[REVIEW]: GridapDistributed: a massively parallel finite element toolbox in Julia #4157

whedon · 2022-02-13T07:46:58Z

Submitting author: @amartinhuertas (Dr. Alberto F. Martin)
Repository: https://github.com/gridap/GridapDistributed.jl/
Branch with paper.md (empty if default branch): joss_paper
Version: v0.2.6
Editor: @Kevin-Mattheus-Moerman
Reviewers: @PetrKryslUCSD, @Leticia-maria, @jedbrown
Archive: 10.5281/zenodo.6622081

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Review checklist for @PetrKryslUCSD

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Documentation

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Software paper

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General checks

Repository: Is the source code for this software available at the repository url?
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Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 and who the target audience is?
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?

Review checklist for @jedbrown

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@amartinhuertas) 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

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 and who the target audience is?
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?

The text was updated successfully, but these errors were encountered:

whedon · 2022-02-13T07:47:01Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @PetrKryslUCSD, @Leticia-maria, @jedbrown it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon · 2022-02-13T07:47:09Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.04 s (1178.8 files/s, 104503.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           30            547            154           2627
TOML                             4            110              1            459
Markdown                        12             97              0            226
YAML                             2              0              6            110
Bourne Shell                     1              1              3              3
-------------------------------------------------------------------------------
SUM:                            49            755            164           3425
-------------------------------------------------------------------------------


Statistical information for the repository '35bcbf2144fe0509a1393d8a' was
gathered on 2022/02/13.
No commited files with the specified extensions were found.

whedon · 2022-02-13T07:47:11Z

PDF failed to compile for issue #4157 with the following error:

 Can't find any papers to compile :-(

Kevin-Mattheus-Moerman · 2022-02-13T07:49:51Z

@PetrKryslUCSD, @Leticia-maria, @jedbrown, @amartinhuertas this is where the review takes places. The reviewers may now start their review, guided by the check lists at the top of those issue.
Reviewers can provide feedback here or open dedicated issues on the projects repository and link to them here.

jedbrown · 2022-02-13T13:35:25Z

@whedon generate pdf from branch joss_paper

whedon · 2022-02-13T13:35:27Z

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

jedbrown · 2022-02-13T13:35:35Z

@whedon check references from branch joss_paper

whedon · 2022-02-13T13:35:40Z

Attempting to check references... from custom branch joss_paper

whedon · 2022-02-13T13:35:55Z

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

OK DOIs

- 10.1137/141000671 is OK
- 10.21105/JOSS.02520 is OK
- 10.1137/20M1328786 is OK
- 10.1007/978-3-030-23957-2 is OK
- 10.5194/GMD-6-2099-2013 is OK
- 10.1137/100791634 is OK
- 10.1006/JCPH.1996.0047 is OK
- 10.3402/TELLUSA.V56I5.14436 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2022-02-13T13:36:21Z

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

Leticia-maria · 2022-02-23T09:45:58Z

@whedon Should I send a PDF with my comments/reviews here?

danielskatz · 2022-02-23T13:21:35Z

👋 @Leticia-maria - @whedon is a bot, now in the processing of being replaced by @editorialbot. Your editor is @Kevin-Mattheus-Moerman, and he will be able to help you submit review comments,

Kevin-Mattheus-Moerman · 2022-02-23T14:09:02Z

@Leticia-maria you can try to attach a file here perhaps or give your feedback here in comments. Alternatively, and for longer discussions or larger issues, you could also open issues on the software repository and link to them here.

If you do create comments here you could use - [ ] to have checkboxes for individual items.

whedon · 2022-02-27T07:47:17Z

👋 @Leticia-maria, please update us on how your review is going (this is an automated reminder).

Kevin-Mattheus-Moerman · 2022-02-28T10:23:05Z

@arfon it looks like whedon still does the reminders. ☝️

arfon · 2022-02-28T11:17:03Z

@arfon it looks like whedon still does the reminders. ☝️

Yeah, that will stop being the case over the next ~2 weeks. Apologies for any confusion caused.

