[REVIEW]: NEoST: A Python package for nested sampling of the neutron star equation of state

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@drannawatts@adonath<!--end-editor-- Reviewers: @chaitanyaafle, @adonath Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c6d09ac472ec540a2d1f6507c5c277e0"><img src="https://joss.theoj.org/papers/c6d09ac472ec540a2d1f6507c5c277e0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c6d09ac472ec540a2d1f6507c5c277e0/status.svg)](https://joss.theoj.org/papers/c6d09ac472ec540a2d1f6507c5c277e0)

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

@ziatdinovmax & @chaitanyaafle, 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 @adonath 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 @chaitanyaafle

📝 Checklist for @adonath

editorialbot commented 1 year ago

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 commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (894.1 files/s, 130426.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          24            587            421           1755
Cython                           3            487             63            815
TeX                              1             46              0            498
Jupyter Notebook                 6              0           1994            357
reStructuredText                16            299            237            353
YAML                             4             11              7            135
Markdown                         1             18              0             65
make                             1              4              7             10
-------------------------------------------------------------------------------
SUM:                            56           1452           2729           3988
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 891

editorialbot commented 1 year ago

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
- 10.21105/joss.04977 is OK
- 10.3847/2041-8213/ab451a is OK
- 10.3847/2041-8213/ab822f is OK
- 10.3847/2041-8213/ac089a is OK
- 10.1103/PhysRevD.107.103051 is OK
- 10.1093/mnras/stz654 is OK
- 10.3847/2041-8213/ac03b8 is OK
- 10.3847/2041-8213/ac089b is OK
- 10.1103/PhysRevX.9.011001 is OK
- 10.1016/j.physrep.2015.12.005 is OK
- 10.1146/annurev-nucl-102313-025446 is OK
- 10.1016/j.ppnp.2020.103770 is OK
- 10.1103/PhysRev.55.364 is OK
- 10.1103/PhysRev.55.374 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
- 10.21105/joss.03021 is OK
- 10.21105/joss.00024 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

adonath commented 1 year ago

@drannawatts @ziatdinovmax @chaitanyaafl this is the review thread for the paper. All of our communications will happen here from now on. Thanks again for the submission and for agreeing to review!

The instructions for the review are given at the beginning of the page. I would like to emphasize again that reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER 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 any 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 (@adonath) if you have any questions/concerns.

chaitanyaafle commented 8 months ago

Review checklist for @chaitanyaafle

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/xpsi-group/neost?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

adonath commented 8 months ago

@editorialbot remove @ziatdinovmax from reviewers

editorialbot commented 8 months ago

@ziatdinovmax removed from the reviewers list!

drannawatts commented 8 months ago

Just checking in on this (since we're about to submit a new NICER results EoS paper using NEoST). If there's anything you need from us please let us know!

adonath commented 8 months ago

Thanks @drannawatts for checking in. I'm currently looking for a second reviewer to replace @ziatdinovmax. Meanwhile @chaitanyaafle please proceed with your review and aim to finish within the next ~2 weeks.

adonath commented 7 months ago

@editorialbot add @tddesjardins as reviewer

editorialbot commented 7 months ago

@tddesjardins added to the reviewers list!

adonath commented 7 months ago

@tddesjardins You can find some more instructions for the review process here: https://github.com/openjournals/joss-reviews/issues/6003#issuecomment-1790661927 and here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

adonath commented 5 months ago

@tddesjardins please start the review

adonath commented 3 months ago

@editorialbot remove @tddesjardins from reviewers

editorialbot commented 3 months ago

@tddesjardins removed from the reviewers list!

drannawatts commented 3 months ago

A couple of updates from our side! We had been planning to hold off on v1.0 release until the JOSS review was complete but since this seems to be taking a bit longer we will likely go ahead and do this since we've made quite a few updates associated with a new NICER EoS publication so it's a good moment to do this.

With that in mind, @adonath, would there be any objection to adding a couple of additional authors to the JOSS paper submission? We have some folks from TU Darmstadt who have contributed a lot of the code in the most recent updates and it would be nice to acknowledge that if we still have the chance. We can also update to include a reference to the new NICER EoS paper.

@chaitanyaafle I see that you have one box still unchecked in your review checklist - have you run into issues with the software there that we need to address? If so let us know and we'll try to fix them ASAP!

adonath commented 3 months ago

Thanks @drannawatts for the update! There is no objection to add more authors, as long as they made a substantial contribution to the package.

We had a bit of bad luck with the second reviewers, I'm in the process of finding one, once again. If the search is not successful within a reasonable timeline of ~4 weeks I will assign myself.

drannawatts commented 3 months ago

Thanks @adonath - we'll update the JOSS manuscript within the next few days once we have the final publication details for the new papers. And no worries on the timeline, as an Editor for MNRAS I know how tricky finding referees can be, and JOSS is asking for a lot more work than a standard paper review!!

nr1118 commented 2 months ago

Hi @adonath, we have updated the NEoST JOSS manuscript and tagged v1.0 as mentioned by @drannawatts. I am also going to run the editorialbot below to generate the new pdf for convenience. Please let us know if you have any questions :)

nr1118 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

nr1118 commented 2 months ago

I apologize for any confusion this may cause (found a few typos in the manuscript), but please use the generated pdf of the JOSS manuscript below this message.

nr1118 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

adonath commented 2 months ago

Thanks @nr1118 for the update!

adonath commented 2 months ago

@editorialbot assign @adonath as reviewer

editorialbot commented 2 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

adonath commented 2 months ago

@editorialbot add @adonath as reviewer

editorialbot commented 2 months ago

@adonath added to the reviewers list!

chaitanyaafle commented 1 month ago

@adonath I have completed all the checkpoints for the review. Had to redo certain things after the update last month, but the update actually addressed some of the concerns I had prior to it, mostly pertaining to installation and example usage. These seem to be fixed now.

What are the next steps?

adonath commented 1 month ago

Thanks @chaitanyaafle for the summary of the status and review! At this point there is nothing to do anymore for you. I will do the second review myself now, as I did not have any luck finding a 2nd reviewer.

@drannawatts I will finish the review by the end of the week.

adonath commented 1 month ago

Review checklist for @adonath

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/xpsi-group/neost?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

drannawatts commented 1 month ago

We have a fairly major update to NEoST (v2.0) coming that will add dark matter inference functionality, associated with this recent paper by @nr1118 (https://arxiv.org/abs/2410.00140). Does it completely mess up your review process for v1.0 @adonath if we roll this out? We don't want to make things unnecessarily difficult for you, but we're also keen to get it out there if we can.

adonath commented 3 weeks ago

@drannawatts I think can live with the fact that part of the review was done on an older version of the package. However it is up to you which version you would like to describe in the paper and which development model you have. We should probably aim for concistency. From the JOSS perspective I think we can handle both. There is no requirement that the version must be the most recent one. So the options are:

Keep the paper mostly as is and describe v1.0. I will finish the review and comments must be back ported to the v1.0 branch. This would also require versioned docs, such that I can take a look at the respective documentation. Once the review is done you release v1.1 or v1.0.1
Update the paper and describe v2.0. I would finish the review on the basis of the latest changes than. And ask @chaitanyaafle for any objections.

It seems to me option 2 is simpler.

drannawatts commented 3 weeks ago

Agreed, Option 2 seems simpler! We'll update the paper, we only need to modify a couple of lines.

editorialbot commented 2 weeks ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

drannawatts commented 2 weeks ago

@editorialbot generate pdf

editorialbot commented 2 weeks ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

adonath commented 1 day ago

I have finished my review. From the JOSS perspective I think it would be good to improve the following two points:

Verify the performance claim / improvement of Cython: https://github.com/xpsi-group/neost/issues/63
Either improve the M1 installation or clarify that Python it is not supported https://github.com/xpsi-group/neost/issues/48. The documentation mentions some hints: https://xpsi-group.github.io/neost/install.html#installing-on-mac-m-series-chips-arm-64, however even with those the it cannot succeed. See https://github.com/xpsi-group/neost/pull/64 for some details.

openjournals / joss-reviews