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[PRE REVIEW]: Gridap: An extensible Finite Element toolbox in Julia #2464

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whedon opened this issue Jul 10, 2020 · 47 comments
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[PRE REVIEW]: Gridap: An extensible Finite Element toolbox in Julia #2464

whedon opened this issue Jul 10, 2020 · 47 comments
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@Kevin-Mattheus-Moerman @PetrKryslUCSD @TeroFrondelius
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@whedon
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whedon commented Jul 10, 2020 •
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Submitting author: @fverdugo (Francesc Verdugo)
Repository: https://github.com/gridap/Gridap.jl
Version: v0.12.0
Editor: @Kevin-Mattheus-Moerman
Reviewers: @PetrKryslUCSD, @TeroFrondelius
Managing EiC: Kyle Niemeyer

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

Thanks for submitting your paper to JOSS @fverdugo. Currently, there isn't an JOSS editor assigned to your paper.

@fverdugo if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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
@whedon
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whedon commented Jul 10, 2020

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

@whedon
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whedon commented Jul 10, 2020

Failed to discover a Statement of need section in paper

@whedon
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whedon commented Jul 10, 2020 

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.01 s (292.5 files/s, 24204.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1              0              0            234
Markdown                         2             10              0             57
JSON                             1              0              0             30
-------------------------------------------------------------------------------
SUM:                             4             10              0            321
-------------------------------------------------------------------------------


Statistical information for the repository '2464' was gathered on 2020/07/10.
No commited files with the specified extensions were found.

@whedon
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whedon commented Jul 10, 2020

Failed to discover a valid open source license.

@whedon whedon added the TeX label Jul 10, 2020
@whedon
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whedon commented Jul 10, 2020 

Reference check summary:

OK DOIs

- 10.1145/1163641.1163644 is OK
- 10.1145/1268776.1268779 is OK
- 10.5281/zenodo.3357100 is OK
- 10.1007/978-3-319-52462-7 is OK
- 10.1145/1644001.1644009 is OK
- 10.1137/141000671 is OK
- 10.1145/2998441 is OK
- 10.1016/j.cpc.2019.107059 is OK
- 10.1007/s11831-017-9244-1 is OK
- 10.5334/jors.151 is OK
- 10.5334/jors.182 is OK
- 10.1145/1731022.1731030 is OK
- 10.11588/ans.2015.100.20553 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented Jul 10, 2020

👉 Check article proof 📄 👈

@kyleniemeyer
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Hi @fverdugo, it looks like you have placed your paper in a separate repository from the software itself. We strongly encourage authors to put the paper in the same repository as the software, and in fact a lot of the checks that our bot @whedon does relies on this. (Right now we have no connection to the software repository.)

Do you have a particular reason for putting the paper in a separate repo? We do support the whole publication process with the paper being in a non-default branch, so if you prefer to not include the paper in your main/master branch, you could do that.

cc @arfon

@fverdugo
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Hi @kyleniemeyer,

I have moved the paper to the repo https://github.com/gridap/Gridap.jl branch joss. Hope it is now OK!

cc @santiagobadia

@kyleniemeyer
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Thanks @fverdugo!

@arfon, could you update the repo URL in the system?

@arfon
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arfon commented Jul 11, 2020

@whedon generate pdf from branch joss

@whedon
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whedon commented Jul 11, 2020 

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

@whedon
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whedon commented Jul 11, 2020

👉 Check article proof 📄 👈

@arfon
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arfon commented Jul 11, 2020

@whedon check repository

@whedon
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whedon commented Jul 11, 2020 

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.45 s (794.1 files/s, 100237.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                          324           8272           1289          32523
Markdown                        21            350              0           1294
Lisp                             6            226              0            687
YAML                             2              6              1            109
TOML                             2              5              0             49
-------------------------------------------------------------------------------
SUM:                           355           8859           1290          34662
-------------------------------------------------------------------------------


Statistical information for the repository '2464' was gathered on 2020/07/11.
No commited files with the specified extensions were found.

@whedon whedon added the Julia label Jul 11, 2020
@Kevin-Mattheus-Moerman
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@kyleniemeyer this looks very interesting to me!! If others (e.g. @labarba or @meg-simula ? ) cannot take this to edit I'd be interested. Alternatively I can join as a reviewer.
Also folks from the Julia FEM community might be good candidates to serve as reviewers: https://github.com/JuliaFEM

I just wanted to point out their pre-print as well https://arxiv.org/abs/1910.01412

@Kevin-Mattheus-Moerman
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@whedon assign @Kevin-Mattheus-Moerman as editor

@whedon
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whedon commented Jul 21, 2020

OK, the editor is @Kevin-Mattheus-Moerman

@Kevin-Mattheus-Moerman
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@maikkirapo @ahojukka5 @KristofferC @ChrisRackauckas @burcugrbz would you be interested in reviewing this submission for JOSS?

Gridap: An extensible Finite Element toolbox in Julia
Paper: https://github.com/openjournals/joss-papers/blob/joss.02464/joss.02464/10.21105.joss.02464.pdf
Software: https://github.com/gridap/Gridap.jl

The review process takes place on GitHub and focuses on the software and a short paper.

Let me know if you are interested and I'll add you as reviewer.

Thanks!

@Kevin-Mattheus-Moerman
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@fverdugo can you comment on this pre-print https://arxiv.org/abs/1910.01412 ? We do not allow duplicate publication at JOSS. Can you please clarify the difference between this pre-print (has it been published/submitted anywhere else yet?) and the JOSS paper?

@fverdugo
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The preprint in arxiv is a completely different and separate thing. It is just a paper-like version of our tutorials in https://github.com/gridap/Tutorials. Not under review nor published anywhere.

If you open the two PDFs, you would clearly see the differences. E.g.,

https://arxiv.org/abs/1910.01412 has 31 pages.

Our JOSS submission has 3 pages.

@Kevin-Mattheus-Moerman
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@fverdugo thanks that is what I thought. Good to formally confirm it here.

@Kevin-Mattheus-Moerman
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@fverdugo as you can see I started inviting reviewers. Mainly those related to the JuliaFEM community. Let me know if you had any other reviewers in mind. You can mention any suggested reviewers here if you like (leave out @ in their GitHub handles please).

@fverdugo
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fverdugo commented Jul 22, 2020 •
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Perhaps PetrKryslUCSD would like to review

@Kevin-Mattheus-Moerman
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@PetrKryslUCSD would you be interested in reviewing this submission for JOSS?

Gridap: An extensible Finite Element toolbox in Julia
Paper: https://github.com/openjournals/joss-papers/blob/joss.02464/joss.02464/10.21105.joss.02464.pdf
Software: https://github.com/gridap/Gridap.jl

The review process takes place on GitHub and focuses on the software and a short paper.

Let me know if you are interested and I'll add you as reviewer.

Thanks!

@PetrKryslUCSD
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PetrKryslUCSD commented Jul 22, 2020 via email

@ChrisRackauckas
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I'm sorry but I won't have time right now.

@Kevin-Mattheus-Moerman
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@whedon assign @PetrKryslUCSD as reviewer

@whedon
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whedon commented Jul 23, 2020

OK, @PetrKryslUCSD is now a reviewer

@Kevin-Mattheus-Moerman
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@maikkirapo @ahojukka5 @KristofferC @burcugrbz would you be interested in reviewing this submission for JOSS?

Gridap: An extensible Finite Element toolbox in Julia
Paper: https://github.com/openjournals/joss-papers/blob/joss.02464/joss.02464/10.21105.joss.02464.pdf
Software: https://github.com/gridap/Gridap.jl

The review process takes place on GitHub and focuses on the software and a short paper.

Let me know if you are interested and I'll add you as reviewer.

Thanks!

@TeroFrondelius
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I am on vacation, but I can do the review in the beginning of August (after a week or so). Also, this would be my first JOSS review, thus possible some learning due to this.

@Kevin-Mattheus-Moerman
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Excellent @TeroFrondelius could you also share (or add on your GitHub profile) a professional profile or ORCID link (is this you?: http://orcid.org/0000-0003-2288-0902)

@Kevin-Mattheus-Moerman
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@whedon add @TeroFrondelius as reviewer

@Kevin-Mattheus-Moerman
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@TeroFrondelius do you think you could convince another juliafem person to join this review?

@PetrKryslUCSD
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PetrKryslUCSD commented Jul 25, 2020 via email

@PetrKryslUCSD
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I guess what confuses me is the variety of conversations here. This does not seem to be focused on the review itself.
But looking at the other issues, perhaps this is how it is supposed to look. Meaning reviewers submitting their comments here. Am I right?

@Kevin-Mattheus-Moerman
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I guess what confuses me is the variety of conversations here. This does not seem to be focused on the review itself.
But looking at the other issues, perhaps this is how it is supposed to look. Meaning reviewers submitting their comments here. Am I right?

Apologies for any confusion, let me clarify. This is a prereview issue where we assign editors/reviewers. The actual review will take place in a dedicated review issue. I'm hoping to recruit one more reviewer.
In the review issue there will be a checkbox list to guide you through the process. You can leave comments to the authors there and also link to issues on their main repository for larger issues.

@Kevin-Mattheus-Moerman
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@whedon add @TeroFrondelius as reviewer

@Kevin-Mattheus-Moerman
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@arfon @openjournals/dev it seems whedon is stuck. It won't assign a reviewer. Can you help?

@arfon
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arfon commented Jul 26, 2020

@whedon add @TeroFrondelius as reviewer

@whedon
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whedon commented Jul 26, 2020

OK, @TeroFrondelius is now a reviewer

@arfon
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arfon commented Jul 26, 2020

@arfon @openjournals/dev it seems whedon is stuck. It won't assign a reviewer. Can you help?

Not sure what was going on here sorry. Minor hiccup...

@TeroFrondelius
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another juliafem person to join this review

@ahojukka5 what you think, would you have time for this review?

@Kevin-Mattheus-Moerman
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@PetrKryslUCSD @TeroFrondelius I'll start the review issue now to avoid further delay. @ahojukka5 if you are able to help that would be great and I can still add you as a reviewer later.

@Kevin-Mattheus-Moerman
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@whedon start review

@whedon
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whedon commented Jul 26, 2020

OK, I've started the review over in #2520.

@whedon whedon closed this as completed Jul 26, 2020
@KristofferC
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FWIW, if still needed, I can probably look at it as well.

@Kevin-Mattheus-Moerman
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@KristofferC great I'll add you over at the review issue #2520

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@arfon @kyleniemeyer @KristofferC @ChrisRackauckas @Kevin-Mattheus-Moerman @PetrKryslUCSD @TeroFrondelius @whedon @fverdugo