[REVIEW]: flowTorch - a Python library for analysis and reduced-order modeling of fluid flows

[whedon]

Submitting author: @AndreWeiner (Andre Weiner)
Repository: https://github.com/FlowModelingControl/flowtorch
Version: v1.0
Editor: @Kevin-Mattheus-Moerman
Reviewer: @akaptano, @JaroslavHron, @salrm8, @hkjeldsberg
Archive: 10.5281/zenodo.5770244

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Status

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Markdown: [![status](https://joss.theoj.org/papers/57b32d31997c90a40b3f4bdc20782e55/status.svg)](https://joss.theoj.org/papers/57b32d31997c90a40b3f4bdc20782e55)

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

@akaptano & @JaroslavHron & @salrm8 & @hkjeldsberg, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @akaptano

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@AndreWeiner) 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 and who the target audience is?
• 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?

Review checklist for @JaroslavHron

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@AndreWeiner) 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 and who the target audience is?
• 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?

Review checklist for @salrm8

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@AndreWeiner) 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 and who the target audience is?
• 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?

Review checklist for @hkjeldsberg

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@AndreWeiner) 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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @akaptano, @JaroslavHron, @salrm8, @hkjeldsberg it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1749

[whedon]

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

OK DOIs

- 10.24355/dbbs.084-202007011404-0 is OK
- 10.1017/S0022112010001217 is OK
- 10.1126/sciadv.abf5006 is OK
- 10.1137/1.9781611974508 is OK
- 10.1017/9781108380690.002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.19 s (409.9 files/s, 224929.5 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
Python                                  42            744           1404           3333
Jupyter Notebook                         9              0          34940            902
Markdown                                 4             80              0            263
Bourne Shell                             9             30             29             95
Windows Module Definition                2             10              3             74
TeX                                      1              5              0             66
reStructuredText                         6             57            109             53
DOS Batch                                1              8              1             26
make                                     1              4              7              9
CSS                                      1              0              0              3
SVG                                      1              0              0              3
---------------------------------------------------------------------------------------
SUM:                                    77            938          36493           4827
---------------------------------------------------------------------------------------


Statistical information for the repository '200fba7b798fff4df08afdfb' was
gathered on 2021/10/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Andre Weiner                    84          7007           1959           94.57
Jannis Anderson                  3           161              5            1.75
Mehdimak                         2           313             36            3.68

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Andre Weiner               5462           78.0          5.8                8.77
Mehdimak                     19            6.1          8.6                0.00

[whedon]

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

[akaptano]

All,

I have already completed most of my review (only thing left to do is check the documentation within the code), and you can see my comments at https://github.com/FlowModelingControl/flowtorch/issues. @Kevin-Mattheus-Moerman I recommend publication after a mix of mostly minor revisions. I will tick off my remaining checklist boxes as these issues get resolved.

[AndreWeiner]

@whedon generate pdf

[whedon]

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

[akaptano]

All, I have finished my review, and the authors have now made suitable revisions to all my comments. I recommend publication.

[hkjeldsberg]

Dear all,

The library looks good from my end, and I think @akaptano already addressed the most pressing issues.

From a developer perspective I would recommend collecting the tests in a separate test-folder, as this would clean up the current project structure.
Furthermore, a possible improvement is adding some sort of continuous integration, i.e., TravisCI., CircleCI, or AppVeyor for automated testing.

However, I do not consider these blocking issues, and I am therefore happy to recommend this library for publication.

[Kevin-Mattheus-Moerman]

@JaroslavHron @salrm8 just checking in if can give an update me on review progress? Are you able to get started or have you started already? Thanks again for your help!

[salrm8]

@Kevin-Mattheus-Moerman, I have already started the review. I will leave my feedback by the end of the week. I hope this is fine. Thank you!

[Kevin-Mattheus-Moerman]

@salrm8 that is fine thanks!

[JaroslavHron]

Hi, i like the paper/library. Especially the the documentation (https://flowmodelingcontrol.github.io/flowtorch-docs/1.0/) is nicely written.

Apart of the already resolved issues pointed out by @akaptano, I have no further remarks and I would recommend this for publication as it is now.

May be a small one:

• from a user point of view I might be tempted to look in the documentation for some hints on writing custom data reader to import flow data in some other format. For example I might have computed flow data in the XDMF format - probably this might be easily derived from the available hdf5, vtk and openfoam readers.

[AndreWeiner]

Hi @JaroslavHron,
thank you very much for your feedback. I already thought about the idea of adding also more advanced programming tutorials to the documentation (there is something like that already for simple linear algebra and tensor operations with PyTorch). The data loaders are probably the first structure one might want to extend.
Best, Andre

[whedon]

👋 @JaroslavHron, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @salrm8, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @akaptano, please update us on how your review is going (this is an automated reminder).

[AndreWeiner]

Dear @Kevin-Mattheus-Moerman,
a quick question: I guess the DOI printed in the draft is not going to be the final DOI but acts as a placeholder, right?
I'll have to submit another article next week, in which I'd like to cite flowTorch using a proper DOI.
Thanks,
Andre

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.24355/dbbs.084-202007011404-0 is OK
- 10.1017/S0022112010001217 is OK
- 10.1126/sciadv.abf5006 is OK
- 10.21105/joss.02104 is OK
- 10.1017/S0022112003006694 is OK
- 10.1137/1.9781611974508 is OK
- 10.1017/9781108380690.002 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.21105/joss.00530 is INVALID because of 'https://doi.org/' prefix

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2822

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2822, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[Kevin-Mattheus-Moerman]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03860 joss-papers#2823
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03860
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...

[Kevin-Mattheus-Moerman]

@openjournals/dev I just accepted this paper but accidentally did so before fixing an invalid DOI, can this still be fixed?

https://doi.org/10.21105/joss.00530 is INVALID because of 'https://doi.org/' prefix

[arfon]

Sure. I can fix this.

[whedon]

🎉🎉🎉 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.03860/status.svg)](https://doi.org/10.21105/joss.03860)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03860">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03860/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03860/status.svg
   :target: https://doi.org/10.21105/joss.03860

This is how it will look in your documentation:

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