[REVIEW]: libCEED: Fast algebra for high-order element-based discretizations #2945

whedon · 2021-01-07T01:34:43Z

Submitting author: @jedbrown (Jed Brown)
Repository: https://github.com/CEED/libCEED
Version: v0.9.0
Editor: @diehlpk
Reviewers: @thelfer, @FreddieWitherden,
Archive: 10.5281/zenodo.5080235

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Review checklist for @thelfer

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General checks

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Functionality

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Documentation

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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?
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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 @FreddieWitherden

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 (@jedbrown) 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: Do the authors clearly state 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 · 2021-01-07T01:34:47Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @thelfer, @FreddieWitherden, @pbauman 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.

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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 · 2021-01-07T01:35:25Z

PDF failed to compile for issue #2945 with the following error:

Can't find any papers to compile :-(

jedbrown · 2021-01-07T01:42:49Z

@whedon generate pdf from branch joss-paper

whedon · 2021-01-07T01:42:52Z

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon · 2021-01-07T01:43:56Z

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

jedbrown · 2021-01-07T01:46:52Z

FYI, we intend to release v0.8.0 no later than March. It's feature-complete from our perspective, but I'd love to include reviewer feedback (which could involve API changes). In any case, we'll tag v0.8.0 by the time this review completes.

Also note that the branch joss-paper is just branch main plus the paper. We plan to merge it upon completion of the review.

diehlpk · 2021-01-12T20:19:01Z

@whedon commands

whedon · 2021-01-12T20:19:03Z

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

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@whedon re-invite @username as reviewer

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@whedon remove @username as reviewer

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@whedon list editors

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EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
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# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

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EiC TASKS

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diehlpk · 2021-01-12T20:20:39Z

@whedon remind @thelfer, @FreddieWitherden, @pbauman in 2 weeks

whedon · 2021-01-12T20:20:42Z

Reminder set for @thelfer, @FreddieWitherden, @pbauman in 2 weeks

FreddieWitherden · 2021-01-16T23:01:34Z

Would it be possible to get a re-invite so I can accept the invitation? (The previous one has expired.)

diehlpk · 2021-01-18T01:22:44Z

@whedon commands

whedon · 2021-01-18T01:22:46Z

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

diehlpk · 2021-01-18T01:23:17Z

@whedon re-invite @FreddieWitherden as reviewer

whedon · 2021-01-18T01:23:21Z

OK, the reviewer has been re-invited.

@FreddieWitherden please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

diehlpk · 2021-01-18T01:23:42Z

@FreddieWitherden Sure, the link expires after two weeks.

whedon · 2021-01-21T01:34:57Z

👋 @FreddieWitherden, please update us on how your review is going.

whedon · 2021-01-21T01:34:57Z

👋 @thelfer, please update us on how your review is going.

whedon · 2021-01-21T01:34:57Z

👋 @pbauman, please update us on how your review is going.

jedbrown · 2021-07-07T20:32:49Z

BTW, I intend to squash-merge the branch upon acceptance, but I would like to wait for AEiC approval first (for repository hygiene).

diehlpk · 2021-07-07T21:06:33Z

@whedon recommend-accept from branch joss-paper

whedon · 2021-07-07T21:06:36Z

Attempting dry run of processing paper acceptance...

whedon · 2021-07-07T21:06:53Z

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

OK DOIs

- 10.1007/s10915-010-9396-8 is OK
- 10.1177/10943420211020803 is OK
- 10.5281/zenodo.2641316 is OK
- 10.5281/zenodo.3860804 is OK
- 10.1177/1094342020915762 is OK
- 10.1137/141000671 is OK
- 10.5281/zenodo.4895340 is OK
- 10.25080/Majora-342d178e-00c is OK
- 10.11578/dc.20171025.1248 is OK
- 10.1016/j.camwa.2020.06.009 is OK
- 10.1145/2833157.2833162 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/0021-9991(80)90005-4 is OK
- 10.1002/fld.1650170103 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1515/jnma-2020-0043 is OK
- 10.1145/1498765.1498785 is OK
- 10.1137/1036141 is OK
- 10.1007/s10915-004-4787-3 is OK
- 10.1109/TPDS.2021.3084070 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-07-07T21:07:09Z

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

Check final proof 👉 openjournals/joss-papers#2437

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2437, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-paper

kyleniemeyer · 2021-07-09T16:56:46Z

Hi @jedbrown, I was looking over the paper before accepting, and it looks to be missing the required Statement of Need section. Can you please add this? The easiest thing is probably to just add it to the Summary section (i.e., "Summary and Statement of Need") or something.

