[REVIEW]: SICOPOLIS-AD v2: tangent linear and adjoint modeling framework for ice sheet modeling enabled by automatic differentiation tool Tapenade

[editorialbot]

Submitting author: @Shreyas911 (Shreyas Sunil Gaikwad)
Repository: https://gitlab.awi.de/sicopolis/sicopolis
Branch with paper.md (empty if default branch): ad
Version: ad-v2
Editor: @crvernon
Reviewers: @svchb, @ifthompson
Archive: 10.5281/zenodo.7648249

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/28110e3febdba655f8f30f1aeaacd5b1"><img src="https://joss.theoj.org/papers/28110e3febdba655f8f30f1aeaacd5b1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/28110e3febdba655f8f30f1aeaacd5b1/status.svg)](https://joss.theoj.org/papers/28110e3febdba655f8f30f1aeaacd5b1)

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

@svchb & @kris-rowe, 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 @crvernon 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 @svchb

📝 Checklist for @ifthompson

[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=0.45 s (468.7 files/s, 315669.7 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Fortran 90                       85          19201          14442          52559
C/C++ Header                     36           5350            203          23348
C                                23           1615           1088          13208
TeX                               6            342            104           2477
Fortran 77                        6            147            210           1992
Bourne Shell                     19            335            347           1028
Python                            6            311            434            868
XML                               1              1              0            779
reStructuredText                  9            520            785            455
Markdown                          5             88              0            207
Bourne Again Shell                5             36              8            152
Jupyter Notebook                  1              0            491            101
HTML                              2              3              0             50
DOS Batch                         2             11              1             35
YAML                              2              6              6             34
JSON                              1              0              0             26
make                              2              7              7             24
CSS                               2              2              6             20
--------------------------------------------------------------------------------
SUM:                            213          27975          18132          97363
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2574

[editorialbot]

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

OK DOIs

- 10.5194/gmd-13-1845-2020 is OK
- 10.1088/2515-7620/ab6368 is OK
- 10.1007/978-3-642-03415-2 is OK
- 10.1175/1520-0442(1997)010<0901:AOAPTD>2.0.CO;2 is OK
- 10.3189/172756411797252068 is OK
- 10.3189/172756409789624256 is OK
- 10.1175/1520-0477(1997)078<2577:WIAAM>2.0.CO;2 is OK
- 10.1145/2450153.2450158 is OK
- 10.3189/2014JoG13J214 is OK
- 10.1080/10556789208805505 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[crvernon]

👋 @Shreyas911 @svchb @kris-rowe - the review takes place in this issue.

❗ Also, please don't forget to add a link to this review issue in any issues or pull requests you may generate in the https://gitlab.awi.de/sicopolis/sicopolis repository. This will help everyone have a single point of reference.

[svchb]

Review checklist for @svchb

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://gitlab.awi.de/sicopolis/sicopolis?
• 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 (@Shreyas911) 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?

[svchb]

@Shreyas911 What is the timeline to merge this branch into the main branch? Because having the paper refer to a version of the code in a development branch might be a bit premature?

[Shreyas911]

@svchb, It will be merged in a few months, per my discussions with Dr. Ralf Greve, who maintains the base SICOPOLIS code. The code on the ad branch is fully merged with develop already. Before the next release, we will merge the ad branch with the master.

[svchb]

@crvernon Is this fine?

[Shreyas911]

@crvernon @svchb, If absolutely necessary, we can speed it up but I think this is just a logistical issue, that will get sorted in a few months.

[crvernon]

@Shreyas911 by in a few months, do you mean holding publication until then as well?

[Shreyas911]

@crvernon, let me elaborate, apologies for the confusion.

We intend to merge the ad branch into the master once the review of the paper is complete and all necessary changes have been made to the ad branch. We thought it was fine to keep everything on the ad branch and there was no rush to merge it, so we had set a timeline of a few months to do the merge, which will be fairly painless.

If the rules of JOSS require it, we can make the merge immediately, but I would have to check with Dr. Ralf Greve (the maintainer of the base SICOPOLIS code) if that is fine.

Best,
Shreyas

[svchb]

@Shreyas911 @crvernon I would suggest holding the publication till it is merged with the main branch, but starting the review process now since the documentation needs a bit of work.

[Shreyas911]

@svchb, yes, I will speak to Ralf and get started on the merging. We can continue the review since we are likely to be done merging before the review process concludes.

[svchb]

@Shreyas911 The paper is too long. The guideline is about 1000 words. You mention a lot of stuff that is also is just repeated from your documentation. Just reference your documentation. Following best development practices, i.e. having a documentation, CI etc. is not a major feature.

I will follow up on documentation improvement suggestions in an issue in your gitlab.

[crvernon]

Working via a development branch is OK while conducting the review. This is often done to not disturb the stable main branch representing a current version used by the public. However, changes made during the review that are done to meet the requirements and feedback from the review should be made available on your main branch before publication is finalized.

[svchb]

@Shreyas911 I am not able to login to the awi gitlab even though I should be able to. (I work for an AWI associated research center) So I am not able to create an issue in your gitlab. You might need to change the settings to allow public issue creation.

[Shreyas911]

@svchb, I will email Ralf, he has the control.

[Shreyas911]

Hi @svchb, I need to add you as a Guest member to the project. Can you share your AWI-affiliated email address or username?

[svchb]

@Shreyas911 Thanks got the invite. Currently waiting on tech support fixing the Identity Provider config between Hereon-HIFIS-AWI.

[svchb]

@Shreyas911
Todo:

• shorten paper
  The paper is too long. The guideline is about 1000 words. You mention a lot of stuff that is also is just repeated from your documentation. Just reference your documentation. Following best development practices, i.e. having a documentation, CI etc. is not a major feature.
• Fix the stuff in issues [1] and [2]

[crvernon]

👋 - @Shreyas911 @svchb @ @kris-rowe Will you please provide an update to the status of this review in this thread?

[Shreyas911]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

@Shreyas911 - thanks for putting together a really nice software product! Thanks to @svchb and @ifthompson for a constructive review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

[crvernon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.5194/gmd-13-1845-2020 is OK
- 10.1088/2515-7620/ab6368 is OK
- 10.1145/2450153.2450158 is OK
- 10.1007/978-3-642-03415-2 is OK
- 10.1175/1520-0442(1997)010<0901:AOAPTD>2.0.CO;2 is OK
- 10.3189/172756411797252068 is OK
- 10.3189/172756409789624256 is OK
- 10.1175/1520-0477(1997)078<2577:WIAAM>2.0.CO;2 is OK
- 10.1145/2450153.2450158 is OK
- 10.3189/2014JoG13J214 is OK
- 10.1080/10556789208805505 is OK
- 10.1111/j.2153-3490.1981.tb01726.x is OK
- 10.1145/293686.293695 is OK
- 10.1145/1377596.1377598 is OK
- 10.3189/002214307783258396 is OK
- 10.5194/gmd-6-1299-2013 is OK
- 10.1080/10556788.2017.1396600 is OK
- 10.1029/2003JF000065 is OK
- 10.5194/gmd-11-3747-2018 is OK
- 10.1029/2011JF002140 is OK
- 10.5194/tc-8-2335-2014 is OK
- 10.5194/gmd-9-4521-2016 is OK
- 10.1029/2020GL091741 is OK
- 10.1007/s003820050149 is OK
- 10.1029/2008JF001015 is OK
- 10.1007/BF00207423 is OK
- 10.1038/nature07809 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4018, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kthyng]

• Check that version was updated
• Check that software archive exists, has been input to JOSS, and title and author list look good
• Check paper

[kthyng]

Everything looks good! Ready to accept.

[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.04679 joss-papers#4026
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04679
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 @Shreyas911! Many thanks to editor @crvernon and reviewers @svchb and @ifthompson for your hard work, time, 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.04679/status.svg)](https://doi.org/10.21105/joss.04679)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04679">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04679/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04679/status.svg
   :target: https://doi.org/10.21105/joss.04679

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://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[Shreyas911]

Hi @crvernon,

Thanks a lot but I think since we made changes after the Zenodo archive was created and tagging was done, we need a new tag and a new DOI for the Zenodo archive. Can you withdraw the paper for just a day or so till we do that? Can you guide me through any other steps needed? I had mentioned retagging in my previous response, so I thought publication would be put on hold till then.

Thanks to you and the reviewers @svchb, @ifthompson. Thanks, @kthyng as well! :)

Best,
Shreyas

[kthyng]

Hi @Shreyas911! Are these changes in code that were part of the JOSS review in the past 5 days since your previous archive and tagging? If they are just changes to the paper then it's fine for them not to be included.

[Shreyas911]

Hi @kthyng ,

@crvernon noticed some minor things to change after the archiving and tagging were done.

1. We made a few changes to the bib file of the paper, but you say this is fine.

2. I added a how-to-contribute section to the docs, but it was already present in the README. I guess this is not that essential either.

If you approve, we could just leave the current archive and tag as it is.

Thanks,
Shreyas

[kthyng]

@Shreyas911 Sounds fine to me to leave as is, but we can certainly reprocess if you'd prefer that. Let me know either way.

[Shreyas911]

Hi @kthyng ,

I have emailed my co-author Ralf, who maintains the SICOPOLIS repo to seek his opinion. I will get back shortly.

Thanks,
Shreyas

[Shreyas911]

Hi @kthyng ,

We would prefer to leave it as it is. Thanks to everyone for their constructive views and suggestions!

Best,
Shreyas

[kthyng]

Ok sounds good. Congrats again!

[mashadab]

Congratulations on publishing this exciting work, Shreyas!