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[PRE REVIEW]: pylbm: A Flexible Python Package for Lattice Boltzmann Method #1016

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whedon opened this issue Oct 14, 2018 · 24 comments

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commented Oct 14, 2018

Submitting author: @gouarin (Loic Gouarin)
Repository: https://github.com/pylbm/pylbm
Version: 0.3.2
Editor: @kyleniemeyer
Reviewer: Pending

Author instructions

Thanks for submitting your paper to JOSS @gouarin. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@gouarin if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
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commented Oct 14, 2018

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

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

@whedon commands
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commented Oct 14, 2018

Attempting PDF compilation. Reticulating splines etc...
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commented Oct 14, 2018

PDF failed to compile for issue #1016 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/lib/whedon.rb:91:in block in check_orcids': Problem with ORCID (0000-0000-0000-0000) for Benjamin Graille (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/lib/whedon.rb:89:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/lib/whedon.rb:89:in check_orcids' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/lib/whedon.rb:70:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-626f701dd525/bin/whedon:98:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

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commented Oct 14, 2018

👋 @kyleniemeyer - would you be able to edit this submission for JOSS?

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commented Oct 14, 2018

@gouarin - please take a look at the errors from @whedon's attempt to compile the paper above. Once you have pushed some fixes, you can ask Whedon to compile again with @whedon generate pdf

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commented Oct 14, 2018

@whedon generate pdf

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commented Oct 14, 2018

Attempting PDF compilation. Reticulating splines etc...
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commented Oct 14, 2018

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commented Oct 23, 2018

Hi @gouarin, do you have any suggested reviewers for this submission? I will try to identify at least one from the JOSS reviewer pool, but I would also like at least one reviewer who is an expert on the topic.

@danielskatz

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commented Oct 23, 2018

And just as a general comment, it would be good to say something about why one would want to run LB simulations in the readme and the docs - for example, in what science/engineering disciplines and for what problems is the LB method a good choice?

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commented Oct 23, 2018

@kyleniemeyer I will try to give you a name soon.

@danielskatz it's difficult to answer to that question. It's like to answer what science/engineering disciplines and for what problems is the finite element, finite difference or finite volume methods a good choice. LB method can be used in computational fluid dynamics and for a lot of problems.

cc @bgraille

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commented Oct 23, 2018

@gouarin @danielskatz I do think including some example problems is important for the paper. Also, I notice that right now about half the paper is decided to future extensions/features; I don't really think that is appropriate, as most of the paper should be motivating and describing the current software. I'd encourage you to check out some of the recent published articles, and work on revising the paper at this stage.

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commented Oct 23, 2018

As @kyleniemeyer said, I don't think there needs to be an exhaustive list of problems for which this is used, but some examples would really help.

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commented Oct 23, 2018

@kyleniemeyer , @danielskatz thanks for your comments. We will modify the article and give various examples. We didn't do it to have a short article. With examples, the article will give more information about what we can do with pylbm and probably more interesting.

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commented Oct 23, 2018

The examples can be really brief (under a paragraph overall), and probably should be in the readme and docs, not just the article. Once the review starts, it's likely the reviewers will ask for this too ...

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commented Oct 23, 2018

We already have various examples in the documentation

https://pylbm.readthedocs.io/en/latest/gallery.html

I can add a link about the gallery in the readme file.

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commented Oct 23, 2018

I'm not sure those graphics really explain what's going on - at least labeling the axes/colors would help

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commented Jan 19, 2019

Hi @kyleniemeyer — I could recommend some reviewer(s) for this submission.

What we're missing, though, is a clear Statement of Need, and some statements in the paper to illustrate how this software has been or can be used in research.

The Lattice Boltzmann Method is like a whole branch of CFD, with thousands of papers published on the topic every year.

Several open-source software packages implementing LBM are already available, big and small. For example:

Therefore, even if we find reviewers and start the review, they (and the editor) will be asking you, @gouarin, to write in the paper how your software sits in the field, what special or different feature it offers, and—for sure—to cite other software in the field.

@gouarin

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commented Jan 20, 2019

Hi @labarba,

thanks for your comments.

We have taken into account the remarks made by @kyleniemeyer and @danielskatz and we have decided to make a new release of pylbm with some of the features described in the paper because it seemed important to us to have them. We will also make new graphics with all the information needed to understand what we draw.

We will make a comparison with the other open-source packages implementing LBM and we will probably give a little example in 1D to understand how it works.

We plan to make all these modifications before the end of February.

So, it would be preferable to wait for the new paper before to start the review process.

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commented Jan 20, 2019

Sure! Just ping us all here when you're ready.

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commented Mar 16, 2019

👋 @gouarin — We'll add this label here 👇 and pause the review. Ping us back when you feel the review can restart.

@labarba labarba added the paused label Mar 16, 2019

@arfon arfon removed the TeX label May 11, 2019

@danielskatz

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commented May 20, 2019

👋 @gouarin - Given that this review hasn't started, I plan to withdraw the paper, with the idea that it can be submitted when the modifications have been made and it is ready to be reviewed. Please let me know if you disagree.

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commented May 21, 2019

@danielskatz I agree. Sorry for the delay.

We will do better next time !

@danielskatz danielskatz added withdrawn and removed paused labels May 21, 2019

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commented May 21, 2019

Thanks - we look forward to your future submission!

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