Joss-reviews: [REVIEW]: PyCM: Multi class confusion matrix library in python

[whedon]

Submitting author: @sepandhaghighi (Sepand Haghighi)
Repository: https://github.com/sepandhaghighi/pycm
Version: v0.8.1
Editor: @arokem
Reviewer: @NickleDave
Archive: 10.5281/zenodo.1250175

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/8268642abd7b142426722c0c39123ff4"><img src="http://joss.theoj.org/papers/8268642abd7b142426722c0c39123ff4/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/8268642abd7b142426722c0c39123ff4/status.svg)](http://joss.theoj.org/papers/8268642abd7b142426722c0c39123ff4)

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

@NickleDave, 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 @arokem know.

Review checklist for @NickleDave

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS 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: Does the release version given match the GitHub release (v0.8.1)?
• [x] Authorship: Has the submitting author (@sepandhaghighi) 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)?

[whedon]

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

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. 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 :page_facing_up: <--

[NickleDave]

review in progress, would say "accept with minor revisions".
added issue about documenting API.
https://github.com/sepandhaghighi/pycm/issues/16

[NickleDave]

added one other minor revision, asking for more specific example usages:
https://github.com/sepandhaghighi/pycm/issues/17

[arokem]

Thanks @NickleDave !

@sepandhaghighi : please let me know here when you've had a chance to address these comments!

[sepandhaghighi]

Hi

@NickleDave Thanks again for review ;-)

@arokem I fixed first issue and working on second

[NickleDave]

added two other issues, after those are closed, this should be ready to accept
https://github.com/sepandhaghighi/pycm/issues/19
https://github.com/sepandhaghighi/pycm/issues/18

[sepandhaghighi]

@NickleDave @arokem
Thank you for your time
The issues have been fixed. ;-)

[sepandhaghighi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[sepandhaghighi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[sepandhaghighi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[NickleDave]

@sepandhaghighi thank you!
@arokem LGTM

[sepandhaghighi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[arokem]

@sepandhaghighi : Great! I believe your paper is ready to be accepted.

At this point, please create a new release of the software and create an archive for it (e.g., using https://zenodo.org/). Once you have that, please reply here with the DOI, so we can set that as the archive to be included in the paper.

[sepandhaghighi]

@arokem
Done !
10.5281/zenodo.1250175

[sepandhaghighi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #729 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse': (tmp/729/paper/paper.md): could not find expected ':' while scanning a simple key at line 12 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:inparse_stream'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in parse' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:inload'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in block in load_file' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:inopen'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in load_file' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/lib/whedon.rb:65:ininitialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/lib/whedon/processor.rb:29:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/lib/whedon/processor.rb:29:inset_paper'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/bin/whedon:99:in from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

[sepandhaghighi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[arokem]

@whedon set 10.5281/zenodo.1250175 as archive

[whedon]

OK. 10.5281/zenodo.1250175 is the archive.

[arokem]

@arfon : I think this paper is ready to go!

[arfon]

@NickleDave - many thanks for your review here and to @arokem for editing this one ✨

@sepandhaghighi - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00729 :zap: :rocket: :boom:

[whedon]

: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 snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00729/status.svg)](https://doi.org/10.21105/joss.00729)

This is how it will look in your documentation:

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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://www.flipcause.com/secure/cause_pdetails/Mjk3Nzk=

[sepandhaghighi]

@NickleDave @arokem @arfon

Thank you for your time ;-)

[NickleDave]

Nice work @sepandhaghighi
Have you thought about sharing PyCM on the scikit-learn mailing list ([email protected] )? I bet a lot of people there would be interested

[sepandhaghighi]

@NickleDave Thanks
Good point, I will post there as soon as possible ;-)