Joss-reviews: [REVIEW]: CluSim: a Python package for the comparison of clusterings and dendrograms

Created on 19 Feb 2019  ·  75Comments  ·  Source: openjournals/joss-reviews

Submitting author: @ajgates42 (Alexander Gates)
Repository: https://github.com/Hoosier-Clusters/clusim
Version: v0.3.2
Editor: @VivianePons
Reviewers: @pajaskowiak, @adavidzh
Archive: 10.5281/zenodo.2601868

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/16ce8a38d204c773202405e1c7da518c"><img src="http://joss.theoj.org/papers/16ce8a38d204c773202405e1c7da518c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/16ce8a38d204c773202405e1c7da518c/status.svg)](http://joss.theoj.org/papers/16ce8a38d204c773202405e1c7da518c)

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

@pajaskowiak, 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 @VivianePons know.

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

Review checklist for @pajaskowiak

Conflict of interest

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: v0.3.2
  • [x] Authorship: Has the submitting author (@ajgates42) 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)?

Review checklist for @adavidzh

Conflict of interest

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: v0.3.2
  • [x] Authorship: Has the submitting author (@ajgates42) 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)?
accepted published recommend-accept review
Source
picture whedon

All 75 comments

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

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@whedon commands
whedon picture whedon on 19 Feb 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 19 Feb 2019

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

whedon picture whedon on 19 Feb 2019

I have a few fundamental comments from the pre-review which I would hope the authors can comment on.

adavidzh picture adavidzh on 19 Feb 2019

👋 @ajgates42 - it seems like @adavidzh is waiting on your feedback on their comments here: https://github.com/openjournals/joss-reviews/issues/1192#issuecomment-457099152

arfon picture arfon on 4 Mar 2019

Thanks @adavidzh for the close reading of our work! I understand the lack of details in our first write-up made it difficult to decode the examples, we were trying to illustrate the breadth of the package which staying within the constraints of the word limits.

To improve the readability and ease of use, we have followed your suggestion and exchanged one of those examples with a simplified version of the Arxiv behavior examples. We chose to retain the random model example because it illustrates another core functionality of the package, but we tried to simplify the explanation in the writeup.

I also included a new example jupyter notebook that recreates the examples discussed in the text.

All updates can be found in the joss-reviews branch.

ajgates42 picture ajgates42 on 13 Mar 2019

@whedon generate pdf from branch joss-reviews

ajgates42 picture ajgates42 on 13 Mar 2019 
Attempting PDF compilation from custom branch joss-reviews
. Reticulating splines etc...
whedon picture whedon on 13 Mar 2019

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

whedon picture whedon on 13 Mar 2019

@whedon generate pdf from branch joss-reviews

ajgates42 picture ajgates42 on 13 Mar 2019 
Attempting PDF compilation from custom branch joss-reviews. Reticulating splines etc...
whedon picture whedon on 13 Mar 2019

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

whedon picture whedon on 13 Mar 2019

Quick question for @VivianePons: the review checklist is addressed to @pajaskowiak. Does this mean that only they should check items or can I also do it?

adavidzh picture adavidzh on 14 Mar 2019

I used the wrong command when I added the second reviewer I said "assign" instead of "add". You are both reviewers but only @pajaskowiak is listed. I'm not sure how I should fix it.

VivianePons picture VivianePons on 14 Mar 2019

Just read the manuscript. Excelent work, easy to follow and understand. My only minor point is w.r.t. the fact that the authors mention that all measures are bounded to the [0,1] interval. This is not the case for Adjusted Rand Index (ARI), which can be negative. Other than that, I have no concerns at all.

pajaskowiak picture pajaskowiak on 15 Mar 2019

@VivianePons: perhaps @whedon add @adavidzh as reviewer :smile:
@ajgates42: thanks for the changes. I would not mention reviewers in the acknowledgments, but that's in my field. Other than that, nothing to add.

adavidzh picture adavidzh on 17 Mar 2019

@whedon add @adavidzh as reviewer

VivianePons picture VivianePons on 17 Mar 2019

OK, @adavidzh is now a reviewer

whedon picture whedon on 17 Mar 2019

The command added you in the list but didn't create the list of checkboxes, I just did manually. Please, just check that you can check them all ;)

Thanks and sorry for the confusion!

