[REVIEW]: NiaPy: Python microframework for building nature-inspired algorithms

[whedon]

Submitting author: @GregaVrbancic (Grega Vrbančič)
Repository: https://github.com/NiaOrg/NiaPy
Version: 1.0.0
Editor: @arfon
Reviewer: @ljvmiranda921
Archive: 10.5281/zenodo.1205048

Status

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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

@ljvmiranda921, 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 @arfon know.

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: Does the release version given match the GitHub release (1.0.0)?
• Authorship: Has the submitting author (@GregaVrbancic) 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. I'm here to help you with some common editorial tasks. @ljvmiranda921 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:

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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...

[arfon]

@ljvmiranda921 - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines

Any questions/concerns please let me know.

[whedon]

--> Check article proof 📄 <--

[ljvmiranda921]

Hello @GregaVrbancic , I have opened-up some issues from my review, please check them out.

General Review

Date: 3/19/2018
Based on JOSS reviewer guidelines.

• Software License: Acceptable. Using OSI-approved MIT license
• Installation Instructions: Ok. There is a list of dependencies in documentation must be made explicit in README
• API Documentation: Ok. Core classes are documented. I suggest that the methods inside these classes be documented as well.
• Tests: Good. Good use of pytest and Makefile for abstracting some tests

Community guidelines are present and contributing is easy for other developers.

[GregaVrbancic]

Hello @ljvmiranda921 , thank you for your time and effort to review our software. We'll take a look at opened issues and will try to address them as soon as possible.

[ljvmiranda921]

Hello @GregaVrbancic ,

I appreciate the swift response on the issues. Overall the library looks good once the remaining branches are merged. Once we close the issues, we can complete the checklist above and call-in the Editor.

[GregaVrbancic]

@ljvmiranda921 thank you again for such a quick responses on opened issues. We are working on closing those remaining opened issues. If I understood correctly, after closing those issues and completing the checklist above, we have to make a new release of software and archive it on zenodo?

[ljvmiranda921]

If I understood correctly, after closing those issues and completing the checklist above, we have to make a new release of software and archive it on zenodo?

Yes I believe that's correct. But I'd prefer we wait for the editor's go signal first before making a new release so we won't miss anything and avoid making multiple releases.

[GregaVrbancic]

Sure, I agree, It's better to wait for editors confirmation.

[ljvmiranda921]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the reviewer of this submission
@whedon assign @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

[ljvmiranda921]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[ljvmiranda921]

Hi @arfon ,

I am done reviewing NiaPy. The issues I opened (referenced here in this issue) have now been closed. All boxes have been checked.

Review Summary

NiaPy is a Python library for nature-inspired optimization. It offers a simple and easy-to-use solution to minimize algorithm implementation from scratch. Overall, the software is a good candidate for publication in JOSS.

Functionality

The software functions as claimed in the basic examples and guides. There are no performance claims so I checked that one off. I've also played around and tested their ParticleSwarmOptimization classes and it works as expected.

Documentation

The installation instructions are clear and works on my Linux (Ubuntu 16.04) and Windows 10 machines as stated. The dependencies, together with the dev requirements, are also listed in both the README and Documentation. API documentation for both methods and classes are also included. Overall, the software works as advertised in the documentation.

There is a clear statement of need in the README. The contributing guidelines are complete (development, testing, git collab) and can be found in the documentation. A code of conduct is also included.

Paper

The paper is clear and gives a good overview of the problem, a statement of need, and a short survey of existing works. The library architecture is also included, which I consider as a plus. The references are also complete.

---

Recommendation for future releases

Although I considered it optional, I hope that class methods and package names will follow the PEP8 style. PEP8 is prescriptive, but it is a good standard for Python projects, especially for something useful as NiaPy. However, changing everything into PEP8 will most likely introduce breaking changes, so it's up to the discretion of the authors to follow this suggestion.

---

[lucijabrezocnik]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[arfon]

Wonderful, many thanks @ljvmiranda921!

@lucijabrezocnik - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[lucijabrezocnik]

Hi @arfon !

We have prepared a new release and archived the current version of NiaPy on Zenodo (https://zenodo.org/record/1205048). Here is the DOI: 10.5281/zenodo.1205048.

[arfon]

@whedon set 10.5281/zenodo.1205048 as archive

[whedon]

OK. 10.5281/zenodo.1205048 is the archive.

[arfon]

@ljvmiranda921 - many thanks for your review here ✨

@GregaVrbancic - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00613 ⚡️:rocket: :boom:

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.00613/status.svg)](https://doi.org/10.21105/joss.00613)

This is how it will look in your documentation:

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