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[REVIEW]: ngsPETSc: A coupling between NETGEN/NGSolve 2 and PETSc #7359

Open editorialbot opened 1 month ago

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@uzerbinati<!--end-author-handle-- (Umberto Zerbinati) Repository: https://github.com/NGSolve/ngsPETSc Branch with paper.md (empty if default branch): Version: v.0.0.5 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @thelfer, @knepley Archive: Pending

Status

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 commented 1 month 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:

@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 commented 1 month ago

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 commented 1 month ago 
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 commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1201

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

knepley commented 1 month ago

Review checklist for @knepley

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

danielskatz commented 1 month ago

@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 commented 1 month ago

Review checklist for @thelfer

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

knepley commented 1 month ago

@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 commented 1 month ago

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

👋 @UZerbinati - can you say something about this?

knepley commented 1 month ago

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

danielskatz commented 1 month ago

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 commented 1 month ago

@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 commented 1 month ago

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

UZerbinati commented 1 month ago

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 commented 3 weeks ago

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

thelfer commented 3 weeks ago

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

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

danielskatz commented 1 week ago

👋 @thelfer - How are things going now?

thelfer commented 1 week ago

@danielskatz Slowly for sure.

I made issues on the installation process.

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

thelfer commented 1 week ago

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 commented 3 days ago

@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 commented 1 day ago

@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 commented 1 day ago

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

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