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[REVIEW]: Ripser.py: A Lean Persistent Homology Library for Python #925

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whedon opened this Issue Sep 2, 2018 · 25 comments

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whedon commented Sep 2, 2018

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

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/a8774cc066969ab17e9a0e9c39c6a81c"><img src="http://joss.theoj.org/papers/a8774cc066969ab17e9a0e9c39c6a81c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/a8774cc066969ab17e9a0e9c39c6a81c/status.svg)](http://joss.theoj.org/papers/a8774cc066969ab17e9a0e9c39c6a81c)

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

@lmcinnes, 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 @arokem know.

Please try and complete your review in the next two weeks

Review checklist for @lmcinnes

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 (0.2.4)?
  • Authorship: Has the submitting author (@sauln) 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 Sep 2, 2018

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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lmcinnes it looks like you're currently assigned as the reviewer for this paper 🎉.

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whedon commented Sep 2, 2018

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

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

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lmcinnes Sep 5, 2018

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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?
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lmcinnes commented Sep 5, 2018

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?
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sauln Sep 5, 2018

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.

sauln commented Sep 5, 2018

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.

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lmcinnes Sep 7, 2018

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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.

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lmcinnes commented Sep 7, 2018

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.

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sauln Sep 7, 2018

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

sauln commented Sep 7, 2018

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

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sauln commented Sep 7, 2018

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Here are some things you can ask me to do:

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whedon commented Sep 7, 2018

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

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@whedon generate pdf

sauln commented Sep 7, 2018

@whedon generate pdf

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@whedon generate pdf

sauln commented Sep 7, 2018

@whedon generate pdf

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sauln Sep 7, 2018

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.

sauln commented Sep 7, 2018

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.

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arokem Sep 10, 2018

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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.

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arokem commented Sep 10, 2018

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.

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sauln Sep 11, 2018

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

DOI

sauln commented Sep 11, 2018

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

DOI

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ctralie Sep 11, 2018

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

ctralie commented Sep 11, 2018

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

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arokem Sep 13, 2018

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@whedon set 10.5281/zenodo.1412867 as archive

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arokem commented Sep 13, 2018

@whedon set 10.5281/zenodo.1412867 as archive

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OK. 10.5281/zenodo.1412867 is the archive.

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whedon commented Sep 13, 2018

OK. 10.5281/zenodo.1412867 is the archive.

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

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arokem commented Sep 13, 2018

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

@arfon arfon added the accepted label Sep 13, 2018

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@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 ⚡️ 🚀 💥

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arfon commented Sep 13, 2018

@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 ⚡️ 🚀 💥

@arfon arfon closed this Sep 13, 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 snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.00925/status.svg)](https://doi.org/10.21105/joss.00925)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00925">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00925/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00925/status.svg
   :target: https://doi.org/10.21105/joss.00925

This is how it will look in your documentation:

DOI

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whedon commented Sep 13, 2018

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

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.00925/status.svg)](https://doi.org/10.21105/joss.00925)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00925">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00925/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00925/status.svg
   :target: https://doi.org/10.21105/joss.00925

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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