[PRE REVIEW]: Xono2L: an eXtensible, LabVIEW-compatible real-time sONOgraphic data capture and processing TOOL

[whedon]

Submitting author: @dzhoshkun (Dzhoshkun Ismail Shakir) Repository: https://github.com/gift-surg/Xono2L Version: v0.1.0 Editor: @Kevin-Mattheus-Moerman Reviewer: Pending

Author instructions

Thanks for submitting your paper to JOSS @dzhoshkun. 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.

@dzhoshkun 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, a robot that can help you with some common editorial tasks. @yochannah it looks like you're currently assigned as the editor for this paper :tada:

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

@whedon commands

What happens now?

This submission is currently in a pre-review state which means we are waiting for the assigned editor (@yochannah) to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1104 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Dzhoshkun Shakir<sup>*</sup>, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:17:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:inblock in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:inparse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:52:inprepare' 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:ininvoke_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:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:113: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: @yochannah - the submitting author suggested you as the handling editor.

[yochannah]

Hey! @arfon @dzhoshkun - I'm not sure if I'm the best person to edit this. I'm not familiar with C++ or Labview, and it's not a scientific domain I'm really familiar with either.

[arfon]

OK np @yochannah. @kyleniemeyer can you find someone else to edit this for us?

[kyleniemeyer]

Hey @brainstorm @Kevin-Mattheus-Moerman would one of you be able to edit this submission?

[brainstorm]

I would love to, but LabVIEW is not OSS but proprietary, closed software. Is there any other means to review this software that does not require to run LabVIEW?

[dzhoshkun]

Thanks @yochannah No worries. I wasn't sure about whom to suggest either, but just saw the keyword "API" in your short biography, so this is why I suggested you.

[Kevin-Mattheus-Moerman]

I'm contacting some potential reviewers.

[dzhoshkun]

Thanks @brainstorm

The software is conceptualised as an extensible API that builds into a DLL (please note that it still needs the proprietary Sonix SDK for capturing live ultrasound data). We had to make some effort for making it LabVIEW compatible. And therefore we wanted to make it available to the community, such that for instance other research groups with similar setups could benefit from and/or extend its capabilities.

This probably does not answer your question, but I guess my point is that as LabVIEW compatibility is a main selling point, it'd make more sense for it to be reviewed by someone who has access to LabVIEW.

[dzhoshkun]

Thanks @Kevin-Mattheus-Moerman

[dzhoshkun]

Regarding the PDF compilation error (https://github.com/openjournals/joss-reviews/issues/1104#issuecomment-442479759): it seems to be related to the fake markdown footnote I've introduced for indicating joint first authorship. Any recommendation how this should/could be achieved in the journal's manuscript format ?

[jedbrown]

Try Pandoc footnotes

[dzhoshkun]

@whedon commands

[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

# Compile the paper
@whedon generate pdf

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper from a custom git branch
@whedon generate pdf from branch custom-branch-name

[dzhoshkun]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1104 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Dzhoshkun Shakir[, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:17:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:inblock in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:inparse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:52:inprepare' 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:ininvoke_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:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:113: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 `

'

[dzhoshkun]

@whedon generate pdf from branch fix-joint-1-author-fn

[whedon]

Attempting PDF compilation from custom branch fix-joint-1-author-fn. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1104 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Dzhoshkun Shakir[, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:17:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:inblock in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:inparse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:52:inprepare' 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:ininvoke_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:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:113: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 `

'

[dzhoshkun]

@whedon generate pdf from branch fix-joint-1-author-fn

[whedon]

Attempting PDF compilation from custom branch fix-joint-1-author-fn. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1104 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Dzhoshkun Shakir[, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:17:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:inblock in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:inparse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:52:inprepare' 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:ininvoke_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:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:113: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 `

'

[dzhoshkun]

@whedon generate pdf from branch fix-joint-1-author-fn

[whedon]

Attempting PDF compilation from custom branch fix-joint-1-author-fn. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1104 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Dzhoshkun Shakir[, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/author.rb:17:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:109:inblock in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:106:inparse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:52:inprepare' 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:ininvoke_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:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:113: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 `

'

[dzhoshkun]

Even though I added quotes around multiple affiliation indices as shown in the example, the PDF generation still fails with the same error. Any ideas?

[dzhoshkun]

@jedbrown Thanks for the hint on pandoc footnotes.

[dzhoshkun]

@whedon generate pdf from branch fix-joint-1-author-fn

[whedon]

Attempting PDF compilation from custom branch fix-joint-1-author-fn. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1104 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Dzhoshkun Shakir[, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:57:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:17:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:109:inblock in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:106:inparse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/processor.rb:32:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/bin/whedon:52:inprepare' 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:ininvoke_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:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/bin/whedon:113: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 `

'

[dzhoshkun]

@whedon generate pdf from branch fix-joint-1-author-fn

[whedon]

Attempting PDF compilation from custom branch fix-joint-1-author-fn. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1104 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Dzhoshkun Shakir[, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:57:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:17:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:109:inblock in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:106:inparse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/processor.rb:32:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/bin/whedon:52:inprepare' 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:ininvoke_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:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/bin/whedon:113: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 `

'

[dzhoshkun]

@whedon generate pdf from branch this-branch-does-not-exist

[whedon]

Attempting PDF compilation from custom branch this-branch-does-not-exist. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1104 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Dzhoshkun Shakir[, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:57:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/author.rb:17:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:109:inblock in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:106:inparse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/processor.rb:32:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/bin/whedon:52:inprepare' 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:ininvoke_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:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/bin/whedon:113: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 `

'

[dzhoshkun]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[dzhoshkun]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[dzhoshkun]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[dzhoshkun]

Apologies for cluttering the thread with the PDF generation commands. I'm giving up on using/faking footnotes for indicating co-first authorship, as this yields undesired artefacts in the generated PDF. Doing it inline instead. @arfon I hope this is acceptable?

[danielskatz]

I think the way you've done it is fine.