[REVIEW]: pyclustering

[whedon]

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:

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 @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)?

[whedon]

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 🎉.

⭐ 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:

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

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[adavidzh]

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]

@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]

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]

Thanks @annoviko, I missed the tag.

[annoviko]

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

[poulson]

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

[adavidzh]

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]

@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]

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]

@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]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[annoviko]

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]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[annoviko]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[adavidzh]

• 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]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[annoviko]

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]

Thank you, @annoviko !

[poulson]

@whedon set 10.5281/zenodo.1491324 as archive

[whedon]

OK. 10.5281/zenodo.1491324 is the archive.

[poulson]

@whedon set 0.8.2 as version

[whedon]

OK. 0.8.2 is the version.

[poulson]

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

[labarba]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[labarba]

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]

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]

@whedon set 10.5281/zenodo.2636831 as archive

[whedon]

OK. 10.5281/zenodo.2636831 is the archive.

[labarba]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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]

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]

@whedon accept deposit=true

[whedon]

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

[whedon]

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

Here's what you must now do:

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

Any issues? notify your editorial technical team...

[labarba]

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

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

[whedon]

🎉🎉🎉 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]

Thanks to everyone :-) !