Skip to content

[REVIEW]: nnde: A Python package for solving differential equations using neural networks #3465

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Closed
40 tasks done
whedon opened this issue Jul 9, 2021 · 129 comments
Closed
40 tasks done

[REVIEW]: nnde: A Python package for solving differential equations using neural networks #3465

whedon opened this issue Jul 9, 2021 · 129 comments
Assignees
@diehlpk @hayesall @taless474
Labels
accepted Makefile published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX

Comments

@whedon
Copy link

whedon commented Jul 9, 2021 •
edited
Loading

Submitting author: @elwinter (Eric Winter)
Repository: https://github.com/elwinter/nnde
Version: v1.0
Editor: @diehlpk
Reviewer: @taless474, @hayesall
Archive: 10.5281/zenodo.5879387

⚠️ 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.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/928f78def0b6f73aecf73326fd390aeb"><img src="https://joss.theoj.org/papers/928f78def0b6f73aecf73326fd390aeb/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/928f78def0b6f73aecf73326fd390aeb/status.svg)](https://joss.theoj.org/papers/928f78def0b6f73aecf73326fd390aeb)

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

@taless474 & @hayesall, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk 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 ✨

Review checklist for @taless474

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

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 (@elwinter) 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 @hayesall

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

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 (@elwinter) 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 whedon mentioned this issue Jul 9, 2021
Closed
@whedon
Copy link
Author

whedon commented Jul 9, 2021

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @taless474, @hayesall 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:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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
Copy link
Author

whedon commented Jul 9, 2021 

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (969.6 files/s, 99205.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          86           2298           2106           4781
Markdown                         2             27              0             47
TeX                              1              3              0             32
make                             1              3              0              8
JSON                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            91           2331           2106           4874
-------------------------------------------------------------------------------


Statistical information for the repository 'be66f95afd6266cb60f8d390' was
gathered on 2021/07/09.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Eric Winter                    192         18132           8947          100.00

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
Eric Winter                9185           50.7          8.3               13.41

@whedon whedon added the TeX label Jul 9, 2021
@whedon
Copy link
Author

whedon commented Jul 9, 2021 

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

OK DOIs

- 10.1109/72.712178 is OK
- 10.1007/978-94-017-9816-7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
Copy link
Author

whedon commented Jul 9, 2021

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

@hayesall
Copy link

hayesall commented Jul 13, 2021 •
edited
Loading

I made the first review pass @elwinter. I need some additional time to check functionality, but all of the points below should be possible to do parallel to that.

Overall Feedback

All of the components are here (software, docstrings, tests), the final step is to make these components accessible to a user. Many of these could be addressed by incorporating a documentation system (e.g. sphinx) to pull docstrings and present them alongside a high-level overview.

If possible: After writing the high-level documentation; schedule a meeting with a colleague (someone who is fairly comfortable in Python and knows a little about this problem setting), give them links to the software and documentation, and watch them get started with it. This almost always helps reveal theories of the software that are inaccessible.

Functionality / Installation

Documentation, Testing, and Community Guidelines

Paper Feedback

@elwinter
Copy link

elwinter commented Jul 13, 2021 via email

@diehlpk
Copy link
Member

diehlpk commented Jul 21, 2021

Hey @taless474 how is your review going?

@whedon
Copy link
Author

whedon commented Jul 23, 2021

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

@whedon
Copy link
Author

whedon commented Jul 23, 2021

👋 @taless474, please update us on how your review is going (this is an automated reminder).

@diehlpk
Copy link
Member

diehlpk commented Jul 26, 2021

@whedon remind @taless474 in 2 weeks

@whedon
Copy link
Author

whedon commented Jul 26, 2021

Reminder set for @taless474 in 2 weeks

@taless474
Copy link

I made the first review pass at @elwinter's nnde. As @hayesall did a great job on creating on-point issues, I went through the functionality check first. Executing this:

pip install nnde
git clone https://github.com/elwinter/nnde_demos
cd nnde_demos; python lagaris01_demo.py

(--update does not work the first time), the demo was successful. However, the demos are located in another repository.

I also ran the tests and they all pass.
I will test it further after elwinter/nnde#9 is resolved.

@diehlpk
Copy link
Member

diehlpk commented Aug 9, 2021

Hey @elwinter how is your revision going?

@elwinter
Copy link

elwinter commented Aug 11, 2021 via email

@diehlpk
Copy link
Member

diehlpk commented Aug 16, 2021

@hayesall The author has addressed most of your concerns. Would you mind to check if you are satisfied.

@hayesall
Copy link

I'll check this evening. I saw the last main change got cleared over the weekend.

