Joss-reviews: [REVIEW]: Opycleid: A Python package for transformational music theory

[whedon]

Submitting author: @AlexPof (Alexandre Popoff)
Repository: https://github.com/AlexPof/opycleid
Version: 0.2.5
Editor: @danielskatz
Reviewer: @drvinceknight, @danielskatz
Archive: 10.5281/zenodo.1857913

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/9cce385bc676b84853e8026ac452eb33"><img src="http://joss.theoj.org/papers/9cce385bc676b84853e8026ac452eb33/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/9cce385bc676b84853e8026ac452eb33/status.svg)](http://joss.theoj.org/papers/9cce385bc676b84853e8026ac452eb33)

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

@drvinceknight & @adammichaelwood, 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 @danielskatz know.

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

Review checklist for @drvinceknight

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 (0.2.5)?
• [x] Authorship: Has the submitting author (@AlexPof) 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 @danielskatz

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 (0.2.5)?
• [x] Authorship: Has the submitting author (@AlexPof) 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. @drvinceknight, 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:

[danielskatz]

@drvinceknight and @adammichaelwood - thanks for agreeing to be reviewers.

Please see the instructions above in the start of this issue, and let me know if you have any problems.

[drvinceknight]

Just back from paternity leave so will be looking at this next week.

[danielskatz]

👋 @adammichaelwood - please let us know how you are getting along on this

[adammichaelwood]

I've reviewed the literature and browsed the code. I have not had the
space to do the complete install and use it. I should be able to do that
in the next week.

On Sun, Oct 7, 2018 at 7:16 AM Daniel S. Katz [e-mail]
wrote:

👋 @adammichaelwood https://github.com/adammichaelwood - please let us
know how you are getting along on this

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/981#issuecomment-427656746,
or mute the thread
https://github.com/notifications/unsubscribe-auth/ABsacWDFyM4t3-pAbWVruQy59q2tJP4_ks5uigyjgaJpZM4W9RoJ
.

[drvinceknight]

@AlexPof I have opened https://github.com/AlexPof/opycleid/issues/1 with some initial queries/suggestions. :) :+1:

[AlexPof]

@drvinceknight Thank you for your remarks. I will have time during the week-end to make the necessary modifications. I realize now that most of the information is in the mkdocs, and this sure calls for an improved README.

[AlexPof]

@drvinceknight I have made the requested modifications in the repository. I also added some missing DOIs to the paper.md.

[AlexPof]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[danielskatz]

👋 @adammichaelwood - any update from your side?

[danielskatz]

👋 @adammichaelwood - We're still waiting to hear from you

[danielskatz]

👋 @drvinceknight - note that a number of changes have been made since your initial remarks - perhaps you can check on the response? And continue your review?

[drvinceknight]

Thanks for the changes @AlexPof, everything looks good to me now. I've left one very minor/small suggestion on https://github.com/AlexPof/opycleid/issues/1 but it's in no way a blocker.

[AlexPof]

@drvinceknight Thanks for everything. I might be mistaken, but I checked on the issue opened on the repository and I didn't find the remaining suggestion you mention. Could you please tell me more about it ?

[drvinceknight]

How strange! It does seem to not be there (perhaps I didn't click "Comment" properly or something). My only comment was that in the README:

>>> pip install opycleid

should probably be:

$ pip install opycleid

The >>> implies that it's a python command (as opposed to the $ which implies that it's a shell command) which could be confusing. Very minor.

[AlexPof]

This is ok, I've corrected it in the repository, and closed the issue.

[AlexPof]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[danielskatz]

I've pinged @adammichaelwood here and in email (5 days ago) will no answer back...

👋 @arfon what do you suggest?

[ooo[bot]]

:wave: Hey @danielskatz...

Letting you know, @arfon is currently OOO until Monday, October 29th 2018. :heart:

[adammichaelwood]

Sorry I've been unresponsive. I will try to work on this today, and leave a note about whether I have gotten through it or what my status is.

[danielskatz]

@adammichaelwood - What's happened in the last 9 days?

[danielskatz]

@adammichaelwood - What's happened in the last 14 days?

[danielskatz]

@adammichaelwood - What's happened in the last 22 days?

[danielskatz]

👋 @adammichaelwood - What's happened in the last 28 days?

[AlexPof]

@danielskatz I was hoping to be able to cite this in a manuscript submission which is due mid-January, do you think it will possible by then ?

[danielskatz]

@AlexPof - sorry for the delay on this. I've started looking at it myself from the point of view of a reviewer, and once I'm ok with it, we'll go ahead, which hopefully will be quick.

[danielskatz]

@adammichaelwood - I'm going to take you off this and do the second review myself

[AlexPof]

Thank you for your answer. I have responded to the issue you opened on the repository. Please do not hesitate to contact me if you have additional remarks.

[danielskatz]

@AlexPof - please add non PyPi build instructions to the README and docs as well.

[danielskatz]

You can also upload this version to PyPi.

After that, you should upload the repo to zenodo or similar, and let me know the DOI of the archived version.

[AlexPof]

I have added the necessary instructions, uploaded the new version on PyPi, and also uploaded the repo to zenodo. The DOI of the zenodo archived version is 10.5281/zenodo.1857913

[danielskatz]

@whedon set 10.5281/zenodo.1857913 as archive

[whedon]

OK. 10.5281/zenodo.1857913 is the archive.

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/96

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/96, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[danielskatz]

@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/97
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00981
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...

[danielskatz]

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

[danielskatz]

@drvinceknight - thanks for your review!

[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.00981/status.svg)](https://doi.org/10.21105/joss.00981)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00981">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00981/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00981/status.svg
   :target: https://doi.org/10.21105/joss.00981

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://www.flipcause.com/secure/cause_pdetails/Mjk3Nzk=