VivianePons picture VivianePons on 17 Mar 2019

@VivianePons: all good, thanks.
@ajgates42: while going through the review checklist:

  1. Can you point me to the contribution guidelines? IMO, this can be as simple as adding a section to README.md.
  2. I can't quite find how the 0.3.1 version is tagged: I see that version in PyPI but there is no branch nor tag that I can find on github.
adavidzh picture adavidzh on 17 Mar 2019

@adavidzh, you can now find a contribution guidelines and code of conduct in the README. I've also tagged a new release v0.3.2 and updated the version in the __init__.py. The PyPI version will be updated shortly.
Thanks!

ajgates42 picture ajgates42 on 18 Mar 2019
👍1

Thanks @ajgates42.

adavidzh picture adavidzh on 19 Mar 2019

@whedon set v0.3.2 as version

adavidzh picture adavidzh on 19 Mar 2019

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

whedon picture whedon on 19 Mar 2019

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

Hi @VivianePons, is it correct to say that the version number should change, given the additions to the repo?

adavidzh picture adavidzh on 19 Mar 2019

@whedon set v0.3.2 as version

VivianePons picture VivianePons on 19 Mar 2019

OK. v0.3.2 is the version.

whedon picture whedon on 19 Mar 2019

Yes, it seems to make sense. I just updated it.

Do we have a green light from both reviewers now to accept the paper?

VivianePons picture VivianePons on 19 Mar 2019

✅ from me.

adavidzh picture adavidzh on 19 Mar 2019

Yes! Everything is fine.

pajaskowiak picture pajaskowiak on 19 Mar 2019

Perfect!

@ajgates42 could you create an archive of your repo on Zenodo or figshare and generate a DOI? Thanks

VivianePons picture VivianePons on 19 Mar 2019

Great! Thank you all for the valuable feedback!

DOI: https://doi.org/10.5281/zenodo.2598682
Record: https://zenodo.org/record/2598682

On Tue, Mar 19, 2019 at 1:13 PM Viviane Pons notifications@github.com
wrote:

Perfect!

@ajgates42 https://github.com/ajgates42 could you create an archive of
your repo on Zenodo or figshare and generate a DOI? Thanks

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1264#issuecomment-474475617,
or mute the thread
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.

--
Alexander Gates
Postdoctoral Research Scholar
Center for Complex Network Research
Northeastern University
http://alexandergates.net

ajgates42 picture ajgates42 on 19 Mar 2019

@whedon generate pdf

VivianePons picture VivianePons on 19 Mar 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 19 Mar 2019

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

whedon picture whedon on 19 Mar 2019

@whedon check references

VivianePons picture VivianePons on 19 Mar 2019 
Attempting to check references...
whedon picture whedon on 19 Mar 2019

```Reference check summary:

OK DOIs

  • 10.1103/PhysRevE.78.046110 is OK
  • 10.1103/PhysRevE.80.016118 is OK
  • 10.1137/080734315 is OK
  • 10.3389/fnhum.2012.00145 is OK
  • 10.1109/SBRN.2012.25 is OK
  • 10.3389/fnins.2013.00133 is OK
  • 10.1126/sciadv.1602548 is OK

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 19 Mar 2019

@ajgates42 it seems like some references are missing their dois. For example, I see: "The impact of random models on clustering similarity" has doi https://doi.org/10.1101/196840 which is not in the bib file. Can you check? whedon has put the list of all references without dois.

Thanks

VivianePons picture VivianePons on 19 Mar 2019

@ajgates42 - you might also want to remove entries from your bibtex that you're not actually using in this paper?

arfon picture arfon on 19 Mar 2019

@VivianePons https://github.com/VivianePons: JMLR actually doesn't
actually give a DOI yet, but I guess we can use the BioRxiv version instead.

On Tue, Mar 19, 2019 at 5:04 PM Arfon Smith notifications@github.com
wrote:

@ajgates42 https://github.com/ajgates42 - you might also want to remove
entries from your bibtex that you're not actually using in this paper?

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1264#issuecomment-474583783,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AZk97aMXsnUI7P0-dyJavQNHFY8_SrTbks5vYVDQgaJpZM4bDUad
.

--
Alexander Gates
Postdoctoral Research Scholar
Center for Complex Network Research
Northeastern University
http://alexandergates.net

ajgates42 picture ajgates42 on 19 Mar 2019

@whedon https://github.com/whedon check references

On Tue, Mar 19, 2019 at 6:14 PM Alexander Gates ajgates42@gmail.com wrote:

@VivianePons https://github.com/VivianePons: JMLR actually doesn't
actually give a DOI yet, but I guess we can use the BioRxiv version instead.

On Tue, Mar 19, 2019 at 5:04 PM Arfon Smith notifications@github.com
wrote:

@ajgates42 https://github.com/ajgates42 - you might also want to
remove entries from your bibtex that you're not actually using in this
paper?

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1264#issuecomment-474583783,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AZk97aMXsnUI7P0-dyJavQNHFY8_SrTbks5vYVDQgaJpZM4bDUad
.

--
Alexander Gates
Postdoctoral Research Scholar
Center for Complex Network Research
Northeastern University
http://alexandergates.net

--
Alexander Gates
Postdoctoral Research Scholar
Center for Complex Network Research
Northeastern University
http://alexandergates.net

ajgates42 picture ajgates42 on 19 Mar 2019

@whedon check references

VivianePons picture VivianePons on 19 Mar 2019 
Attempting to check references...
whedon picture whedon on 19 Mar 2019

