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[PRE REVIEW]: FSharpGephiStreamer: An idiomatic bridge between F# and network visualization #1214

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whedon opened this issue Jan 28, 2019 · 45 comments

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commented Jan 28, 2019

Submitting author: @muehlhaus (Timo Mühlhaus)
Repository: https://github.com/CSBiology/FSharpGephiStreamer
Version: v1.1.0
Editor: @danielskatz
Reviewers: @cgravill, @PrashantVaidyanathan

Author instructions

Thanks for submitting your paper to JOSS @muehlhaus. The JOSS editor Pending, will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@muehlhaus 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 whedon added the pre-review label Jan 28, 2019

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commented Jan 28, 2019

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

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 an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience 😸

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.

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commented Jan 28, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jan 28, 2019

PDF failed to compile for issue #1214 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1214/paper/paper.md): invalid leading UTF-8 octet at line 1 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse_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:in load'
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:in open'
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-c5f29247288e/lib/whedon.rb:68:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c5f29247288e/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c5f29247288e/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c5f29247288e/bin/whedon:52:in prepare' 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:in invoke_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:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c5f29247288e/bin/whedon:113:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

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commented Jan 28, 2019

Hi @muehlhaus - I suspect this failure is from having á in a bib entry. I would suggest changing it to an a, since it's just a label, and then changing the same in the \cite part of the .md file. I also notice some odd bits in the entry itself, which should be cleaned up - eg the "EP -" and "SN -" at the end of fields.
Once you have done this, you can enter a new comment here that says @whedon generate pdf to start the PDF processing again.

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commented Jan 28, 2019

@whedon generate pdf

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commented Jan 28, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jan 28, 2019

PDF failed to compile for issue #1214 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 15 0 15 0 0 131 0 --:--:-- --:--:-- --:--:-- 132
Error producing PDF.
! Illegal parameter number in definition of \temp@a.

l.101 ...l{https://doi.org/10.21105/joss.01214}}}}

Looks like we failed to compile the PDF

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commented Jan 28, 2019

👋 @arfon - can you help with this one?

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commented Jan 29, 2019

👋 @yochannah - would you be willing to edit this?
(Note that there's a pdf problem that I'm hoping @arfon will help us solve as well)

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commented Jan 29, 2019

@danielskatz Sure!

@muehlhaus we don't seem to have any F# reviewers on our list so it could take a little while longer to find someone. Do you have any suggestions? No worries if not.

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commented Jan 29, 2019

@whedon assign @yochannah as editor

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commented Jan 29, 2019

OK, the editor is @yochannah

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commented Jan 30, 2019

This looks to be a bug in our LaTeX template at the # in the title. I've been trying to fix this for the last hour and haven't found an easy fix yet sorry.

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commented Jan 30, 2019

@yochannah - I am afraid that people I would recommend with the necessary expertise might not be completely free regarding conflicts of interest. I am very sorry.

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commented Jan 30, 2019

That's fine and makes absolute sense. I'll send out some emails and see who we can find :)

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commented Feb 3, 2019

@swoodhouse 👋 I wonder if you might be interested in reviewing this paper by any chance?

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commented Feb 4, 2019

@whedon generate pdf

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commented Feb 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Feb 4, 2019

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commented Feb 6, 2019

The article proof looks fine. Thank you for fixing the pdf generator that it can cope with our article.

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commented Feb 9, 2019

Hi @tpetricek - I know you're busy reviewing another item on JOSS at the minute so I won't ask you to look at another (unless you want to!) - but I was wondering if you could recommend any F#-ers who might be interested in reviewing this?

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commented Feb 15, 2019

This looks like a nice project! I'd try asking @cgravill or maybe @sylvanc.

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commented Feb 17, 2019

Thanks @tpetricek!

@cgravill, @sylvanc, are either or both of you interested in reviewing this paper by any chance?

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commented Mar 10, 2019

Still looking for a reviewer on this at the minute - most of the people I've managed to find through searches so far either have no research experience or have collaborated with the current authors 😆 I did find another name to try, though - @gbaydin, is this something we could interested you in reviewing?

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commented Mar 11, 2019

Hi @yochannah,
Thank you for your continued efforts in finding a reviewer for our paper. I guess a factor why it is so hard finding people for this may be that all the fsharpers go straight to industry, which in my opinion is a pity as we see F# as a language suited very well for research in bioinformatics (and for all kinds of data analysis).

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commented Mar 19, 2019

I’m also more on the industry side. Still, it seems like you’re having a challenge engaging an ideal reviewer, so I’d be willing to assist if that helps.

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commented Mar 19, 2019

@cgravill I would be very happy to take you up on this one. Ideally I'd like a second reviewer as well - any chance you know anyone who might be interested?

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commented Mar 24, 2019

I'd tag @tpetricek but I fear we'd have a cycle going then! :-) I'll try asking around.

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commented Apr 15, 2019

@yochannah 👋 — how are you getting on searching for reviewers for this submission?

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commented Apr 23, 2019

@PrashantVaidyanathan may also be able to help

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commented May 12, 2019

Hi folks! @yochannah will be stepping down from the JOSS board, due to other obligations making it hard for her to volunteer time currently. I would like to reassign this submission to another editor.

@danielskatz — given current loads, could you take over on this one?

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commented May 12, 2019

@whedon assign @danielskatz as editor

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commented May 12, 2019

OK, the editor is @danielskatz

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commented May 12, 2019

👋 @PrashantVaidyanathan - would you be willing to review this submission?

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commented May 12, 2019

👋 @cgravill - thanks for agreeing to review - once I get one more reviewer, we'll start the review

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commented May 12, 2019

@whedon assign @cgravill as reviewer

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commented May 12, 2019

OK, the reviewer is @cgravill

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commented May 12, 2019

👋 @TahaHachana, @dsyme, @jackfoxy, @tpetricek - would one of you be willing be the 2nd reviewer for this JOSS submission? (See our reviewer guidelines if needed)

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commented May 13, 2019

@danielskatz thanks for the invitation. I'm going to have to beg out...too many other commitments, and I'm probably the least qualified for this topic.

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commented May 13, 2019

@danielskatz I'm happy to help. I'm travelling this week so the earliest I can send in my reviews is 20th May if that's alright?

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commented May 13, 2019

@PrashantVaidyanathan - Thanks! You will see as we start the review that a JOSS review is not a one-time read, but a set of suggestions and requests to the author, and an iterative process with the author to improve the submission (both the paper and the software)

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commented May 13, 2019

@whedon add @PrashantVaidyanathan as reviewer

@whedon whedon assigned cgravill and danielskatz and unassigned cgravill and danielskatz May 13, 2019

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commented May 13, 2019

OK, @PrashantVaidyanathan is now a reviewer

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commented May 13, 2019

@whedon start review

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commented May 13, 2019

OK, I've started the review over in #1445. Feel free to close this issue now!

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