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]: qtools: A Python toolset for the Q molecular simulation package. #935

Closed
whedon opened this issue Sep 11, 2018 · 31 comments

Comments

Projects
None yet
9 participants
@whedon
Copy link
Collaborator

commented Sep 11, 2018

Submitting author: @mpurg (Miha Purg)
Repository: https://github.com/mpurg/qtools
Version: v0.6.1
Editor: @kyleniemeyer
Reviewers: @malramsay64, @fdroessler
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/6dc33648ae23a49031b9c305cbd8300f"><img src="http://joss.theoj.org/papers/6dc33648ae23a49031b9c305cbd8300f/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/6dc33648ae23a49031b9c305cbd8300f/status.svg)](http://joss.theoj.org/papers/6dc33648ae23a49031b9c305cbd8300f)

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

@malramsay64 & @esguerra & @fdroessler, 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 @kyleniemeyer know.

Please try and complete your review in the next two weeks

Review checklist for @malramsay64

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 (v0.6.1)?
  • Authorship: Has the submitting author (@mpurg) 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 @fdroessler

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 (v0.6.1)?
  • Authorship: Has the submitting author (@mpurg) 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 Sep 11, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @malramsay64, 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 Sep 11, 2018

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

This comment has been minimized.

Copy link
Collaborator Author

commented Sep 11, 2018

@kyleniemeyer

This comment has been minimized.

Copy link

commented Sep 11, 2018

@mpurg @malramsay64 @esguerra @fdroessler 👋 you each have individual checklists above. Detailed review criteria are at https://joss.readthedocs.io/en/latest/review_criteria.html

@malramsay64

This comment has been minimized.

Copy link

commented Sep 11, 2018

@mpurg I have taken an initial look and raised a number of issues. To be clear, only the issues with '[review]' in the title are the ones which require action based on the review criteria. The others are more suggestions which I think would make the software better. I am happy to help fix or discuss any issues.

@esguerra

This comment has been minimized.

Copy link

commented Sep 18, 2018

@mpurg @malramsay64 @fdroessler @kyleniemeyer
Sorry this reply has taken so long.
Only until now do I have time to read the COI policy in detail.
The author of this software and I are coauthors in a paper published less than four years ago, so, I cannot act as a reviewer, sadly.

Thanks for the invitation and what a great idea this is,

Mauricio

@kyleniemeyer

This comment has been minimized.

Copy link

commented Sep 22, 2018

@esguerra OK, thanks for letting me know!

@kyleniemeyer

This comment has been minimized.

Copy link

commented Sep 22, 2018

@whedon remove @esguerra as reviewer

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Sep 22, 2018

OK, @esguerra is no longer a reviewer

@kyleniemeyer

This comment has been minimized.

Copy link

commented Sep 22, 2018

@fdroessler @malramsay64 Have your reviews progressed? I noticed that many/most of the checkboxes in the review list above are not filled.

@fdroessler

This comment has been minimized.

Copy link

commented Sep 22, 2018

@kyleniemeyer I should be able to get to it beginninof next week. I am currently traveling in Africa but have looked at the paper and can start the full review process shortly.

@malramsay64

This comment has been minimized.

Copy link

commented Sep 24, 2018

@kyleniemeyer I have some time this week set aside to continue my review. I had somewhat put it on the side expecting some response from @mpurg to the issues I have raised.

@mpurg

This comment has been minimized.

Copy link

commented Sep 24, 2018

Hi all, sorry for vanishing.
I just submitted my phd thesis and took a much needed week off.

@malramsay64 thanks for all the comments and issues you raised, I will address them later today.

@fdroessler

This comment has been minimized.

Copy link

commented Oct 2, 2018

Sorry I wanted to check if the following item: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)? refers to the references in the paper or the reference of the software itself.

@fdroessler

This comment has been minimized.

Copy link

commented Oct 2, 2018

@kyleniemeyer @mpurg I have been through my checklist now and will wait till some of the issues that @malramsay64 and myself have raised are addressed.

@kyleniemeyer

This comment has been minimized.

Copy link

commented Oct 2, 2018

@fdroessler the item about archival references mean in the paper

@malramsay64

This comment has been minimized.

Copy link

commented Oct 10, 2018

@mpurg The updates you have been making to the code are all great. There is still the documentation which needs more explanation aimed at a new user. Feel free to get in contact if you want some ideas or feedback as you make changes.

@mpurg

This comment has been minimized.

Copy link

commented Oct 10, 2018

Hi @malramsay64, @kyleniemeyer, @fdroessler
I've already addressed some of the issues as well as ported the whole codebase to Py3+, but as @malramsay64 points out, the documentation needs quite some work. Unfortunately, I'm juggling this revision with studying for a final exam and preparing for my PhD defense, making the whole process at this moment painfully slow and inefficient. Considering the extent of the revisions, would it be possible to postpone the revision process until the 3rd of Nov?

@malramsay64

This comment has been minimized.

Copy link

commented Oct 10, 2018

@mpurg fine by me, just ping me when your ready.

@kyleniemeyer

This comment has been minimized.

Copy link

commented Oct 11, 2018

@mpurg 👍

@kyleniemeyer

This comment has been minimized.

Copy link

commented Nov 5, 2018

Hi @mpurg, just wanted to check on the status of your revisions—hope your PhD defense went well!

@mpurg

This comment has been minimized.

Copy link

commented Nov 6, 2018

@labarba

This comment has been minimized.

Copy link
Member

commented Jan 19, 2019

👋 @mpurg — We haven't heard from you in a while. What's your status? Are you able to work on the revisions soon?

@labarba

This comment has been minimized.

Copy link
Member

commented Jan 19, 2019

@kyleniemeyer — I manually removed the checklist for the unassigned reviewer, to avoid confusion and left-over un-ticked marks.

@mpurg

This comment has been minimized.

Copy link

commented Jan 20, 2019

@labarba

This comment has been minimized.

Copy link
Member

commented Jan 20, 2019

Thanks, @mpurg. We'll add this label here ☝️ and pause the review. Ping us back when you feel the review can restart.

@labarba labarba added the paused label Jan 20, 2019

@arfon arfon added paused and removed paused labels May 11, 2019

@danielskatz

This comment has been minimized.

Copy link

commented May 20, 2019

👋 @mpurg @kyleniemeyer - Given the long delay at this point, I suggest that withdrawing the submission might be a good option, with the idea that it can be submitted again later.

Your thoughts?

@kyleniemeyer

This comment has been minimized.

Copy link

commented May 20, 2019

I agree, if @mpurg feels the same.

@labarba

This comment has been minimized.

Copy link
Member

commented May 20, 2019

If this submission is withdrawn (and given the long delay, I agree that it should), we would ask the authors to please provide a link to this issue when they submit again (via a comment in the Pre-Review issue). This way, we can recall the history and possibly ask the same reviewers if they are still willing to contribute a review.

@mpurg

This comment has been minimized.

Copy link

commented May 20, 2019

@danielskatz danielskatz added withdrawn and removed paused labels May 20, 2019

@danielskatz

This comment has been minimized.

Copy link

commented May 20, 2019

Thanks - I will go ahead and withdraw this.
If/when do you resubmit, please add a comment that this was already partially reviewed, so as @labarba suggests, we can reference this issue and potentially get the same review back

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.