[REVIEW]: bayes_spec: A Bayesian Spectral Line Modeling Framework for Astrophysics

[editorialbot]

Submitting author: @tvwenger (Trey Wenger)
Repository: https://github.com/tvwenger/bayes_spec
Branch with paper.md (empty if default branch):
Version: 1.7.2
Editor: @ivastar
Reviewers: @ConorMacBride, @kbwestfall, @larryshamalama
Archive: 10.5281/zenodo.13947167

Status

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Reviewers and authors:

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Reviewer instructions & questions

@ConorMacBride & @kbwestfall & @larryshamalama, 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 @ivastar 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 @kbwestfall

📝 Checklist for @larryshamalama

📝 Checklist for @ConorMacBride

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.3847/1538-4357/ac2f42 is OK
- 10.7717/peerj-cs.1516 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (664.7 files/s, 249416.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21            839           1999           2462
Jupyter Notebook                 4              0           9435            613
Markdown                         2             73              0            151
YAML                             6             11             21            147
reStructuredText                 5             74             82             83
TOML                             1              5              0             32
TeX                              1              1              0             28
DOS Batch                        1              8              1             26
JSON                             1              0              0             23
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            43           1015          11545           3574
-------------------------------------------------------------------------------

Commit count by author:

    25	Trey Wenger

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 291

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[ivastar]

@ConorMacBride, @kbwestfall, @larryshamalama thank you for agreeing to review this submission! Please check out the review instructions above. Each reviewer creates their own checklist and goes through the items. If you have any questions or concerns, please do not hesitate to reach out to me either via this issue or via e-mail. We are looking for the first round of reviews on this submission to be completed by end of September.

[larryshamalama]

Review checklist for @larryshamalama

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/tvwenger/bayes_spec?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tvwenger) 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?

[kbwestfall]

Review checklist for @kbwestfall

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/tvwenger/bayes_spec?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tvwenger) 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?

[ConorMacBride]

Review checklist for @ConorMacBride

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/tvwenger/bayes_spec?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tvwenger) 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?

[ivastar]

@ConorMacBride, @kbwestfall, @larryshamalama thank you all for kicking off the review. Reminder that it would be great to complete the checklists in the next week or so. Let me know if you need more time.

[ivastar]

@ConorMacBride, @kbwestfall, @larryshamalama pinging the thread as a reminder to complete the review at your earliest convenience. Do let me know if you have any questions or problems. Thanks!

[larryshamalama]

Hi @tvwenger, great work! Apologies for the delay, many things going on on my side 😅 I did not have a change to fully look into all the physics details (which seem interesting!), so I looked more at the package overall + Bayesian stats side of things. My comments are below:

Main comments

• Quickstart: Can you include a quickstart tutorial ready to run after installation in both your README and paper? Perhaps something fairly encapsulated that generates data and fits it (via GaussModel?). It seems that you have one ready to go here: https://bayes-spec.readthedocs.io/en/latest/notebooks/basic_tutorial.html . In the paper, it can be after the "Statement of need" section under a "Usage" section or something.
  Since the GaussModel in the basic tutorial is very similar to the one your have in bayes_spec/models/gauss_models.py, why not just use the latter for the intro tutorial? Perhaps you can then add another example with more differences/nuances as a separate page under tutorials.
• What is the main benefit that this package offers to users (primarily astrophysical researchers)? I believe that I understand it from your Statement of need, but I just want to clarify, since my background is in statistics and not astrophysics. Perhaps it can be simply to reduce additional overhead of knowledge in Bayesian statistics + implementation for commonly used models, which is my guess.
• When you say "Bayesian models of spectral line observations are rare in astrophysics", do you mean that the use of Bayesian modelling is rare (A), ready-to-use implemented Bayesian models for spectral line modelling are rare (B) or both (A because of B)?
• Are there other packages that focus on spectral line modelling, Bayesian or not? If so, this can also be added to statement of need. For instance, this paper seems to list some packages, but I don't know how relevant each are.

Minor/nitpicks

• You are the sole author of this paper. Is there a way to remove "These authors contributed equally"? Or maybe this is not so important...
• I will create a PR that solves some minor documentation items

[tvwenger]

Thanks for agreeing to referee this project, @larryshamalama! I really appreciate your insight.

I've addressed all of your concerns, and you will find the answers to your questions in the new paper draft. Please let me know what else I can clear up!

[tvwenger]

@editorialbot generate pdf

[editorialbot]

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

[kbwestfall]

@ConorMacBride, @kbwestfall, @larryshamalama pinging the thread as a reminder to complete the review at your earliest convenience. Do let me know if you have any questions or problems. Thanks!

HI @ivastar , @tvwenger . I'm so sorry for my late review. Things have been extraordinarily busy for me. I'm hoping to provide a review this weekend or early next week.

[ConorMacBride]

Hi @tvwenger, this is a great package, very well done! I hadn't fitted spectra with techniques like MCMC before (only least squares) so this was really interesting!

I think the paper provides a very nice overview of the value bayes_spec provides to astrophysics and also how it compares to alternative tools. I like the inclusion of the Usage section in the paper as it lets us see how easy it is to use and what needs to be provided. The paper shouldn’t include software documentation, however this section feels more illustrative than documentary to me, so I think it should be fine (and I see other JOSS papers include a section like this).

