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[REVIEW]: TimeSeriesClustering: An extensible framework in Julia #1573

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whedon opened this issue Jul 16, 2019 · 87 comments

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@whedon
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commented Jul 16, 2019

Submitting author: @holgerteichgraeber (Holger Teichgraeber)
Repository: https://github.com/holgerteichgraeber/TimeSeriesClustering.jl
Version: v0.5.2
Editor: @danielskatz
Reviewer: @jgoldfar, @ahwillia
Archive: 10.5281/zenodo.3385349

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/e3975d642975a19f5e2d7e43e3752066"><img src="http://joss.theoj.org/papers/e3975d642975a19f5e2d7e43e3752066/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/e3975d642975a19f5e2d7e43e3752066/status.svg)](http://joss.theoj.org/papers/e3975d642975a19f5e2d7e43e3752066)

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) by leaving comments 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

@jgoldfar & @ahwillia, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.

Please try and complete your review in the next two weeks

Review checklist for @jgoldfar

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: v0.5.2
  • Authorship: Has the submitting author (@holgerteichgraeber) 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)?

Review checklist for @ahwillia

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: v0.5.2
  • Authorship: Has the submitting author (@holgerteichgraeber) 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)?
@whedon

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commented Jul 16, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jgoldfar, @ahwillia it looks like you're currently assigned to review 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:

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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
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commented Jul 16, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 16, 2019

@danielskatz

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commented Jul 16, 2019

Note: @ahwillia is traveling for the next few weeks. It will be about 3 weeks until he can work on this review.

@danielskatz

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commented Jul 16, 2019

👋 @jgoldfar, @ahwillia - We'll do the review here - please read the comments above, and get started when you can. If you have any questions, please ask.

@holgerteichgraeber

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commented Jul 23, 2019

👋 @jgoldfar, @ahwillia - We'll do the review here - please read the comments above, and get started when you can. If you have any questions, please ask.

👋Thank you all for offering to review, I look forward to your comments.
Tagging along co-authors @YoungFaithful and @arbrandt for reference.

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commented Jul 26, 2019

👋 @jgoldfar - have you had a chance to get started?

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commented Aug 1, 2019

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commented Aug 2, 2019

@whedon remind @ahwillia in 7 days

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commented Aug 2, 2019

Reminder set for @ahwillia in 7 days

@danielskatz

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commented Aug 9, 2019

Yes; I will post my review within a few days

@jgoldfar - any update on this?

@ahwillia

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commented Aug 9, 2019

Looking through this now. I'm generally very impressed and think we should be able to approve this in short order. I am confirming that I can install and execute the package now.

My biggest piece of feedback is that the README and description of the package should emphasize even more applications. I think this package will be broadly useful to many fields! For example, the first sentence of the README might lead users to think the package is for a very specialized purpose I would recommend editing to something like...

Current: "ClustForOpt is a julia implementation of unsupervised machine learning methods for finding representative periods for energy systems optimization problems."

Revised: "ClustForOpt is a julia implementation of unsupervised machine learning methods for detecting motifs, clustering, and quantifying similarity between time series datasets."

Likewise, in the subsequent paragraphs, I recommend adding some more example applications with citations. Segmentation and clustering of audio datasets should be an easy one to find.

It is of course okay to say something like "this package was originally developed for energy systems optimization" but I think emphasizing the generality of the package and the methods as much as possible will increase the impact of this work.

Full disclosure, I've worked on using very simple time warping methods for neural data (https://www.biorxiv.org/content/10.1101/661165v1), though those data show very different statistics and call for different modeling approaches. But I'm quite enthusiastic about this area of research.

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commented Aug 9, 2019

One final thought, I don't insist on changing the name of the repo, but something like "TimeSeriesClustering.jl" would seem to better capture the function of the package. The name ClustForOpt doesn't make it super clear what the package does...

Also can the authors comment on the differences between this package and other time series packages in julia (e.g TimeSeries.jl) in the paper / README? It would be nice to give users more guidance on the broader tools available in Julia for these kinds of modeling problems.

