[PRE REVIEW]: ngsPETSc: A coupling between NETGEN/NGSolve 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
Managing EiC: Daniel S. Katz

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/c42278c469f63f9f3420333d6654a599/status.svg)](https://joss.theoj.org/papers/c42278c469f63f9f3420333d6654a599)

Author instructions

Thanks for submitting your paper to JOSS @UZerbinati. Currently, there isn't a JOSS editor assigned to your paper.

@UZerbinati if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (651.8 files/s, 365512.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1          12092              0          11876
Python                          26            353            626           2244
reStructuredText                14            349            345           1179
TeX                              1              1              0            184
YAML                             4             29             17            161
Markdown                         2             23              0             77
Dockerfile                       1              0             11             54
make                             2              6              7             50
DOS Batch                        1              8              1             26
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            53          12861           1007          15854
-------------------------------------------------------------------------------

Commit count by author:

   223	Umberto Zerbinati
    11	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

- 10.5281/zenodo.12650574 is OK
- 10.1137/15M1025785 is OK
- 10.5802/smai-jcm.72 is OK
- 10.1007/s10208-005-0183-0 is OK

MISSING DOIs

- 10.1007/s007910050004 may be a valid DOI for title: NETGEN An advancing front 2D/3D-mesh generator bas...
- No DOI given, and none found for title: C++ 11 implementation of finite elements in NGSolv...
- No DOI given, and none found for title: Firedrake user manual
- No DOI given, and none found for title: PETSc/TAO Users Manual
- No DOI given, and none found for title: Parallel distributed computing using Python
- 10.1137/050646421 may be a valid DOI for title: An Augmented Lagrangian–Based Approach to the Osee...
- No DOI given, and none found for title: OpenCASCADE
- No DOI given, and none found for title: ML3.1 Smoothed Aggregation User’s Guide
- 10.1142/s0218202594000133 may be a valid DOI for title: Stability of higher order triangular Hood–Taylor m...
- No DOI given, and none found for title: A numerical solution of the Navier–Stokes equation...
- No DOI given, and none found for title: hypre: A Library of High Performance Preconditione...
- 10.1137/0907058 may be a valid DOI for title: GMRES: A Generalized Minimal Residual Algorithm fo...

INVALID DOIs

- https://doi.org/10.1016/S0021-9991(03)00194-3 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/nme.1620121010 is INVALID because of 'https://doi.org/' prefix

[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 📄 👈

[editorialbot]

Five most similar historical JOSS papers:

DMStag: Staggered, Structured Grids for PETSc
Submitting author: @psanan
Handling editor: @kyleniemeyer (Active)
Reviewers: @elauksap, @mbarzegary
Similarity score: 0.7462

OpenCMP: An Open-Source Computational Multiphysics Package
Submitting author: @nasserma
Handling editor: @lucydot (Active)
Reviewers: @bonh, @WilkAndy
Similarity score: 0.7422

GridapDistributed: a massively parallel finite element toolbox in Julia
Submitting author: @amartinhuertas
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @Leticia-maria, @jedbrown
Similarity score: 0.7406

scikit-fem: A Python package for finite element assembly
Submitting author: @kinnala
Handling editor: @meg-simula (Retired)
Reviewers: @thelfer, @AnjaliSandip
Similarity score: 0.7384

NGSTrefftz: Add-on to NGSolve for Trefftz methods
Submitting author: @PaulSt
Handling editor: @Nikoleta-v3 (Active)
Reviewers: @mscroggs, @thelfer
Similarity score: 0.7284

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

👋 @jedbrown - would you be able to edit this submission?

[danielskatz]

@editorialbot invite @jedbrown as editor

[editorialbot]

Invitation to edit this submission sent!

[danielskatz]

👋 @UZerbinati - your readme appears blank, which will need to be changed to satisfy JOSS review criteria, such as in https://joss.readthedocs.io/en/latest/review_criteria.html#documentation

[UZerbinati]

Hi @danielskatz ! Thank you for letting me know: I've updated the README to include a statement of need, installation instructions and a minimal example on how to test the code.
Also, I now realise that I miss-typed the title of the paper during submission, the correct title should be: "ngsPETSc: A coupling between NETGEN/NGSolve and PETSc"

[danielskatz]

I've changed the title here. The editor may also need to change it once the review starts and that issue is created.

