[REVIEW]: pyclustering #1230

whedon · 2019-02-04T13:48:11Z

Submitting author: @annoviko (Andrei Novikov)
Repository: https://github.com/annoviko/pyclustering
Version: 0.8.2
Editor: @poulson
Reviewer: @adavidzh
Archive: 10.5281/zenodo.2636831

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/3dec2a6a7d9cb29a15363a3ecfcf7967"><img src="http://joss.theoj.org/papers/3dec2a6a7d9cb29a15363a3ecfcf7967/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/3dec2a6a7d9cb29a15363a3ecfcf7967/status.svg)](http://joss.theoj.org/papers/3dec2a6a7d9cb29a15363a3ecfcf7967)

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

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

Make sure you're logged in to your GitHub account
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 @poulson know.

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

Review checklist for @adavidzh

Conflict of interest

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

I confirm that I read and will adhere to the JOSS 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: 0.8.2
Authorship: Has the submitting author (@annoviko) 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)?

The text was updated successfully, but these errors were encountered:

whedon · 2019-02-04T13:48:14Z

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

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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 😿

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whedon · 2019-02-04T13:48:15Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-02-04T13:48:37Z

👉 Check article proof 📄 👈

adavidzh · 2019-02-12T00:01:26Z

Hi @poulson, I'm not sure how to check the "release version".

The repo has a 0.8.2.rel branch whose README.rst identifies the version as 0.8.2. PyPi mentions 0.8.2. So, while things looks consistent, I'm not sure if "the release version given match[es] the GitHub release (0.8.2)".

poulson · 2019-02-20T16:32:17Z

@adavidzh I apologize for missing the ping on this! I will reach out to the author to confirm.

@annoviko Andrei, Could you confirm that 0.8.2rel is the proper branch? It would be great if you could take a minute and create a 0.8.2 branch so that there is a complete match.

annoviko · 2019-02-20T16:44:15Z

Hello, @poulson, yes, I can confirm that '0.8.2.rel' is the proper branch that was created to release version 0.8.2. There is already '0.8.2' tag as you can see it on pyclustering release page: https://github.com/annoviko/pyclustering/tree/0.8.2 (release page: https://github.com/annoviko/pyclustering/releases/tag/0.8.2).

adavidzh · 2019-02-20T17:40:01Z

Thanks @annoviko, I missed the tag.

annoviko · 2019-02-21T13:04:03Z

@adavidzh, you welcome, do not hesitate to ask me any questions related to pyclustering.

poulson · 2019-03-03T15:14:49Z

Hi Andre (@adavidzh) 👋. Are there any other roadblocks with the review that I could help address?

adavidzh · 2019-03-04T09:15:33Z

I have run into the following issues:

manual installation instructions need to be updated: Installation instructions annoviko/pyclustering#492.
pip installation works, even in unsupported architectures; I'm on Darwin so I'll have to fire-up a VM to continue.

The paper itself could benefit a lot from:

putting in tables the running text where available algorithms are listed.
breaking the monolithic Summary section into the four main parts of the library, viz. Clustering algorithms, Oscillatory networks and neural networks, Graph Coloring Algorithms, and Containers, each with a table and its own statement of need.

annoviko · 2019-03-04T19:31:37Z

@adavidzh , I have updated instruction in line with annoviko/pyclustering#492.

About installation on MAC OS using pip. Yes, it works, but CCORE (fast code - C/C++ implementation) is not supported, python implementation is used instead. CCORE is build only for Linux and Windows as you can see it in CI:

Travis-CI (Linux builds): https://travis-ci.org/annoviko/pyclustering
AppVeyor (Windows builds): https://ci.appveyor.com/project/annoviko/pyclustering/branch/master

But pyclustering itself works on every other platform if it is supported by python and libraries that are used by pyclustering.

About the paper. I will provide changes soon.

adavidzh · 2019-03-04T22:10:47Z

Thanks @annoviko. I now understand that only the CCORE does not work in Darwin. I am working through the examples and reported one issue here annoviko/pyclustering#493. As for the paper, that would be great, thanks.

annoviko · 2019-03-09T20:22:45Z

@adavidzh, I have updated the paper (see 'master' branch: paper/paper.md). And updated example section in README file ('master' and '0.8.2.rel' branches).

annoviko · 2019-03-10T10:15:18Z

@whedon generate pdf

whedon · 2019-03-10T10:15:20Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-03-10T10:15:43Z

👉 Check article proof 📄 👈

annoviko · 2019-03-10T11:17:32Z

Just for your information: PDF generator does not support symbol '✓' (see @Wheldon's previous post - tables have empty columns), therefore I have changed it to 'v'.

annoviko · 2019-03-10T11:17:52Z

@whedon generate pdf

whedon · 2019-03-10T11:17:54Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-03-10T11:18:38Z

👉 Check article proof 📄 👈

annoviko · 2019-03-10T11:20:27Z

@whedon generate pdf

whedon · 2019-03-10T11:20:29Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-03-10T11:20:59Z

👉 Check article proof 📄 👈

adavidzh · 2019-03-10T17:33:29Z

Paper: this looks much better, thanks. Based on the instructions, I suggest trying $\checkmark$ , $\Checkmark$ , $\ding{51}$ , $\ballotcheck$ , and others like those from fontawesome in a single try to see if JOSS supports any of them.
README: also good progress; Installation instructions annoviko/pyclustering#492 is not yet finished but should be close to that.