The example notebooks are very useful and easy to follow; I was able to modify the notebooks and the GaussModel to fit a multi-component spectrum with an absorption and an emission component typical of the Sun’s atmosphere. I was also able to redefine the parameters of GaussModel, changing velocity & line area to wavelength & amplitude. This was really straightforward and the rest of the example notebook was able to sample and plot the modified model without any hassle. Just one suggestion:

• [JOSS Review] Add type checking to add_priors methods tvwenger/bayes_spec#43

I also tried to replace the gaussian function with the Voigt function, however it looks like PyMC requires it to be compatible with PyTensor so I would need to implement a gradient method. Some documentation updates would be nice:

• [JOSS Review] Documentation on creating user-defined models tvwenger/bayes_spec#42

Some other items:

• [JOSS Review] Does jax and jaxlib need to be pinned? tvwenger/bayes_spec#41
• [JOSS Review] Set docs website default version to stable tvwenger/bayes_spec#44

I’m not totally sure but I think GPL-3.0 requires downstream dependencies to also use this licence, so anyone who includes bayes_spec as a dependency in their package may need to adopt GPL-3.0. If you think that would be an issue for you, it might be worth researching further and considering a different license, for example, PyMC uses Apache. (Minor suggestion: maybe consider removing the licence text from the API documentation as it’s repeated many times.) GPL-3.0 is OSI approved so all good review-wise!

[tvwenger]

Thanks for the helpful feedback @ConorMacBride @kbwestfall @larryshamalama ! I have addressed all of your feedback thus far.

Pinging the editor @ivastar regarding some outstanding questions:

1. In [JOSS Review] Dependencies tvwenger/bayes_spec#40 @kbwestfall requests clarification regarding the checkbox: "Is there a clearly-stated list of dependencies?" Does the inclusion of a requirements.txt and environment.yml file satisfy this requirement?
2. @kbwestfall and @larryshamalama disagree on whether or not a "Usage" section is appropriate in the paper. @larryshamalama recommends it, @kbwestfall does not. What is your preference as the editor?
3. @kbwestfall made the following comment:

The review criteria say the paper should include: "A description of how this software compares to other commonly-used packages in this research area." This feels slightly different than the "list of key references" listed for authors under "What should my paper contain?", so it would be useful to get some editor input on the following: It would be interesting to provide more detail on the comparison of bayes_spec and McFine, while still keeping the comparison brief. Am I right that the last sentence of this paragraph implies that McFine is only for hyperfine spectroscopy?

To which I replied:

I will defer to the editor about this. McFine was published while bayes_spec was under review, so I have not yet had a chance to dive in and compare McFine to bayes_spec. You are correct that McFine is for hyperfine spectroscopy only.

It is my opinion that a thorough comparison of bayes_spec and McFine is warranted but beyond the scope of this "paper".

I am looking forward to finalizing this review. Thanks again for your help!

[tvwenger]

@editorialbot generate pdf

[warrickball]

Sorry, one last typo in this PR!

[tvwenger]

Merged!

[warrickball]

@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

- 10.1088/0004-6256/149/4/138 is OK
- 10.1051/0004-6361/201935335 is OK
- 10.3847/1538-4357/ac2f42 is OK
- 10.3847/1538-3881/ac695a is OK
- 10.7717/peerj-cs.1516 is OK
- 10.1093/mnras/stae030 is OK
- 10.1093/mnras/stae2130 is OK

🟡 SKIP DOIs

- None

❌ 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#6085, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[warrickball]

@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: Wenger
  given-names: Trey V.
  orcid: "https://orcid.org/0000-0003-0640-7787"
doi: 10.5281/zenodo.13947167
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Wenger
    given-names: Trey V.
    orcid: "https://orcid.org/0000-0003-0640-7787"
  date-published: 2024-11-01
  doi: 10.21105/joss.07201
  issn: 2475-9066
  issue: 103
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7201
  title: "bayes_spec: A Bayesian Spectral Line Modeling Framework for
    Astrophysics"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07201"
  volume: 9
title: "bayes_spec: A Bayesian Spectral Line Modeling Framework for
  Astrophysics"

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]

🦋🦋🦋 👉 Bluesky post 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.07201 joss-papers#6086
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07201
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...

[warrickball]

@openjournals/dev — The DOI still isn't resolving after ~40 hours. Is the Crossref queue just backed up? I noticed the Crossref status page reports various recent issues but none are obviously related (at least, not to someone who's never looked at the Crossref status before).

The deposit itself looked okay to me.

[tvwenger]

Could it be the ampersand in my affiliation? A la pkp/pkp-lib#9959

[warrickball]

Nice find, and probably! I think the dev teams are going to have a go a fixing the JOSS pipeline to catch this and correctly generate the XML for the Crossref deposit. Hopefully we'll sort this out in a few days but if not we can work around it if you're in a hurry. The paper does appear on the JOSS website; this is about getting the automatic DOI resolution fixed (which I acknowledge does have knock on effects).

[warrickball]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#6095

[warrickball]

@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

- 10.1088/0004-6256/149/4/138 is OK
- 10.1051/0004-6361/201935335 is OK
- 10.3847/1538-4357/ac2f42 is OK
- 10.3847/1538-3881/ac695a is OK
- 10.7717/peerj-cs.1516 is OK
- 10.1093/mnras/stae030 is OK
- 10.1093/mnras/stae2130 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance.

[warrickball]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#6098

[warrickball]

Thanks once again to @ConorMacBride, @kbwestfall & @larryshamalama for reviewing and @ivastar for editing this submission! JOSS simply wouldn't be possible without its community of volunteers.

Congratulations @tvwenger, your paper has been published in JOSS (and the DOI now resolves too)!

Huge thanks also to @tarleb for quickly fixing the Crossref pipeline.

[editorialbot]

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

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

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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07201/status.svg
   :target: https://doi.org/10.21105/joss.07201

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