[REVIEW]: Pyret: A Python package for analysis of neurophysiology data

[whedon]

Submitting author: @nirum (Niru Maheswaranathan)
Repository: https://github.com/baccuslab/pyret
Version: v0.5.0
Editor: @arokem
Reviewer: @kdesimone
Archive: 10.5281/zenodo.232521

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/73e486788290a6386e90a21c7e71bbe0/status.svg)](http://joss.theoj.org/papers/73e486788290a6386e90a21c7e71bbe0)

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 questions

Conflict of interest

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

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 (v0.5.0)?
• Authorship: Has the submitting author (@nirum) made major contributions to the software?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: Have any performance claims of the software been confirmed?

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. I'm here to help you with some common editorial tasks for JOSS.

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

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[arokem]

@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 reviewer of this submission
@whedon assign @username as reviewer

# List the GitHub usernames of the JOSS editors
@whedon list editors

# List of JOSS 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

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This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update).

[arokem]

@whedon assign @kdesimone as reviewer

[whedon]

OK, the reviewer is @kdesimone

[kdesimone]

The authors have satisfactorily addressed (and closed) all the issues, which I've linked below.

baccuslab/pyret#88
baccuslab/pyret#86
baccuslab/pyret#85
baccuslab/pyret#83

[arokem]

@arfon: what's the next step here?

IIUC, @nirum and colleagues need to create a DOI for the package that incorporates the fixes from the review. Is that correct?

[arfon]

IIUC, @nirum and colleagues need to create a DOI for the package that incorporates the fixes from the review. Is that correct?

Yes, that's correct. @nirum - please create the archive and update this thread with the DOI so we can accept this submission.

[nirum]

Thanks @kdesimone and @arokem!

I've uploaded the package using zenodo, here is the DOI:

[arfon]

@whedon set 10.5281/zenodo.232521 as archive

[whedon]

OK. 10.5281/zenodo.232521 is the archive.

[arfon]

@arokem thanks for editing this one and for your review @kdesimone ⚡

@nirum - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00137 ⚡️ 🚀 💥