Joss-reviews: [REVIEW]: AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System.

[whedon]

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 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

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (1.0.0)?
• [x] Authorship: Has the submitting author (@melund) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

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

Review checklist for @acolum

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (1.0.0)?
• [x] Authorship: Has the submitting author (@melund) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

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

[whedon]

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 :tada:.

:star: Important :star:

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:

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

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[trallard]

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 👩🏻‍💻

[melund]

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

[acolum]

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

[trallard]

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

[melund]

@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.

[trallard]

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

[melund]

Yes. I believe he is :)

[tonygon]

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!

[tonygon]

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

Cheers!

[trallard]

@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:

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

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

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

Once these tasks are completed I can finalise the editorial tasks

[melund]

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

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

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

• [x] 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

[trallard]

@whedon commands

[whedon]

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

[trallard]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[trallard]

@whedon set 10.5281/zenodo.2450121 as archive

[whedon]

OK. 10.5281/zenodo.2450121 is the archive.

[melund]

@trallard PDF looks good :)

[trallard]

@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 🙌🏻

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/425

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/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...

[melund]

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

[arfon]

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

@melund - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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:

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