[REVIEW]: starry_process: Interpretable Gaussian processes for stellar light curves

[whedon]

Submitting author: @rodluger (Rodrigo Luger)
Repository: https://github.com/rodluger/starry_process
Version: v0.9.6
Editor: @arfon
Reviewer: @nespinoza, @j-faria
Archive: 10.5281/zenodo.4665400

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/e35db3c9bac38b270a827dce462bd7d2/status.svg)](https://joss.theoj.org/papers/e35db3c9bac38b270a827dce462bd7d2)

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

@nespinoza & @j-faria, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon 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 ✨

Review checklist for @nespinoza

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 repository url?
• 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 (@rodluger) 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

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: Does the paper have a section titled 'Statement of Need' that clearly states 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @j-faria

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 repository url?
• 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 (@rodluger) 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

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: Does the paper have a section titled 'Statement of Need' that clearly states 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @nespinoza, @j-faria it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[arfon]

@nespinoza, @j-faria - One thing I forgot to mention when inviting you both to review is that this JOSS submission/paper is a joint publication with AAS Journals, i.e. this JOSS paper will be published together with another paper in one of the AAS journals. As part of this collaboration, AAS publishing makes a small donation to the running costs of JOSS.

If this is unacceptable to you, please let me know and I can look for alternative reviewers.

Some related links:

• Blog post describing the collaboration: https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing
• Summary of JOSS financial model: https://joss.theoj.org/about#costs

[whedon]

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

OK DOIs

- 10.21105/joss.02103 is OK
- 10.3847/1538-3881/ab4fee is OK
- 10.1109/TPAMI.2015.2448083 is OK
- 10.3847/1538-3881/aa9332 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[arfon]

@nespinoza, @j-faria – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. 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 #3071 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 make a start well 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.

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=5.66 s (280.5 files/s, 56619.8 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C/C++ Header                    532          23772          32795         127515
C++                             733           8403           5536          43116
Fortran 77                       51             17          13727          24137
CMake                            85           1470           1480           6782
Python                           88           1391           1940           6660
C                                21            796           2076           3792
CUDA                             14            681            173           2732
SVG                               1              0              0           2671
Markdown                          4            500              0           1642
Jupyter Notebook                  6              0           2662            623
HTML                              6             45              6            426
Bourne Shell                      9            113             40            380
YAML                              8             49              1            350
PO File                           4            120            154            322
CSS                               5             60             21            217
JavaScript                        3             27             54            210
XML                               1             15             10            210
TeX                               1              8              0            131
JSON                              1              0              0             81
Bourne Again Shell                4             18             21             77
reStructuredText                  4             32             46             44
DTD                               1              1              0             30
make                              3             12             11             23
TOML                              1              1              0             19
Dockerfile                        1              6              0             13
INI                               1              0              0              8
--------------------------------------------------------------------------------
SUM:                           1588          37537          60753         222211
--------------------------------------------------------------------------------


Statistical information for the repository 'b4b80f621b1d1b2e4dfc3c18' was
gathered on 2021/02/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Dan F-M                         10           312            198            0.16
Rodrigo Luger                  332        286182          28294           99.84

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Dan F-M                     293           93.9          0.9                1.71
Rodrigo Luger            257709           90.1          5.8               16.38

[nespinoza]

Hi @arfon, thanks for the breakdown! I'm ready to start marking checkboxes but my invitation link has expired (oops). Can I get a new one :-)? Thanks!

N.

[danielskatz]

@whedon re-invite @nespinoza as reviewer

[whedon]

OK, the reviewer has been re-invited.

@nespinoza please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[j-faria]

Hi @arfon, any problem in cross-referencing the issues as I did above? Please let me know if there's a more standard approach.

[nespinoza]

Hi everyone,

I have reviewed the submitted manuscript and software presented by @rodluger. This is a fantastic piece of software --- thanks for writing this Rodrigo! I checked all the claims and functionalities following the tutorials in the documentation. I found them very helpful and as a developer that will be implementing this in its own library, I found them to be enlightening on how easy the software is to use. Thanks for that!

