Joss-reviews: [PRE REVIEW]: BVPy: A Python package based on FEniCS and Gmsh for solving boundary value problems in cell and tissue mechanics.
Submitting author: @oalii (Olivier Ali)
Repository: https://gitlab.inria.fr/mosaic/bvpy
Version: v1.0.0
Editor: @Kevin-Mattheus-Moerman
Reviewers: @IgorBaratta, @chennachaos, @finsberg
Managing EiC: Arfon Smith
:warning: JOSS reduced service mode :warning:
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Author instructions
Thanks for submitting your paper to JOSS @oalii. Currently, there isn't an JOSS editor assigned to your paper.
@oalii 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
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whedon
All 38 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
:warning: JOSS reduced service mode :warning:
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
Software report (experimental):
github.com/AlDanial/cloc v 1.84 T=0.19 s (445.2 files/s, 73502.3 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 52 1587 3096 3458
Jupyter Notebook 9 0 3472 443
DOS Batch 1 29 3 212
Markdown 2 110 0 198
reStructuredText 9 206 170 174
YAML 3 16 10 173
make 1 29 8 143
JSON 3 0 0 130
TeX 1 8 0 118
Dockerfile 1 14 8 39
CSS 1 0 0 9
Bourne Shell 1 2 0 4
-------------------------------------------------------------------------------
SUM: 84 2001 6767 5101
-------------------------------------------------------------------------------
Statistical information for the repository 'cc5650abca4dd4ceef557bd6' was
gathered on 2020/10/28.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Florian 229 20229 15304 70.44
GACON Florian 4 228 2 0.46
Olivier Ali 138 11490 3192 29.10
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
Florian 4524 22.4 1.0 16.53
Olivier Ali 3617 31.5 1.0 9.43
PDF failed to compile for issue #2793 with the following error:
/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (890fd4099fd333577252941f/paper/paper.md): found character that cannot start any token while scanning for the next token at line 4 column 1 (Psych::SyntaxError)
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:127:inload_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:87:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:58:inprepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
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from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart'
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from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `
whedon
on 28 Oct 2020
@oalii - there are a number of issues with your paper.md. I've attempted to address them in: https://gist.githubusercontent.com/arfon/fe64794a79cbe9d0004b8ede620df49f/raw/4752f38cb5db08998161c43fda197b64929c81b9/paper.md
arfon
on 28 Oct 2020
@whedon invite @Kevin-Mattheus-Moerman as editor
:wave: @Kevin-Mattheus-Moerman - I realise you already have a number of papers on your plate but would you be able to take this one too?
arfon
on 29 Oct 2020
@Kevin-Mattheus-Moerman has been invited to edit this submission.
whedon
on 29 Oct 2020
@whedon assign me as editor
Kevin-Mattheus-Moerman
on 29 Oct 2020
OK, the editor is @Kevin-Mattheus-Moerman
whedon
on 29 Oct 2020
Hello @arfon, thanks for your editing of the paper.md. https://gist.githubusercontent.com/arfon/fe64794a79cbe9d0004b8ede620df49f/raw/4752f38cb5db08998161c43fda197b64929c81b9/paper.md
Since this is my first submission to JOSS I don't know how it works: Do I need to do anything with these modifications (update and push the file on our gitlab repo ?).
oalii
on 30 Oct 2020
Hi @oalii. Yes, please update your paper and test is compiles with either the Whedon paper preview service (http://whedon.theoj.org) or here by issuing the command @whedon generate pdf.
The entire JOSS editorial process happens in the GitHub review issues and so it's essential that the paper can be compiled by Whedon here.
arfon
on 30 Oct 2020
@whedon generate pdf
oalii
on 30 Oct 2020
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
whedon
on 30 Oct 2020
@arfon,
ok I updated paper.md with your modifications, the pdf is properly generated and all our tests pass. Again a stupid newbie question : I pushed the modify in the develop branch, should I merge it in the master or should I wait the end of the review process before pushing everything on the master ?
oalii
on 30 Oct 2020
馃憤. There are no stupid questions here, these are all good ones :-)
Whedon can compile from the default (master in your case) or a named branch so it's up to you. Some authors never merge the JOSS paper into their default branch (preferring to keep it on a named branch for the entire process).
arfon
on 30 Oct 2020
Thanks @arfon ,
So maybe the best in our case would be to switch on the develop branch for the reviewing process and merge at the end in the master once all the improvements generated by the review will be made ?
In that case, how can I specify to Whedon that the default branch to check is the develop one ?
oalii
on 30 Oct 2020
Yes, that sounds good. We can ask Whedon to build from a custom branch with e.g.:
@whedon generate pdf from branch develop
arfon
on 30 Oct 2020
@whedon generate pdf from branch develop
oalii
on 4 Nov 2020
Attempting PDF compilation from custom branch develop. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
whedon
on 4 Nov 2020
@oalii I will be looking for suitable reviewers for this submission. If you have any suggested reviewers in mind please list them here (remove @ from github handles for now).
Kevin-Mattheus-Moerman
on 7 Nov 2020
@chrisrichardson, @garth-wells, @IgorBaratta, @trallard, @meg-simula, @pefarrell, @SteveMaas1978, @sebastkm would you be interested in reviewing this submission for JOSS?
Kevin-Mattheus-Moerman
on 7 Nov 2020
Hi @Kevin-Mattheus-Moerman ,
I'm happy to review this one!
IgorBaratta
on 7 Nov 2020
@whedon assign @IgorBaratta as reviewer
Kevin-Mattheus-Moerman
on 7 Nov 2020
OK, @IgorBaratta is now a reviewer
whedon
on 7 Nov 2020
@oalii are you able to suggest any reviewers at this points? Thanks
Kevin-Mattheus-Moerman
on 9 Nov 2020
Hi @Kevin-Mattheus-Moerman ,
Thanks for accepting to edit this manuscript.
I quickly checked online and came up with some suggestions:
@finsberg authored an FEniCS-based, biophysical-related paper in JOSS last year.
@jessdtate, @dlagrava, @jhill1, @chennachaos and @JaroslavHron already reviewed some FEniCS-based pieces for JOSS in the past, maybe they could fit ?
oalii
on 9 Nov 2020
I am happy to help out reviewing this.
finsberg
on 10 Nov 2020
Hi @finsberg ,
Thanks for your help !
oalii
on 10 Nov 2020
I am happy to help to review this submission.
chennachaos
on 10 Nov 2020
@oalii it looks like you have already two reviewers. Good luck!
dlagrava
on 10 Nov 2020
Thanks @chennachaos for jumping in !
And thanks also to @dlagrava for answering as well.
Let's wait for @Kevin-Mattheus-Moerman's ruling, I think he is the one in charge here :)
oalii
on 10 Nov 2020
@whedon add @chennachaos as reviewer
Kevin-Mattheus-Moerman
on 10 Nov 2020
OK, @chennachaos is now a reviewer
whedon
on 10 Nov 2020
@whedon add @finsberg as reviewer
Kevin-Mattheus-Moerman
on 10 Nov 2020
OK, @finsberg is now a reviewer
whedon
on 10 Nov 2020
@whedon start review
Kevin-Mattheus-Moerman
on 10 Nov 2020
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2831.
whedon
on 10 Nov 2020
@dlagrava we've started the review over at #2831. If you are able to/interested in helping as well I can add you as a reviewer there. Let me know. Thanks either way.
Kevin-Mattheus-Moerman
on 10 Nov 2020
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