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]: Visualizing alpha-helical peptides in R with helixvis #1008

Open
whedon opened this Issue Oct 9, 2018 · 4 comments

Comments

Projects
None yet
3 participants
@whedon
Collaborator

whedon commented Oct 9, 2018

Submitting author: @rrrlw (Raoul R. Wadhwa)
Repository: https://github.com/rrrlw/helixvis
Version: v1.0.0
Editor: @yochannah
Reviewer: @nagoue, @tomsing1
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/f28ccdaa9e62646cf673f36dac630eab"><img src="http://joss.theoj.org/papers/f28ccdaa9e62646cf673f36dac630eab/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/f28ccdaa9e62646cf673f36dac630eab/status.svg)](http://joss.theoj.org/papers/f28ccdaa9e62646cf673f36dac630eab)

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

@nagoue & @tomsing1, 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 @yochannah know.

Please try and complete your review in the next two weeks

Review checklist for @nagoue

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: Does the release version given match the GitHub release (v1.0.0)?
  • Authorship: Has the submitting author (@rrrlw) 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)?

Review checklist for @tomsing1

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: Does the release version given match the GitHub release (v1.0.0)?
  • Authorship: Has the submitting author (@rrrlw) 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.

Show comment
Hide comment
@whedon

whedon Oct 9, 2018

Collaborator

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

whedon commented Oct 9, 2018

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

Show comment
Hide comment
@whedon

whedon Oct 9, 2018

Collaborator
Attempting PDF compilation. Reticulating splines etc...
Collaborator

whedon commented Oct 9, 2018

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

This comment has been minimized.

Show comment
Hide comment
@whedon
Collaborator

whedon commented Oct 9, 2018

@rrrlw

This comment has been minimized.

Show comment
Hide comment
@rrrlw

rrrlw Oct 9, 2018

Collaborator

First off, thank you @yochannah for editing and @tomsing1, @nagoue for reviewing! Very grateful for the time and effort you all are contributing.

A couple of quick notes for the reviewers:

  • The CRAN version of helixvis is very much out-of-date (will update on CRAN when the review on this thread is complete, even if helixvis is not accepted to JOSS), so please use devtools::install_github("rrrlw/helixvis") to install the package
  • I have added a document reflecting the reviewer checklist for this JOSS submission here, which could save the reviewers some time on the checklists above. Hope it helps.

Looking forward to everyone's feedback!

Collaborator

rrrlw commented Oct 9, 2018

First off, thank you @yochannah for editing and @tomsing1, @nagoue for reviewing! Very grateful for the time and effort you all are contributing.

A couple of quick notes for the reviewers:

  • The CRAN version of helixvis is very much out-of-date (will update on CRAN when the review on this thread is complete, even if helixvis is not accepted to JOSS), so please use devtools::install_github("rrrlw/helixvis") to install the package
  • I have added a document reflecting the reviewer checklist for this JOSS submission here, which could save the reviewers some time on the checklists above. Hope it helps.

Looking forward to everyone's feedback!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment