editorialbot commented 11 months ago

Submitting author: !--author-handle-->@prappleizer@eloisabentivegna<!--end-editor-- Reviewers: @AstroBarker, @JBorrow Archive: 10.5281/zenodo.8335352

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4214c6e588774490458e34630e8052c1"><img src="https://joss.theoj.org/papers/4214c6e588774490458e34630e8052c1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4214c6e588774490458e34630e8052c1/status.svg)](https://joss.theoj.org/papers/4214c6e588774490458e34630e8052c1)

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

@AstroBarker & @JBorrow, 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 @eloisabentivegna 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 @AstroBarker

📝 Checklist for @JBorrow

editorialbot commented 11 months 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 11 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (218.7 files/s, 72841.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             26              0            547
Markdown                         1             29              0             64
-------------------------------------------------------------------------------
SUM:                             2             55              0            611
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 11 months ago

Wordcount for paper.md is 1068

editorialbot commented 11 months ago

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

OK DOIs

- 10.48550/arXiv.2012.15797 is OK
- 10.3847/1538-4357/ab290a is OK
- 10.1093/mnras/stu2467 is OK
- 10.3847/1538-4357/ac1f21 is OK
- 10.1088/0004-637X/799/2/226 is OK
- 10.1086/340952 is OK
- 10.1093/mnras/stw3039 is OK
- 10.21105/joss.04475 is OK
- 10.48550/arXiv.2111.08721 is OK
- 10.21105/joss.03283 is OK
- 10.1093/mnras/stz1796 is OK
- 10.3847/1538-3881/ac5908 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.6825092 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.7697295 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00024 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.5281/zenodo.7799772 is OK
- 10.21105/joss.01143 is OK

MISSING DOIs

- 10.1007/978-1-4842-2677-3_5 may be a valid DOI for title: pytest

INVALID DOIs

- None

editorialbot commented 11 months ago

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

eloisabentivegna commented 11 months ago

Dear @AstroBarker and @JBorrow, thanks again for agreeing to review this submission, as well as for making me aware of your different expertise and time constraints. Please reach out to me if you bump into a roadblock -- I'd be happy to help!

AstroBarker commented 11 months ago

Review checklist for @AstroBarker

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/pysersic/pysersic?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@prappleizer) 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?

JBorrow commented 11 months ago

Review checklist for @JBorrow

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/pysersic/pysersic?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@prappleizer) 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?

JBorrow commented 11 months ago

All of my concerns have been addressed. I am happy to accept the paper. Congratulations @prappleizer on this wonderful work, and thank you for sharing it with the community.

prappleizer commented 11 months ago

Thank you for reviewing @JBorrow -- All great suggestions and comments for things the repo needed!

eloisabentivegna commented 11 months ago

Thanks @JBorrow and @AstroBarker for your hard work, and @JBorrow for the recommendation. Your suggestions improve this package even further, and ensure it's community-ready. Much appreciated.

AstroBarker commented 11 months ago

Sorry for the delay here -- all of my suggestions have been addressed and I am happy to accept as well. Great work.

eloisabentivegna commented 10 months ago

Great news! Thanks @AstroBarker.

I will start reviewing the current manuscript now and then move to the pre-publication stage.

eloisabentivegna commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- 10.48550/arXiv.2012.15797 is OK
- 10.3847/1538-4357/ab290a is OK
- 10.1093/mnras/stu2467 is OK
- 10.3847/1538-4357/ac1f21 is OK
- 10.1088/0004-637X/799/2/226 is OK
- 10.1086/340952 is OK
- 10.1093/mnras/stw3039 is OK
- 10.21105/joss.04475 is OK
- 10.48550/arXiv.2111.08721 is OK
- 10.21105/joss.03283 is OK
- 10.1093/mnras/stz1796 is OK
- 10.3847/1538-3881/ac5908 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.6825092 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.7697295 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00024 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.5281/zenodo.7799772 is OK
- 10.21105/joss.01143 is OK

MISSING DOIs

- 10.1007/978-1-4842-2677-3_5 may be a valid DOI for title: pytest

INVALID DOIs

- None

eloisabentivegna commented 10 months ago

@editorialbot generate pdf

eloisabentivegna commented 10 months ago

MISSING DOIs

10.1007/978-1-4842-2677-3_5 may be a valid DOI for title: pytest

@prappleizer, could you take care of the missing DOI above?

editorialbot commented 10 months ago

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

prappleizer commented 10 months ago

@eloisabentivegna DOI has been added!