```Reference check summary:

OK DOIs

  • 10.1007/BF01908075 is OK
  • 10.1186/1471-2105-9-497 is OK
  • 10.1145/1553374.1553511 is OK
  • 10.1101/196840 is OK
  • 10.1093/bioinformatics/btq228 is OK

MISSING DOIs

  • None

INVALID DOIs

  • None
    ```
whedon picture whedon on 19 Mar 2019

@whedon generate pdf

VivianePons picture VivianePons on 19 Mar 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 19 Mar 2019

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

whedon picture whedon on 19 Mar 2019

We're still missing a doi for "Data clustering: a review" (not listed by whedon for some reason...). Other missing ones are from "misc" paper, arxiv preprint, so I guess this is ok.

Also the date on the scipy citation prints weirdly, @arfon do you know if it's the correct way to do it?

VivianePons picture VivianePons on 19 Mar 2019

Also the date on the scipy citation prints weirdly, @arfon do you know if it's the correct way to do it?

Not sure, I think it's probably because of the bibtex entry not actually having a date range https://github.com/Hoosier-Clusters/clusim/blob/master/paper.bib#L85

arfon picture arfon on 20 Mar 2019

Thats the standard citation from the scipy website
https://www.scipy.org/citing.html. But the reference isn't essential for
the work, so lets, just drop it from the paper. I've updated the bib
accordingly.

Thanks!

On Wed, Mar 20, 2019 at 6:10 AM Arfon Smith notifications@github.com
wrote:

Also the date on the scipy citation prints weirdly, @arfon
https://github.com/arfon do you know if it's the correct way to do it?

Not sure, I think it's probably because of the bibtex entry not actually
having a date range
https://github.com/Hoosier-Clusters/clusim/blob/master/paper.bib#L85

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1264#issuecomment-474766604,
or mute the thread
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.

--
Alexander Gates
Postdoctoral Research Scholar
Center for Complex Network Research
Northeastern University
http://alexandergates.net

ajgates42 picture ajgates42 on 20 Mar 2019

@whedon generate pdf

VivianePons picture VivianePons on 20 Mar 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 20 Mar 2019

