[REVIEW]: Ripser.py: A Lean Persistent Homology Library for Python

whedon commented 6 years ago

Submitting author: @sauln (Nathaniel Saul) Repository: https://github.com/scikit-tda/ripser.py Version: 0.2.4 Editor: @arokem Reviewer: @lmcinnes Archive: 10.5281/zenodo.1412867

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@lmcinnes, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @lmcinnes

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?
[ ] Version: Does the release version given match the GitHub release (0.2.4)?
[x] Authorship: Has the submitting author (@sauln) 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 commented 6 years ago

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whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

lmcinnes commented 6 years ago

First off, this is clearly a mature library with significant documentation available. It looks great!

I'm still working through the checklist, but some initial comments, all minor:

the versions don't match, but I presume there were further patch releases after the initial submission?
In the paper the reference for the original Ripser library isn't resolving; I think this is a capitalisation issue in the bibtex name.
When testing the installation via pip there were errors in building the wheel (since pip hadn't installed numpy yet; it seemed to get around that and work, but the errors were disconcerting). Perhaps it would be best to add numpy as a dependency up front in the installation instructions?
In contributions in the README it would be beneficial to cover how to report issues or questions.
The checklist suggests everything that does have a DOI in the references should -- I believe many of the papers referenced have DOIs but the references don't list them. Perhaps @arokem can clarify this one?

sauln commented 6 years ago

Hi @lmcinnes, thanks for the initial feedback.

We have moved forward a bit since the initial submission. I think once this process is complete, we'll bump to version 0.3. Do we need to fix the version numbers somewhere in the joss system?
Reference fixed, thanks for catching that.
I am concerned about the errors. My experience is that everything marked in install_requires will install before trying to install Ripser.py. We have no way around install Cython first, but numpy should come along easily. Could we debug this together? Do you have the system information and error messages handy?
blurb added
I added many more DOIs to the bib. For some references I'm sure have DOIs, but I have been unable to find them (scikit-learn, cavannageometric, edelsbrunner2010computational, carlsson2009topology, stolz2017persistent, tralie2018slomoloops, and tralie2018autism). I'll try tracking them down over the next few days.

Thanks again for the feedback. I look forward to helping move this forward however I can.

lmcinnes commented 6 years ago

Hi @sauln,

It all looks good -- thanks for patching up the minor issues. My only remaining concern is the README provides example code that doesn't quite work. I think for the sklearn API version you want to remove the ['dgm']. Beyond that I think everything has been addressed.

sauln commented 6 years ago

@lmcinnes, thanks for catching that example issue. I've fixed the bug and added an example image for the output.

sauln commented 6 years ago

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whedon commented 6 years ago

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# Compile the paper
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sauln 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:

sauln 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:

sauln commented 6 years ago

The paper looks good to me. I did notice some of the references are rendering strangely, print the first name only some of the time. I'm not sure if this is intentional or if there is something wrong with our .bib.

arokem commented 6 years ago

I have seen author first names in other JOSS papers as well, so I don't think this is anything unique to your paper.

Regarding DOIs: I was also not able to find DOIs for these articles. I am surprised in particular that JMLR doesn't have DOIs (for the sklearn paper), but it does seem like it doesn't.

One small comment: The paper currently suggests using pip install ripser (with a lower-case 'r'), while the README suggests using pip install Ripser (with a capital 'R'). Having just tried this, I realize that it doesn't matter which one you use, but I think that this might still confuse some readers of the article.

Other than that - nice work! I think that the paper is ready to be accepted (thanks @lmcinnes for the review!). Once you have corrected this small item, please create an archive for the accepted version of the software (e.g., using Zenodo) and post it here.

lmcinnes commented 6 years ago

Thanks @arokem and @sauln! Glad to see this getting published.

On Sun, Sep 9, 2018 at 10:29 PM Ariel Rokem notifications@github.com wrote:

I have seen author first names in other JOSS papers as well, so I don't think this is anything unique to your paper.

Regarding DOIs: I was also not able to find DOIs for these articles. I am surprised in particular that JMLR doesn't have DOIs (for the sklearn paper), but it does seem like it doesn't.

One small comment: The paper currently suggests using pip install ripser (with a lower-case 'r'), while the README suggests using pip install Ripser (with a capital 'R'). Having just tried this, I realize that it doesn't matter which one you use, but I think that this might still confuse some readers of the article.

Other than that - nice work! I think that the paper is ready to be accepted (thanks @lmcinnes https://github.com/lmcinnes for the review!). Once you have corrected this small item, please create an archive for the accepted version of the software (e.g., using Zenodo) and post it here.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/925#issuecomment-419769845, or mute the thread https://github.com/notifications/unsubscribe-auth/ALaKBXl9w-4kYWznbAlWJ645-qdBRb8fks5uZc6OgaJpZM4WWul9 .

sauln commented 6 years ago

Thank you both @lmcinnes and @arokem for pushing this through. @ctralie and I are both excited to have this accepted.

I have incremented the version to 0.3.0, made a release, and uploaded it to zenodo. The badge with DOI is below

ctralie commented 6 years ago

Thank you @lmcinnes and @arokem both for getting to this so quickly! We appreciate the attention to detail and are both very excited to have this through

arokem commented 6 years ago

@whedon set 10.5281/zenodo.1412867 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1412867 is the archive.

arokem commented 6 years ago

@arfon: I think that this article is ready to go!

arfon commented 6 years ago

@lmcinnes - many thanks for your review here and to @arokem for editing this submission ✨

@sauln - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00925 :zap: :rocket: :boom:

whedon commented 6 years ago

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

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