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[REVIEW]: hdbscan: A high performance implementation of HDBSCAN* clustering. #205

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whedon opened this issue Mar 13, 2017 · 17 comments

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@whedon
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commented Mar 13, 2017

Submitting author: @lmcinnes (Leland McInnes)
Repository: https://github.com/scikit-learn-contrib/hdbscan
Version: v0.8.8
Editor: @danielskatz
Reviewer: @zhaozhang
Archive: 10.5281/zenodo.401403

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/b5c5dd4b7491890b711c06225dcc9649"><img src="http://joss.theoj.org/papers/b5c5dd4b7491890b711c06225dcc9649/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/b5c5dd4b7491890b711c06225dcc9649/status.svg)](http://joss.theoj.org/papers/b5c5dd4b7491890b711c06225dcc9649)

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

Conflict of interest

  • 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).

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 (v0.8.8)?
  • Authorship: Has the submitting author (@lmcinnes) made major contributions to the software?

Functionality

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

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)?
@whedon

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commented Mar 13, 2017

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @zhaozhang 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 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:

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
@danielskatz

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commented Mar 13, 2017

Hi @lmcinnes

Please fix the formatting of the paper part of your submission. See https://github.com/mpastell/Weave.jl/blob/master/paper/paper.md for an example of another current submission that has a properly formatted paper. By this, I refer to two things:

  1. the metadata: your line 12 needs one more space at the start.
  2. references to items in the bibliography. Only items that are referenced in the text will be shown in the bibliography when the paper is compiled, and you currently don't refer to any of them.

Thanks.

@lmcinnes

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commented Mar 13, 2017

@danielskatz

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commented Mar 13, 2017

Thanks - there were also a couple more things I saw, so I put in a pull request.

@lmcinnes

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commented Mar 13, 2017

Thank you! Merged.

@zhaozhang

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commented Mar 17, 2017

Hi @lmcinnes,

I have found the following points during installation:

  1. hdbscan depends on scipy also, it was not documented in the instruction manual.
  2. it works with both Python2 and Python3, please document this.
  3. The code examples in README.md are not self-contained, please replace "data" with some example dataset.

Please also include community guidelines:

  1. Contribute to the software.
  2. Report issues or problems with the software.
  3. Seek support.

Please add DOI for the references in paper.bib.

Best,
Zhao

@lmcinnes

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commented Mar 18, 2017

Hi @zhaozhang

Thanks for taking the time to look through everything. I've attempted to remedy each of these points. My only issue is that there does not appear to be a DOI for "Rates of convergence for the cluster tree" from NIPS 2010 (NIPS proceedings seem to forego DOIs for reasons that are not clear to me). Any recommendations on that front would be appreciated.

@danielskatz

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commented Mar 18, 2017

If there's no DOI for a reference, then you don't need to supply one :)

JOSS just wants to be sure that where there is a DOI, it's used.

@danielskatz

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commented Mar 20, 2017

Hi @zhaozhang

If the authors have addressed your points, please update the checkboxes and let me know here that you think is ready to be accepted.

If not, please continue to work with the authors on what you think is needed.

@zhaozhang

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commented Mar 20, 2017

Hi @danielskatz

Yes, I have update the checkboxes. I think it is ready to be accepted.

@danielskatz

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commented Mar 20, 2017

@arfon, over to you for the next steps.

@zhaozhang, thanks for the quick work in suggesting changes

@lmcinnes, thanks for your quick work in responding to the suggestions.

@lmcinnes

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commented Mar 20, 2017

@arfon

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commented Mar 21, 2017

@lmcinnes - 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.

@lmcinnes

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commented Mar 21, 2017

@arfon

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commented Mar 21, 2017

@whedon set 10.5281/zenodo.401403 as archive

@whedon

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commented Mar 21, 2017

OK. 10.5281/zenodo.401403 is the archive.

@arfon arfon added the accepted label Mar 21, 2017

@arfon

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commented Mar 21, 2017

@zhaozhang many thanks for the review here and @danielskatz for editing this paper

@lmcinnes - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00205 ⚡️ 🚀 💥

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