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]: imager: an R package for image processing #1012

Open
whedon opened this issue Oct 10, 2018 · 69 comments

Comments

Projects
None yet
7 participants
@whedon
Copy link
Collaborator

commented Oct 10, 2018

Submitting author: @dahtah (Simon BARTHELME)
Repository: https://github.com/dahtah/imager
Version: 0.42
Editor: @Kevin-Mattheus-Moerman
Reviewers: @jeroen
Archive: 10.5281/zenodo.3235256

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/489ba37ed9daff3376bbf3dcd06ca4cd"><img src="http://joss.theoj.org/papers/489ba37ed9daff3376bbf3dcd06ca4cd/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/489ba37ed9daff3376bbf3dcd06ca4cd/status.svg)](http://joss.theoj.org/papers/489ba37ed9daff3376bbf3dcd06ca4cd)

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) 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

@jeroen, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

Please try and complete your review in the next two weeks

Review checklist for @jeroen

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?
  • Version: 0.42
  • Authorship: Has the submitting author (@dahtah) 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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Oct 10, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jeroen, it looks like you're currently assigned as the reviewer for 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
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Oct 10, 2018

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Oct 10, 2018

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Oct 23, 2018

@jeroen, @NikEfth can you update me on when you plan to work on this review? Thanks. 🚀 🤖

@jeroen

This comment has been minimized.

Copy link
Collaborator

commented Oct 23, 2018

@dahtah in the brief overview of imaging libraries available in R, could you compare imager to the magick package? This package interfaces to the ImageMagick C++ library and is probably the most comprehensive imaging toolkit in R currently available.

@NikEfth

This comment has been minimized.

Copy link

commented Nov 2, 2018

@jeroen @dahtah I would need a bit of support to get this started. I am using arch linux and I cannot find the dependency ibfftw3-dev. Any help?

@dahtah

This comment has been minimized.

Copy link

commented Nov 5, 2018

@NikEfth I don't know much about arch linux, but I guess this should be the right package, assuming the include files are in there. Could you please confirm?

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Nov 20, 2018

@dahtah, @jeroen, @NikEfth can you give an update as to where we are on the review process?

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Nov 20, 2018

@dahtah can you clarify the license for this work and where it can be found? Thanks.

@dahtah

This comment has been minimized.

Copy link

commented Nov 21, 2018

@Kevin-Mattheus-Moerman The license can be found in the DESCRIPTION file of the R package, as per recommend practice. Do you mean clarify the license in the manuscript?

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Nov 21, 2018

Thanks for the clarification. You do not need to mention the license in the paper. But here are some steps I think you should take:

  • The DESCRIPTION file simply reads: License: LGPL, however this license type has three variations i.e. LGPL-2.0, LGPL-2.1 and LGPL-3.0, which one does your project carry?

  • Can you also add an actual LICENSE file to your project? If you choose LGPL-3.0 you'd paste this text in there. This way it is clear what the license is. Also this way GitHub will render a little statement on the top right on your project front page clarifying the license, like this:
    screenshot from 2018-11-21 09-04-24

  • Perhaps consider also rendering a license badge at the top of your readme and have it link to your LICENSE file, e.g. : License

@dahtah

This comment has been minimized.

Copy link

commented Nov 26, 2018

@Kevin-Mattheus-Moerman Thank you for your suggestions. They are implemented in the current master.

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Nov 28, 2018

@arfon this repository is currently on the release 0.20 but the version label here and on CRAN is 0.41.1. Is this okay or should we suggest that the repo release carries the same version number as the CRAN number?

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Nov 28, 2018

@NikEfth have you resolved the linux arch issue you had? Are you still able to help with this review? Let me know if you cannot. Thanks.

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Nov 28, 2018

@jeroen I see you have two unticked boxes remaining. The version number will be fixed once the submission is accepted. In terms of the license this has now been clarified to be an OSI approved license (LGPL-3.0). Are you able to tick the last boxes and perhaps formulate a recommendation (e.g. accept or not). Thanks!

@arfon

This comment has been minimized.

Copy link
Member

commented Nov 28, 2018

@arfon this repository is currently on the release 0.20 but the version label here and on CRAN is 0.41.1. Is this okay or should we suggest that the repo release carries the same version number as the CRAN number?

I think we want to be clear about which version we've reviewed here. Is GitHub version 0.20 the same as CRAN version 0.41.1?

