[REVIEW]: GASTLI: A Python package for coupled interior–atmosphere modelling of volatile-rich planets

[editorialbot]

Submitting author: @lorenaacuna (Lorena Acuña)
Repository: https://github.com/lorenaacuna/GASTLI
Branch with paper.md (empty if default branch): main
Version: v0.9
Editor: @JBorrow
Reviewers: @ivalaginja, @MartianColonist
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c7f7fcd6e5c8c909cf237eb5aff9d0c4"><img src="https://joss.theoj.org/papers/c7f7fcd6e5c8c909cf237eb5aff9d0c4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c7f7fcd6e5c8c909cf237eb5aff9d0c4/status.svg)](https://joss.theoj.org/papers/c7f7fcd6e5c8c909cf237eb5aff9d0c4)

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

@ivalaginja & @MartianColonist, 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 @JBorrow 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 @ivalaginja

📝 Checklist for @MartianColonist

[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]

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

✅ OK DOIs

- 10.1088/0067-0049/192/1/3 is OK
- 10.1088/0067-0049/208/1/4 is OK
- 10.1088/0067-0049/220/1/15 is OK
- 10.3847/1538-4365/aaa5a8 is OK
- 10.3847/1538-4365/ab2241 is OK
- 10.1093/mnras/stac1133 is OK
- 10.1093/mnras/stab2250 is OK
- 10.3847/0004-637X/831/2/180 is OK
- 10.3390/atmos10110664 is OK
- 10.48550/arXiv.2402.19466 is OK
- 10.1051/0004-6361/201833873 is OK
- 10.1088/0004-637X/792/1/1 is OK
- 10.3847/0004-637X/831/1/64 is OK
- 10.1088/0004-637X/775/2/105 is OK
- 10.1088/0004-637X/813/1/47 is OK
- 10.1051/0004-6361/201629800 is OK
- 10.3847/2041-8205/831/2/L16 is OK
- 10.3847/1538-4357/aa965a is OK
- 10.3847/2041-8213/ab9530 is OK
- 10.3847/1538-4357/abfa99 is OK
- 10.3847/1538-4357/ac66e2 is OK
- 10.1051/0004-6361/202039885 is OK
- 10.1051/0004-6361/202142374 is OK
- 10.1051/0004-6361/202245736 is OK
- 10.1051/0004-6361/202243207 is OK
- 10.1051/0004-6361/201833963 is OK
- 10.3847/1538-4357/abfc48 is OK
- 10.48550/arXiv.2302.07902 is OK
- 10.1051/0004-6361/202038367 is OK
- 10.48550/arXiv.2406.10032 is OK
- 10.1088/0004-637X/775/1/80 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Structure interne et minéralogie des exoplanètes t...
- No DOI given, and none found for title: Sesame: the Los Alamos National Laboratory equatio...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1078.0 files/s, 287482.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Fortran 95                      10           1951           1731           3335
Python                          22            779           1038           1627
TeX                              1             36              0            557
reStructuredText                 8            361           1175            207
Meson                            1             43             18            153
Fortran 90                       2             43             18             79
Markdown                         1             18              0             46
YAML                             2              4              4             29
DOS Batch                        1              8              1             26
TOML                             1              2              0             25
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            50           3249           3992           6093
-------------------------------------------------------------------------------

Commit count by author:

   178	lorenaacuna

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1383

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[editorialbot]

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

[ivalaginja]

Review checklist for @ivalaginja

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/lorenaacuna/GASTLI?
• 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 (@lorenaacuna) 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?

[MartianColonist]

Review checklist for @MartianColonist

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/lorenaacuna/GASTLI?
• 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 (@lorenaacuna) 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?

[MartianColonist]

@lorenaacuna, I'm looking forward to reviewing your JOSS manuscript and Python package!

One quick thing: the embedded images aren't showing in the notebooks in the docs (probably because they are PDFs). Can you try converting them to pngs to see if they'll render that way?

[ivalaginja]

@lorenaaacuna, could you elaborate why in the package documentation under https://gastli.readthedocs.io/en/latest/#development, there are six people listed as main developers, while the paper only lists five co-authors? I see that the sixth one is mentioned in the acknowledgments of the paper. How come? This could be totally fine, I am just trying to make sure I understand how the choice was made.

[JBorrow]

Hi @lorenaacuna, just wondering if you could provide an update to our reviewers on their questions?

