[REVIEW]: vSmartMOM.jl: an Open-Source Julia Package for Atmospheric Radiative Transfer and Remote Sensing Tools

[editorialbot]

Submitting author: @RupeshJey (Rupesh Jeyaram)
Repository: https://github.com/RemoteSensingTools/vSmartMOM.jl
Branch with paper.md (empty if default branch): joss
Version: v1.0.1
Editor: @pdebuyl
Reviewers: @jimmielin, @arjunsavel
Archive: 10.5281/zenodo.7373457

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e19083ce4cadbe34b1b740413a54007e"><img src="https://joss.theoj.org/papers/e19083ce4cadbe34b1b740413a54007e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e19083ce4cadbe34b1b740413a54007e/status.svg)](https://joss.theoj.org/papers/e19083ce4cadbe34b1b740413a54007e)

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

@jimmielin & @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 @pdebuyl 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 @arjunsavel

📝 Checklist for @jimmielin

[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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.21 s (720.8 files/s, 125841.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           97           2760           3061          10537
TOML                             6            401              1           1740
Markdown                        20            419              0           1027
YAML                            18             55            484            679
Jupyter Notebook                 5              0           4424            425
TeX                              1             17              0            203
Python                           3             18             30             53
JSON                             1              0              0             27
-------------------------------------------------------------------------------
SUM:                           151           3670           8000          14691
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2709

[editorialbot]

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

OK DOIs

- 10.1016/j.jqsrt.2013.09.004 is OK
- 10.1016/j.jqsrt.2013.12.015 is OK
- 10.1088/0004-637X/691/2/1909 is OK
- 10.1016/j.jqsrt.2015.03.007 is OK
- 10.1016/S0022-4073(99)00147-8 is OK
- 10.3847/1538-4357/aadf94 is OK
- 10.3847/1538-4357/ab1b4e is OK
- 10.3847/1538-4357/abcd99 is OK

MISSING DOIs

- 10.1093/astrogeo/atab102 may be a valid DOI for title: ExoMol at 10
- 10.1111/j.1365-2966.2012.21440.x may be a valid DOI for title: Exomol: molecular line lists for exoplanet and other atmospheres
- 10.3847/1538-4365/ab7a1a may be a valid DOI for title: An accurate, extensive, and practical line list of methane for the HITEMP database
- 10.1016/j.jqsrt.2010.05.001 may be a valid DOI for title: HITEMP, the high-temperature molecular spectroscopic database

INVALID DOIs

- https://doi.org/10.1016/j.jqsrt.2017.06.038 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.rse.2020.112053 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[arjunsavel]

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

• 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/RemoteSensingTools/vSmartMOM.jl?
• 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 (@RupeshJey) 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: 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?

[jimmielin]

Review checklist for @jimmielin

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/RemoteSensingTools/vSmartMOM.jl?
• 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 (@RupeshJey) 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: 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. - note: dependencies were automatically handled by pkg. installation was great.
• 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 - there is support and contributing information in the README, but no clear guidelines for submitting code (whether PRs are supported or changes are to be submitted through another venue). Adding one or two sentences to the README should be able to clarify this. A community conduct was added very early in the project, so that's great.

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?

[jimmielin]

Hello all, I've had an opportunity to look at this package during the pre-review phase, and have just went through the software and manuscript again. Please find my comments below.

Summary

vSmartMOM.jl is a Julia package for computing atmospheric optical properties and fully-polarized multiple-scattering radiance simulations with the Matrix Operator Method. The software is open-source licensed, is modular (including Absorption.jl and Scattering.jl and having separate documentation sections for these is highly positive, in my view, it shows that modularity was not an afterthought), and takes advantage of specific strengths of the Julia ecosystem, including GPU-acceleration and automatic differentiation. The development of a fully Julia-based package for remote sensing applications is also a good step in improving software capabilities for researchers. The manuscript is well written to showcase its strengths, and the documentation is clear and covers the functionality of the package. I recommend publication after the following comments are addressed:

Functionality

• The RT parameters are well documented. However, I had to dig into the documentation then into the DefaultParameters.yaml to configure the architecture property for testing CPU and GPUs. Also, using GPU() and CPU() as specified in the yaml comments did not work out-of-the-box:

➜  julia  julia vSmartMOMtest.jl
[ Info: CUDA-enabled GPU(s) detected
[ Info: CUDA.CuDevice(0): NVIDIA GeForce RTX 3050 Ti Laptop GPU
WARNING: both KernelAbstractions and Architectures export "CPU"; uses of it in module CoreRT must be qualified

...
  # Architecture (default_architecture, GPU(), CPU())
  architecture:       default_architecture
...

Simply noting Architectures.GPU(), Architectures.CPU() instead would help, so that the documentation is accurate out-of-the-box.