My suggestions, therefore, are all very minor, but are directly related to the checkmarks we must mark as reviewers for JOSS:

1. I think it would benefit users if you add a section in the README.md file on how to install the package (i.e., the pip install starry-process). This is explained in the documentation, but folks might check the Github before the docs and wonder how to quickly install the package to try it out (this actually happened to me!).

2. While the dependencies are listed in the setup.py file and are even handled automatically, a clear list of dependencies in text form is still missing. I opened an issue in the repo about this: [JOSS review] List dependencies on README.md and/or documentation rodluger/starry_process#22.

3. I'm also missing some Community Guidelines for contribution. Also opened an issue on this: [JOSS review] List Community Guidelines rodluger/starry_process#23

Once again, thanks for this software --- if you have any comments regarding this review, please let me know.

Best,
Néstor

[whedon]

👋 @nespinoza, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @j-faria, please update us on how your review is going (this is an automated reminder).

[j-faria]

I finished reviewing the paper and the software. There were a couple of minor issues with the README (some that @nespinoza also identified) and a plot/animation; they were all fixed.
Everything else looks good so all lights are green from my side to accept this submission.

This is an outstanding piece of work, congratulations to @rodluger and the other contributors.
I'm looking forward to using starry_process myself so I'll be sure to keep in touch to see what your plans are regarding RVs :)

PS: only the app doesn't work for me, but I'll check if it's my problem before opening an issue. Nothing that should delay publication.

[rodluger]

@j-faria Can you tell me more about your issues with the app? Or just raise an issue in the repo when you get a chance. Thanks!

[nespinoza]

Thanks for all the additions @rodluger. On my end, I can call this review complete then --- happy to accept this paper for publication in JOSS on my end. Congrats @rodluger on this awesome piece of software!

[rodluger]

Thanks @nespinoza ! @arfon, anything else you need from me?

[rodluger]

@whedon generate pdf

[whedon]

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

[rodluger]

@arfon

I created a new release and published it to Zenodo: https://zenodo.org/record/4665400

The DOI is https://doi.org/10.5281/zenodo.4665400

Thanks!

[rodluger]

@arfon The two associated AAS papers are still in review (one has just been accepted, the other should be accepted in the next couple days). Is there a way to synchronize the release to get the cross-refs correct?

https://ui.adsabs.harvard.edu/abs/2021arXiv210200007L/abstract
https://ui.adsabs.harvard.edu/abs/2021arXiv210201697L/abstract

[arfon]

@rodluger - yes, the AAS office should be asking me for the DOI of this paper. Do you have the DOIs for the AAS papers yet? We can cite them both in this paper, and link to one of them in the side-bar too using the metadata in the JOSS paper Markdown header (although you will have to pick just one of them for this).

[danielskatz]

👋 @rodluger - just a ping to see if there's any news from AAS at this point...

[rodluger]

@danielskatz No word -- not sure what the hangup is. I just pinged them: will let you know as soon as I hear back.

[arfon]

I just heard from the AAS that their DOI is 10.3847/1538-3881/abfdb9.

@rodluger - could you add the relevant information to your paper.md:

aas-doi: 10.3847/1538-3881/abfdb9 
aas-journal: Astrophysical Journal <- (or whatever AAS journal you submitted to)

[arfon]

@rodluger – friendly bump on this. Could you please add the AAS paper DOI to your JOSS paper?

[rodluger]

@whedon generate pdf

[whedon]

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

[rodluger]

@arfon Done! So sorry for the delay.

[arfon]

@whedon set 10.5281/zenodo.4665400 as archive

[whedon]

OK. 10.5281/zenodo.4665400 is the archive.

[arfon]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.21105/joss.02103 is OK
- 10.3847/1538-3881/ab4fee is OK
- 10.1109/TPAMI.2015.2448083 is OK
- 10.3847/1538-3881/aa9332 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2442

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2442, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03071 joss-papers#2445
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03071
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...

[arfon]

@nespinoza, @j-faria – 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 ✨

@rodluger – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 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.03071/status.svg)](https://doi.org/10.21105/joss.03071)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03071">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03071/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03071/status.svg
   :target: https://doi.org/10.21105/joss.03071

This is how it will look in your documentation:

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