[PRE REVIEW]: DIFFICE-jax: Differentiable neural-network solver for data assimilation of ice shelves in JAX

[editorialbot]

Submitting author: @wangyji (Yongji Wang)
Repository: https://github.com/YaoGroup/DIFFICE_jax
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @AnjaliSandip
Reviewers: @daniel-cheng, @nmcardoso, @RahulSundar
Managing EiC: Kristen Thyng

Status

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Markdown: [![status](https://joss.theoj.org/papers/4cf986d53809937f2352b5fc2b7a6120/status.svg)](https://joss.theoj.org/papers/4cf986d53809937f2352b5fc2b7a6120)

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (878.8 files/s, 210320.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          31           1208           1834           4130
Jupyter Notebook                 5              0           1013           1436
TeX                              1            205              0           1172
Markdown                        11            227              0            660
MATLAB                           1             12             13             32
YAML                             1              1              4             19
-------------------------------------------------------------------------------
SUM:                            50           1653           2864           7449
-------------------------------------------------------------------------------

Commit count by author:

   410	yjwang
    94	Yao Lai
     3	Yongi Wang

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2277

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

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- 10.1098/rspa.1953.0161 may be a valid DOI for title: The flow law of ice from measurements in glacier t...
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- No DOI given, and none found for title: Physics-informed machine learning
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- 10.1126/science.aaw4741 may be a valid DOI for title: Hidden fluid mechanics: Learning velocity and pres...
- 10.1016/j.jcp.2018.10.045 may be a valid DOI for title: Physics-informed neural networks: A deep learning ...
- No DOI given, and none found for title: Euler operators for mis-specified physics-informed...
- 10.1103/physrevlett.130.244002 may be a valid DOI for title: Asymptotic self-similar blow-up profile for three-...
- 10.1029/2021ms002621 may be a valid DOI for title: Data-Driven Inference of the Mechanics of Slip Alo...
- 10.31223/x5x07f may be a valid DOI for title: Variational inference of ice shelf rheology with p...
- 10.1016/j.cam.2021.113887 may be a valid DOI for title: Optimally weighted loss functions for solving pdes...
- No DOI given, and none found for title: Adam: A method for stochastic optimization
- 10.1007/bf01589116 may be a valid DOI for title: On the limited memory BFGS method for large scale ...
- No DOI given, and none found for title: Neural networks for pattern recognition
- 10.1017/jfm.2012.21 may be a valid DOI for title: Dynamics of a viscous layer flowing radially over ...
- No DOI given, and none found for title: Automatic differentiation in machine learning: a s...
- 10.4208/cicp.oa-2020-0085 may be a valid DOI for title: Frequency principle: Fourier analysis sheds light ...
- No DOI given, and none found for title: In-situquantification of ice rheology and direct m...
- 10.1029/2018gl078356 may be a valid DOI for title: Greenland Ice Sheet: Higher nonlinearity of ice fl...
- 10.1029/2011jf002140 may be a valid DOI for title: Continental scale, high order, high spatial resolu...
- 10.1007/s11214-009-9619-1 may be a valid DOI for title: Rheological and thermal properties of icy material...
- No DOI given, and none found for title: Computational methods for inverse problems
- 10.1029/2010gl043853 may be a valid DOI for title: Spatial patterns of basal drag inferred using cont...
- 10.1017/s0022143000023327 may be a valid DOI for title: Stability of the junction of an ice sheet and an i...
- 10.1029/2021jf006346 may be a valid DOI for title: Controls on Larsen C Ice Shelf Retreat From a 60-Y...
- 10.3189/s0022143000024710 may be a valid DOI for title: Deformation of floating ice shelves
- 10.1016/j.cma.2019.112732 may be a valid DOI for title: Surrogate modeling for fluid flows based on physic...
- 10.1017/jfm.2021.135 may be a valid DOI for title: Flow over an espresso cup: inferring 3-D velocity ...
- 10.1007/s10409-021-01148-1 may be a valid DOI for title: Physics-informed neural networks (PINNs) for fluid...
- 10.1016/j.jcp.2023.112435 may be a valid DOI for title: One-dimensional ice shelf hardness inversion: Clus...
- No DOI given, and none found for title: The flow of glaciers and ice-sheets as a problem i...
- 10.1029/rg019i004p00664 may be a valid DOI for title: Flow law for polycrystalline ice in glaciers: comp...
- No DOI given, and none found for title: Experiments on the deformation of ice
