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[REVIEW]: PySwarms: a research toolkit for Particle Swarm Optimization in Python #433
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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @stsievert 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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS reviews 😿 To fix this do the following two things:
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I've looked this over briefly today, and here's some comments:
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Hi @stsievert , Thank you so much for your comments. An aside, PSO is a class of search algorithms that can be used to optimize functions even if they're differentiable or not. This library provides implementations of these algorithms that should solve any optimization problem. Of course, the performance will depend on the PSO parameters (you can control if the particles are independent from one another, follows the herd, etc.), and to the type of PSO used in a certain problem. As for your comments:
Thank you so much, I hope it clears things up! 😄 [1] Dario Floreano, Peter Durr, and Claudio Mattiussi. “Neuroevolution: from architectures to |
Thanks – that clears this up. I don't think the above is expressed clearly in your docs. I would like to see the same sentence, maybe with "high-level interface" expanded.
It does! Thank you. |
Thank you @stsievert . Unfortunately, I'm on a trip so I might be able to handle this on Thursday, (UTC+09 :00). |
No worries – take your time! |
Hi @stsievert , I've made the changes you've requested both in Paper.md and the README.rst. Hope it's much better now. Thanks a lot! |
Thanks – this looks better! I've commented in ljvmiranda921/pyswarms#56 for some more small edits. |
@stsievert thanks for your comments so far! I noticed that a few of the checkboxes at the top are still empty, is your review still in progress? (Also, please do check off that first one about the conflict of interest) |
Merged to resolve #56. Reference: openjournals/joss-reviews#433 Author: ljvmiranda921 E-mail: ljvmiranda@gmail.com
Update: The latest commit resolves ljvmiranda921/pyswarms#56 Hi @stsievert , the latest commit applies the changes needed. 👍 |
@kyleniemeyer my review is still in progress. I still need to download and verify the claims in the documentation. Plus I'd like @oesteban's comment too. |
This commit modifies the TOC tree and moves the API documentation into its own Section (not a Subsection).Turns out that the submodules header is unnecessary and can be omitted. Reference: openjournals/joss-reviews#433 Author: ljvmiranda921 E-mail: ljvmiranda@gmail.com
Update: The latest commit resolves ljvmiranda921/pyswarms#61 |
I've updated the review, and all boxes are checked. |
Hi @oesteban, have you had a chance to look at the software package and paper, if you are still able to? |
Hi @kyleniemeyer , sorry I wasn't able to check this recently. Thank you for the review @stsievert ! |
Hi @kyleniemeyer ! :) I am just wondering what the status of this would be. Thanks a lot! |
Hi @ljvmiranda921, sorry for the delay on this. It looks like your software is good to go, but I do have some feedback on the article before accepting. Right now, the article is a bit short; we don't want a full-length paper, but per the author guidelines we do expect between 250-1000 words. Perhaps you could describe the implementation a bit more, or better yet explain some example use cases. Examples of the software being used in research (whether published already, or in progress) are also helpful. In addition, it may be helpful to explain PSO in a sentence or two, with an appropriate reference, at the beginning. |
Reference: openjournals/joss-reviews#433 Extends the previous version of the paper (very short) into a longer and more explicit version. A short introduction for PSO was added, some design principles, and a brief mention to some use-cases. Author: @ljvmiranda921 E-mail: ljvmiranda@gmail.com
Hi @kyleniemeyer , thanks a lot! I have updated the paper and the changes can be seen in ljvmiranda921/pyswarms#71 . If everything looks good, I can already merge the branch to master. 😄 |
@ljvmiranda921 looks good! Please merge that, and I'll try generating the article PDF. |
@kyleniemeyer , merged! 👍 |
@whedon generate pdf |
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@ljvmiranda921 alright, looks good. Can you now archive the entire software repository (e.g., using Zenodo) and report the DOI back here? That'll be the last thing needed. |
Thanks! Hmmm, I currently have a Zenodo DOI of the latest version v.0.1.7 (link, DOI: 10.5281/zenodo.996029). Do I still need to make a new one? |
It should reflect the latest version including the changes you made to address the reviewer comments here—if that version was archived in September, then I don't think it would have the newer changes you made. |
Got it, will archive via Zenodo |
Hi @kyleniemeyer , sorry for my confusion and I just want to be careful: if I am to archive via Zenodo, then that means I will create a new release, thus bumping the version number of my submission (just following the instructions from this link). This will then be v0.1.8 and is now "different" to v0.1.7, is it okay to proceed? Thanks a lot! 👍 |
@ljvmiranda921 yeah that's no problem, we typically expect the version number to change after the code goes through review. |
Here is the DOI: 10.5281/zenodo.1145432 (link) |
@whedon set 10.5281/zenodo.1145432 as archive |
OK. 10.5281/zenodo.1145432 is the archive. |
@arfon this is now accepted and ready to publish |
Thank you @kyleniemeyer for helping me improve my paper, and to @stsievert for reviewing my submission! 😃 |
@stsievert - many thanks for your review and to @kyleniemeyer for editing this submission ✨. @ljvmiranda921 - your submission is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00433 ⚡️ 🚀 💥 |
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Submitting author: @ljvmiranda921 (Lester James Miranda)
Repository: https://github.com/ljvmiranda921/pyswarms
Version: v0.1.7
Editor: @kyleniemeyer
Reviewer: @stsievert
Archive: 10.5281/zenodo.1145432
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