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

whedon picture whedon on 20 Mar 2019

@whedon check references

VivianePons picture VivianePons on 20 Mar 2019 
Attempting to check references...
whedon picture whedon on 20 Mar 2019

```Reference check summary:

OK DOIs

  • 10.1007/BF01908075 is OK
  • 10.1145/331499.331504 is OK
  • 10.1186/1471-2105-9-497 is OK
  • 10.1145/1553374.1553511 is OK
  • 10.1101/196840 is OK
  • 10.1093/bioinformatics/btq228 is OK

MISSING DOIs

  • None

INVALID DOIs

  • None
    ```
whedon picture whedon on 20 Mar 2019

Perfect, could you update the Zenodo metadata so that the title matches the paper name? (At the moment, the Zenodo title is only "CluSim" whereas the title paper is: "CluSim: a Python package for the comparison of clusterings and dendrograms")

Also, you might wanna udpate the paper.md and paper.bib on the the Zenodo archive if that's possible (sorry, I should probably have asked you to create the archive AFTER checking the references)

VivianePons picture VivianePons on 20 Mar 2019

OK. The Zenodo metadata and files have been brought up to date. The new
DOI is 10.5281/zenodo.2601868

On Wed, Mar 20, 2019 at 5:50 PM Viviane Pons notifications@github.com
wrote:

Perfect, could you update the Zenodo metadata so that the title matches
the paper name? (At the moment, the Zenodo title is only "CluSim" whereas
the title paper is: "CluSim: a Python package for the comparison of
clusterings and dendrograms")

Also, you might wanna udpate the paper.md and paper.bib on the the Zenodo
archive if that's possible (sorry, I should probably have asked you to
create the archive AFTER checking the references)

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1264#issuecomment-475042484,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AZk97dNC-iBOWgBWa9c9VPXLi05V_06-ks5vYq0-gaJpZM4bDUad
.

--
Alexander Gates
Postdoctoral Research Scholar
Center for Complex Network Research
Northeastern University
http://alexandergates.net

ajgates42 picture ajgates42 on 21 Mar 2019

@whedon set 10.5281/zenodo.2601868 as archive

VivianePons picture VivianePons on 21 Mar 2019

OK. 10.5281/zenodo.2601868 is the archive.

whedon picture whedon on 21 Mar 2019

@whedon generate pdf

VivianePons picture VivianePons on 21 Mar 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 21 Mar 2019

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

whedon picture whedon on 21 Mar 2019

Thank you @ajgates42 @adavidzh and @pajaskowiak for the great work! This paper is ready to be accepted. It's now up to you @openjournals/joss-eics

VivianePons picture VivianePons on 21 Mar 2019

@whedon accept

arfon picture arfon on 21 Mar 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 21 Mar 2019

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/572

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/572, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

whedon picture whedon on 21 Mar 2019

```Reference check summary:

OK DOIs

  • 10.1007/BF01908075 is OK
  • 10.1145/331499.331504 is OK
  • 10.1186/1471-2105-9-497 is OK
  • 10.1145/1553374.1553511 is OK
  • 10.1101/196840 is OK
  • 10.1093/bioinformatics/btq228 is OK

MISSING DOIs

  • None

INVALID DOIs

  • None
    ```
whedon picture whedon on 21 Mar 2019

@whedon accept deposit=true

arfon picture arfon on 21 Mar 2019 
Doing it live! Attempting automated processing of paper acceptance...
whedon picture whedon on 21 Mar 2019

🚨🚨🚨 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/573
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01264
  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...

whedon picture whedon on 21 Mar 2019

@pajaskowiak, @adavidzh - many thanks for your reviews here and to @VivianePons for editing this submission :sparkles:

@ajgates42 - your paper is now accepted into JOSS :zap::rocket::boom:

arfon picture arfon on 21 Mar 2019
🎉1

: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.01264/status.svg)](https://doi.org/10.21105/joss.01264)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01264">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01264/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01264/status.svg
   :target: https://doi.org/10.21105/joss.01264

This is how it will look in your documentation:

DOI

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whedon picture whedon on 21 Mar 2019

Awesome! Thank you everyone for the insightful feedback and great
submission experience.

On Thu, Mar 21, 2019 at 1:21 PM Arfon Smith notifications@github.com
wrote:

@pajaskowiak https://github.com/pajaskowiak, @adavidzh
https://github.com/adavidzh - many thanks for your reviews here and to
@VivianePons https://github.com/VivianePons for editing this submission
✨

@ajgates42 https://github.com/ajgates42 - your paper is now accepted
into JOSS ⚡️🚀💥

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
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or mute the thread
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.

--
Alexander Gates
Postdoctoral Research Scholar
Center for Complex Network Research
Northeastern University
http://alexandergates.net

ajgates42 picture ajgates42 on 21 Mar 2019
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