- No DOI given, and none found for title: Creep and fracture of ice
- 10.1017/s0022143000003658 may be a valid DOI for title: Flow-law hypotheses for ice-sheet modeling
- No DOI given, and none found for title: Creep deformation of ice
- 10.1038/318082b0 may be a valid DOI for title: Flow law for ice in polar ice sheets
- 10.1017/jog.2020.16 may be a valid DOI for title: A non-local continuum poro-damage mechanics model ...
- 10.1016/j.cma.2016.09.034 may be a valid DOI for title: An updated-Lagrangian damage mechanics formulation...
- 10.5194/tc-8-2101-2014 may be a valid DOI for title: Combining damage and fracture mechanics to model c...
- 10.1029/2004jb003104 may be a valid DOI for title: Dynamic damage model of crevasse opening and appli...
- 10.3189/s0022143000007474 may be a valid DOI for title: Textural characteristics and impurity content of m...
- 10.1137/1.9780898717921 may be a valid DOI for title: Inverse problem theory and methods for model param...
- No DOI given, and none found for title: Antarctic ice sheet response to sudden and sustain...
- 10.1017/s0260305500016165 may be a valid DOI for title: The steady-state crystal size of deforming ice
- 10.3189/2014jog14j051 may be a valid DOI for title: Improved representation of East Antarctic surface ...
- 10.1002/9780470750636.ch60 may be a valid DOI for title: Superplastic flow of ice relevant to glacier and i...
- No DOI given, and none found for title: Using a composite flow law to model deformation in...
- No DOI given, and none found for title: Grain growth of natural and synthetic ice at 0^∘ C
- 10.3389/feart.2021.702213 may be a valid DOI for title: Microstructure and crystallographic preferred orie...
- 10.3389/feart.2022.828313 may be a valid DOI for title: Tidal modulation of a lateral shear margin: Priest...
- 10.1016/j.jsg.2006.02.008 may be a valid DOI for title: Quartz veins deformed by diffusion creep-accommoda...
- 10.5194/egusphere-egu22-731 may be a valid DOI for title: Large interannual variability in supraglacial lake...
- 10.1029/2020ms002292 may be a valid DOI for title: A generalized interpolation material point method ...
- 10.1038/35832 may be a valid DOI for title: Breakup and conditions for stability of the northe...
- 10.1038/nclimate3359 may be a valid DOI for title: Impacts of the Larsen-C Ice Shelf calving event
- 10.3189/s0022143000031233 may be a valid DOI for title: On the rates of growth of grains and crystals in S...
- No DOI given, and none found for title: Deep core studies of the crystal structure and fab...
- No DOI given, and none found for title: Nonlinear partial differential equations for scien...
- 10.3189/002214310792447743 may be a valid DOI for title: Propagation of long fractures in the Ronne Ice She...
- 10.1038/s41467-019-13539-x may be a valid DOI for title: Seawater softening of suture zones inhibits fractu...
- 10.1002/2013jf002935 may be a valid DOI for title: The structure and effect of suture zones in the La...
- No DOI given, and none found for title: A systematic study of the fracturing of Ronne-Filc...
- 10.1002/2017gl072648 may be a valid DOI for title: Fracture propagation and stability of ice shelves ...
- 10.31223/x5pm16 may be a valid DOI for title: The highly nonlinear viscosity of fast-flowing gla...
- 10.1017/jog.2018.30 may be a valid DOI for title: The effect of buttressing on grounding line dynami...
- 10.1016/s0012-821x(97)00193-3 may be a valid DOI for title: Anisotropic behavior of GRIP ices and flow in Cent...
- 10.1016/j.jsg.2018.07.014 may be a valid DOI for title: Mechanics and microstructure of deformed natural a...
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- 10.31223/x5w31w may be a valid DOI for title: Recrystallization of ice enhances the creep and vu...
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- 10.4208/cicp.oa-2020-0164 may be a valid DOI for title: Extended physics-informed neural networks (XPINNs)...
- 10.1016/0165-232x(89)90014-1 may be a valid DOI for title: A review of ice rheology for ice sheet modelling
- 10.1029/rg019i004p00664 may be a valid DOI for title: Flow law for polycrystalline ice in glaciers: comp...
- No DOI given, and none found for title: Modelling the climate and surface mass balance of ...
- 10.1002/jgrf.20054 may be a valid DOI for title: Alternative ice shelf equilibria determined by oce...
- 10.1007/s005310000149 may be a valid DOI for title: Grain size reduction by dynamic recrystallization:...
- 10.1016/j.jsg.2023.104987 may be a valid DOI for title: A process-based theory for subgrain-size and grain...
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- 10.1016/0165-232x(94)00011-l may be a valid DOI for title: A flow law for anisotropic polycrystalline ice und...
- 10.3189/s0260305500013458 may be a valid DOI for title: An anisotropic flow law for ice-sheet ice and its ...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...

