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

editorialbot commented 4 hours ago

Submitting author: !--author-handle-->@BodeTobias@danielskatz<!--end-editor-- 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

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

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

editorialbot commented 4 hours ago

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 commented 4 hours ago

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 commented 4 hours ago

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 commented 4 hours ago

:warning: An error happened when generating the pdf.

editorialbot commented 4 hours ago

Paper file info:

📄 Wordcount for paper.md is 451

✅ The paper includes a Statement of need section

editorialbot commented 4 hours ago

License info:

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

danielskatz commented 4 hours ago

@editorialbot generate pdf

editorialbot commented 4 hours ago

:warning: An error happened when generating the pdf.

danielskatz commented 4 hours ago

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

danielskatz commented 4 hours ago

👋 @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 commented 4 hours ago

👋 @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 commented 4 hours ago

(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)

openjournals / joss-reviews