Kevin-Mattheus-Moerman · 2022-03-07T09:39:07Z

@PetrKryslUCSD, @Leticia-maria, @jedbrown I am just checking in to see how things are going. Could you please provide an update on review progress? If you need more time that is okay too. Thanks again for your help!

PetrKryslUCSD · 2022-03-08T16:07:12Z

@whedon generate pdf from branch joss_paper

editorialbot · 2022-03-08T16:07:13Z

My name is now @editorialbot

PetrKryslUCSD · 2022-03-08T16:07:37Z

@editorialbot generate pdf from branch joss_paper

editorialbot · 2022-03-08T16:07:38Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

PetrKryslUCSD · 2022-03-08T16:07:56Z

@editorialbot generate pdf

Kevin-Mattheus-Moerman · 2022-06-09T08:04:16Z

@openjournals/dev hmmm can you check what is going on here? ☝️

xuanxu · 2022-06-09T09:13:34Z

The code for a couple of figures with multiple images with the same caption was invalid. This PR changes it to use a single image with multiple panels and using valid syntax.

Kevin-Mattheus-Moerman · 2022-06-09T09:14:53Z

@amartinhuertas can you check this ☝️

Thanks for your help @xuanxu!

Kevin-Mattheus-Moerman · 2022-06-09T09:15:44Z

@xuanxu this does not explain the reference checking to behave differently though right? ☝️

xuanxu · 2022-06-09T09:20:49Z

@Kevin-Mattheus-Moerman Right. About the reference checking: it seems that the first time when trying to find suggestions for "MPI: A Message-Passing Interface Standard Version ..." the Crossref API failed to respond or errored. The second time probably it just responded with no suggestions.

amartinhuertas · 2022-06-09T09:32:59Z

@amartinhuertas can you check this point_up

I already accepted the PR. Thanks @xuanxu !

Kevin-Mattheus-Moerman · 2022-06-09T09:43:17Z

@editorialbot recommend-accept

editorialbot · 2022-06-09T09:43:19Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-06-09T09:43:21Z

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

OK DOIs

- 10.1016/j.cpc.2022.108341 is OK
- 10.1137/141000671 is OK
- 10.21105/JOSS.02520 is OK
- 10.1137/20M1328786 is OK
- 10.1007/978-3-030-23957-2 is OK
- 10.5194/GMD-6-2099-2013 is OK
- 10.1137/100791634 is OK
- 10.1006/JCPH.1996.0047 is OK
- 10.3402/TELLUSA.V56I5.14436 is OK
- 10.48550/ARXIV.2203.04629 is OK
- 10.1016/j.camwa.2020.06.009 is OK
- 10.1515/jnum-2012-0013 is OK
- 10.1007/s11831-017-9244-1 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.1515/jnma-2021-0081 is OK
- 10.1145/1163641.1163644 is OK
- 10.1007/978-3-642-23099-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-06-09T09:45:17Z

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

Check final proof 👉 openjournals/joss-papers#3270

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3270, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2022-06-09T14:31:25Z

@editorialbot accept

editorialbot · 2022-06-09T14:31:27Z

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

editorialbot · 2022-06-09T14:33:32Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-06-09T14:33:33Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04157 joss-papers#3271
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04157
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

editorialbot · 2022-06-09T15:10:27Z

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

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

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.04157/status.svg)](https://doi.org/10.21105/joss.04157)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04157">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04157/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04157/status.svg
   :target: https://doi.org/10.21105/joss.04157

This is how it will look in your documentation:

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Kevin-Mattheus-Moerman · 2022-06-09T15:12:08Z

Congratulations @amartinhuertas et al. 🎉 on your publication in JOSS!