Also, the Zenodo archive appears to have a number of authors listed that do not appear in the paper. Usually we ask that these match up, unless you are purposely including additional folks.

jedbrown · 2021-07-09T17:26:33Z

Thanks, I revised the heading and have matched the author list in the archive.

kyleniemeyer · 2021-07-09T17:30:02Z

@whedon generate pdf from branch joss-paper

whedon · 2021-07-09T17:30:05Z

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon · 2021-07-09T17:30:30Z

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

kyleniemeyer · 2021-07-09T17:34:46Z

Thanks @jedbrown, this now looks good to me to accept. Did you want to merge the branch now, or after we publish?

jedbrown · 2021-07-09T17:40:04Z

Great, I have merged the branch.

kyleniemeyer · 2021-07-09T17:41:35Z

@whedon accept

whedon · 2021-07-09T17:41:38Z

To recommend a paper to be accepted use @whedon recommend-accept

kyleniemeyer · 2021-07-09T17:41:49Z

@whedon accept deposit=true

whedon · 2021-07-09T17:41:52Z

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

whedon · 2021-07-09T17:42:32Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-07-09T17:42:32Z

🚨🚨🚨 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.02945 joss-papers#2439
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02945
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2021-07-09T17:48:04Z

Congrats @jedbrown on your article's publication in JOSS!

Many thanks to @thelfer and @FreddieWitherden for reviewing this submission, and @diehlpk for editing it.

whedon · 2021-07-09T17:48:07Z

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

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Markdown:
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HTML:
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   :target: https://doi.org/10.21105/joss.02945

This is how it will look in your documentation:

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jedbrown · 2021-07-09T17:49:04Z

Thanks, everyone!

whedon added C Makefile review Shell labels Jan 7, 2021

whedon assigned diehlpk Jan 7, 2021

whedon mentioned this issue Jan 7, 2021

[PRE REVIEW]: libCEED: Fast algebra for high-order element-based discretizations #2938

Closed

whedon assigned pbauman Jan 8, 2021

openjournals deleted a comment from whedon Jan 12, 2021

whedon assigned FreddieWitherden Jan 17, 2021

This was referenced Jan 23, 2021

Error/Exception Handling CEED/libCEED#696

Closed

Obtaining libCEED version at compile time/run time CEED/libCEED#697

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whedon added accepted published Papers published in JOSS labels Jul 9, 2021

kyleniemeyer closed this as completed Jul 9, 2021

ShantanuDash mentioned this issue Jul 16, 2021

Update Requirements.txt benjaminbolling/RSW#1

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editorialbot mentioned this issue Oct 10, 2023

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[PRE REVIEW]: MOLE: Mimetic Operators Library Enhanced #6005

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[PRE REVIEW]: NebulaSEM: A high-order discontinuous Galerkin spectral element code for atmospheric modeling #6180

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[PRE REVIEW]: CNearest: A C++ toolkit to use the nearest-neighbour method of regularised stokeslets algorithm to solve viscous flow problems #7191

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[PRE REVIEW]: gpu-ISTL - Extending OPM Flow with GPU Linear Solvers #7524

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[REVIEW]: libCEED: Fast algebra for high-order element-based discretizations #2945

[REVIEW]: libCEED: Fast algebra for high-order element-based discretizations #2945

Comments

whedon commented Jan 7, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @thelfer

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @FreddieWitherden

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Jan 7, 2021

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diehlpk commented Jan 12, 2021

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FreddieWitherden commented Jan 16, 2021

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