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[REVIEW]: ExoTiC-LD: thirty seconds to stellar limb-darkening coefficients #6816

Closed editorialbot closed 1 month ago

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@DavoGrant<!--end-author-handle-- (David Grant) Repository: https://github.com/Exo-TiC/ExoTiC-LD Branch with paper.md (empty if default branch): Version: v3.2.1 Editor: !--editor-->@warrickball<!--end-editor-- Reviewers: @nenasedk, @LorenzoMugnai Archive: 10.5281/zenodo.13224465

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status

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Markdown: [![status](https://joss.theoj.org/papers/6b6b5840e6d23b5d8d50a82f2d3171c3/status.svg)](https://joss.theoj.org/papers/6b6b5840e6d23b5d8d50a82f2d3171c3)

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

@nenasedk & @LorenzoMugnai, 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 @warrickball 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 @LorenzoMugnai

📝 Checklist for @nenasedk

editorialbot commented 3 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:

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

@editorialbot generate pdf
editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1374.2 files/s, 140131.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            365            614           1487
TeX                              1             19              0            288
reStructuredText                11            121            139            178
Jupyter Notebook                 5              0            620            144
Markdown                         3             33              0            140
YAML                             3             15              4             61
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            42            565           1385           2333
-------------------------------------------------------------------------------

Commit count by author:

    86  David Grant
    30  Hannah Wakeford
    17  hrwakeford
editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 540

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 3 months ago

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

LorenzoMugnai commented 3 months ago

Review checklist for @LorenzoMugnai

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

editorialbot commented 3 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1051/0004-6361/200913675 is OK
- 10.1093/mnras/stw224 is OK
- 10.1093/mnras/stt1435 is OK
- 10.1038/s41586-022-05591-3 is OK
- 10.3847/2041-8213/acfc3b is OK
- 10.3847/2041-8213/acebf0 is OK
- 10.3847/2041-8213/ad20e4 is OK
- 10.3847/2041-8213/accb9c is OK
- 10.3847/1538-3881/ad19df is OK
- 10.21105/joss.04503 is OK
- 10.1093/mnras/stv1857 is OK
- 10.5281/zenodo.4556063 is OK

MISSING DOIs

- No DOI given, and none found for title: A new non-linear limb-darkening law for LTE stella...
- 10.1051/0004-6361/201219058 may be a valid DOI for title: A new extensive library of PHOENIX stellar atmosph...
- No DOI given, and none found for title: ATLAS9 Stellar Atmosphere Programs and 2km/s grid
- No DOI given, and none found for title: The Stagger-grid: A grid of 3D stellar atmosphere ...
- 10.3847/2515-5172/acc180 may be a valid DOI for title: MPS-ATLAS library of stellar model atmospheres and...
- No DOI given, and none found for title: Stellar limb darkening. A new MPS-ATLAS library fo...
- No DOI given, and none found for title: JKTLD: Limb darkening coefficients
- 10.21105/joss.01834 may be a valid DOI for title: ExoTETHyS: tools for exoplanetary transits around ...

INVALID DOIs

- None
warrickball commented 3 months ago

Hi @nenasedk & @LorenzoMugnai, and thanks again for agreeing to review (and so quickly!). This is the review thread for the paper. All of our correspondence will now happen here.

Please read the "Reviewer instructions & questions" in the first comment above. @nenasdk, you can generate your checklist by commenting @editorialbot generate my checklist on this issue. (I usually advise both reviewers but @LorenzoMugnai has already created his!) 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. We aim to work with the authors to help them meet our criteria instead of merely passing judgement on the submission. We also encourage reviewers to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6816 so that the issue/PR is linked to this thread. Please also feel free to comment and ask questions on this thread. JOSS editors have found it 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 start whenever you can. JOSS reviews are iterative and the authors can start responding while you continue to review other parts of the submission.

Finally, don't hesitate to ask many any questions you might have about the process.