@PetrKryslUCSD, @Leticia-maria, @jedbrown thank you so much for your review efforts!!!

whedon added Julia review Shell labels Feb 13, 2022

whedon assigned Kevin-Mattheus-Moerman Feb 13, 2022

whedon mentioned this issue Feb 13, 2022

[PRE REVIEW]: GridapDistributed: a massively parallel finite element toolbox in Julia #4085

Closed

whedon assigned jedbrown, Leticia-maria and PetrKryslUCSD Feb 14, 2022

xuanxu mentioned this issue Jun 9, 2022

Use single image per figure with markdown syntax gridap/GridapDistributed.jl#90

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 9, 2022

editorialbot added accepted published Papers published in JOSS labels Jun 9, 2022

Kevin-Mattheus-Moerman closed this as completed Jun 9, 2022

editorialbot mentioned this issue Oct 10, 2023

[PRE REVIEW]: hp3D: A Scalable MPI/OpenMP hp-Adaptive Finite Element Software Library for Complex Multiphysics Applications #5936

Closed

editorialbot mentioned this issue Feb 5, 2024

[PRE REVIEW]: HealpixMPI.jl: an MPI-parallel implementation of the Healpix tessellation scheme in Julia #6324

Closed

editorialbot mentioned this issue Jun 27, 2024

[PRE REVIEW]: DelaunayTriangulation.jl: A Julia package for Delaunay triangulations and Voronoi tessellations in the plane #6937

Closed

This was referenced Jul 16, 2024

[PRE REVIEW]: dlr.esy.grid.match: A Grid Matching & Conversion Tool #6993

Closed

[PRE REVIEW]: ngsPETSc: A coupling between NETGEN/NGSolve and PETSc #7014

Closed

editorialbot mentioned this issue Oct 9, 2024

[PRE REVIEW]: PyLops-MPI - MPI Powered PyLops with mpi4py #7339

Closed

This was referenced Oct 22, 2024

[PRE REVIEW]: PointClouds.jl: Fast & flexible processing of lidar data #7394

Open

[PRE REVIEW]: XCALibre.jl: an XPU unstructured finite volume Computational Fluid Dynamics library #7408

Closed

editorialbot mentioned this issue Nov 18, 2024

[PRE REVIEW]: CurvilinearGrids.jl: A Julia package for curvilinear coordinate transformations #7494

Closed

[REVIEW]: GridapDistributed: a massively parallel finite element toolbox in Julia #4157

[REVIEW]: GridapDistributed: a massively parallel finite element toolbox in Julia #4157

Comments

whedon commented Feb 13, 2022 • edited by editorialbot Loading

Status

Reviewer instructions & questions

Review checklist for @PetrKryslUCSD

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @Leticia-maria

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @jedbrown

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Feb 13, 2022

whedon commented Feb 13, 2022

whedon commented Feb 13, 2022

Kevin-Mattheus-Moerman commented Feb 13, 2022

jedbrown commented Feb 13, 2022

whedon commented Feb 13, 2022

jedbrown commented Feb 13, 2022

whedon commented Feb 13, 2022

whedon commented Feb 13, 2022

whedon commented Feb 13, 2022

Leticia-maria commented Feb 23, 2022

danielskatz commented Feb 23, 2022

Kevin-Mattheus-Moerman commented Feb 23, 2022

whedon commented Feb 27, 2022

Kevin-Mattheus-Moerman commented Feb 28, 2022

arfon commented Feb 28, 2022

Kevin-Mattheus-Moerman commented Mar 7, 2022

PetrKryslUCSD commented Mar 8, 2022

editorialbot commented Mar 8, 2022

PetrKryslUCSD commented Mar 8, 2022

editorialbot commented Mar 8, 2022

PetrKryslUCSD commented Mar 8, 2022

Kevin-Mattheus-Moerman commented Jun 9, 2022

xuanxu commented Jun 9, 2022

Kevin-Mattheus-Moerman commented Jun 9, 2022

Kevin-Mattheus-Moerman commented Jun 9, 2022

xuanxu commented Jun 9, 2022

amartinhuertas commented Jun 9, 2022

Kevin-Mattheus-Moerman commented Jun 9, 2022

editorialbot commented Jun 9, 2022

editorialbot commented Jun 9, 2022

editorialbot commented Jun 9, 2022

Kevin-Mattheus-Moerman commented Jun 9, 2022

editorialbot commented Jun 9, 2022

editorialbot commented Jun 9, 2022

editorialbot commented Jun 9, 2022

editorialbot commented Jun 9, 2022

Kevin-Mattheus-Moerman commented Jun 9, 2022

whedon commented Feb 13, 2022 •

edited by editorialbot

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