[UZerbinati]

I've added DOIs for the papers I could find a DOI for.
I suspect there are no DOIs for the remaining papers.
@editorialbot generate pdf
@editorialbot check references

[danielskatz]

@UZerbinati - A JOSS command needs to be the first thing in a new comment

[UZerbinati]

@editorialbot check references

[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

MISSING 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

INVALID DOIs

- None

[UZerbinati]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

DMStag: Staggered, Structured Grids for PETSc
Submitting author: @psanan
Handling editor: @kyleniemeyer (Active)
Reviewers: @elauksap, @mbarzegary
Similarity score: 0.7412

OpenCMP: An Open-Source Computational Multiphysics Package
Submitting author: @nasserma
Handling editor: @lucydot (Active)
Reviewers: @bonh, @WilkAndy
Similarity score: 0.7377

GridapDistributed: a massively parallel finite element toolbox in Julia
Submitting author: @amartinhuertas
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @Leticia-maria, @jedbrown
Similarity score: 0.7324

scikit-fem: A Python package for finite element assembly
Submitting author: @kinnala
Handling editor: @meg-simula (Retired)
Reviewers: @thelfer, @AnjaliSandip
Similarity score: 0.7322

FEniCS-arclength: A numerical continuation package in FEniCS for nonlinear problems in solid mechanics
Submitting author: @pprachas
Handling editor: @prashjha (Active)
Reviewers: @w-luo-academic, @kingyin3613
Similarity score: 0.7253

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[jedbrown]

@editorialbot assign @jedbrown as editor

👋 Hi, sorry to be slow picking this up.

[editorialbot]

Assigned! @jedbrown is now the editor

[danielskatz]

thanks @jedbrown

[editorialbot]

Assigned! @danielskatz is now the editor

[danielskatz]

@UZerbinati - Please suggest ~5 potential reviewers. You can search the list of people that have already agreed to review and may be suitable for this submission. Or people who aren't in the JOSS system would also be ok. If you know their GitHub usernames, then please mention them here in this thread (without tagging them with an @).

[jedbrown]

I'm very sorry about my extended lapse here. Thanks for picking it up, Dan.

[UZerbinati]

Dear @danielskatz ,
may I suggest:

Paul Stocker: PaulSt
Christopher Lehrenfeld: schruste
Robert Kirby: rckirby
Matt Knepley: knepley
Christopher Lackner: ChrLackner

[danielskatz]

👋 @schruste - Would you be willing to review this JOSS submission?

[danielskatz]

👋 @PaulSt & @rckirby, would one or both of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[danielskatz]

👋 @knepley & @ChrLackner, would one or both of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[rckirby]

What are your conflict of interest guidelines? I am a co-author/collaborator with one of the authors.

[danielskatz]

@rckirby - see https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#joss-conflict-of-interest-policy Basically, it depends on how long ago the collaboration ended (the work was done), assuming it is not current.

[PaulSt]

@danielskatz I am sorry, but I believe reviewing this matter would present a conflict of interest for me. However, I can additionally suggest @thelfer & @mscroggs as reviewers.

[danielskatz]

👋 @thelfer & @mscroggs, would one or both of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[rckirby]

I've read the CoI policy and will decline.

[ChrLackner]

Sorry, @danielskatz I have COI as well here.

[thelfer]

@danielskatz I am interested.

[danielskatz]

Thanks @thelfer - I'll add you in the system, but we won't start the review until we get at least one more reviewer.

[danielskatz]

@editorialbot add @thelfer as reviewer

[editorialbot]

@thelfer added to the reviewers list!

[knepley]

@danielskatz I don't think I am conflicted, so I can do it.

[danielskatz]

Thanks @knepley! I'll add you, and start the review

[danielskatz]

@editorialbot add @knepley as reviewer

[editorialbot]

@knepley added to the reviewers list!

[danielskatz]

@editorialbot start review

[danielskatz]

@editorialbot start review

let's try that again...

[danielskatz]

Sorry, we're have a systems issue, but hopefully we'll be able to start the review soon

[schruste]

Sorry for the late reply. I also think that that I have a COI here.

[danielskatz]

@editorialbot start review

We think this is fixed - let's see

[editorialbot]

OK, I've started the review over in #7359.