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[REVIEW]: PyDMD: Python Dynamic Mode Decomposition #530

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whedon opened this Issue Jan 11, 2018 · 23 comments

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whedon commented Jan 11, 2018

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

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/734e4326edd5062c6e8ee98d03df9e1d"><img src="http://joss.theoj.org/papers/734e4326edd5062c6e8ee98d03df9e1d/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/734e4326edd5062c6e8ee98d03df9e1d/status.svg)](http://joss.theoj.org/papers/734e4326edd5062c6e8ee98d03df9e1d)

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

@jkmacc-LANL, 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 @jakevdp know.

Conflict of interest

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 (v0.1.0)?
  • Authorship: Has the submitting author (@mtezzele) 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)?
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whedon Jan 11, 2018

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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 🎉.

⭐️ Important ⭐️

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:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

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whedon commented Jan 11, 2018

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 🎉.

⭐️ Important ⭐️

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:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands
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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 11, 2018

Attempting PDF compilation. Reticulating splines etc...
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https://github.com/openjournals/joss-papers/blob/joss.00530/joss.00530/10.21105.joss.00530.pdf
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whedon commented Jan 11, 2018

https://github.com/openjournals/joss-papers/blob/joss.00530/joss.00530/10.21105.joss.00530.pdf
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jakevdp Jan 11, 2018

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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!

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jakevdp commented Jan 11, 2018

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!

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jkmacc-LANL Jan 25, 2018

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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.

  • 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

  • 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

  • Please add DOIs to the references, where possible.
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jkmacc-LANL commented Jan 25, 2018

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.

  • 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

  • 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

  • Please add DOIs to the references, where possible.
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mtezzele Jan 25, 2018

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

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mtezzele commented Jan 25, 2018

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

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mtezzele Jan 29, 2018

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@whedon generate pdf

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mtezzele commented Jan 29, 2018

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 29, 2018

Attempting PDF compilation. Reticulating splines etc...
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https://github.com/openjournals/joss-papers/blob/joss.00530/joss.00530/10.21105.joss.00530.pdf
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whedon commented Jan 29, 2018

https://github.com/openjournals/joss-papers/blob/joss.00530/joss.00530/10.21105.joss.00530.pdf
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mtezzele Jan 29, 2018

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

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mtezzele commented Jan 29, 2018

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

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jkmacc-LANL Jan 29, 2018

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@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👍

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jkmacc-LANL commented Jan 29, 2018

@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👍

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mtezzele Jan 29, 2018

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

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mtezzele commented Jan 29, 2018

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

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

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jakevdp commented Jan 30, 2018

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

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jkmacc-LANL Feb 5, 2018

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Yes, they are addressed. Thanks!

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jkmacc-LANL commented Feb 5, 2018

Yes, they are addressed. Thanks!

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mtezzele Feb 9, 2018

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@jakevdp what do I have to do now?

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mtezzele commented Feb 9, 2018

@jakevdp what do I have to do now?

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arfon Feb 12, 2018

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@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.

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arfon commented Feb 12, 2018

@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.

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ndem0 Feb 12, 2018

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

ndem0 commented Feb 12, 2018

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

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arfon Feb 12, 2018

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@whedon set 10.5281/zenodo.1171787 as archive

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arfon commented Feb 12, 2018

@whedon set 10.5281/zenodo.1171787 as archive

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OK. 10.5281/zenodo.1171787 is the archive.

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whedon commented Feb 12, 2018

OK. 10.5281/zenodo.1171787 is the archive.

@arfon arfon added the accepted label Feb 12, 2018

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@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 ⚡️ 🚀 💥

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arfon commented Feb 12, 2018

@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 ⚡️ 🚀 💥

@arfon arfon closed this Feb 12, 2018

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippet:

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

This is how it will look in your documentation:

DOI

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:

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whedon commented Feb 12, 2018

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippet:

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

This is how it will look in your documentation:

DOI

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:

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mtezzele Feb 12, 2018

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

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mtezzele commented Feb 12, 2018

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

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jkmacc-LANL Feb 13, 2018

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

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jkmacc-LANL commented Feb 13, 2018

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

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