll most likely try to address them all together unless you feel that they are so serious that they are holding you up in which case we'll get them fixed straight away!

adonath · 2023-01-06T21:01:27Z

Happy new year everyone! This is just a quick reminder for @JohannesBuchner and @matteobachetti to continue their review.
Usually JOSS aims for a short review phase between 2-4 weeks, so let's try to aim for concluding the review soon. Please also let me know whether there are any open questions or anything else I can help with. Thanks!

matteobachetti · 2023-01-08T13:51:28Z

Hi @adonath , thanks for the reminder. I got a little lost, I was expecting some updates on if the issues got solved, in particular the ones about installation

drannawatts · 2023-01-08T15:43:13Z

Hi @matteobachetti, what you were still waiting for from us on installation? Did the fix that @thjsal gave you on Dec 9 not solve the problem?

We have a github issue raised to make sure that this step (which currently appears only on the HPC installation page) is also copied to the main install instructions, but as I mentioned in my comment on Dec 9 we were thinking to do this 'en masse' with any other issues raised during the review process. But as I mentioned above we're happy to fix things straight away if they are holding you up!!

editorialbot · 2023-02-13T14:38:55Z

👋 @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#3964, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

drannawatts · 2023-02-13T18:19:46Z

Looks good to us!

dfm · 2023-02-13T19:59:04Z

@drannawatts — I've submitted a PR with some minor edits, but I have one other request before the final processing: Can you update the metadata for the Zenodo archive so that the title and author list exactly match the paper? There should be an "edit" button at the top right of that page.

drannawatts · 2023-02-13T20:23:30Z

Metadata updated (middle initial for my name, and full addresses instead of abbreviated ones), and title. Just checking the PR now!

dfm · 2023-02-14T12:51:47Z

@editorialbot generate pdf

editorialbot · 2023-02-14T12:53:23Z

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

dfm · 2023-02-14T12:56:43Z

@editorialbot recommend-accept

editorialbot · 2023-02-14T12:56:45Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-02-14T12:57:36Z

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

OK DOIs

- 10.3847/2041-8213/ac0a81 is OK
- 10.3847/2041-8213/ab481c is OK
- 10.5281/zenodo.4697625 is OK
- 10.5281/zenodo.3386449 is OK
- 10.3847/2041-8213/ab451a is OK
- 10.3847/2041-8213/ab53e7 is OK
- 10.1007/s11433-017-9188-4 is OK
- 10.48550/arXiv.1903.03035 is OK
- 10.1051/0004-6361/201630261 is OK
- 10.3847/1538-4357/aacea0 is OK
- 10.21105/joss.00849 is OK
- 10.1093/mnras/sty3090 is OK
- 10.1214/17-BA1075 is OK
- 10.21105/joss.00916 is OK
- 10.1051/0004-6361/201322971 is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1109/MCSE.2007.53 is OK
- 10.5281/zenodo.1202077 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.jpdc.2007.09.005 is OK
- 10.1109/99.660313 is OK
- 10.1109/MCSE.2010.118 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1109/MCSE.2007.58 is OK
- 10.1117/12.2231304 is OK
- 10.1086/670067 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-02-14T12:58:43Z

👋 @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#3966, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm · 2023-02-14T13:04:23Z

@editorialbot accept

editorialbot · 2023-02-14T13:04:25Z

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

editorialbot · 2023-02-14T13:07:17Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-02-14T13:07:18Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-02-14T13:07:20Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04977 joss-papers#3967
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04977
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

dfm · 2023-02-14T13:12:48Z

Many thanks to @JohannesBuchner and @matteobachetti for reviewing and to @adonath for editing! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@drannawatts et al. — Your paper is now accepted and published in JOSS! ⚡🚀💥

editorialbot · 2023-02-14T13:12:55Z

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

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adonath · 2023-02-14T13:30:46Z

Congratulations @drannawatts and co-authors! Thanks @dfm for chief editing!

drannawatts · 2023-02-14T14:56:17Z

Thank you to all of you @adonath @dfm @JohannesBuchner @matteobachetti , this has been a really great experience and both code and paper are much improved as a result of your efforts!

editorialbot added Cython Python review TeX Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences labels Nov 28, 2022

editorialbot assigned adonath Nov 28, 2022

editorialbot mentioned this issue Nov 28, 2022

[PRE REVIEW]: X-PSI: A Python package for neutron star X-ray Pulse Simulation and Inference #4803

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Feb 13, 2023

dfm mentioned this issue Feb 13, 2023

Small edits for JOSS submission xpsi-group/xpsi#284

Merged

editorialbot added accepted published Papers published in JOSS labels Feb 14, 2023

dfm closed this as completed Feb 14, 2023

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[PRE REVIEW]: CompactObject: An open-source Python package for full-scope neutron star equation of state inference #7487

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[REVIEW]: X-PSI: A Python package for neutron star X-ray Pulse Simulation and Inference #4977

[REVIEW]: X-PSI: A Python package for neutron star X-ray Pulse Simulation and Inference #4977

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Review checklist for @matteobachetti

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General checks

Functionality

Documentation

Software paper

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General checks

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Documentation

Software paper

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thjsal commented Dec 9, 2022 •

edited

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drannawatts commented Feb 13, 2023 •

edited

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