[lorenaacuna]

With the JWST cycle 4 deadline and a conference this week, I'll be able to address their questions and comments next week if that's ok

[lorenaacuna]

@ivalaginja Yes, exactly. Iva Momcheva helped with optimisation and debugging. I invited her to be co-author of this software paper, but she declined and said she preferred to be mentioned in the acknowledgements.

[lorenaacuna]

@MartianColonist Thanks so much for catching this. I changed this in the documentation, now you should see the .png version of the plots rendered in the notebooks.

[ivalaginja]

@editorialbot generate pdf

[editorialbot]

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

[ivalaginja]

Hey @lorenaacuna, I am slowly working through the checklist. As expected, the installation is the most time-consuming part, but in the meantime, could I ask you to address lorenaacuna/GASTLI#3 please?

[ivalaginja]

And I opened another issue with the goal to clarify the documentation somewhat: lorenaacuna/GASTLI#4

[ivalaginja]

The third issue that is part of my review is here: lorenaacuna/GASTLI#5
It addresses the installation instructions.

[ivalaginja]

@lorenaacuna @JBorrow I have now finished my review and am waiting for responses from the lead author. The submission looks very good to me, but a couple of things will have to be addressed (see the three issues above), in particular a clarification of the installation instructions.

[MartianColonist]

Hi all, I'm just wrapping up some travel right now, but will be ready to complete my review shortly!

[lorenaacuna]

@JBorrow I'm waiting for a co-author to get back to us to clarify one last comment in issue #5 before I close it.

I'm looking forward to @MartianColonist's review.

[lorenaacuna]

@JBorrow I'm just waiting until @ivalaginja succesfully installs GASTLI in their system to close issue #5.

Can we send a kind reminder to the second reviewer (@MartianColonist) to send his comments soon?

[MartianColonist]

Reminder received, I'll have my review complete within the week!

[MartianColonist]

@editorialbot generate pdf

[editorialbot]

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

[MartianColonist]

Hi @lorenaacuna,

This first part of my review offers feedback on the software paper. The paper overall is very good and will make a great addition to JOSS (well done!). I hope my feedback and suggestions on the paper below will help improve its clarity.

Feedback on the software paper

General comments:

• There are a few missing sections commonly seen in JOSS papers:

1. Similar Tools (the JOSS docs requires "A list of key references, including to other software addressing related needs"): all this section needs is links to the code repositories of similar open source codes, such as MESA and MAGRATHEA.
2. Documentation: a single-sentence section pointing the user to the GASTLI documentation.
3. Future Developments (optional): it would be nice to mention any planned future developments / new applications of GASTLI after v1.0. For example, are there plans to support other atmospheric model grids in the future (besides pRT)?

• The Summary section is quite light on references to the exoplanet and interior modelling literature. I've noted below a few specific lines, but I do feel the first paragraph, in particular, needs additional citations to contextualise the field for beginners to GASTLI (and interior structure models more broadly).
• From a quick look at the Exoplanet Modeling and Analysis Center, there may be a few other open source interior structure models (e.g., VPLanet and HARDCORE). In the Statement of Need / Similar Tools, it could be helpful to differentiate between open source packages that interpolate / fit existing interior model grids (e.g. plaNETic and SMINT) vs. full interior structure calculation codes like GASTLI.
• A Figure illustrating use cases of GASTLI would be a great addition that would significantly enhance the paper. For example, a schematic of a planet cross section with the GASTLI logo and text annotations stating applications. Such a Figure would tell a prospective user what problems GATLI can solve and the inputs and outputs of the code.
• The paper doesn't mention that GASTLI can be used to perform interior retrievals, but the code documentation highlights how to use GASTLI for this application. It would be nice to advertise this important feature in the paper.

Line-by-line specific feedback:

• Line 12: "Their bulk composition..." 'Their' is ambiguous in this sentence, as it could be referring to hot Jupiters (from the previous sentence) or gas giant exoplanets more broadly (from the paragraph subject). I'd presume the latter, but it would be good to update the wording to be specific. E.g. "The bulk composition of gaseous giant exoplanets..."
• Line 13-14: It would be helpful to provide a few more citations for how bulk compositions inform planet formation pathways and planet-star interactions.
• Line 16: please provide an example reference for the wide variety of mass fractions across the exoplanet population (e.g. a review paper).
• Lines 19-21: please include citations for at least one paper that uses inverse methods to infer the bulk composition of giant exoplanets.
• Lines 22-24: please provide an example citation for a paper/review discussing modelling inputs required for interior structure models.
• Line 31: typo "EOS" -> "EOSs".
• Line 41: 'retrieval' can be jargon for some readers, so I would recommend something like "Bayesian inverse fitting of mass and radius data ('retrieval')".
• Line 45: "The compositions of the envelope are limited to low metal content" - please clarify in this sentence if this limitation refers to just MESA or both codes mentioned (MESA and MAGRATHEA). Also, how low is 'low' here? Given Neptune is roughly 80x solar, where is the limit?
• Line 49: "FORTRAN inlists" - I haven't encountered the term 'inlist' before, so perhaps this is specialised terminology for MESA? Is there an alternative more general term?
• Lines 49-51: "The computational time of one simple forward model is at least 1 minute. This renders MESA..." - I recommend merging these two sentences, since it isn't clear from the first alone that the quoted runtime is referring to MESA.
• Line 53: "computationally fast" - since a 1 minute runtime was mentioned for MESA, please also provide a rough forward model runtime for MAGRATHEA.
• Line 55: typo "type of planets" -> "types of planet".
• Line 56: please provide an example citation for the need to use non-ideal high-pressure H/He envelopes to model sub-Neptune interiors.
• Line 57: This section is very well-written and comprehensively referenced, nicely done.

Great work @lorenaacuna on the paper!

I am currently working through the code documentation and verifying GASTLI on my Linux machine. I will shortly provide further feedback on this in a separate comment and/or issues in the GASTLI GitHub repository.

[MartianColonist]

Editorial question for @JBorrow:

I noticed in reviewing the software paper that there is another paper on GASTLI with a similar title, also advertising the package as an open source code, published in Astronomy & Astrophysics (GASTLI: An open-source coupled interior-atmosphere model to unveil gas-giant composition). The main difference between this JOSS submission and the published methods paper is the description of the code classes and runtime in the JOSS submission.

I presume these papers are sufficiently distinct that everything is good on JOSS's end?

Also, is there any way to link the Astronomy & Astrophysics paper to this JOSS submission (in the same way an AAS Journal paired paper can appear in the margin of a JOSS paper)?

[MartianColonist]

Hi @lorenaacuna,

I've raised four issues on the GASTLI repository. They are mostly minor issues that cover suggestions to improve the installation instructions and documentation (thanks to @ivalaginja for your previous helpful suggestions!).

For the final part of my review, I am trying to run GASTLI to verify the functionality.

I have installed GASTLI following the instructions, but I received an error message upon importing the package (issue #10). Please let me know once you have a solution to this, and then I'll continue running the tutorials.

[lorenaacuna]

Editorial question for @JBorrow:

I noticed in reviewing the software paper that there is another paper on GASTLI with a similar title, also advertising the package as an open source code, published in Astronomy & Astrophysics (GASTLI: An open-source coupled interior-atmosphere model to unveil gas-giant composition). The main difference between this JOSS submission and the published methods paper is the description of the code classes and runtime in the JOSS submission.

I presume these papers are sufficiently distinct that everything is good on JOSS's end?

Also, is there any way to link the Astronomy & Astrophysics paper to this JOSS submission (in the same way an AAS Journal paired paper can appear in the margin of a JOSS paper)?

Thanks @MartianColonist for bringing this up.

We submitted a science paper to A&A before the software paper to JOSS for two reasons:

1. To make sure that the methodology - particularly the new implementation of H/He layer - and the scientific validations (comparison to Solar System planets and mass-radius relations from previous works) were peer-reviewed.

2. To highlight new scientific results that extend beyond the scope of a software paper. These include the intercomparison of interior models, illustrating how different assumptions influence the inferred metal mass fraction, as well as a retrieval analysis of HAT-P-26 b.

We believed these results would fall outside the intended scope of a JOSS software paper, which focuses more on the technical aspects, such as the description of code classes and runtime. Thus, we decided to submit the papers separately.

@JBorrow Please let us know if further clarification is needed.

[lorenaacuna]

@MartianColonist thanks a lot for the review! I'm going to start addressing first your comments on the manuscript this week. After that I'll move to the docs and functionality suggestions/issues, but I may finish addressing those after the New Year. Thanks a lot for your patience.

[MartianColonist]

Sounds great, thanks for putting together such a useful package! I'm excited to try GASTLI.

Have a great New Year.