[REVIEW]: PyDMD: Python Dynamic Mode Decomposition

whedon commented 6 years ago

Submitting author: @mtezzele (Marco Tezzele) Repository: https://github.com/mathLab/PyDMD Version: v0.1.0 Editor: @jakevdp Reviewer: @jkmacc-LANL Archive: 10.5281/zenodo.1171787

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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 (v0.1.0)?
[x] Authorship: Has the submitting author (@mtezzele) 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?
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[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 6 years ago

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @jkmacc-LANL it looks like you're currently assigned as the reviewer for this paper :tada:.

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whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

https://github.com/openjournals/joss-papers/blob/joss.00530/joss.00530/10.21105.joss.00530.pdf

jakevdp commented 6 years ago

Hi @jkmacc-LANL – the review will take place in this issue. Please see the instructions and checklist above, and feel free to let me know if you have any questions!

jkmacc-LANL commented 6 years ago

PyDMD is a well-documented, well-tested, easy to install software package. Congratulations! It was a pleasure to review this (...and thanks for your patience). I only had a few minor requests (below). These aren't show-stoppers, so I didn't create issues for them in the project repo. With these minor tweaks, this contribution is easily ready to be accepted.

Functionality

I installed and ran the tutorial notebooks on OS X 10.12.6 with Python 3.6.4. It went very smoothly.

[x] Tutorial notebook 2 requires ffmpeg. I recommended that this be explicit at the top of the notebook, or in the cell (7) that uses it.

Documentation

[x] A slightly longer description of the software on the documentation website landing page would be helpful. Some of the text from the JOSS paper would be appropriate.

Software Paper

[x] Please add DOIs to the references, where possible.

mtezzele commented 6 years ago

@jkmacc-LANL thank you very much! I will proceed in implementing your suggestions in the next few days!

mtezzele commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

https://github.com/openjournals/joss-papers/blob/joss.00530/joss.00530/10.21105.joss.00530.pdf

mtezzele commented 6 years ago

@jakevdp I have implemented all the suggestions and regenerated the pdf. What do I have to do now?

jkmacc-LANL commented 6 years ago

@mtezzele I see your changes, and they look good. Regarding the middle point, my suggestion was to add a slightly longer description to https://mathlab.github.io/PyDMD/, not on the README. I apologize for the confusion. Everything else is great👍

mtezzele commented 6 years ago

Done! I'm sorry I misread, my fault.

jakevdp commented 6 years ago

@jkmacc-LANL, has @mtezzele addressed all your comments?

jkmacc-LANL commented 6 years ago

Yes, they are addressed. Thanks!

mtezzele commented 6 years ago

@jakevdp what do I have to do now?

arfon commented 6 years ago

@mtezzele - 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.

ndem0 commented 6 years ago

@arfon We have upload the package and this is the DOI for all the versions: https://doi.org/10.5281/zenodo.1171787

arfon commented 6 years ago

@whedon set 10.5281/zenodo.1171787 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1171787 is the archive.

arfon commented 6 years ago

@jkmacc-LANL - many thanks for your review here and to @jakevdp for editing this submission ✨

@ndem0 @mtezzele - your paper is now accepted in JOSS and your DOI is https://doi.org/10.21105/joss.00530 ⚡️ 🚀 💥

whedon commented 6 years ago

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

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[![DOI](http://joss.theoj.org/papers/10.21105/joss.00530/status.svg)](https://doi.org/10.21105/joss.00530)

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mtezzele commented 6 years ago

Thank you very much @jkmacc-LANL, @jakevdp, and @arfon for your time and efforts!

jkmacc-LANL commented 6 years ago

Yes, thanks everyone. 10/10, would review again 😉 !

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