I am planning to make a PR against paper.md regarding some text issues after you give a try to the checkmark options above. If there is prior art somewhere on how to do it, I couldn't find it.

annoviko · 2019-03-10T18:41:05Z

@whedon generate pdf

whedon · 2019-03-10T18:41:07Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-03-10T18:41:31Z

👉 Check article proof 📄 👈

annoviko · 2019-04-08T11:41:54Z

Hello, Jack (@poulson) ,

There is already DOI for 0.8.2 release that is described in the paper: https://zenodo.org/record/1491324#.XKszIlUzaUk

    doi          = {10.5281/zenodo.1491324},
    url          = {https://doi.org/10.5281/zenodo.1491324}

poulson · 2019-04-09T21:57:08Z

Thank you, @annoviko !

poulson · 2019-04-09T21:57:41Z

@whedon set 10.5281/zenodo.1491324 as archive

whedon · 2019-04-09T21:57:44Z

OK. 10.5281/zenodo.1491324 is the archive.

poulson · 2019-04-09T21:57:52Z

@whedon set 0.8.2 as version

whedon · 2019-04-09T21:57:55Z

OK. 0.8.2 is the version.

poulson · 2019-04-09T21:59:07Z

The paper is ready to be accepted! @openjournals/joss-eics

labarba · 2019-04-10T17:00:39Z

@whedon generate pdf

whedon · 2019-04-10T17:00:41Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-10T17:01:20Z

👉 Check article proof 📄 👈

labarba · 2019-04-10T17:04:34Z

The Zenodo archive in DOI 10.5281/zenodo.1491324 is Version 0.8.2 from Nov 19, 2018. If you've made changes during this review, then you would have to make a new tagged version in your software repository, and an update to the Zenodo deposit.

annoviko · 2019-04-11T19:41:48Z

Hello, @labarba, there were changes related to project description, functionality wasn't changed. But anyway, I have prepare special 0.8.2 JOSS release with these changes if it is required. Here is DOI: 10.5281/zenodo.2636831 - version 0.8.2. Link: https://doi.org/10.5281/zenodo.2636831 .

labarba · 2019-04-14T12:58:51Z

@whedon set 10.5281/zenodo.2636831 as archive

whedon · 2019-04-14T12:58:55Z

OK. 10.5281/zenodo.2636831 is the archive.

labarba · 2019-04-14T12:59:57Z

@whedon accept

whedon · 2019-04-14T12:59:59Z

Attempting dry run of processing paper acceptance...

whedon · 2019-04-14T13:00:28Z

Check final proof 👉 openjournals/joss-papers#623

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#623, 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 · 2019-04-14T13:00:43Z


OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1145/1273442.1250746 is OK
- 10.1007/BFb0033313 is OK
- 10.1145/235968.233324 is OK
- 10.1109/TKDE.2002.1033770 is OK
- 10.1007/s10618-005-1396-1 is OK
- 10.1145/276305.276312 is OK
- 10.1007/BF02289263 is OK
- 10.1561/2000000034 is OK
- https://doi.org/10.1016/S0898-1221(99)00090-5 is OK
- 10.1109/TKDE.2012.32 is OK
- 10.1145/304181.304187 is OK
- 10.1109/ICDE.1999.754967 is OK
- 10.1016/0377-0427(87)90125-7 is OK
- 10.1134/S1054661814030146 is OK
- 10.1109/5.58325 is OK
- 10.5220/0004906703050309 is OK
- 10.1134/S1054661809020151 is OK
- https://doi.org/10.1016/j.neunet.2009.02.002 is OK
- 10.1109/ISCAS.2003.1206418 is OK
- 10.1162/neco.1997.9.4.805 is OK
- 10.1007/978-3-642-36877-6 is OK
- 10.1016/j.physrep.2008.09.002 is OK
- 10.1109/TNNLS.2014.2345572 is OK
- 10.1007/978-3-319-21909-7_20 is OK
- 10.1145/359094.359101 is OK
- https://doi.org/10.1016/j.physd.2011.09.010 is OK
- https://doi.org/10.1016/0098-3004(91)90117-V is OK

MISSING DOIs

- None

INVALID DOIs

- None

labarba · 2019-04-14T13:13:27Z

@whedon accept deposit=true

whedon · 2019-04-14T13:13:30Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2019-04-14T13:14:07Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01230 joss-papers#624
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01230
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

labarba · 2019-04-14T13:15:55Z

Congratulations, @annoviko, your JOSS paper is now published!

Big thanks to our editor: @poulson, and reviewer: @adavidzh — your valuable contribution makes JOSS possible! 🙏

whedon · 2019-04-14T13:16:10Z

🎉🎉🎉 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.01230/status.svg)](https://doi.org/10.21105/joss.01230)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01230">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01230/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01230/status.svg
   :target: https://doi.org/10.21105/joss.01230

This is how it will look in your documentation:

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annoviko · 2019-04-14T13:17:09Z

Thanks to everyone :-) !

whedon assigned poulson Feb 4, 2019

whedon added the review label Feb 4, 2019

whedon mentioned this issue Feb 4, 2019

[PRE REVIEW]: pyclustering #1195

Closed

poulson added the accepted label Apr 9, 2019

labarba closed this as completed Apr 14, 2019

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

This was referenced Oct 30, 2023

[PRE REVIEW]: CM++ - A Meta-method for Well-Connected Community Detection #5998

Closed

[PRE REVIEW]: linkinglines: Using the Hough Transform to Cluster Line Segments and for Mesoscale Feature Extraction #6007

Closed

[REVIEW]: pyclustering #1230

[REVIEW]: pyclustering #1230

Comments

whedon commented Feb 4, 2019 • edited Loading

Status

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Review checklist for @adavidzh

Conflict of interest

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Software paper

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