[REVIEW]: AutoPDEx: An Automized Partial Differential Equation solver based on JAX

[editorialbot]

Submitting author: @BodeTobias (Tobias Bode)
Repository: https://github.com/BodeTobias/AutoPDEx
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @danielskatz
Reviewers: @celliern, @basileMarchand
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d89578e18c80a90afeb1093fa1e25545"><img src="https://joss.theoj.org/papers/d89578e18c80a90afeb1093fa1e25545/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d89578e18c80a90afeb1093fa1e25545/status.svg)](https://joss.theoj.org/papers/d89578e18c80a90afeb1093fa1e25545)

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

@celliern & @basileMarchand, 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 @danielskatz 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 @celliern

📝 Checklist for @basileMarchand

[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]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Efficient and modular implicit differentiation
- No DOI given, and none found for title: Flax: A neural network library and ecosystem for J...
- No DOI given, and none found for title: Equinox: neural networks in JAX via callable PyTre...
- No DOI given, and none found for title: PETSc users manual
- No DOI given, and none found for title: Gmsh: A 3-D finite element mesh generator with bui...
- No DOI given, and none found for title: 36-paraview: An end-user tool for large-data visua...
- No DOI given, and none found for title: Automation of Finite Element Methods

❌ MISSING DOIs

- 10.1016/s0167-739x(03)00188-2 may be a valid DOI for title: Solving unsymmetric sparse systems of linear equat...
- 10.21105/joss.01450 may be a valid DOI for title: PyVista: 3D plotting and mesh analysis through a s...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.33 s (1382.7 files/s, 246540.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           193           5424            579          47362
Python                          45           2249           4040          13264
SVG                              5              0              0           2698
CSS                             12            307             92           1793
JavaScript                      18            185            283           1203
reStructuredText               178            610            833            546
Jupyter Notebook                 1              0            454            100
YAML                             3             14             10             80
TeX                              1              9              0             79
TOML                             1              6              0             46
Markdown                         3             18              0             35
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           462           8834           6299          67241
-------------------------------------------------------------------------------

Commit count by author:

    22	BodeTobias

[editorialbot]

⚠️ An error happened when generating the pdf.

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 451

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU Affero General Public License v3.0 (Check here for OSI approval)

[danielskatz]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[danielskatz]

@openjournals/dev - Any idea what's going on with generating the PDF here? This looks like some type of system error

[danielskatz]

👋 @BodeTobias - please work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[danielskatz]

👋 @celliern and @basileMarchand - 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. There are also links to the JOSS reviewer guidelines.

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#7300 so that a link is created to this 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 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

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

[danielskatz]

(and sorry the PDF isn't immediately available - we'll figure this out and get it made ASAP - you can refer to the version from the pre-review issue for now: https://github.com/openjournals/joss-papers/blob/joss.07261/joss.07261/10.21105.joss.07261.pdf)

[editorialbot]

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

[xuanxu]

Paper compiled, it looks like it was a temporary GitHub issue

[danielskatz]

thanks @xuanxu!

[celliern]

Review checklist for @celliern

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://github.com/BodeTobias/AutoPDEx?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@BodeTobias) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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?

[celliern]

A small error make the lib non-importable in an empty env (easily fixable)

BodeTobias/AutoPDEx#1

[BodeTobias]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Flax: A neural network library and ecosystem for J...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.48550/arXiv.2105.15183 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.48550/arXiv.2111.00254 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.2172/1577437 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.future.2003.07.011 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/nme.2579 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/B978-012387582-2/50038-1 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1007/978-3-319-39005-5 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.21105/joss.01450 is INVALID because of 'https://doi.org/' prefix

[BodeTobias]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.48550/arXiv.2105.15183 is OK
- 10.48550/arXiv.2111.00254 is OK
- 10.2172/1577437 is OK
- 10.1016/j.future.2003.07.011 is OK
- 10.1002/nme.2579 is OK
- 10.1016/B978-012387582-2/50038-1 is OK
- 10.1007/978-3-319-39005-5 is OK
- 10.21105/joss.01450 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Flax: A neural network library and ecosystem for J...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[BodeTobias]

@editorialbot generate pdf

[editorialbot]

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

[basileMarchand]

Review checklist for @basileMarchand

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://github.com/BodeTobias/AutoPDEx?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@BodeTobias) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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?