Joss-reviews: [REVIEW]: The psyplot interactive visualization framework

[whedon]

Submitting author: @Chilipp (Philipp S. Sommer)
Repository: https://github.com/Chilipp/psyplot.git
Version: v1.0.0
Editor: @arfon
Reviewer: @Fil
Archive: 10.5281/zenodo.845455

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/3535c28017003f0b5fb63b1b64118b60"><img src="http://joss.theoj.org/papers/3535c28017003f0b5fb63b1b64118b60/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/3535c28017003f0b5fb63b1b64118b60/status.svg)](http://joss.theoj.org/papers/3535c28017003f0b5fb63b1b64118b60)

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

@Fil, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Conflict of interest

• [x] 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).

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 (v1.0.0)?
• [x] Authorship: Has the submitting author (@Chilipp) made major contributions to the software?

Functionality

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

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 for JOSS. @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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS 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

[arfon]

@Fil - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines

Any questions/concerns please let me know.

[Fil]

@arfon this is my first review, so maybe my question is obvious: where is the "thing" that I'm reviewing? (not the software, which I found, but the paper that will be published — probably something named paper.md)

[arfon]

Hi @Fil. JOSS reviews are primarily about the software (https://github.com/Chilipp/psyplot.git). We also ask that you check that the associated paper (https://github.com/Chilipp/psyplot/blob/master/paper.md) meets the recommended structure/content requirements.

[Fil]

Yes absolutely. I'm mostly offline atm so was doing the simple admin things — will do the install later next week

[Fil]

@chilipp I've followed the installation procedure (conda in a virtualenv) and I can't seem to get the plot as a graphics. Here's what I get in a jupyter notebook (after conda install nb_conda).

I was hoping to get the map as in the example http://psyplot.readthedocs.io/en/latest/getting_started.html

Alternatively, I couldn't find how to launch the psyplot gui (from http://psyplot.readthedocs.io/projects/psyplot-gui/en/latest/getting_started.html). (EDIT: found it via spotlight…)

[Fil]

With psyplot-gui running, I was able to get the map plotted, and change its projection as in the example.

Minor corrections to the install procedure to explain if it is possible to use from jupyter notebook, and how to launch the gui would be welcome.

[Chilipp]

@Fil , thanks a lot for the feedback and your typo corrections!

I added notes to the docs of psyplot, which should solve this problem (see the 2 first notes in the Getting started example. Additionally I included a section in the psyplot-gui docs on how to start the GUI.

[Fil]

About the "Community Guidelines" item: the package's README only hints a github issues; it could say a bit more clearly how to contribute, and for example if pull requests, examples, and documentation are welcome.

[Fil]

About "References", please fix the references DOI:

• xarray according to http://xarray.pydata.org/en/stable/faq.html#how-should-i-cite-xarray
• matplotlib according to http://ieeexplore.ieee.org/document/4160265/

[Fil]

all set @arfon (@whedon too 🤖)
thank you @Chilipp for your patience

[Chilipp]

Thanks for your comments and your time!

[arfon]

@Chilipp - 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.

[Chilipp]

@arfon, I will use Zenodo for it. However I encountered a bug on their page. A couple of months ago, the psyplot repository has been deleted and created new from scratch. Now I cannot enable it again for Zenodo.

I contacted Zenodo and would like to wait for their response. Otherwise I could only provide a DOI of the psyplot-conda repository, which provides the installers for psyplot.

[arfon]

I contacted Zenodo and would like to wait for their response. Otherwise I could only provide a DOI of the psyplot-conda repository, which provides the installers for psyplot.

Agreed. Let's wait for their response here.

[Chilipp]

@arfon, I thought a bit more about it and I now think that it makes the most sense to use the DOI for psyplot-conda I just created

This would be the best for the JOSS paper, I think, because this archive then also includes the plugins psy-simple, psy-maps and psy-reg and the GUI, plus the installers, which have also been tested by @Fil.

[Chilipp]

@whedon set 10.5281/zenodo.845455 as archive

[whedon]

I'm sorry @Chilipp, I'm afraid I can't do that. That's something only JOSS editors are allowed to do.

[arfon]

@whedon set 10.5281/zenodo.845455 as archive

[whedon]

OK. 10.5281/zenodo.845455 is the archive.

[arfon]

@Fil - many thanks for your review here ✨

@Chilipp - your paper now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00363 ⚡️ 🚀 💥

[Chilipp]

Great! Many thanks from me, too @arfon and @Fil