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[REVIEW]: AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System. #1108

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whedon opened this Issue Nov 29, 2018 · 32 comments

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whedon commented Nov 29, 2018

Submitting author: @melund (Morten Enemark Lund)
Repository: https://github.com/AnyBody-Research-Group/AnyPyTools
Version: 1.0.0
Editor: @trallard
Reviewer: @tonygon, @acolum
Archive: 10.5281/zenodo.2450121

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/03757b9d4a0d730af5d712006c762719"><img src="http://joss.theoj.org/papers/03757b9d4a0d730af5d712006c762719/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/03757b9d4a0d730af5d712006c762719/status.svg)](http://joss.theoj.org/papers/03757b9d4a0d730af5d712006c762719)

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

@tonygon & @marcopus & @acolum, 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 @trallard know.

Please try and complete your review in the next two weeks

Review checklist for @tonygon

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 (1.0.0)?
  • Authorship: Has the submitting author (@melund) 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 @acolum

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 (1.0.0)?
  • Authorship: Has the submitting author (@melund) 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)?
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whedon commented Nov 29, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tonygon, 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
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whedon commented Nov 29, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Nov 29, 2018

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trallard commented Nov 29, 2018

Hi reviewers and @melund! This is the issue we will be using to conduct the review.
@tonygon, @marcopus, @acolum each of you have a checklist to guide you through the review process.

If any of you encounters any issues / need any guidance during the review process feel free to ping me here 👩🏻‍💻

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melund commented Nov 29, 2018

Thanks, @trallard. I am really looking forward to the review process here :)

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acolum commented Dec 9, 2018

Just completed my review!
The paper, documentation, and code were all excellent, and I was glad to check off all of the requirements above.

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trallard commented Dec 10, 2018

Great, thanks for that speedy review @acolum. I will just wait for @tonygon and @marcopus 's reviews

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melund commented Dec 11, 2018

@trallard. I just browsed the JOSS conflict of interest policy and I think one of the reviewers I suggested could cause a problem. I knew one of my supervisors (Michael Skipper Andersen @msan00) had worked with @marcopus in the past but didn't realize that they also recently (2017) co-authored a paper.

I am sorry about that. But I think that disqualifies @marcopus as a reviewer.

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trallard commented Dec 11, 2018

hey @melund thanks for double checking. I am going to then remove @marcopus (apologies). Is @tonygon still a suitable reviewer?

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melund commented Dec 11, 2018

Yes. I believe he is :)

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tonygon commented Dec 18, 2018

hey @melund thanks for double checking. I am going to then remove @marcopus (apologies). Is @tonygon still a suitable reviewer?

@trallard My apologies for the delay. As I mentioned to Morten before agreeing, I'm able to do the review, I work with AnyPython tools and AnyBody, I used both regularly for a project.
But, I'm in the transition between jobs, so time is a bit limited ;)
Since we have holidays by the end of the week I will finish the review then.
I already know/did most of all AnyPython tools part, I just need to seat down and finish the formal procedure from the JOSS side.

I hope there is still time.
Cheers!

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tonygon commented Dec 30, 2018

@trallard
Just finished checking the JOSS requirements)
Thanks for the patience!
And continue the great work @melund!!

Cheers!

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trallard commented Jan 2, 2019

@tonygon thanks for your review and hope you had a nice holiday season


@melund now that the reviews are completed and the paper has been recommended for acceptance, we need you to complete the following actions:

  • make a new release of the package (unless the latest release is up to date with the recent modifications)

  • upload the revised software to your DOI-granting data/software repository, and post the DOI here

  • double check the submission paper to ensure it is up-to-date

Once these tasks are completed I can finalise the editorial tasks

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melund commented Jan 2, 2019

Thanks a lot @trallard. I have finished the remaining tasks.

  • make a new release of the package (unless the latest release is up to date with the recent modifications)

  • upload the revised software to your DOI-granting data/software repository, and post the DOI here

  • double check the submission paper to ensure it is up-to-date

The library is achived with Zenodo and the DOI for version 1.0.1 is:

10.5281/zenodo.2450121

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trallard commented Jan 7, 2019

@whedon commands

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whedon commented Jan 7, 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

# Open the review issue
@whedon start review

# Compile the paper
@whedon generate pdf

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

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trallard commented Jan 7, 2019

@whedon generate pdf

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whedon commented Jan 7, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 7, 2019

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trallard commented Jan 7, 2019

@whedon set 10.5281/zenodo.2450121 as archive

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whedon commented Jan 7, 2019

OK. 10.5281/zenodo.2450121 is the archive.

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melund commented Jan 7, 2019

@trallard PDF looks good :)

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trallard commented Jan 7, 2019

@melund all looks good to me so I will proceed with the acceptance recommendation

@arfon: this submission is accepted and ready to be published 🎉👾

@tonygon @acolum thank you very much for your time and valuable contribution to JOSS as reviewers for this submission 🙌🏻

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arfon commented Jan 7, 2019

@whedon accept

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whedon commented Jan 7, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Jan 7, 2019

Check final proof 👉 openjournals/joss-papers#425

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#425, 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 commented Jan 7, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Jan 7, 2019

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whedon commented Jan 7, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Jan 7, 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#426
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01108
  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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melund commented Jan 7, 2019

Woohoo... Awesome, it is online. Thanks a lot everyone...

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arfon commented Jan 7, 2019

@tonygon, @acolum - many thanks for your reviews and to @trallard for editing this submission

@melund - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Jan 7, 2019

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whedon commented Jan 7, 2019

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.01108/status.svg)](https://doi.org/10.21105/joss.01108)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01108">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01108/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01108/status.svg
   :target: https://doi.org/10.21105/joss.01108

This is how it will look in your documentation:

DOI

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