LorenzoMugnai commented 3 months ago

Hello @DavoGrant,

First of all, congratulations on your work. The package is very well put together, and I see it is already widely used by the community.

I was reviewing your documentation and have a few comments and suggestions for improvements, in line with the JOSS guidelines:

Thank you for considering these suggestions, and great work once again!

DavoGrant commented 3 months ago

Hi @LorenzoMugnai -- thanks for taking the time to review our repository. We really appreciate the work that goes into reviewing.

We have addressed each of your initial comments, and I think the documentation is looking much improved thanks to your suggestions. Here is what we have done:

nenasedk commented 3 months ago

@DavoGrant

I just wanted to give you a heads up that I'm on vacation this week without my laptop. This review is my first priority for next week, so I'll get back to you then!

LorenzoMugnai commented 3 months ago

Hi @LorenzoMugnai -- thanks for taking the time to review our repository. We really appreciate the work that goes into reviewing.

We have addressed each of your initial comments, and I think the documentation is looking much improved thanks to your suggestions. Here is what we have done:

  • Community guidelines: We have added a “contributing” page to the documentation and signposted to this from the homepage. We have also updated the contributing.md file in the package root.
  • Functionality documentation: We have added all the class methods and submodule functions to the API index page. In this page we have added text to help orientate the user. Additionally, we have improved the docstrings for the limb-darkening laws, now showing the latex-typed functional forms in the docs.
  • Installation instructions: We have added a subsection on installing from source to the installation page in the documentation.

Hi @DavoGrant I just saw your updated documentation: it looks so much better to me. Great work!

nenasedk commented 3 months ago

Review checklist for @nenasedk

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

nenasedk commented 3 months ago

Hi @DavoGrant

Great writeup, and ExoTIC-LD was super easy to install and get running. I have a few small recommendations for your consideration:

  1. Statement of need: what does ExoTic provide that other limb darkening codes (Espinoza limb-darkening, LDTk) do not?

  2. What is specific about this version that justifies the JOSS publication? Were there recently major updates, or is the JOSS paper meant to cover ExoTic in general? If so, maybe a bit more detail about the features would be appropriate (e.g. probabilistic computations).

  3. API documentation: there are functions for 3 parameter, 4 parameter limb darkening coefficients. Maybe add a line to the API documentation stating that the coefficients can be found in exotic_ld.ls_laws.whatever_the_law_is.

  4. It would be helpful if the tutorials explained why the user should choose one parameterisation or another.

  5. Bibliography/DOI links should be included for the Husser, Kostogryz N, Kostogryz NM, Magic and Morello papers.

  6. Line 20 and throughout: either use limb-darkening or limb darkening (hyphenation)

  7. Line 22: Minor quibble - Then retrieve the wavelength-dependent... should be rephrased as Then the wavelength-dependent sensitivity must be retrieved... or Then one retrieves... or something to that effect, right now the sentence lacks a subject.

  8. phoenix models are usually stylised as PHOENIX models. (all caps)

DavoGrant commented 3 months ago

Hi @nenasedk -- many thanks for your suggestions and your quick turn around on this. Let me go through each point in turn (same numbering as above):

  1. Our aim with ExoTiC-LD was to make a complete and frictionless tool for limb-darkening computation. Ease of use was our top priority, and this seems to be working based on usership in the community. Beyond this, the code provides access to a more extensive collection of stellar grids than most, and under the hood we have developed a tree structure for selecting stellar models within the 3D parameters space. I feel the statement of need already speaks to this, but let us know if you had any specific additions in mind.
  2. This JOSS submission is for ExoTiC-LD in general. Publication was prompted by reaching feature completeness and an uptick in usership.
  3. We have added additional signposts in the main API docs page to the ld_laws subpackage. We have added a few words explaining that this is where to inspect the functional forms and coefficients for each limb-darkening law.
  4. We have added some text to the first tutorial explaining that choosing a parameterisation is very much application dependent. We signpost to some good literature that goes into these choices in more detail.
  5. Done. See commit 897d194.
  6. Hyphenation is (I believe) used when it is a compound modifier; e.g., limb-darkening coefficient.
  7. Done.
  8. Done.
warrickball commented 2 months ago

Hi @LorenzoMugnai and @nenasedk, I just wanted to check in and ask whether you'd had a chance to review @DavoGrant's most recent changes?

  1. Hyphenation is (I believe) used when it is a compound modifier; e.g., limb-darkening coefficient.

My understanding is that yes, we write about the phenomenon of "limb darkening" without a hyphen but would hyphenate when described things related to that phenomenon, like a "limb-darkening coefficient". See e.g. these titles of ApJ articles with "limb darkening" or "limb-darkening".

nenasedk commented 2 months ago

@warrickball @DavoGrant

I've updated my checklist, everything looks good to me.

LorenzoMugnai commented 2 months ago

Hello, sorry for my late reply. I was testing the tutorials and I found an error raised for an apparently missing file. Following the JOSS directions, I raised an Issue (https://github.com/Exo-TiC/ExoTiC-LD/issues/49#issue-2371928351) ticket in the repository with (hopefully) all the information to reproduce the issue.

Other than that, the software and the manuscript look very good to me. Great job!

DavoGrant commented 2 months ago

@LorenzoMugnai, bug now fixed in (see https://github.com/Exo-TiC/ExoTiC-LD/pull/50).

DavoGrant 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:

LorenzoMugnai commented 2 months ago

@LorenzoMugnai, bug now fixed in (see Exo-TiC/ExoTiC-LD#50).

Briliant! Thank you! I have no other comments. I completed my checklist. Thanks

warrickball commented 2 months ago

Just to confirm @LorenzoMugnai and @nenasedk, are you happy to recommend this package for publication? I just want to double check that I'm interpeting everything correctly.

LorenzoMugnai commented 2 months ago

Yes, I am happy to recommend the package for publication

warrickball commented 2 months ago

Hi @DavoGrant, I've had a look at the paper myself and I think you should expand on what ExoTiC-LD does that other codes don't. I appreciate you've mentioned four other codes but it raises the question: why do we need another one? I don't doubt there's a good reason—compactness or ease of use alone are enough—but it should be included in the paper.

Also, the ASCL entry for JKTLD suggests citing Southworth (2008) as the appropriate reference. This seems to be more widely used, with ~334 citations vs ~18 for the ASCL record. (You're welcome to cite both.)

DavoGrant commented 1 month ago

@warrickball, just made those updates you have suggested.

Thanks, let us know the next steps.

warrickball commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

warrickball commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1051/0004-6361/200913675 is OK
- 10.1093/mnras/stw224 is OK
- 10.1093/mnras/stt1435 is OK
- 10.1038/s41586-022-05591-3 is OK
- 10.3847/2041-8213/acfc3b is OK
- 10.3847/2041-8213/acebf0 is OK
- 10.3847/2041-8213/ad20e4 is OK
- 10.3847/2041-8213/accb9c is OK
- 10.3847/1538-3881/ad19df is OK
- 10.21105/joss.04503 is OK
- 10.1051/0004-6361/201219058 is OK
- 10.1051/0004-6361/201423804 is OK
- 10.3847/2515-5172/acc180 is OK
- 10.1051/0004-6361/202243722 is OK
- 10.1111/j.1365-2966.2008.13145.x is OK
- 10.1093/mnras/stv1857 is OK
- 10.21105/joss.01834 is OK
- 10.5281/zenodo.4556063 is OK

MISSING DOIs

- No DOI given, and none found for title: A new non-linear limb-darkening law for LTE stella...
- No DOI given, and none found for title: ATLAS9 Stellar Atmosphere Programs and 2km/s grid

INVALID DOIs

- None
warrickball commented 1 month ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

warrickball commented 1 month ago

Hi @DavoGrant, I'm happy with these changes and that the @nenasedk and @LorenzoMugnai have recommended the paper for publication. There's just a bit more housekeeping to do as noted in the Additional Author Tasks After Review is Complete above, which mostly boils down to making a tagged release of the code and archiving that version in a Zenodo repository. (I'll check off the editor tasks as we proceed.)