@dahtah

This comment has been minimized.

Copy link

commented Nov 28, 2018

@arfon It's my fault, I haven't consistently tagged releases on github to coincide with CRAN. If you'd like to know which version you have installed, run:
packageVersion('imager')
I'll try to pay more attention to tags in the future.

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jan 4, 2019

@NikEfth any luck resuming the review process? Let me know if you are still able to review this work or not. Thanks.

@NikEfth

This comment has been minimized.

Copy link

commented Jan 5, 2019

Hi @Kevin-Mattheus-Moerman this slipped under my radar. Sorry.
I will give it a try the coming week and let you know soon.
Cheers,

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jan 12, 2019

Great, thanks @NikEfth

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jan 12, 2019

@jeroen I see you have 3 unticked boxes remaining. The version number will be fixed once the submission is accepted. In terms of the license this has now been clarified to be an OSI approved license (LGPL-3.0). Are you able to tick the last boxes and perhaps formulate a recommendation (e.g. accept or not). Thanks!

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jan 31, 2019

@NikEfth can you give an update on your review? Thanks

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jan 31, 2019

@jeroen see my comments ☝️, do you think you are able to tick the last boxes? Thanks!

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Feb 10, 2019

@jeroen 👋 do you think you can tick those last boxes at this point? Thanks

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Feb 10, 2019

@NikEfth are you still able to help with this review? Thanks

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Mar 1, 2019

@NikEfth can you please complete the review at your earliest convenience to avoid further delays with this submission? Thanks.

@jeroen

This comment has been minimized.

Copy link
Collaborator

commented Mar 1, 2019

OK accept.

PS: I don't understand why I have to check for Version: Does the release version given match the GitHub release (0.41.1)? and then you say The version number will be fixed once the submission is accepted ... so what am I checking for here?

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented May 15, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented May 15, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented May 15, 2019

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented May 15, 2019

@dahtah can you add the following sections/headings to your paper:

  • Acknowledgements

  • References

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented May 15, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented May 15, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented May 15, 2019

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented May 15, 2019

@dahtah thanks for making those changes. at this point can you:

  • Please archive a copy of the reviewed software on Zenodo (some find the steps defining this automated process useful). Once you've done that can you provide us with the DOI of the archived version?
  • Can you please list the final version label for the reviewed software?
@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented May 28, 2019

@dahtah 👋 ☝️

@dahtah

This comment has been minimized.

Copy link

commented May 30, 2019

Sorry for the delay, and thanks for reviewing this. Zenodo gave me the following DOI: 10.5281/zenodo.3235256. The archived version is 0.42

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jun 4, 2019

@whedon set 10.5281/zenodo.3235256 as archive

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 4, 2019

OK. 10.5281/zenodo.3235256 is the archive.

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jun 4, 2019

@whedon set 0.42 as version

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 4, 2019

OK. 0.42 is the version.

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jun 4, 2019

@dahtah can you do the following:

  • Can you change the Zenodo archive title from "dahtah/imager: JOSS release" to match that of this submission "imager: an R package for image processing"

  • Can you update the author list on Zenodo so it matches the paper?

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jun 10, 2019

@dahtah 👋 can you work on the above? Thanks

@dahtah

This comment has been minimized.

Copy link

commented Jun 11, 2019

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jun 11, 2019

@dahtah did you create a new Zenodo archive? It does not seem updated yet on this link: https://zenodo.org/record/3235256

@dahtah

This comment has been minimized.

Copy link

commented Jun 11, 2019

@Kevin-Mattheus-Moerman Is it good now? I had saved but hadn't clicked the publish button

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jun 11, 2019

@dahtah yep looks good

@Kevin-Mattheus-Moerman

This comment has been minimized.

Copy link
Member

commented Jun 11, 2019

@openjournals/joss-eics this submission is ready to be accepted 🎉

@arfon

This comment has been minimized.

Copy link
Member

commented Jun 11, 2019

@whedon accept

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 11, 2019

Attempting dry run of processing paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 11, 2019

Check final proof 👉 openjournals/joss-papers#747

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#747, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 11, 2019


OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None
@arfon

This comment has been minimized.

Copy link
Member

commented Jun 11, 2019

@whedon accept deposit=true

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 11, 2019

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

@whedon whedon added the accepted label Jun 11, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 11, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 11, 2019

🚨🚨🚨 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#748
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01012
  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...

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.