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[REVIEW]: SICOPOLIS-AD v2: tangent linear and adjoint modeling framework for ice sheet modeling enabled by automatic differentiation tool Tapenade
Submitting author: @Shreyas911 (Shreyas Sunil Gaikwad) Repository: https://gitlab.awi.de/sicopolis/sicopolis Branch with paper.md (empty if default branch): ad Version: SICOPOLIS-AD v2 (SICOPOLIS v_5.3) Editor: @crvernon Reviewers: @svchb, @kris-rowe Archive: Pending
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: [](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
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
Software report:
github.com/AlDanial/cloc v 1.88 T=0.45 s (468.7 files/s, 315669.7 lines/s)
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Language files blank comment code
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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
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SUM: 213 27975 18132 97363
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gitinspector failed to run statistical information for the repository
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
👋 @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.
Review checklist for @svchb
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://gitlab.awi.de/sicopolis/sicopolis?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] 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?
- [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Functionality
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] 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?
- [x] 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).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [x] 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?
- [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)?
- [x] 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?
@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?
@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.
@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.
@Shreyas911 by in a few months, do you mean holding publication until then as well?
@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
@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.
@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.
@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.
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.
@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.
Hi @svchb, I need to add you as a Guest member to the project. Can you share your AWI-affiliated email address or username?
@Shreyas911 Thanks got the invite. Currently waiting on tech support fixing the Identity Provider config between Hereon-HIFIS-AWI.
@Shreyas911 Todo:
- [x] 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.
- [x] Fix the stuff in issues [1] and [2]
:wave: - @Shreyas911 @svchb @ @kris-rowe Will you please provide an update to the status of this review in this thread?
@crvernon Shreyas911 started working on my comments a week ago and is finished with like 80-90% of my first round of comments.
@crvernon We hope to be done addressing almost all issues over this weekend. I think some Gitlab issues are not exactly under our purview, so I will address them in the comments in Gitlab itself.
@Shreyas911 This is not true. Papers published in JOSS don't address a single feature of a program but the whole program! So the forward version of your program is also under review. Actually, everything in your repository is attached as a file to the JOSS publication and is part of the publication.
Hello @svchb @crvernon,
It is not common to have features like documentation, and CI in softwares that are used in our field. We therefore would prefer to mention them in the paper explicitly. We have reduced the size of the paper from 2500 words to about 1500 words. We have also addressed the issues raised on Gitlab.
Hello @svchb @crvernon,
Just checking in to see what we are supposed to do next, we have done our best to address the issues raised before.
Thanks, Shreyas