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[REVIEW]: Pingouin: statistics in Python #1026

Closed whedon closed 6 years ago

whedon commented 6 years ago

Submitting author: @raphaelvallat (Raphael Vallat) Repository: https://github.com/raphaelvallat/pingouin Version: v0.1.10 Editor: @cMadan Reviewer: @snastase Archive: 10.5281/zenodo.1491783

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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

@snastase, 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 @cMadan know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @snastase

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 6 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @snastase 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

:point_right: Check article proof :page_facing_up: :point_left:

raphaelvallat commented 6 years ago

Hi @cMadan and @snastase!

I was hoping to release the version 0.2.0 of Pingouin by early next week and ideally I would really love to include the JOSS paper in it. Do you think that it would be possible to do the review by then? If not, no worries, I'll just include it in a future release.

Thank you and have a great day! Raphael

cMadan commented 6 years ago

@snastase, how is the review coming? Do you have any questions about the review procedures?

snastase commented 6 years ago

@cMadan @raphaelvallat Sorry for holding this up!

I’m not a very experienced developer (also my first JOSS review), so take this as the perspective of an intermediate-skill-level user. Overall, I think this is a great contribution. Documentation and examples are stellar. I worked through the checklist and point out some minor issues below (most of which I suspect are installation issues that may be peculiar to my environment).

General checklist: general checks are all good (version has progressed to 0.1.10).

Functional checklist: Installation with pip (on Mac) was smooth, although it might be worth including a note for folks like me who still have a python 2.7 installation floating around; e.g., pip3 install pingouin. I get some incompatibility warnings for requirements (mock, future, jsonschema, decorator), but these do not derail installation. Install via pip was smooth enough on a Linux machine. Module imports fine in IPython. Developer install via git clone was smooth.

I followed the “10 Minutes to Pingouin” walkthrough in IPython on both Mac and Linux machines, and most of it ran smoothly. I ran into the following handful of errors.

I also walked through all of the tutorial notebooks on Binder. This is an excellent approach to interactive examples. I ran into the following issues:

Documentation checklist: Regarding the statement of need, it might be helpful to include in the introductory documentation how this relates to adjacent packages such as statsmodels, whether it provides complementary functionality, etc. Regarding installation instructions, you might go into a bit more detail as to pandas requirements—I'm curious whether that would pre-empt some of the errors I ran into. I spot-checked the tests, and they seem comprehensive enough. Community guidelines are fine, e.g,. code of conduct, gitter, etc. Documentation (tutorials, docstrings) and examples are excellent. The flowchart guidelines are really nice too.

Paper checklist: Everything in order. You might do a final pass over the references to make sure formatting is correct; e.g., most of the journal names in your list are abbreviated, but the Berens reference is not—should be “J. Stat. Softw.”; also capitalize the proceedings name for the McKinney reference.

Random highly-specific feature request: In the corr function, it would be nice to have separate implementations of Kendall’s tau-a, tau-b, and tau-c. This occurs to me because in representational similarity analysis in neuroimaging, the recommended metric for comparing representational similarity matrices is Kendall’s tau-a (Nili et al., PLOS Comp Biol, 2014). As far as I know, there’s no python implementation of tau-a.

Again, sorry for the delay! Let me know if I can be of help.

Sam

raphaelvallat commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 6 years ago

:point_right: Check article proof :page_facing_up: :point_left:

raphaelvallat commented 6 years ago

Hi @snastase!

Thank you so much for your review and your positive feedback, I really appreciate it!

Please find below the answers to the main points that you mentioned in your review:

1) I never tried to run Pingouin on Python 2.7. My idea when I started working on the project was that it would be a Python 3 only package. I uploaded the installation instructions to emphasize that it works better with Python 3 and that users should be careful when using Python 2.7

2) Thank you for noticing the pandas.drop() error in the pairwise_ttests() function. I realized that the columns argument has only been added since Pandas 0.21. I have therefore updated the requirements.txt file to make sure that the pip installation also updates the pandas version.

3) I have just uploaded the version 0.2.0 of Pingouin to PyPi, which should solve all the bugs that you have encountered in the Binder notebooks (i.e. no linear regression, missing example datasets...). Just make sure to upgrade your version: pip install --upgrade pingouin

4) I liked the idea of adding a section explaining how Pingouin relates to similar packages. Therefore, I have just added a FAQ section in the documentation to explain the differences between Statsmodels, Scipy and Pingouin, as well as to answer some of the most basic functions that users may ask when they first start to use Python and/or Pingouin.

5) I have updated the Berens reference in the paper, however, I am not able to capitalize the proceedings name for the McKinney reference (the automatic PDF generation somehow does not take it into account).

6) I was not aware of these alternatives metrics of the Kendall tau. The Pingouin implementation relies on the scipy.stats.kendalltau() function, which, according to the documentation, uses the tau-b when ties are present and tau-a in absence of ties. Therefore, it seems that only the tau-c implementation is missing. I will definitely keep that in mind and maybe try to add it in a future release.

Thank you again, Samuel, for your review! Please let me know if there is anything else that I can do. Have a great day, Raphael

raphaelvallat commented 6 years ago

Hi @snastase and @cMadan !

I am just wondering what should be the next step(s) for this review. Is there anything else that I can do? This is my very first JOSS paper so I am new to this process,

Thank you and have an excellent day! Raphael

cMadan commented 6 years ago

@raphaelvallat, I think you're all set for now.

@snastase, can you look over the reviewer checklist in the first post in this issue and check off what's all sorted, and see what still needs to be addressed? Apart from that, please look over @raphaelvallat's response and revisions and let us know what you think of the current state of the submission.

snastase commented 6 years ago

Okay, I think the author has adequately addressed my comments! New v0.2.0 fixes my import problems for linear_regression and mediation_analysis. The pairwise_ttests functionality now works normally for me. I like the mention of statsmodels in the FAQ. I've completed the review checklist above and am satisfied with the current state of the package—I endorse it for acceptance/publication.

cMadan commented 6 years ago

@snastase, perfect, thank you for your thorough review!

@raphaelvallat, you're almost done! I just need the DOI for an archived version of the current code (i.e., deposit it on Zenodo or FigShare).

raphaelvallat commented 6 years ago

@snastase Great! thank you so much, Samuel, for your review!

@cMadan The DOI number of the current release is: https://zenodo.org/badge/latestdoi/127584791

DOI

Have a great day! Raphael

cMadan commented 6 years ago

@whedon set 10.5281/zenodo.1491783 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1491783 is the archive.

cMadan commented 6 years ago

@whedon accept

whedon commented 6 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 6 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/68

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/68, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
arfon commented 6 years ago

@whedon accept deposit=true

whedon commented 6 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 6 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/71
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01026
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? notify your editorial technical team...

arfon commented 6 years ago

@snastase - many thanks for your review and to @cMadan for editing this submission ✨

@raphaelvallat - your paper is now accepted into JOSS :zap::rocket::boom:

whedon commented 6 years ago

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

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

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01026/status.svg)](https://doi.org/10.21105/joss.01026)

HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.01026/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01026/status.svg
   :target: https://doi.org/10.21105/joss.01026

This is how it will look in your documentation:

DOI

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