[REVIEW]: ngsPETSc: A coupling between NETGEN/NGSolve 2 and PETSc

[editorialbot]

Submitting author: @UZerbinati (Umberto Zerbinati)
Repository: https://github.com/NGSolve/ngsPETSc
Branch with paper.md (empty if default branch):
Version: v.0.0.5
Editor: @danielskatz
Reviewers: @thelfer, @knepley
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c42278c469f63f9f3420333d6654a599"><img src="https://joss.theoj.org/papers/c42278c469f63f9f3420333d6654a599/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c42278c469f63f9f3420333d6654a599/status.svg)](https://joss.theoj.org/papers/c42278c469f63f9f3420333d6654a599)

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

@thelfer & @knepley, 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 @knepley

📝 Checklist for @thelfer

[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]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (608.1 files/s, 343173.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1          12092              0          11876
Python                          26            372            651           2331
reStructuredText                14            349            345           1179
TeX                              1              0              0            183
YAML                             4             29             17            164
Markdown                         2             29              0             92
Dockerfile                       1              0             11             51
make                             2              6              7             50
TOML                             1              3              0             38
DOS Batch                        1              8              1             26
-------------------------------------------------------------------------------
SUM:                            53          12888           1032          15990
-------------------------------------------------------------------------------

Commit count by author:

   266	Umberto Zerbinati
    21	Patrick Farrell
    14	Jack Betteridge
     8	Francesco Ballarin
     8	Stefano Zampini
     4	Matthew Scroggs
     2	Connor Ward
     1	Nacime Bouziani
     1	Pablo Brubeck

[editorialbot]

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

✅ OK DOIs

- 10.1007/s007910050004 is OK
- 10.25561/104839 is OK
- 10.2172/2205494 is OK
- 10.1016/j.advwatres.2011.04.013 is OK
- 10.5281/zenodo.12650574 is OK
- 10.1137/15M1025785 is OK
- 10.1016/S0021-9991(03)00194-3 is OK
- 10.1137/050646421 is OK
- 10.1002/nme.1620121010 is OK
- 10.5802/smai-jcm.72 is OK
- 10.1142/S0218202594000133 is OK
- 10.1016/0045-7930(73)90027-3 is OK
- 10.1007/3-540-47789-6_66 is OK
- 10.1137/0907058 is OK
- 10.1007/s10208-005-0183-0 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: C++ 11 implementation of finite elements in NGSolv...
- No DOI given, and none found for title: OpenCASCADE
- No DOI given, and none found for title: ML3.1 Smoothed Aggregation User’s Guide

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1201

✅ 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 📄 👈

[knepley]

Review checklist for @knepley

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/NGSolve/ngsPETSc?
• 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 (@UZerbinati) 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?

[danielskatz]

@thelfer & @knepley - 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#7359 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.

[thelfer]

Review checklist for @thelfer

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/NGSolve/ngsPETSc?
• 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 (@UZerbinati) 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?

[knepley]

@danielskatz Looking at the repo, based on the number of commits, number of lines, and recently opened MRs, the authors should probably also include JDBetteridge in the author list. How do you normally approach this at JOSS?

[danielskatz]

@knepley - This is really a question for the author, rather than for JOSS.

👋 @UZerbinati - can you say something about this?

[knepley]

@danielskatz Oh, I meant "I am allowed to talk directly to the author", so I guess the answer is yes :)

[danielskatz]

Yes! JOSS reviewers are meant to be interactive between the author(s) and reviewers, with my role being to keep things on track and progressing. Think of this like any other open source software discussion.

[knepley]

@UZerbinati There is not really a State of the Field in the paper, which would be a brief list of packages with similar capabilities, maybe DUNE or FreeFEM?

[knepley]

@UZerbinati I don't see guidelines for contributing. Perhaps it would be enough to point to the Firedrake guidelines in the documentation?

[UZerbinati]

Dear @danielskatz and @knepley, the reason why Jack is not among the authors is the fact that most of his contributions were made after the submission of this manuscript. After talking with the other authors and Jack, we decided to add Jack among the paper's authors.

[danielskatz]

👋 @thelfer - Will you be able to start on your review soon?

[thelfer]

👋 @thelfer - Will you be able to start on your review soon?

I'll start my review next week after my vacations :)

[danielskatz]

👋 @thelfer - How are things going now?

[thelfer]

@danielskatz Slowly for sure.

I made issues on the installation process.

• [JOSS review] Installation link in README.md is broken NGSolve/ngsPETSc#54
• [JOSS Review] Feedback on the installation proccess NGSolve/ngsPETSc#55
• [JOSS REVIEW] first example fails NGSolve/ngsPETSc#56

I must now recompile ngsolve with OpenCascade enabled for the tests to work.

[thelfer]

I am pretty busy this week and the next one, but after that sky is blue, so I think that the review will be over at the end of the month

[UZerbinati]

@thelfer it might be helpful that we started distributing a wheel for ngsPETSc (it is still in alpha phase because wheels with petsc4py and mpi4py are always tricky): PyPI

[danielskatz]

@knepley - I think your concerns (or some of them) might have been addressed. Can you take another look and see if there's more that you can check off your review checklist?

[thelfer]

it might be helpful that we started distributing a wheel for ngsPETSc

Thanks for the input. I'll have a look quickly.

[thelfer]

@danielskatz I almost finished my review. There are still a few questions left regarding the availability of the tests cases exhibited in the paper: NGSolve/ngsPETSc#64

[thelfer]

Issue NGSolve/ngsPETSc#64 has been quickly fixed. On my side, everything is ok and the paper is ready to be published.

[danielskatz]

Thanks @thelfer!

[danielskatz]

@thelfer - can you check off the last item in your checklist?

[danielskatz]

👋 @knepley - How are you doing on this? It looks like you just have a few items left to check off. I wonder if they have been addressed by the authors now.

[thelfer]

@thelfer - can you check off the last item in your checklist?

Which one ?

I did not check for automated tests and did not see any "state of the art" section in the documentation. Are they required ?

[danielskatz]

👋 @thelfer

Note that the definition for Automated tests (which might be slightly misnamed) is "Are there automated tests or manual steps described so that the functionality of the software can be verified?"

And yes, the paper is required to discuss the state of the field - "Do the authors describe how this software compares to other commonly-used packages?"

If neither of these can be checked off by you currently, the authors will need to address them before we can say that your review is complete and the work can be published.

[thelfer]

@danielskatz

"Are there automated tests or manual steps described so that the functionality of the software can be verified?"

Digging in the Contributing section of the documentation, there is a paragraph showing how to run the tests.
It works.

"Do the authors describe how this software compares to other commonly-used packages?"

I would say that this point is questionnable.

The paper shows how useful it is for NGSolve and Firedrake, and what new features are brought to those solvers.

I don't even know if this criterion is applicable in this context.

[UZerbinati]

@danielskatz @thelfer

Regarding automated testing, we also have a CI which was running smoothly until yesterday. I'm planning to find out the bug that is causing its failure this weekend. Here is the GitHub workflow for the CI: https://github.com/NGSolve/ngsPETSc/blob/main/.github/workflows/ngsPETSc.yml.

Regarding the state of the art, as suggested by @knepley we added a paragraph where we briefly list packages with similar capabilities, including DUNE and FreeFEM, here you can find the MR: NGSolve/ngsPETSc#62

[thelfer]

@UZerbinati Thanks for the inputs
@danielskatz Everything is now ok on my side

[danielskatz]

Thanks again @thelfer

[thelfer]

Thanks again @thelfer

My pleasure.