eloisabentivegna commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- 10.48550/arXiv.2012.15797 is OK
- 10.3847/1538-4357/ab290a is OK
- 10.1093/mnras/stu2467 is OK
- 10.3847/1538-4357/ac1f21 is OK
- 10.1088/0004-637X/799/2/226 is OK
- 10.1086/340952 is OK
- 10.1093/mnras/stw3039 is OK
- 10.21105/joss.04475 is OK
- 10.48550/arXiv.2111.08721 is OK
- 10.21105/joss.03283 is OK
- 10.1093/mnras/stz1796 is OK
- 10.3847/1538-3881/ac5908 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.6825092 is OK
- 10.1007/978-1-4842-2677-3_5 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.7697295 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00024 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.5281/zenodo.7799772 is OK
- 10.21105/joss.01143 is OK

MISSING DOIs

- None

INVALID DOIs

- None

eloisabentivegna commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

eloisabentivegna commented 10 months ago

I've just finished reading the paper (great work!) and suggested a tiny fix. Once that has been taken care of, we can start preparing the repo for publication, following the checklist below.

eloisabentivegna commented 10 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

eloisabentivegna commented 10 months ago

@prappleizer, if you can take care of the first five tasks, I will complete the post-review phase and recommend acceptance.

prappleizer commented 10 months ago

Thanks! I'll try to get to these this evening.

prappleizer commented 10 months ago

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper. [version 0.1.3]
[x] Archive the release on Zenodo/figshare/etc and post the DOI here. [https://doi.org/10.5281/zenodo.8335352]
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

eloisabentivegna commented 10 months ago

Hi @prappleizer, the title I see on Zenodo is "pysersic v0.1.3". It should be identical to the one for this submission.

prappleizer commented 10 months ago

Done, thanks for the clarification.

eloisabentivegna commented 10 months ago

@editorialbot set 10.5281/zenodo.8335352 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.8335352

eloisabentivegna commented 10 months ago

@editorialbot set version 0.1.3 as version

editorialbot commented 10 months ago

Done! version is now version 0.1.3

eloisabentivegna commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

eloisabentivegna commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- 10.48550/arXiv.2012.15797 is OK
- 10.3847/1538-4357/ab290a is OK
- 10.1093/mnras/stu2467 is OK
- 10.3847/1538-4357/ac1f21 is OK
- 10.1088/0004-637X/799/2/226 is OK
- 10.1086/340952 is OK
- 10.1093/mnras/stw3039 is OK
- 10.21105/joss.04475 is OK
- 10.48550/arXiv.2111.08721 is OK
- 10.21105/joss.03283 is OK
- 10.1093/mnras/stz1796 is OK
- 10.3847/1538-3881/ac5908 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.6825092 is OK
- 10.1007/978-1-4842-2677-3_5 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.7697295 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00024 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.5281/zenodo.7799772 is OK
- 10.21105/joss.01143 is OK

MISSING DOIs

- None

INVALID DOIs

- None

eloisabentivegna commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 10 months ago

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

OK DOIs

- 10.48550/arXiv.2012.15797 is OK
- 10.3847/1538-4357/ab290a is OK
- 10.1093/mnras/stu2467 is OK
- 10.3847/1538-4357/ac1f21 is OK
- 10.1088/0004-637X/799/2/226 is OK
- 10.1086/340952 is OK
- 10.1093/mnras/stw3039 is OK
- 10.21105/joss.04475 is OK
- 10.48550/arXiv.2111.08721 is OK
- 10.21105/joss.03283 is OK
- 10.1093/mnras/stz1796 is OK
- 10.3847/1538-3881/ac5908 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.6825092 is OK
- 10.1007/978-1-4842-2677-3_5 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.7697295 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.21105/joss.00024 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.5281/zenodo.7799772 is OK
- 10.21105/joss.01143 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 10 months ago

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.


              ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

F_{\rm total}
       ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

editorialbot commented 10 months ago

:wave: @openjournals/aass-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4573, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 10 months ago

I'm sorry @prappleizer, I'm afraid I can't do that. That's something only eics are allowed to do.

eloisabentivegna commented 10 months ago

I am observing the pdf compilation error above, but the pdf in https://github.com/openjournals/joss-papers/pull/4573 seems fine.

Is this a problem, @openjournals/aass-eics?

dfm commented 10 months ago

Thanks all! I've opened a PR with some small typographical edits which should also fix the metadata issue above. Once merged, I'll proceed with acceptance.

prappleizer commented 10 months ago

PR has been accepted!

eloisabentivegna commented 10 months ago

Thanks, @dfm. Also a big thanks to @AstroBarker and @JBorrow for sharing their comments on the submission. Your help is very appreciated!

Congratulations, @prappleizer!

dfm commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

openjournals / joss-reviews

[REVIEW]: Pysersic: A Python package for determining galaxy structural properties via Bayesian inference, accelerated with jax #5703

Status

Reviewer instructions & questions

Checklists

Review checklist for @AstroBarker

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @JBorrow

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance