[REVIEW]: model-traits: Model attribute definitions for scientific simulations in C++ #3389

whedon · 2021-06-21T13:53:38Z

Submitting author: @jacobmerson (Jacob Merson)
Repository: https://github.com/jacobmerson/model-traits
Version: v0.2.0
Editor: @diehlpk
Reviewer: @daniellivingston, @pratikvn
Archive: 10.5281/zenodo.5247209

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Review checklist for @daniellivingston

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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 (@jacobmerson) 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

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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?
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 @pratikvn

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 (@jacobmerson) 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 · 2021-06-21T13:53:42Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @daniellivingston, @pratikvn 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:

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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 · 2021-06-21T13:53:49Z

PDF failed to compile for issue #3389 with the following error:

 Can't find any papers to compile :-(

whedon · 2021-06-21T13:53:50Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.18 s (326.5 files/s, 233198.6 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C/C++ Header                     20           6588            975          30382
C++                              19            169            201           2436
YAML                              4              0              3            731
Bourne Again Shell                2            115             74            564
CMake                            11             65             45            364
Markdown                          2             36              0             93
Bourne Shell                      2              0              0              9
--------------------------------------------------------------------------------
SUM:                             60           6973           1298          34579
--------------------------------------------------------------------------------


Statistical information for the repository '8ec564d2a729cd29c15b098b' was
gathered on 2021/06/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jacob Merson                    57         45198           4447          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Jacob Merson              40751           90.2          0.4                2.89

daniellivingston · 2021-06-24T02:34:12Z

@whedon generate pdf

whedon · 2021-06-24T02:34:20Z

PDF failed to compile for issue #3389 with the following error:

 Can't find any papers to compile :-(

daniellivingston · 2021-06-24T02:53:25Z

@diehlpk Is there supposed to be a PDF of the paper here, or am I missing something?

diehlpk · 2021-06-24T03:02:23Z

@whedon commands

whedon · 2021-06-24T03:02:26Z

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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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:

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@whedon generate pdf

# Compile the paper from alternative branch
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@whedon remind @reviewer in 2 weeks

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@whedon recommend-accept

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@whedon check references

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@whedon check repository

EiC TASKS

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

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

diehlpk · 2021-06-24T03:03:13Z

@whedon generate pdf from branch joss

whedon · 2021-06-24T03:03:15Z

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

whedon · 2021-06-24T03:03:35Z

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

diehlpk · 2021-06-24T03:05:19Z

@daniellivingston Yes, please find the links to the PDF above.

daniellivingston · 2021-06-24T03:05:28Z

@diehlpk Thank you!

jacobmerson · 2021-06-28T04:08:54Z

@whedon generate pdf from branch joss

Some minor clarifying changes were made to the figures.

whedon · 2021-06-28T04:08:56Z

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

whedon · 2021-06-28T04:09:16Z

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

whedon · 2021-07-05T13:53:52Z

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

whedon · 2021-07-05T13:53:52Z

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

daniellivingston · 2021-07-10T22:00:49Z

Hi all, sorry for the delay. I expect to have this wrapped up within the next 48 hours.

diehlpk · 2021-07-12T14:24:35Z

Hi all, sorry for the delay. I expect to have this wrapped up within the next 48 hours.

@daniellivingston No rush, just wanted to check how your review is going and if any issues arise.

diehlpk · 2021-07-26T15:22:22Z

@whedon remind @daniellivingston in 2 weeks

whedon · 2021-07-26T15:22:24Z

Reminder set for @daniellivingston in 2 weeks

whedon · 2021-08-24T19:30:29Z

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

@whedon commands

diehlpk · 2021-08-24T19:30:42Z

@whedon commands

whedon · 2021-08-24T19:30:44Z

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 recommend-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 · 2021-08-24T19:31:08Z

@whedon set 10.5281/zenodo.5247209 as archive

whedon · 2021-08-24T19:31:12Z

OK. 10.5281/zenodo.5247209 is the archive.

diehlpk · 2021-08-24T19:32:31Z

@daniellivingston and @pratikvn thanks for reviewing and improving the paper and code.

diehlpk · 2021-08-24T19:32:46Z

@whedon recommend-accept

whedon · 2021-08-24T19:32:49Z

Attempting dry run of processing paper acceptance...

whedon · 2021-08-24T19:32:56Z

PDF failed to compile for issue #3389 with the following error:

 Can't find any papers to compile :-(

diehlpk · 2021-08-24T19:33:29Z

@whedon generate pdf from branch joss

whedon · 2021-08-24T19:33:32Z

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

whedon · 2021-08-24T19:33:53Z

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

danielskatz · 2021-08-24T19:39:36Z

@diehlpk - did you mean to do @whedon recommend-accept from branch joss?

diehlpk · 2021-08-24T19:53:33Z

@whedon recommend-accept from branch joss

whedon · 2021-08-24T19:53:35Z

Attempting dry run of processing paper acceptance...

whedon · 2021-08-24T19:53:41Z

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

OK DOIs

- 10.1002/(SICI)1097-0207(19970515)40:9<1573::AID-NME128>3.0.CO;2-9 is OK
- 10.1080/10255842.2018.1538414 is OK
- 10.1145/2814935 is OK
- 10.1007/s003660200030 is OK
- 10.2172/1349054 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-08-24T19:53:58Z

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

Check final proof 👉 openjournals/joss-papers#2531

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2531, 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

diehlpk · 2021-08-24T19:55:07Z

@diehlpk - did you mean to do @whedon recommend-accept from branch joss?

@danielskatz Yes, we should find some solution to store the branch with the paper.

danielskatz · 2021-08-24T20:11:27Z

👋 @jacobmerson - I'm the AEiC on duty this week, and am finishing the processing of your submission. I've suggested a number of changes to the paper in jacobmerson/model-traits#8. Please either merge this or let me know what you disagree with, then we can complete the publication process.

jacobmerson · 2021-08-24T21:33:03Z

@danielskatz I have merged your pull request with wording changes.

danielskatz · 2021-08-24T23:26:41Z

@whedon accept deposit=true from branch joss

whedon · 2021-08-24T23:26:44Z

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

whedon · 2021-08-24T23:27:18Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-08-24T23:27:18Z

🚨🚨🚨 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.03389 joss-papers#2532
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03389
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2021-08-24T23:35:02Z

Congratulations to @jacobmerson (Jacob Merson) and co-author!!

And thanks to @diehlpk for editing, and @daniellivingston and @pratikvn for reviewing!
We couldn't do this without you!

whedon · 2021-08-24T23:35:05Z

🎉🎉🎉 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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</a>

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.. image:: https://joss.theoj.org/papers/10.21105/joss.03389/status.svg
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whedon added C++ CMake review Shell labels Jun 21, 2021

whedon assigned diehlpk Jun 21, 2021

whedon mentioned this issue Jun 21, 2021

[PRE REVIEW]: model-traits: Model attribute definitions for scientific simulations in C++ #3307

Closed

whedon assigned pratikvn and daniellivingston Jun 22, 2021

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 24, 2021

whedon added accepted published Papers published in JOSS labels Aug 24, 2021

danielskatz closed this as completed Aug 24, 2021

[REVIEW]: model-traits: Model attribute definitions for scientific simulations in C++ #3389

[REVIEW]: model-traits: Model attribute definitions for scientific simulations in C++ #3389

Comments

whedon commented Jun 21, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @daniellivingston

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @pratikvn

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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