• The manuscript claims "optimized techniques have been implemented to speed up the package's performance on both CPU and GPU by orders-of-magnitude compared to existing radiative transfer codes" (L22-24). This claim is not further explained in the Benchmarks section, which only compares the CPU vs. GPU architecture in vSmartMOM.jl. I would be interested in an example of specific order-of-magnitude improvement compared to existing codes (e.g., SCIATRAN?).

Documentation

• The project has a clear Code of Conduct which was added very early in the project, which I highly appreciate. There is also a statement about support and suggestions in the README. However, there is no clear statement of how to contribute to the package, and whether standard GitHub practices (Issues & Pull Requests) are supported or these should be sent by email (as mentioned in the "Support" section of the README). I would recommend the authors to clarify how contributions of the package are accepted, preferably through GitHub and not by email which is private and results in duplicate efforts to report bugs or contribute to the software.
• Docstrings are missing in the "Methods & Types" section of the documentation at https://remotesensingtools.github.io/vSmartMOM.jl/dev/pages/vSmartMOM/Types/

Software paper

• MOM methods date back to at least Liu & Ruprecht, 1996. The authors cite Sanghavi et al., 2013 (L13, L46). While this is a software package paper which implements Sanghavi et al. 2013's vSmartMOM algorithm, I still recommend more references to the basis of the numerical methods. This will also help put this software package in context (what were the codes available before vSmartMOM.jl?)
• L61 first mentions CPU and GPU (CUDA) architectures. I suggest saying CPU core is single-threaded here first, along with L78.

Technical Corrections

• Citations on line 57 are missing (Yurchenko et al., 2012; Rothman et al., 2010)
• The title of Hu et al., 2000 is incorrectly parsed (??-fit instead of $\delta$-fit)

[pdebuyl]

Hi @jimmielin @arjunsavel , thanks for the reviews so far!

@RupeshJey you may already update your repository following the review by @jimmielin and keep us updated here. Reviews with JOSS can be interactive in this way.

[arjunsavel]

Hi all, I've finished my look at this package!

With vSmartMOM, the authors have put together a well-developed package and a welcome addition to the open-source radiative transfer literature. The code is fast, modular, and appears well-tested, and it definitely has sufficient documentation and tutorials. I have a few comments, and pending their resolution I recommend this project for acceptance.

Firstly, I have some minor paper and documentation comments, which are grouped in issues in the code repository:

• Paper comments
• Documentation comments
• Documentation example bug?

Beyond these issues, I was curious about the authors' thoughts on the code's demos. They appear to constitute a potentially valuable set of additional examples and use cases, but there are some obstacles to their immediate application. For instance, they reference what I surmise to be a past name for vSmartMOM (RadiativeTransfer). Additionally, certain modules (RadiativeTransfer.PhaseFunction) and methods (make_univariate_aerosol) appear to be deprecated. If the authors plan to continue packaging these demos with the code, I recommend that they be updated to be executable with the current code version.

[cfranken]

Beyond these issues, I was curious about the authors' thoughts on the code's demos. They appear to constitute a potentially valuable set of additional examples and use cases, but there are some obstacles to their immediate application. For instance, they reference what I surmise to be a past name for vSmartMOM (RadiativeTransfer). Additionally, certain modules (RadiativeTransfer.PhaseFunction) and methods (make_univariate_aerosol) appear to be deprecated. If the authors plan to continue packaging these demos with the code, I recommend that they be updated to be executable with the current code version.

Apologies for the late replies, we just started going through everything. As for demos, we saw now that they are indeed deprecated. It is likely best to remove the demos from that specific folder and make them part of the documentation, so that they are run automatically with every push, allowing us to see deprecation issues immediately. Thanks for catching that. We will go through the remaining issues soon as well.

[pdebuyl]

Hi @cfranken what is the progress regarding the issues raised by the reviewers?

[RupeshJey]

Hi @pdebuyl, @cfranken and I met to discuss the necessary changes and are working on them now. We are trying to finish addressing them in the next few days. Sorry for the delay, both of us have been moving long distances this summer, and it has been hectic.

[RupeshJey]

Just leaving an update that we've made great progress on all the feedback made above. We've made suggested modifications to the paper and documentation. We are in the process of fixing a bunch of the technical issues like dead links, citation issues, etc.

[pdebuyl]

Thanks for the update @RupeshJey , let us know when it is appropriate for the reviewers to take a new look at the repository/doc/paper.

[pdebuyl]

@RupeshJey any news?

[RupeshJey]

Hi Pierre, just wrapped up on our side!