INVALID DOIs

- https://doi.org/10.1016/0165-232X(82)90010-6 is INVALID because of 'https://doi.org/' prefix

[kthyng]

Hi @wangyji and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• OSI-approved license
• Installation instructions
• Documentation
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application/in scope

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

Also @wangyji please comment further on the paper you say is simultaneously under review about this software. Can you post a link to it or is it not available publicly? If that is the case, please describe what is in the paper to compare it with this submission.

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[kthyng]

Hi @wangyji I have some suggestions and questions:

• is there a reason you haven't made a release for your package on PyPI or conda-forge?
• What materials would you call docs?
• How would a user verify the software is running properly once they've set it up?
• fix DOIs
• Shorten your paper by moving "Algorithm Features", "Examples", and "Mathematical Formulation" (or some of those sections if you really want to keep one in the paer) to an actual docs like readthedocs, which you could also add your examples and tutorials to which can then have static versions hosted.

[kthyng]

Hi @wangyji, please get back to me about these questions so we can move forward with your submission processing. I'd like to hear back from you next week otherwise I will withdraw your submission the following week.

[wangyji]

Hi @wangyji, please get back to me about these questions so we can move forward with your submission processing. I'd like to hear back from you next week otherwise I will withdraw your submission the following week.

Hi, I apologize for the late reply. I am still in the process of addressing all the questions and suggestions you have provided. Below are my answers to your questions:

• is there a reason you haven't made a release for your package on PyPI or conda-forge?

Actually, this is my first time writing a formal Python package, and I am not familiar with how to release a package on PyPI. I am currently learning how to do that, but it is proving to be more challenging than I expected. It might take me some time to get it working properly. I have also realized that I need to restructure my repository to make it compatible.

-What materials would you call docs?

The main folder and each subfolder in my GitHub package have README.md files, which I consider as docs
.
-How would a user verify the software is running properly once they've set it up?

I have included a tutorial example in the repository. My thought is for users to verify the proper installation of the software by running that example.

• fix DOIs

I will address this shortly

• Shorten your paper by moving "Algorithm Features", "Examples", and "Mathematical Formulation" (or some of those sections if you really want to keep one in the paer) to an actual docs like readthedocs, which you could also add your examples and tutorials to which can then have static versions hosted.

That's a good suggestion. I will also address this shortly.

[kthyng]

@wangyji Thanks for getting back to me. I'm out of town next week and I will check back the follow week to see where you're at. Some of these are just questions, it's ok to take some time to do things, but please communicate if you do. If you want more than some time, that is ok too, but in that case we might suggest to resubmit (depending on the level of effort required). We can take a look when I'm back. Thank you!

[wangyji]

@kthyng Thanks for understanding. Having one more week should be enough for me to fix most of the issues. I will keep you updated for the change I make next week.

