[REVIEW]: FTorch: a library for coupling PyTorch models to Fortran

[editorialbot]

Submitting author: @jatkinson1000 (Jack Atkinson)
Repository: https://github.com/Cambridge-ICCS/FTorch
Branch with paper.md (empty if default branch): JOSS
Version: v1.0.0
Editor: @matthewfeickert
Reviewers: @parikshitbajpai, @timothyas, @anand-me
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/171ec3ec7deaa00418caab47afdc33ef/status.svg)](https://joss.theoj.org/papers/171ec3ec7deaa00418caab47afdc33ef)

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

@parikshitbajpai & @timothyas, 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 @matthewfeickert 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

@parikshitbajpai, please create your checklist typing: @editorialbot generate my checklist

@timothyas, please create your checklist typing: @editorialbot generate my checklist

[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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1785.6 files/s, 235537.6 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Fortran 90                       11            811            421           2833
Markdown                         24            586              0           1963
Python                           18            357            766            788
C++                               2             29             32            320
CMake                             9             75             82            275
YAML                              5             42             52            240
TeX                               1             21              0            189
C/C++ Header                      1             20            103             54
Bourne Again Shell                1              8             14             47
C                                 1              9              4             47
make                              2             16              8             26
TOML                              2              5             11             12
Bourne Shell                      1              3              9             11
--------------------------------------------------------------------------------
SUM:                             78           1982           1502           6805
--------------------------------------------------------------------------------

Commit count by author:

    69	jatkinson1000
    43	Jack Atkinson
    41	Joe Wallwork
    37	ElliottKasoar
    17	Dominic Orchard
    15	Athena Elafrou
    13	melt
     4	Simon Clifford
     2	SimonClifford
     1	helgehr
     1	mondus
     1	tommelt
     1	vopikamm

[editorialbot]

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

✅ OK DOIs

- 10.1007/s11831-022-09795-8 is OK
- 10.1029/2022GL098174 is OK
- 10.1098/rsta.2020.0093 is OK
- 10.1109/MCSE.2022.3159862 is OK
- 10.1103/RevModPhys.91.045002 is OK
- 10.1029/2024MS004292 is OK
- 10.48550/arXiv.2011.03081 is OK
- 10.1016/j.jocs.2022.101707 is OK
- 10.1029/2024MS004398 is OK
- 10.1145/3323057.3323059 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Fortitude
- No DOI given, and none found for title: fypp
- No DOI given, and none found for title: clang-format
- No DOI given, and none found for title: clang-tidy
- No DOI given, and none found for title: Pytorch: An imperative style, high-performance dee...
- No DOI given, and none found for title: MiMA Machine Learning
- No DOI given, and none found for title: CAM-ML
- No DOI given, and none found for title: DataWave CAM-GW
- No DOI given, and none found for title: forpy
- No DOI given, and none found for title: pytorch-fortran
- No DOI given, and none found for title: TorchFort

❌ MISSING DOIs

- 10.1093/gmo/9781561592630.article.24101 may be a valid DOI for title: ruff

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1767

✅ 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 📄 👈

[jatkinson1000]

Thanks all for agreeing to edit and review.
I look forward to your comments.

Just a note to say - I created the JOSS paper in a separate branch, but as an active piece of software there will likely be additions to main since this was created. I'm not sure how well the JOSS system handles this, but I'm happy to keep the JOSS branch up to date by rebasing if you wish.

[matthewfeickert]

I created the JOSS paper in a separate branch, but as an active piece of software there will likely be additions to main since this was created. I'm not sure how well the JOSS system handles this, but I'm happy to keep the JOSS branch up to date by rebasing if you wish.

That's totally fine, @jatkinson1000. Any edits can happen on the paper branch and then we'll have editorialbot rerender as needed.

[matthewfeickert]

@parikshitbajpai @timothyas @anand-me Thanks for agreeing to review this submission! This is the review thread for the paper. All of our communications will happen here from now on. 👍

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied (and if you leave notes on each item that's even better). There are also links to the JOSS reviewer guidelines. I find it particularly helpful to also use the JOSS review criteria and review checklist docs as supplement/guides to the reviewer checklist @editorialbot will make for you.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7602 so that a link is created to this Issue 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 reviews to be completed within about 4 weeks*. Please let me know if either of you require some more time (that's perfectly okay). We can also use @editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@matthewfeickert) if you have any questions/concerns.

---

*We've already covered that @parikshitbajpai will not be able to start until January, so we can push this back more in general.

[matthewfeickert]

@editorialbot add @anand-me as reviewer

[editorialbot]

@anand-me added to the reviewers list!

[matthewfeickert]

As mentioned in #7573 (comment), we have had some additional potential reviewers respond to agree to also contribute reviews, and I like to accept 3 reviewers when possible. So @anand-me will be joining as a reviewer (thanks!) though has similar time constraint as @parikshitbajpai.

@anand-me, please check out #7602 (comment) for additional information, and if you have any questions please let me know.

[anand-me]

@matthewfeickert - Thank you for adding me as a reviewer! I'm looking forward to contributing.

[timothyas]

Hi folks, I just wanted to let you know that I'm looking forward to reviewing this, but unfortunately won't be able to until I'm back from holidays - around Jan 2/3. I hope that's alright! Happy holidays everybody!

[matthewfeickert]

Thanks for the update, @timothyas. That's totally fine. Happy holidays and 2025 to everyone and thank you all for participating in the open science process.