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[REVIEW]: DEPP - Differential Evolution Parallel Program #1701

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whedon opened this issue Sep 3, 2019 · 138 comments
Closed

[REVIEW]: DEPP - Differential Evolution Parallel Program #1701

whedon opened this issue Sep 3, 2019 · 138 comments

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@whedon
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@whedon whedon commented Sep 3, 2019

Submitting author: @gbertoldo (Guilherme Bertoldo)
Repository: https://github.com/gbertoldo/DEPP
Version: v1.0.0
Editor: @meg-simula
Reviewer: @HaoZeke, @dham
Archive: 10.5281/zenodo.3722436

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/76800aa00f4d57b1695c876c0b936ba3"><img src="https://joss.theoj.org/papers/76800aa00f4d57b1695c876c0b936ba3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/76800aa00f4d57b1695c876c0b936ba3/status.svg)](https://joss.theoj.org/papers/76800aa00f4d57b1695c876c0b936ba3)

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

@HaoZeke & @dham, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @meg-simula know.

Please try and complete your review in the next two weeks

Review checklist for @HaoZeke

Conflict of interest

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 (@gbertoldo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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?

Review checklist for @dham

Conflict of interest

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 (@gbertoldo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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?
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@whedon whedon commented Sep 3, 2019

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

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:

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

watching

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

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
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@whedon whedon commented Sep 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Sep 3, 2019

@meg-simula

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@meg-simula meg-simula commented Sep 3, 2019

@HaoZeke @dham Thanks again for agreeing to review. Reviewer checklists have been generated for each you above - take a look and dig in at will.

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@meg-simula meg-simula commented Sep 3, 2019

@whedon commands

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@whedon whedon commented Sep 3, 2019

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

# 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

# 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 accept the paper and deposit with Crossref
@whedon accept

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

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@meg-simula meg-simula commented Sep 3, 2019

@whedon remind @HaoZeke in 2 weeks

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@whedon whedon commented Sep 3, 2019

Reminder set for @HaoZeke in 2 weeks

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@meg-simula meg-simula commented Sep 3, 2019

@whedon remind @dham in 3 weeks

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@whedon whedon commented Sep 3, 2019

Reminder set for @dham in 3 weeks

@HaoZeke

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@HaoZeke HaoZeke commented Sep 15, 2019

@whedon check references

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@whedon whedon commented Sep 15, 2019

Attempting to check references...
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@whedon whedon commented Sep 15, 2019


OK DOIs

- 10.1111/mice.12124 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Sep 17, 2019

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

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@whedon whedon commented Sep 24, 2019

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

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@meg-simula meg-simula commented Oct 1, 2019

@HaoZeke and @dham, could you give us an update on how the review is going? Is there any additional information needed?

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@HaoZeke HaoZeke commented Oct 1, 2019

@gbertoldo

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@gbertoldo gbertoldo commented Oct 2, 2019

Dear @meg-simula and @HaoZeke, I was not sure about modifying the repository during the review. I will provide changes asked by @HaoZeke as soon as possible.

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@HaoZeke HaoZeke commented Oct 2, 2019

@gbertoldo, sorry I should have clarified the process at the onset. JOSS is an inclusive journal, and as the review progresses, I shall be opening issues to shepard the software towards being in accordance to our guidelines. Once the issues have all been addressed, @meg-simula will give her comments and move forward with the publication. Thanks for getting started on the issues.

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@gbertoldo gbertoldo commented Oct 3, 2019

@whedon generate pdf

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@whedon whedon commented Oct 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 3, 2019

@gbertoldo

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@gbertoldo gbertoldo commented Oct 3, 2019

@whedon generate pdf

@gbertoldo

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@gbertoldo gbertoldo commented Mar 19, 2020

@whedon generate pdf

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@whedon whedon commented Mar 19, 2020

@gbertoldo

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@gbertoldo gbertoldo commented Mar 20, 2020

@whedon generate pdf

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@whedon whedon commented Mar 20, 2020

@gbertoldo

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@gbertoldo gbertoldo commented Mar 20, 2020

Dear, @meg-simula,

We fixed all the issues you raised, except for adding a missing DOI reported by Whedon. There is a paper with the same title as the book we cited. Whedon is claiming for the paper's DOI. Since the book has no DOI, it was not added.

We thank you and the reviewers (@HaoZeke and @dham) for the suggestions that helped us to improve the quality of the software and the quality of the manuscript.

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@ooo ooo bot commented Mar 20, 2020

👋 Hey @gbertoldo...

Letting you know, @meg-simula is currently OOO until Friday, March 27th 2020. ❤️

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@arfon arfon commented Mar 20, 2020

@gbertoldo - I'll take over this submission from here to help out @meg-simula.

One quick stylistic thing, you seem to have an inconsistency in how you refer to the software. Sometimes it's DEPP, other times DEPP. You might want to make sure that when you have made these all the same?

After this, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

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@ooo ooo bot commented Mar 20, 2020

👋 Hey @arfon...

Letting you know, @meg-simula is currently OOO until Friday, March 27th 2020. ❤️

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@gbertoldo gbertoldo commented Mar 20, 2020

@whedon generate pdf

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@whedon whedon commented Mar 20, 2020

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@gbertoldo gbertoldo commented Mar 20, 2020

Hi, @arfon,

We fixed the issue you pointed out. Here is the DOI: 10.5281/zenodo.3722436.

Thanks!

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@arfon arfon commented Mar 20, 2020

@whedon set 10.5281/zenodo.3722436 as archive

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@whedon whedon commented Mar 20, 2020

OK. 10.5281/zenodo.3722436 is the archive.

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@arfon arfon commented Mar 20, 2020

@whedon accept

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@whedon whedon commented Mar 20, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Mar 20, 2020

Reference check summary:

OK DOIs

- 10.1111/mice.12124 is OK
- 10.1023/A:1008202821328 is OK
- 10.1109/TEVC.2009.2014613 is OK

MISSING DOIs

- https://doi.org/10.2307/1270613 may be missing for title: Response surface methodology: process and product optimization using designed experiments

INVALID DOIs

- None
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@whedon whedon commented Mar 20, 2020

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

Check final proof 👉 openjournals/joss-papers#1386

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1386, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@arfon arfon commented Mar 20, 2020

@gbertoldo is this DOI recommendation correct?

- https://doi.org/10.2307/1270613 may be missing for title: Response surface methodology: process and product optimization using designed experiments
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@gbertoldo gbertoldo commented Mar 20, 2020

Hi, @arfon,

No, this DOI refers to a paper, but we cited a book with the same title.

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@arfon arfon commented Mar 20, 2020

@whedon accept deposit=true

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@whedon whedon commented Mar 20, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Mar 20, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Mar 20, 2020

🚨🚨🚨 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 👉 openjournals/joss-papers#1387
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01701
  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...

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@arfon arfon commented Mar 20, 2020

@HaoZeke, @dham - many thanks for your reviews here and to @meg-simula for editing this submission

@gbertoldo - your paper is now accepted into JOSS 🚀💥

@arfon arfon closed this Mar 20, 2020
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@ooo ooo bot commented Mar 20, 2020

👋 Hey @arfon...

Letting you know, @meg-simula is currently OOO until Friday, March 27th 2020. ❤️

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@whedon whedon commented Mar 20, 2020

🎉🎉🎉 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.01701/status.svg)](https://doi.org/10.21105/joss.01701)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01701">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01701/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01701/status.svg
   :target: https://doi.org/10.21105/joss.01701

This is how it will look in your documentation:

DOI

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