[wangyji]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

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WAVI.jl: Ice Sheet Modelling in Julia
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Handling editor: @observingClouds (Active)
Reviewers: @PennyHow, @daniel-cheng, @JordiBolibar
Similarity score: 0.6980

nnde: A Python package for solving differential equations using neural networks
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Submitting author: @Balaje
Handling editor: @diehlpk (Active)
Reviewers: @corentin-dev, @iammix
Similarity score: 0.6717

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[wangyji]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.5194/tc-15-1975-2021 is OK
- 10.1002/2014JF003181 is OK
- 10.22541/essoar.170965007.78479393/v1 is OK
- 10.1017/jog.2020.112 is OK
- 10.1016/j.jcp.2023.112428 is OK
- 10.5194/gmd-16-6671-2023 is OK
- 10.1017/jog.2021.120 is OK
- 10.1017/jog.2022.41 is OK
- 10.1017/jog.2023.73 is OK
- 10.1016/j.jcp.2024.112865 is OK
- 10.21203/rs.3.rs-2135795/v1 is OK
- 10.1029/JB094iB04p04071 is OK
- 10.3189/S0022143000015744 is OK
- 10.1038/s43247-022-00385-x is OK
- 10.1073/pnas.2309788121 is OK
- 10.5194/tc-9-1427-2015 is OK
- 10.1002/jgrf.20125 is OK
- 10.5194/tc-5-315-2011 is OK
- 10.3189/172756403781816338 is OK
- 10.1137/19M1274067 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1029/2021MS002621 is OK
- 10.1017/jog.2023.8 is OK
- 10.1029/2010GL043853 is OK
- 10.1016/j.jcp.2023.112435 is OK
- 10.4208/cicp.oa-2020-0164 is OK

MISSING DOIs

- No DOI given, and none found for title: Deep learning the flow law of Antarctic Ice Shelve...
- 10.1038/s41586-020-2627-8 may be a valid DOI for title: Vulnerability of Antarctica’s ice shelves to meltw...
- No DOI given, and none found for title: MEaSUREs Phase-Based Antarctica Ice Velocity Map, ...
- No DOI given, and none found for title: MEaSUREs BedMachine Antarctica, Version 2
- No DOI given, and none found for title: Deep glacial troughs and stabilizing ridges unveil...
- No DOI given, and none found for title: Physics-informed machine learning
- No DOI given, and none found for title: Euler operators for mis-specified physics-informed...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...

INVALID DOIs

- 10.5555/3618408.3618696 is INVALID

[wangyji]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.5194/tc-15-1975-2021 is OK
- 10.1002/2014JF003181 is OK
- 10.22541/essoar.170965007.78479393/v1 is OK
- 10.1017/jog.2020.112 is OK
- 10.1016/j.jcp.2023.112428 is OK
- 10.5194/gmd-16-6671-2023 is OK
- 10.1017/jog.2021.120 is OK
- 10.1017/jog.2022.41 is OK
- 10.1017/jog.2023.73 is OK
- 10.1016/j.jcp.2024.112865 is OK
- 10.21203/rs.3.rs-2135795/v1 is OK
- 10.1029/JB094iB04p04071 is OK
- 10.3189/S0022143000015744 is OK
- 10.1038/s43247-022-00385-x is OK
- 10.1073/pnas.2309788121 is OK
- 10.5194/tc-9-1427-2015 is OK
- 10.1002/jgrf.20125 is OK
- 10.5194/tc-5-315-2011 is OK
- 10.3189/172756403781816338 is OK
- 10.1137/19M1274067 is OK
- 10.48550/arXiv.2207.02338 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1029/2021MS002621 is OK
- 10.1017/jog.2023.8 is OK
- 10.1029/2010GL043853 is OK
- 10.1016/j.jcp.2023.112435 is OK
- 10.4208/cicp.oa-2020-0164 is OK

MISSING DOIs

- No DOI given, and none found for title: Deep learning the flow law of Antarctic Ice Shelve...
- No DOI given, and none found for title: MEaSUREs Phase-Based Antarctica Ice Velocity Map, ...
- No DOI given, and none found for title: MEaSUREs BedMachine Antarctica, Version 2
- No DOI given, and none found for title: Euler operators for mis-specified physics-informed...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...

INVALID DOIs

- None

[kthyng]

@wangyji I am back in town and just checking in — please let me know how things are going on your end.

[wangyji]

@kthyng glad to hear you are back. I think I tried to fixed all the issues.

1. I have fixed all the DOI. However, the missing DOIs shown above are the reference of either software or raw data in geophysics, which does not have DOI, but only url. I am not sure whether I need to further fix those references or not.

2. I also cut and re-organize the paper. I believe the revised paper is clearer and within the word limit.

3. I also successfully published our package on PYPI and also modify the installation information in the main README file in our GITHUB repo.

