[REVIEW]: Excalibur: An Open Source Molecular and Atomic Cross Section Computation Code for Substellar Atmospheres

editorialbot commented 1 week ago

Submitting author: !--author-handle-->@arnav-agrawal@dfm<!--end-editor-- Reviewers: @LorenzoMugnai, @arjunsavel Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/e58e5b15672fcfe1e358ca99a38ed23c/status.svg)](https://joss.theoj.org/papers/e58e5b15672fcfe1e358ca99a38ed23c)

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

@LorenzoMugnai & @arjunsavel, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @LorenzoMugnai

📝 Checklist for @arjunsavel

editorialbot commented 1 week ago

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editorialbot commented 1 week ago

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

OK DOIs

- 10.1016/j.jqsrt.2020.107228 is OK
- 10.1016/j.jqsrt.2010.05.001 is OK
- 10.1016/j.jqsrt.2021.107949 is OK
- 10.48550/arXiv.1710.10854 is OK
- 10.1088/0004-637X/808/2/182 is OK
- 10.3847/1538-4365/abd773 is OK
- 10.1051/0004-6361/201732531 is OK
- 10.1016/j.jqsrt.2018.09.027 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (877.5 files/s, 188977.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          23           1627           1855           2942
Jupyter Notebook                 6              0           1667            211
TeX                              1             12              0            127
reStructuredText                 6             53             48            106
Markdown                         1             25              0             53
YAML                             2              6             10             33
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            41           1735           3588           3507
-------------------------------------------------------------------------------

Commit count by author:

   162  arnav_agrawal
   125  Ryan MacDonald
    20  rmacdonald
     5  arnav-agrawal

editorialbot commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1335

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

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

dfm commented 1 week ago

@LorenzoMugnai, @arjunsavel — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6894 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible!

editorialbot commented 1 week ago

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

LorenzoMugnai commented 1 week ago

Review checklist for @LorenzoMugnai

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/MartianColonist/Excalibur?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@arnav-agrawal) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] 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?

LorenzoMugnai commented 4 days ago

Hi @arnav-agrawal,

I have been reviewing the documentation and found it to be a bit too minimalist. If I may, here are a few suggestions for improvement:

Installation Instructions: I noticed that you recommend installing the software from source via GitHub. While this is fine, I wonder why you suggest using the pip editable mode (-e). Could you please explain the necessity of this in the documentation?
Functionality Documentation: Your API documentation appears to be built using autoapi (as mentioned on the API page). Could you add some explanatory text around it, at least in the index, to help users navigate the documentation more effectively?
Community Guidelines: I found these either missing or not easily accessible. Could you please add a dedicated section for community guidelines in the documentation?
minors: Regarding the home page, I suggest including a link to the "Introduction" section and to the paper to be cited (unless the paper is the JOSS one and is not published yet, of course).

Thank you for your attention to these suggestions.

LorenzoMugnai commented 3 days ago

Hi again,

Regarding the paper, I found it quite enjoyable to read. I have a few comments, mostly aimed at making it more accessible for non-expert users, whom you identify as the preferred audience for the didactic purpose of your code:

You start with fundamental assumptions in the field (e.g., "Without accurate cross sections, one cannot reliably measure the chemical composition of substellar atmospheres."), which is a nice way to introduce the framework. However, I feel the paper could benefit from additional references or a few more lines to support such statements.
You mention that the code can run on a CPU laptop for "smaller line lists." What do you mean by "smaller"? Can you provide benchmarks, such as reference computation times and memory usage?
You state that the HDF5 output can be used with retrieval codes. Could you provide examples of codes natively supported by your output format (such as Poseidon, Taurex, etc.)? Or does the user need to adapt your output for these codes? Including references or citations for some retrieval codes would be helpful.
You graphically show that the cross sections produced can be used to generate transmission spectra. Can you explain how this can be done for a non-expert user, perhaps by referencing the integration with modelling codes?
I feel the statement of need could be more effective if moved just after the summary, before delving into the details of Excalibur's computational process. Have you considered this?
You close the manuscript by inviting the reader to provide suggestions. It would be useful to reference your "contribution guidelines," encouraging users to join the discussion on a dedicated channel (perhaps GitHub?).

LorenzoMugnai commented 3 days ago

Another note (sorry for the several messages),

I see that there are automated tests in your repository. However, they don't seem to be linked to any CI, GitHub Action, or coverage tool. Have you considered including a GitHub Action for CI with a dedicated badge? Here is an example for POSEIDON, the retrieval code developed by your co-author and hosted in the same repository as Excalibur.

Thank you!

arnav-agrawal commented 18 hours ago

Hi @LorenzoMugnai,

Thank you for your suggestions and comments. We are working on touching up our code and documentation accordingly, and will have updates soon.

arjunsavel commented 16 hours ago

Review checklist for @arjunsavel

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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/MartianColonist/Excalibur?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@arnav-agrawal) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] 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

[x] 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.
[x] 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?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] 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?

arjunsavel commented 15 hours ago

@dfm hope you're well! Just wanted to double-check that I'm not COI-d out of reviewing. I'm on a paper (maybe a few?) with the second author, but it's part of a rather large collaboration (JWST ERS, and the limb asymmetry sub-unit). I don't think I've had much scientific conversation with the second author.

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