[REVIEW]: cottoncandy: scientific python package for easy cloud storage

[whedon]

Submitting author: @anwarnunez (Anwar Nunez-Elizalde)
Repository: https://github.com/gallantlab/cottoncandy
Version: 0.1.0
Editor: @leeper
Reviewer: @vsoch
Archive: 10.5281/zenodo.1402799

Status

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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

@vsoch, 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 @leeper know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @vsoch

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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 (v.0.0.2)?
• Authorship: Has the submitting author (@anwarnunez) 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]

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

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@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[leeper]

Hi, @vsoch, your review checklist is available here (above ^^). Please let me know if you have any questions about the process.

[vsoch]

Thanks @whedon and @leeper ! I'm much looking forward to reviewing this. To give you a time frame, I should be able to get this underway mid to end of this week, finishing up some things this weekend! :)

[vsoch]

I have posted my review and updated the boxes above thus far! Please see the linked issue for discussion on the submission.

[leeper]

Thank you @vsoch for the very detailed review!

[anwarnunez]

Thanks for the review! I'll start working on the fixes to address your comments this weekend.

[vsoch]

Awesome! And I don't know the rules for this sort of thing, but please let me know if I can be of any help! 🍬

[leeper]

Feel free to continue the dialogue here or over there as needed and ping me if I can help on any procedural issues.

[anwarnunez]

Hello!
I submitted my responses to the review:
gallantlab/cottoncandy#63 (comment)

I made a new branch containing all the changes requested here: https://github.com/gallantlab/cottoncandy/tree/joss_review

Looking forward to your feedback!

[leeper]

Great. Thanks, @anwarnunez. @vsoch, please take a look when you can.

[vsoch]

Yes thank you, already noted!

[vsoch]

@whedon generate pdf

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

[vsoch]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[vsoch]

Great job @anwarnunez and thank you @leeper and @whedon. My further comments are here:

gallantlab/cottoncandy#63 (comment)

Happy Monday!

[vsoch]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[vsoch]

@leeper my review is complete, I think we are good to go! @anwarnunez and @leeper we will need the release to be 0.1.0 to coincide with the rc versions, and the (updated) one in this issue board. Great work everyone!

[anwarnunez]

Great!
All done from my end, too.
I merged, tagged and uploaded to pip:
https://pypi.org/project/cottoncandy/
https://github.com/gallantlab/cottoncandy/releases/tag/0.1.0

[anwarnunez]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[leeper]

@whedon set 10.5281/zenodo.1402799 as archive

[whedon]

OK. 10.5281/zenodo.1402799 is the archive.

[leeper]

@anwarnunez Please merge this PR: gallantlab/cottoncandy#68

[anwarnunez]

merged!

[leeper]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[leeper]

@arfon over to you

[arfon]

@vsoch - many thanks for your review here and to @leeper for editing this submission ✨

@anwarnunez - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00890 ⚡ 🚀 💥

[whedon]

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[anwarnunez]

Great, thanks @arfon!
Thanks @vsoch for the great comments and @leeper for editing!