@diehlpk
Copy link
Member

diehlpk commented Aug 23, 2021

I made the first review pass at @elwinter's nnde. As @hayesall did a great job on creating on-point issues, I went through the functionality check first. Executing this:

pip install nnde
git clone https://github.com/elwinter/nnde_demos
cd nnde_demos; python lagaris01_demo.py

(--update does not work the first time), the demo was successful. However, the demos are located in another repository.

I also ran the tests and they all pass.
I will test it further after elwinter/nnde#9 is resolved.

@taless474 I think #9 is resolved and you can start to review again.

@diehlpk
Copy link
Member

diehlpk commented Sep 5, 2021

@hayesall and @taless474 The author has addressed most of your concerns. Would you mind to check if you are satisfied.

@hayesall
Copy link

hayesall commented Sep 6, 2021

Hey @diehlpk I checked off all but "Functionality" from my tasklist a couple days ago (but I didn't want to cause notification noise). I still need a little more time on functionality.

Follow-up: This would be a stronger submission with sphinx/mkdocs and elwinter/nnde#13, but nnde currently meets the baseline requirements.

@hayesall
Copy link

hayesall commented Sep 6, 2021

@whedon generate pdf

@whedon
Copy link
Author

whedon commented Sep 6, 2021

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

@diehlpk
Copy link
Member

diehlpk commented Sep 10, 2021

@elwinter Can you have a look at elwinter/nnde#13 and sphinx/mkdocs?

@elwinter
Copy link

elwinter commented Feb 14, 2022 via email

@elwinter
Copy link

elwinter commented Feb 14, 2022 via email

@danielskatz
Copy link

👋 @diehlpk - can you check again and see if you think this is ready to publish?

@diehlpk
Copy link
Member

diehlpk commented Feb 14, 2022

@whedon generate pdf

@whedon
Copy link
Author

whedon commented Feb 14, 2022

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

@diehlpk
Copy link
Member

diehlpk commented Feb 14, 2022

2. Does your co-author want to go by initials only?

@danielskatz The papers looks good now. The last thing is the question above.

@danielskatz
Copy link

I see "And my co-author prefers to use leading initials and last name" above - so I'll go ahead and process this now

@danielskatz
Copy link

@whedon recommend-accept

@whedon
Copy link
Author

whedon commented Feb 14, 2022 

Attempting dry run of processing paper acceptance...

@whedon
Copy link
Author

whedon commented Feb 14, 2022 

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

OK DOIs

- 10.1109/72.712178 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1007/978-94-017-9816-7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
Copy link
Author

whedon commented Feb 14, 2022

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

Check final proof 👉 openjournals/joss-papers#2960

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2960, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@danielskatz
Copy link

@whedon accept deposit=true

@whedon
Copy link
Author

whedon commented Feb 14, 2022 

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

@whedon whedon added accepted published Papers published in JOSS labels Feb 14, 2022
@whedon
Copy link
Author

whedon commented Feb 14, 2022

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
Copy link
Author

whedon commented Feb 14, 2022

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03465 joss-papers#2961
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03465
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@danielskatz
Copy link

Congratulations to @elwinter (Eric Winter) and co-author!!

And thanks to @taless474 and @hayesall for reviewing, and @diehlpk for editing!
We couldn't do this without you!

@whedon
Copy link
Author

whedon commented Feb 14, 2022

🎉🎉🎉 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.03465/status.svg)](https://doi.org/10.21105/joss.03465)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03465">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03465/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03465/status.svg
   :target: https://doi.org/10.21105/joss.03465

This is how it will look in your documentation:

DOI

We need your help!

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:

@janmandel
Copy link

Trying to install in google colab
!pip install PyAFBF
errors out with
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. albumentations 0.1.12 requires imgaug<0.2.7,>=0.2.5, but you have imgaug 0.2.9 which is incompatible.

@elwinter
Copy link

elwinter commented Feb 20, 2022 via email

@janmandel
Copy link

janmandel commented Feb 21, 2022 via email

@elwinter
Copy link

elwinter commented Feb 21, 2022 via email

@editorialbot editorialbot mentioned this issue Feb 17, 2024
Closed
@editorialbot editorialbot mentioned this issue Jun 23, 2024
Closed
@editorialbot editorialbot mentioned this issue Jul 17, 2024
Closed
@editorialbot editorialbot mentioned this issue Mar 21, 2025
Closed
@editorialbot editorialbot mentioned this issue Mar 31, 2025
Closed
@editorialbot editorialbot mentioned this issue Apr 18, 2025
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@diehlpk diehlpk

@hayesall hayesall

@taless474 taless474

Labels
accepted Makefile published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
8 participants
@danielskatz @kthyng @diehlpk @janmandel @elwinter @hayesall @whedon @taless474