4. I also re-organize the repo and move all the documentation file into the docs subfolder. Basically, all the files in that folder can be considered as the documentation of our package. We also double check the hyperlink to those files. However, I am not sure whether I need to create a website, such as 'readthedocs` to meet the documentation requirement for JOSS.

[wangyji]

@kthyng also for your previou

Hi @wangyji and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• OSI-approved license
• Installation instructions
• Documentation
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application/in scope

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

Also @wangyji please comment further on the paper you say is simultaneously under review about this software. Can you post a link to it or is it not available publicly? If that is the case, please describe what is in the paper to compare it with this submission.

@kthyng also for your question in the above message, the paper that is currently under review in another journal does not have pre-print version during the review process. That paper is a geoscience paper about Antarctica ice shelves, which aims at elucidating the results inferred by this software in order to explore and uncover the hidden mechanisms that govern the motion of Antarctica ice shelves. However, that paper does not provide detailed algorithms and usage of the software.

[kthyng]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1189.2 files/s, 219073.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21            491            777           1510
TeX                              2            247              0           1453
Jupyter Notebook                 5              0            960           1273
Markdown                        10            232              0            634
YAML                             2              8             10             45
TOML                             1              6              0             34
MATLAB                           1             12             13             32
-------------------------------------------------------------------------------
SUM:                            42            996           1760           4981
-------------------------------------------------------------------------------

Commit count by author:

   615	yjwang
   111	Yao Lai
     6	Yongi Wang

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1315

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[AnjaliSandip]

@wangyji, if you have any suggestions for potential reviewers, please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

[wangyji]

Hi @AnjaliSandip, yes, below are our suggestions for 5 potential reviewers.

1. alextbradley; 2. pennyhow; 3. JordiBolibar; 4. daniel-cheng; 5. weiji14

[kthyng]

@editorialbot assign @AnjaliSandip as editor

@AnjaliSandip you'll need to run this command to assign yourself as editor (in the future).

[editorialbot]

Assigned! @AnjaliSandip is now the editor

[AnjaliSandip]

👋 @alextbradley, @PennyHow, @JordiBolibar, @daniel-cheng, & @weiji14 would you review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html.

[weiji14]

Hi 👋, I'd prefer to pass on this one as I'm currently in the queue for reviewing another JOSS submission, but can try to recommend other reviewers (if the other 4 on the list don't put their hand up).

[PennyHow]

Unfortunately I am in a similar position to @weiji14 - I am just finishing up one review and have just put myself forward for another, so I will be too busy to review this one as well.

[daniel-cheng]

Hi all, I am available to review this submission.

[alextbradley]

Hi @AnjaliSandip, unfortunately I'm going to have to decline to review this paper as I feel it would be a conflict of interests for me to do so.

[JordiBolibar]

Hi @AnjaliSandip, I'm afraid I won't have the time to review this in the coming weeks. I hope you can find an alternative reviewer soon :)

[AnjaliSandip]

Hi all, I am available to review this submission.

Thank you!

[AnjaliSandip]

@editorialbot add @daniel-cheng as reviewer

[editorialbot]

@daniel-cheng added to the reviewers list!

[AnjaliSandip]

@weiji14 @wangyji If you have any suggestions for additional potential reviewers, please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

[AnjaliSandip]

@wangyji, Can you suggest additional potential reviewers? We need at least one more to start the review process.

[AnjaliSandip]

👋 @nmcardoso, @RahulSundar, & @jcla490, would you review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html.

[nmcardoso]

Hi @AnjaliSandip I can review this submission

[AnjaliSandip]

@editorialbot add @nmcardoso as reviewer

[editorialbot]

@nmcardoso added to the reviewers list!

[jcla490]

Hi, I am unable to review this article at this time due to other obligations. Apologies!

[RahulSundar]

HI!

👋 @nmcardoso, @RahulSundar, & @jcla490, would you review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html.

I am available to review this submission. Thanks. Would need about 2 weeks for the same.

[AnjaliSandip]

@editorialbot add @RahulSundar as reviewer

[editorialbot]

@RahulSundar added to the reviewers list!

[AnjaliSandip]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7254.