Joss-reviews: [REVIEW]: egtplot: A Python Package for Three-Strategy Evolutionary Games

[whedon]

Submitting author: @drew-williamson (Drew Williamson)
Repository: https://github.com/mirzaevinom/egtplot
Version: v0.5
Editor: @arfon
Reviewer: @fil, @jmbr
Archive: 10.5281/zenodo.1291455

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

@fil & @jmbr, 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 @arfon know.

Review checklist for @fil

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 (v0.3)?
• [x] Authorship: Has the submitting author (@drew-williamson) 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 @jmbr

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 (v0.3)?
• [x] Authorship: Has the submitting author (@drew-williamson) 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. I'm here to help you with some common editorial tasks. @fil, 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]

--> Check article proof :page_facing_up: <--

[jmbr]

Accept with minor revisions: https://github.com/mirzaevinom/egtplot/issues/1

[drew-williamson]

Thanks so much for taking the time to review egtplot! This is our first Python package so it's a bit rough around the edges. We'll make the revisions right away.

[Fil]

So far I haven't been able to install and run the demo notebook. I have struggled with incompatibilities between versions of macos, conda, geopandas, tornado, jupyter etc. (I wanted to try it in an virtual environment.)

I keep hitting those errors:
https://github.com/jupyter/notebook/issues/3407
https://github.com/geopandas/geopandas/issues/556

I might try later but not sure I'll find time.

[arfon]

I might try later but not sure I'll find time.

Thanks for your efforts thus far. Is this something @drew-williamson could help with by being more specific about the version for the required environment?

[Fil]

I finally managed to install almost everything with docker.

Here are my comments so far: https://github.com/mirzaevinom/egtplot/issues/2

[drew-williamson]

@mirzaevinom and I have made the edits requested by @jmbr and are now working on those requested by @Fil. A question for @arfon, though: how do we change the version of the package on JOSS?

[arfon]

@mirzaevinom and I have made the edits requested by @jmbr and are now working on those requested by @Fil. A question for @arfon, though: how do we change the version of the package on JOSS?

@drew-williamson - I can change the version. What will the new version number be?

[drew-williamson]

Let's call it 0.5. Thanks!

[Fil]

All clear from me! ㊗️

[arfon]

👋 @jmbr - could you take a look at this again when you have a chance?

[jmbr]

@arfon I closed the issue https://github.com/mirzaevinom/egtplot/issues/1 some weeks ago. It's good to go as far as I am concerned.

[arfon]

@drew-williamson - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[mirzaevinom]

@arfon, the reviewed software files are on Zenodo now: https://doi.org/10.5281/zenodo.1291455. Thank you!

[arfon]

@whedon set 10.5281/zenodo.1291455 as archive

[whedon]

OK. 10.5281/zenodo.1291455 is the archive.

[arfon]

@Fil, @jmbr - many thanks for your reviews here ✨

@drew-williamson - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00735 :zap: :rocket: :boom:

[whedon]

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

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This is how it will look in your documentation:

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[drew-williamson]

Thank you @jmbr, @Fil , and @arfon!