Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Closed
editorialbot opened this issue Oct 15, 2024 · 71 comments
Closed

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

editorialbot opened this issue Oct 15, 2024 · 71 comments
Assignees
Labels
accepted Dockerfile published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Oct 15, 2024

Submitting author: @UZerbinati (Umberto Zerbinati)
Repository: https://github.com/NGSolve/ngsPETSc
Branch with paper.md (empty if default branch):
Version: 0.0.8
Editor: @danielskatz
Reviewers: @thelfer, @knepley
Archive: 10.5281/zenodo.14295034

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 editorialbot added Dockerfile Python review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Oct 15, 2024
@editorialbot
Copy link
Collaborator Author

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
Copy link
Collaborator Author

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
Copy link
Collaborator Author

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
Copy link
Collaborator Author

Paper file info:

📄 Wordcount for paper.md is 1201

✅ The paper includes a Statement of need section

@editorialbot
Copy link
Collaborator Author

License info:

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

@editorialbot
Copy link
Collaborator Author

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

@knepley
Copy link

knepley commented Oct 15, 2024

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

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
Copy link

@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
Copy link

thelfer commented Oct 15, 2024

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

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
Copy link

knepley commented Oct 16, 2024

@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
Copy link

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

👋 @UZerbinati - can you say something about this?

@knepley
Copy link

knepley commented Oct 16, 2024

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

@danielskatz
Copy link

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
Copy link

knepley commented Oct 16, 2024

@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
Copy link

knepley commented Oct 16, 2024

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

@UZerbinati
Copy link

UZerbinati commented Oct 16, 2024

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.

UZerbinati added a commit to NGSolve/ngsPETSc that referenced this issue Oct 16, 2024
UZerbinati added a commit to NGSolve/ngsPETSc that referenced this issue Oct 16, 2024
@danielskatz
Copy link

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

@thelfer
Copy link

thelfer commented Nov 1, 2024

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

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

@danielskatz
Copy link

👋 @thelfer - How are things going now?

@editorialbot
Copy link
Collaborator Author

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

@danielskatz
Copy link

@editorialbot check references

@editorialbot
Copy link
Collaborator Author

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

✅ OK DOIs

- 10.1007/s007910050004 is OK
- 10.25561/104839 is OK
- 10.1145/2629697 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
- 10.1007/s00607-010-0110-3 is OK
- 10.1515/jnma-2023-0089 is OK
- 10.5281/zenodo.10447666 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
- No DOI given, and none found for title: FreeFem++ manual
- No DOI given, and none found for title: A three-dimensional finite element mesh generator ...
- No DOI given, and none found for title: Flexible, scalable mesh and data management using ...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

@danielskatz
Copy link

@UZerbinati - I have suggested some small changes in NGSolve/ngsPETSc#67 - please merge this.

Also, I note there is no Acknowledgements section in your paper. Should there be, mentioning any funding or anything else?

@danielskatz
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

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

@danielskatz
Copy link

👋 @UZerbinati - thanks for merging the PR. Once you've decided on the Ack section and perhaps made a change to add it, please

  • Make a tagged release of your software, and list the version tag of the archived version here.
  • Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
  • Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

@UZerbinati
Copy link

Dear @danielskatz,
we have updated the paper to include an acknowledgements section. The DOI of the archived version is 10.5281/zenodo.14295034.

@UZerbinati
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

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

@danielskatz
Copy link

@editorialbot set 10.5281/zenodo.14295034 as archive

@editorialbot
Copy link
Collaborator Author

Done! archive is now 10.5281/zenodo.14295034

@danielskatz
Copy link

@editorialbot set 0.0.8 as version

@editorialbot
Copy link
Collaborator Author

Done! version is now 0.0.8

@danielskatz
Copy link

@editorialbot recommend-accept

@editorialbot
Copy link
Collaborator Author

Attempting dry run of processing paper acceptance...

@editorialbot
Copy link
Collaborator Author

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

✅ OK DOIs

- 10.1007/s007910050004 is OK
- 10.25561/104839 is OK
- 10.1145/2629697 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
- 10.2172/974895 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
- 10.1007/s00607-010-0110-3 is OK
- 10.1515/jnma-2023-0089 is OK
- 10.5281/zenodo.10447666 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: FreeFem++ manual
- No DOI given, and none found for title: A three-dimensional finite element mesh generator ...
- No DOI given, and none found for title: Flexible, scalable mesh and data management using ...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6237, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 9, 2024
@danielskatz
Copy link

@editorialbot accept

@editorialbot
Copy link
Collaborator Author

Doing it live! Attempting automated processing of paper acceptance...

@editorialbot
Copy link
Collaborator Author

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Betteridge
  given-names: Jack
  orcid: "https://orcid.org/0000-0002-3919-8603"
- family-names: Farrell
  given-names: Patrick E.
  orcid: "https://orcid.org/0000-0002-1241-7060"
- family-names: Hochsteger
  given-names: Matthias
  orcid: "https://orcid.org/0009-0001-8842-3221"
- family-names: Lackner
  given-names: Christopher
  orcid: "https://orcid.org/0009-0000-3448-3002"
- family-names: Schöberl
  given-names: Joachim
  orcid: "https://orcid.org/0000-0002-1250-5087"
- family-names: Zampini
  given-names: Stefano
  orcid: "https://orcid.org/0000-0002-0435-0433"
- family-names: Zerbinati
  given-names: Umberto
  orcid: "https://orcid.org/0000-0002-2577-1106"
contact:
- family-names: Zerbinati
  given-names: Umberto
  orcid: "https://orcid.org/0000-0002-2577-1106"
doi: 10.5281/zenodo.14295034
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Betteridge
    given-names: Jack
    orcid: "https://orcid.org/0000-0002-3919-8603"
  - family-names: Farrell
    given-names: Patrick E.
    orcid: "https://orcid.org/0000-0002-1241-7060"
  - family-names: Hochsteger
    given-names: Matthias
    orcid: "https://orcid.org/0009-0001-8842-3221"
  - family-names: Lackner
    given-names: Christopher
    orcid: "https://orcid.org/0009-0000-3448-3002"
  - family-names: Schöberl
    given-names: Joachim
    orcid: "https://orcid.org/0000-0002-1250-5087"
  - family-names: Zampini
    given-names: Stefano
    orcid: "https://orcid.org/0000-0002-0435-0433"
  - family-names: Zerbinati
    given-names: Umberto
    orcid: "https://orcid.org/0000-0002-2577-1106"
  date-published: 2024-12-09
  doi: 10.21105/joss.07359
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7359
  title: "ngsPETSc: A coupling between NETGEN/NGSolve and PETSc"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07359"
  volume: 9
title: "ngsPETSc: A coupling between NETGEN/NGSolve and PETSc"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

@editorialbot
Copy link
Collaborator Author

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

@editorialbot
Copy link
Collaborator Author

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

@editorialbot
Copy link
Collaborator Author

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07359 joss-papers#6238
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07359
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Dec 9, 2024
@danielskatz
Copy link

Congratulations to @UZerbinati (Umberto Zerbinati) and co-authors on your publication!!

And thanks to @thelfer and @knepley for reviewing!
JOSS depends on volunteers and we couldn't succeed without you

@editorialbot
Copy link
Collaborator Author

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following

code snippets

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.07359/status.svg)](https://doi.org/10.21105/joss.07359)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07359">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07359/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07359/status.svg
   :target: https://doi.org/10.21105/joss.07359

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
accepted Dockerfile published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics
Projects
None yet
Development

No branches or pull requests

5 participants