[REVIEW]: ronswanson: Building Table Models for 3ML

[editorialbot]

Submitting author: @grburgess (J. Michael Burgess)
Repository: https://github.com/grburgess/ronswanson
Branch with paper.md (empty if default branch):
Version: v0.2.10
Editor: @dfm
Reviewers: @cosimoNigro, @volodymyrss
Archive: 10.5281/zenodo.7778865

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b9ab6f687a9f3018b6b08c6575cfc6ee"><img src="https://joss.theoj.org/papers/b9ab6f687a9f3018b6b08c6575cfc6ee/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b9ab6f687a9f3018b6b08c6575cfc6ee/status.svg)](https://joss.theoj.org/papers/b9ab6f687a9f3018b6b08c6575cfc6ee)

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

@cosimoNigro & @volodymyrss, 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 @volodymyrss

📝 Checklist for @cosimoNigro

[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:

@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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (485.2 files/s, 70510.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1646           1301           3214
Markdown                         4            161              0            405
YAML                             9             82             19            282
TeX                              1              6              0             44
JSON                             1              8              0             33
INI                              1              4              0             20
reStructuredText                 3             10              9             11
TOML                             1              1              0             10
-------------------------------------------------------------------------------
SUM:                            50           1918           1329           4019
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 833

[dfm]

@cosimoNigro, @volodymyrss — This is the review thread for the paper. All of our communications 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#4969 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.

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.5646925 is OK

MISSING DOIs

- 10.1007/10968987_3 may be a valid DOI for title: SLURM: Simple Linux Utility for Resource Management
- 10.22323/1.312.0130 may be a valid DOI for title: The Multi-Mission Maximum Likelihood framework (3ML)

INVALID DOIs

- None

[editorialbot]

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

[volodymyrss]

Review checklist for @volodymyrss

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/grburgess/ronswanson?
• 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 (@grburgess) 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• 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?
• 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?

[volodymyrss]

@editorialbot commands

[editorialbot]

Hello @volodymyrss, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[cosimoNigro]

Review checklist for @cosimoNigro

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/grburgess/ronswanson?
• 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 (@grburgess) 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]

@cosimoNigro, @volodymyrss, @grburgess — 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!

[volodymyrss]

@cosimoNigro, @volodymyrss, @grburgess — 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!

Sorry, when I was going through check boxes I realized I want to request a change but it was not totally clear how. Just writing it here?..

[dfm]

@volodymyrss — Great question! As I mentioned briefly above, the usual workflow is to open issues on the project repo (it is useful to include a link back to this thread) with any suggested changes. You're also welcome to list smaller things directly here in this thread, but that can get things a little cluttered. Let me know if you have further questions!

[volodymyrss]

@editorialbot generate pdf

[editorialbot]

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

[grburgess]

@editorialbot generate pdf

[editorialbot]

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

[volodymyrss]

@editorialbot recommend-accept

for the version at this time

[editorialbot]

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

[volodymyrss]

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

hm, I just extrapolated ordinary review and did not read the guide again. Anyway, I checked all.

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.5646925 is OK
- 10.5281/zenodo.7734804 is OK

MISSING DOIs

- 10.1007/10968987_3 may be a valid DOI for title: SLURM: Simple Linux Utility for Resource Management
- 10.22323/1.312.0130 may be a valid DOI for title: The Multi-Mission Maximum Likelihood framework (3ML)
- 10.22323/1.301.0766 may be a valid DOI for title: Gammapy - A prototype for the CTA science tools

INVALID DOIs

- None

[dfm]

@editorialbot set 10.5281/zenodo.7778865 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7778865

[dfm]

@editorialbot set v0.2.10 as version

[editorialbot]

Done! version is now v0.2.10

[dfm]

@grburgess — Thanks! Can you check the DOIs listed above and add them to the bibliography if they are correct?

[grburgess]

@dfm done!

[dfm]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/10968987_3 is OK
- 10.5281/zenodo.5646925 is OK
- 10.22323/1.312.0130 is OK
- 10.22323/1.301.0766 is OK
- 10.5281/zenodo.7734804 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[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

- 10.1007/10968987_3 is OK
- 10.5281/zenodo.5646925 is OK
- 10.22323/1.312.0130 is OK
- 10.22323/1.301.0766 is OK
- 10.5281/zenodo.7734804 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#4084, 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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.04969 joss-papers#4085
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04969
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...

[grburgess]

Thanks @volodymyrss and @cosimoNigro for a useful and thoughtful review. Thanks for the edits @dfm.

[dfm]

@cosimoNigro, @volodymyrss — 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!!

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

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04969/status.svg)](https://doi.org/10.21105/joss.04969)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04969">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04969/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04969/status.svg
   :target: https://doi.org/10.21105/joss.04969

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[grburgess]

@editorialbot generate preprint

[editorialbot]

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

[grburgess]

@dfm does the preprint function still work?

[grburgess]

oops