[PRE REVIEW]: GB_code: A grain boundary generation code

[whedon]

Submitting author: @oekosheri (raheleh Hadian)
Repository: https://github.com/oekosheri/GB_code
Version: v1.0.0
Editor: @labarba
Reviewers: @vyasr, @trallard

Author instructions

Thanks for submitting your paper to JOSS @oekosheri. 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.

@oekosheri 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

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @labarba 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

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #853 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse': (tmp/853/paper/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse_stream'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in parse' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:in load'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in block in load_file' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in open'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in load_file' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:68:in initialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in <top (required)>'
from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

[arfon]

👋 @labarba - the submitting author suggested you as the handling editor.

[arfon]

@oekosheri - this PR should fix the paper compilation issues oekosheri/GB_code#1

[oekosheri]

Thanks, I edited paper.md and merged. does it look alright now?

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #853 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 12 0 12 0 0 150 0 --:--:-- --:--:-- --:--:-- 151
pandoc-citeproc: reference Sutton:1996 not found
pandoc-citeproc: reference Bollmann:1984 not found
pandoc-citeproc: reference Sutton:1996 not found
pandoc-citeproc: reference Bollmann:1984 not found
Error producing PDF.
! Missing $ inserted.

$
l.283

Looks like we failed to compile the PDF

[oekosheri]

I edited paper.bib and and paper.md again and committed the new changes.

[oekosheri]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #853 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 12 0 12 0 0 28 0 --:--:-- --:--:-- --:--:-- 28
Error producing PDF.
! Missing $ inserted.

$
l.283

Looks like we failed to compile the PDF

[oekosheri]

@arfon Could you tell me what the problem is?

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

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

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

[oekosheri]

@arfon I used pandoc to generate the PDF myself and had no issues. Waiting for your help to see what the problem is.

[arfon]

@oekosheri - I think the underscore in the title needs escaping. I fixed it in oekosheri/GB_code#2

[oekosheri]

Thank you, I merged it. Let me see if I can generate the PDF now.

[oekosheri]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[oekosheri]

I made a minor change,
So:
@whedon generate pdf

[oekosheri]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[oekosheri]

@arfon @labarba the pdf looks good to me. Looking forward to the review process!

[oekosheri]

@arfon Dear Editor, I was wondering about the time frame of the review process. Could you let me know approximately when my code will be reviewed? Thanks and I appreciate it.

[labarba]

It can take between two weeks and two months, typically, to complete the review and acceptance process. Thank you for your patience with our wholly volunteer-staffed journal.

[labarba]

Note that the Pre-review header requests that you provide reviewer suggestions, if possible.

[oekosheri]

@labarba Thank you for your answer. I didn't know I should suggest reviewers. Is there a list I can choose from?

[arfon]

@oekosheri 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.

☝️@oekosheri - I've copied the link from above.

[oekosheri]

Thanks! I would highly appreciate it if any of these reviewers: @bjmorgan @trallard @jochym, would agree to review my code.

[labarba]

@whedon assign @vyasr as reviewer

[whedon]

OK, the reviewer is @vyasr

[labarba]

FYI — I'm waiting for replies from potential second reviewers. Once I get a positive reply, I'll add the reviewer and start the review issue. Stay tuned.

[oekosheri]

Thank you for informing me.

[trallard]

hi @labarba I can jump in as a second reviewer if you are still looking for someone to do it

[labarba]

thank you, @trallard, that's great! I'll add you now and start the review
🙏

[labarba]

@whedon add @trallard as reviewer

[whedon]

OK, @trallard is now a reviewer

[labarba]

@whedon start review

[whedon]

OK, I've started the review over in #900. Feel free to close this issue now!