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commented Aug 9, 2019

👋 @ahwillia, please update us on how your review is going.

@holgerteichgraeber

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commented Aug 10, 2019

Thank you for your feedback, these are great ideas! I am out for the weekend, and will get back to this next week.

@holgerteichgraeber

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commented Aug 10, 2019

In case that there are any papers that you can recommend to read in the suggested application areas, suggestions are greatly appreciated.

@danielskatz

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commented Aug 15, 2019

👋 @jgoldfar, @ahwillia - can you please use your checklists above to indicate what you think is ok, and what needs to be done, in addition to the comments @ahwillia has posted in this thread, and what I expect @jgoldfar to post soon.

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commented Aug 16, 2019

Checked my boxes...

@holgerteichgraeber
In case that there are any papers that you can recommend to read in the suggested application areas, suggestions are greatly appreciated.

Eamonn Keogh has a variety of methods and application papers to check out (e.g. https://www.cs.ucr.edu/~eamonn/MatrixProfile.html). I'm sure many other research groups have relevant papers as well. Please don't worry about being comprehensive, but the more references you can find the better.

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commented Aug 17, 2019

👋 @jgoldfar

Yes; I will post my review within a few days

Can you please go ahead and do this? (and check the boxes for items that are complete)

@holgerteichgraeber

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commented Aug 18, 2019

@whedon generate pdf from branch paper

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commented Aug 18, 2019

Attempting PDF compilation from custom branch paper. Reticulating splines etc...
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commented Aug 18, 2019

@holgerteichgraeber

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commented Aug 18, 2019

@whedon generate pdf from branch paper

Ok, that seems not to have worked. Will push to master branch and revisit.

I will be updating the package to reflect its more general applicability and rename to TimeSeriesClustering.jl. I will update here once complete.

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commented Aug 18, 2019

@whedon generate pdf

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commented Aug 18, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Sep 4, 2019

@holgerteichgraeber

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commented Sep 6, 2019

The current version number is v0.5.2 and the zenodo DOI is 10.5281/zenodo.3385349 (https://doi.org/10.5281/zenodo.3385349).

@danielskatz just following up, this may have gotten lost among the other messages.

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commented Sep 6, 2019

thanks - sorry I missed that

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commented Sep 6, 2019

@whedon set v0.5.2 as version

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commented Sep 6, 2019

OK. v0.5.2 is the version.

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commented Sep 6, 2019

@whedon set 10.5281/zenodo.3385349 as archive

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commented Sep 6, 2019

OK. 10.5281/zenodo.3385349 is the archive.

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commented Sep 6, 2019

@whedon accept

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commented Sep 6, 2019

Attempting dry run of processing paper acceptance...
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commented Sep 6, 2019

Check final proof 👉 openjournals/joss-papers#950

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#950, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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commented Sep 6, 2019

@whedon check references

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commented Sep 6, 2019

Attempting to check references...
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commented Sep 6, 2019


OK DOIs

- 10.1016/j.apenergy.2019.02.012 is OK
- 10.21105/joss.01230 is OK
- 10.18637/jss.v062.i01 is OK
- 10.18637/jss.v031.i07 is OK
- 10.21105/joss.01504 is OK
- 10.5281/zenodo.2547683 is OK
- 10.21105/joss.00825 is OK
- 10.1016/j.energy.2017.09.087 is OK
- 10.1016/j.energy.2017.11.059 is OK
- 10.1016/j.energy.2017.06.082 is OK
- 10.1016/j.renene.2017.10.017 is OK
- 10.1016/j.energy.2016.06.081 is OK
- 10.1016/j.apenergy.2017.03.051 is OK
- 10.1109/IEVC.2012.6183283 is OK
- 10.1016/j.compchemeng.2009.10.009 is OK
- 10.1137/15M1020575 is OK
- 10.1137/141000671 is OK
- 10.1016/j.is.2015.04.007 is OK
- 10.1016/j.patcog.2005.01.025 is OK
- 10.1016/j.engappai.2010.09.007 is OK
- 10.1137/1.9781611972795.41 is OK
- 10.1186/1471-2105-8-S7-S21 is OK
- 10.1002/widm.1119 is OK
- 10.1016/j.knosys.2014.04.035 is OK
- 10.1016/j.dsp.2010.07.003 is OK
- 10.1145/1281192.1281282 is OK
- 10.4018/ijban.2014100104 is OK

MISSING DOIs

- https://doi.org/10.1137/1.9781611972801.73 may be missing for title: Multiresolution motif discovery in time series
- https://doi.org/10.1109/asru.2017.8269008 may be missing for title: An embedded segmental k-means model for unsupervised segmentation and clustering of speech

INVALID DOIs

- 10.1.1.19.6629 is INVALID
@danielskatz

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commented Sep 6, 2019

👋 @holgerteichgraeber - It looks like the two missing DOIs found above are correct - please add them. And the invalid DOI is indeed invalid - either replace it with the right one or remove it.

Then please regenerate the pdf.

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commented Sep 7, 2019

@whedon generate pdf

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commented Sep 7, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Sep 7, 2019

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commented Sep 7, 2019

👋 @holgerteichgraeber - It looks like the two missing DOIs found above are correct - please add them. And the invalid DOI is indeed invalid - either replace it with the right one or remove it.

Then please regenerate the pdf.

@danielskatz Thank you, I updated the two DOIs and removed the third.

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commented Sep 8, 2019

@whedon check references

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commented Sep 8, 2019

Attempting to check references...
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commented Sep 8, 2019


OK DOIs

- 10.1016/j.apenergy.2019.02.012 is OK
- 10.21105/joss.01230 is OK
- 10.18637/jss.v062.i01 is OK
- 10.18637/jss.v031.i07 is OK
- 10.21105/joss.01504 is OK
- 10.5281/zenodo.2547683 is OK
- 10.21105/joss.00825 is OK
- 10.1016/j.energy.2017.09.087 is OK
- 10.1016/j.energy.2017.11.059 is OK
- 10.1016/j.energy.2017.06.082 is OK
- 10.1016/j.renene.2017.10.017 is OK
- 10.1016/j.energy.2016.06.081 is OK
- 10.1016/j.apenergy.2017.03.051 is OK
- 10.1109/IEVC.2012.6183283 is OK
- 10.1016/j.compchemeng.2009.10.009 is OK
- 10.1137/15M1020575 is OK
- 10.1137/141000671 is OK
- 10.1016/j.is.2015.04.007 is OK
- 10.1016/j.patcog.2005.01.025 is OK
- 10.1016/j.engappai.2010.09.007 is OK
- 10.1137/1.9781611972795.41 is OK
- 10.1186/1471-2105-8-S7-S21 is OK
- 10.1002/widm.1119 is OK
- https://doi.org/10.1137/1.9781611972801.73 is OK
- 10.1016/j.knosys.2014.04.035 is OK
- https://doi.org/10.1109/asru.2017.8269008 is OK
- 10.1016/j.dsp.2010.07.003 is OK
- 10.1145/1281192.1281282 is OK
- 10.4018/ijban.2014100104 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Sep 8, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Sep 8, 2019

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commented Sep 8, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented Sep 8, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Sep 8, 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 👉 openjournals/joss-papers#951
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01573
  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...

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commented Sep 8, 2019

Thanks to @jgoldfar & @ahwillia for reviewing!

@danielskatz danielskatz closed this Sep 8, 2019

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commented Sep 8, 2019

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.01573/status.svg)](https://doi.org/10.21105/joss.01573)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01573">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01573/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01573/status.svg
   :target: https://doi.org/10.21105/joss.01573

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:

@holgerteichgraeber

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commented Sep 8, 2019

Thank you @danielskatz @ahwillia @jgoldfar for editing and reviewing! I very much appreciate that you took the time to review, your comments were extremely helpful!

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