Let me know if you need any extra guidance.

DavoGrant commented 1 month ago

@warrickball this is great news.

@hrwakeford has made a Zenodo release, this is v3.2.1, and has the following DOI https://doi.org/10.5281/zenodo.13224465. We have checked the author, affiliations, and licenses too.

warrickball commented 1 month ago

While I check the Zenodo archive, I just noticed that some of the references which you presumably got from NASA ADS aren't showing the journal names because of the shorthands like \apj and \aap. Could you replace these with the journal names (e.g. Astrophysical Journal, Astronomy & Astrophysics)? These don't warrant a new release (though you can make one if you like).

warrickball commented 1 month ago

@editorialbot set 10.5281/zenodo.13224465 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.13224465

warrickball commented 1 month ago

@editorialbot set v3.2.1 as version

editorialbot commented 1 month ago

Done! version is now v3.2.1

DavoGrant commented 1 month ago

While I check the Zenodo archive, I just noticed that some of the references which you presumably got from NASA ADS aren't showing the journal names because of the shorthands like \apj and \aap. Could you replace these with the journal names (e.g. Astrophysical Journal, Astronomy & Astrophysics)? These don't warrant a new release (though you can make one if you like).

Done.

DavoGrant commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

warrickball commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 1 month ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1051/0004-6361/200913675 is OK
- 10.1093/mnras/stw224 is OK
- 10.1093/mnras/stt1435 is OK
- 10.1038/s41586-022-05591-3 is OK
- 10.3847/2041-8213/acfc3b is OK
- 10.3847/2041-8213/acebf0 is OK
- 10.3847/2041-8213/ad20e4 is OK
- 10.3847/2041-8213/accb9c is OK
- 10.3847/1538-3881/ad19df is OK
- 10.21105/joss.04503 is OK
- 10.1051/0004-6361/201219058 is OK
- 10.1051/0004-6361/201423804 is OK
- 10.3847/2515-5172/acc180 is OK
- 10.1051/0004-6361/202243722 is OK
- 10.1111/j.1365-2966.2008.13145.x is OK
- 10.1093/mnras/stv1857 is OK
- 10.21105/joss.01834 is OK
- 10.5281/zenodo.4556063 is OK

MISSING DOIs

- No DOI given, and none found for title: A new non-linear limb-darkening law for LTE stella...
- No DOI given, and none found for title: ATLAS9 Stellar Atmosphere Programs and 2km/s grid

INVALID DOIs

- None
editorialbot commented 1 month 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/5738, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm commented 1 month ago

@editorialbot accept

editorialbot commented 1 month ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 1 month ago

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``` cff-version: "1.2.0" authors: - family-names: Grant given-names: David orcid: "https://orcid.org/0000-0001-5878-618X" - family-names: Wakeford given-names: Hannah R. orcid: "https://orcid.org/0000-0003-4328-3867" contact: - family-names: Grant given-names: David orcid: "https://orcid.org/0000-0001-5878-618X" doi: 10.5281/zenodo.13224465 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Grant given-names: David orcid: "https://orcid.org/0000-0001-5878-618X" - family-names: Wakeford given-names: Hannah R. orcid: "https://orcid.org/0000-0003-4328-3867" date-published: 2024-08-09 doi: 10.21105/joss.06816 issn: 2475-9066 issue: 100 journal: Journal of Open Source Software publisher: name: Open Journals start: 6816 title: "ExoTiC-LD: thirty seconds to stellar limb-darkening coefficients" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06816" volume: 9 title: "ExoTiC-LD: thirty seconds to stellar limb-darkening coefficients" ```

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editorialbot commented 1 month ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 month ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5747
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06816
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

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