[PRE REVIEW]: G3F: Global, Multidimensional Spectral Regression Analysis

[whedon]

Submitting author: @dap-biospec (Denis Proshlyakov) Repository: https://github.com/dap-biospec/G3F Version: v1.0a4 Editor: @kyleniemeyer Reviewers: @tcausgrove, @FaustinCarter

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

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[whedon]

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1568 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1568/paper.md): did not find expected key while parsing a block mapping at line 2 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-5a9319b684e6/lib/whedon.rb:95:inload_yaml' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:78:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:55:inprepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' 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' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

[arfon]

:wave: @dap-biospec - this PR should fix your paper compilation: https://github.com/dap-biospec/G3F/pull/1

[arfon]

:wave: @kyleniemeyer - would you be willing to edit this submission for JOSS?

[dap-biospec]

@arfon @kyleniemeyer Thank you for patching up the paper!

Below are three suggested reviewers. I have no affiliation with any of them.

Christopher Neese: physical chemistry, chemical physics, https://electroscience.osu.edu/people/neese.6

Tim Causgrove: chemistry, protein kinetics and thermodynamics http://faculty.tamucc.edu/tcausgrove/Causgrove_Home.html

Tony Withers: geochemistry; equilibrium and dynamics; spectroscopy; - http://www.bgi.uni-bayreuth.de/?page=4&lng=en&mode=s&id=337

[kyleniemeyer]

@arfon yep, I'll take this one

[kyleniemeyer]

@whedon assign @kyleniemeyer as editor

[whedon]

OK, the editor is @kyleniemeyer

[kyleniemeyer]

@dap-biospec could you merge @arfon's PR for your paper fix, so that we can compile it here?

[dap-biospec]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1568 with the following error:

Error reading bibliography ./paper.bib (line 25, column 9): unexpected "a" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

[dap-biospec]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[dap-biospec]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[dap-biospec]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[dap-biospec]

@kyleniemeyer patch and compilation are done.

[kyleniemeyer]

@whedon add @tcausgrove as reviewer

[whedon]

OK, @tcausgrove is now a reviewer

[dap-biospec]

@tcausgrove, @kyleniemeyer - Documentation has been updated to keep repo transparent. Additional examples are provided in the demo experiment to better illustrate capabilities in three scenarios. A separate performance testing experiment is provided along with the description of testing process and the expected results.

[kyleniemeyer]

Hi @FaustinCarter, I realize the submission #1532 is still in progress, but would you also be willing to review this one?

[FaustinCarter]

In theory, yes. In practice, it depends on whether I can get IgorPro 8 to give me another trial period. I have an older license, but this code does not appear to be backwards compatible. Give me a couple days and I'll have a definite. If you find a different reviewer in the meantime, that is also fine.

[dap-biospec]

@FaustinCarter - I would greatly appreciate it. Please let me know if we can help you with IgorPro 8 in any way. For example, we can set up a remote desktop to one of our computers with IgorPro running site license. I can also reach out to Wavemetrics if you would like.

[FaustinCarter]

Either one of those sound like reasonable options to me. If you can make one of them work I'm on board.

On Mon, Aug 5, 2019 at 12:09 PM dap-biospec notifications@github.com wrote:

@FaustinCarter https://github.com/FaustinCarter - I would greatly appreciate it. Please let me know if we can help you with IgorPro 8 in any way. For example, we can set up a remote desktop to one of our computers with IgorPro running site license. I can also reach out to Wavemetrics if you would like.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1568?email_source=notifications&email_token=ACTQRRA5JAV6JJDVXRSAQ63QDB3GTA5CNFSM4IDSKGAKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3SY4KA#issuecomment-518360616, or mute the thread https://github.com/notifications/unsubscribe-auth/ACTQRRG7DTZICGGIIYQ7RCDQDB3GTANCNFSM4IDSKGAA .

[dap-biospec]

@FaustinCarter I am asking our IT staff to set up a limited time VPN access for you (I have control of my group our workstations). What email address would you like to use? It would be better if it is more official than GMail (not for me, for administration). If you do not want to post it here, email me directly at dapro@chemistry.msu.edu.

Thanks for understanding!

[kyleniemeyer]

Great, thanks @FaustinCarter and @dap-biospec for working something out! I'll go ahead and add you as a reviewer and we can get the formal review started.

[kyleniemeyer]

@whedon add @FaustinCarter as reviewer

[whedon]

OK, @FaustinCarter is now a reviewer

[kyleniemeyer]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1629. Feel free to close this issue now!