We’ve addressed the concerns listed in the above reviews. Here’s a mostly-exhaustive list of the changes:

• The CPU/GPU selection bug in the yaml file is fixed. The user can input either Architectures.GPU/CPU or just GPU/CPU now.
• We discuss “why” GPU and auto-differentiation are so useful for our type of radiative transfer simulation.
• There is now a “How to Contribute” section that describes how contributors can use git’s features to contribute.
• Docstrings are fixed in the Methods & Types section.
• Additional references are added to the paper to discuss the codes available before vSmartMOM.
• The technical citation issues have been addressed
• The paper feedback has all been taken into account. The minor revisions have been made. Some new definitions are added (e.g. auto-differentiation). We briefly discuss other codes and differences – “Different codes use various approximations like…”
• Documentation-wise, the links are fixed, the minor suggestions are addressed, and the tutorials’ plots, variables, and topics are better-explained (e.g. Doppler Broadening).
• The demos folder was indeed outdated and has now been removed, and the use-cases are now covered exclusively in the tutorials section of the documentation.

There were a couple of points on the paper that we wanted to note as well:

• The Q and U benchmarks are not stated as percentages because they are so minuscule that small discrepancies result in huge fractional variation. For example, -0.0019 and -0.0020 are quite acceptably close, but differ by 5% error. Not sure how to better address this.
• We tried to create a few charts to show the benchmarks as compared to established literature, but the graphs became quickly confusing with so many quantities to compare. We feel the tables and summary of the accuracy is still the better way to go.

Main branch: https://github.com/RemoteSensingTools/vSmartMOM.jl
Paper md (on joss branch): https://github.com/RemoteSensingTools/vSmartMOM.jl/blob/joss/paper.md
Web documentation: https://remotesensingtools.github.io/vSmartMOM.jl/dev/

Thanks all!

[pdebuyl]

@editorialbot generate pdf

[editorialbot]

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

[pdebuyl]

Thanks @RupeshJey for the update!

I have Julia 1.5 and tried to install according to the instructions: (] key then add vSmartMOM) and have this error:

(@v1.5) pkg> add vSmartMOM
  Resolving package versions...
ERROR: Unsatisfiable requirements detected for package DelimitedFiles [8bb1440f]:
 DelimitedFiles [8bb1440f] log:
 ├─possible versions are: 1.5.4 or uninstalled
 └─found to have no compatible versions left with vSmartMOM [7ba11eeb] 
   └─vSmartMOM [7ba11eeb] log:
     ├─possible versions are: 0.5.0 or uninstalled
     └─restricted to versions * by an explicit requirement, leaving only versions 0.5.0

Can you remove the data tables from the article file? It is better to have a link to the documentation, not only because tables in pdfs are hard to use but also to keep with JOSS' guidelines to have brief articles.

The citations yurchenko2012exomol:2012 roth-63 man2010hitemp:2010 have a syntax issue.

[pdebuyl]

@jimmielin @arjunsavel can you have a look at the updated version?

[pdebuyl]

@RupeshJey there is also an issue with the copyright text in the README. The "all rights reserved" and the provisions for commercial use are not aligned with the Apache license. Please only keep the mention of apache licensing. You may keep the acknowledgement of course.

[arjunsavel]

Thanks for your patience, all! The issues that I raised earlier have been sufficiently addressed, and I recommend this project for publication. Nicely done!

[pdebuyl]

Thanks for the fixes

[kthyng]

Hi @RupeshJey! I'm helping to wrap up this publication, however, I see some capitalization errors in your references. For example it looks like "Mie" should be capitalized but it isn't always. Also in your Grant et al references, there is an "i" instead of "I". These are just two examples, please look through your references in detail to correct all errors. You can preserve capitalization with {} around characters.

[cfranken]

we added {} for the titles (bibtex should automatically keep capitalization for titles ideally, this has always been annoying!).
Thanks for checking, this is much more thorough than in other journals

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

@cfranken agreed it is annoying about capitalization!

Ok this all looks good to go now.

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

⚠️ Couldn't acccept/publish paper. An error happened.

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot 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.04575 joss-papers#3778
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04575
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...

[kthyng]

Congrats on your new publication @RupeshJey! Many thanks to editor @pdebuyl and reviewers @jimmielin and @arjunsavel for your time, hard work, and expertise!!

[editorialbot]

🎉🎉🎉 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.04575/status.svg)](https://doi.org/10.21105/joss.04575)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04575">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04575/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04575/status.svg
   :target: https://doi.org/10.21105/joss.04575

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[RupeshJey]

@pdebuyl @jimmielin @arjunsavel @kthyng @cfranken

Thank you all very much for your help throughout the process! Really grateful for the JOSS community and contributors.

[cfranken]

I second @RupeshJey, this has been a great process at JOSS, other journals should learn from it (instead of charging an arm and a leg).

[pdebuyl]

Thanks for the feedback!