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[PRE REVIEW]: phyphy: A Python package for facilitating the execution and parsing of HyPhy standard analyses #484

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whedon opened this Issue Dec 6, 2017 · 18 comments

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whedon commented Dec 6, 2017

Submitting author: @sjspielman (Stephanie Spielman)
Repository: https://github.com/sjspielman/phyphy
Version: v0.1
Editor: @mgymrek
Reviewer: @luizirber

Author instructions

Thanks for submitting your paper to JOSS @sjspielman. 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.

@sjspielman 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:

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@whedon whedon added the pre-review label Dec 6, 2017

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

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

@whedon commands
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whedon commented Dec 6, 2017

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

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

@whedon commands
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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Dec 6, 2017

Attempting PDF compilation. Reticulating splines etc...
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PDF failed to compile for issue #484 with the following error: 

 pandoc-citeproc: Could not find paper.bib
CallStack (from HasCallStack):
  error, called at src/Text/CSL/Pandoc.hs:224:39 in pandoc-citeproc-0.10.4-BdOyQb33rzG2TMOLj4Fbp9:Text.CSL.Pandoc
pandoc: Error running filter pandoc-citeproc
Filter returned error status 1
Looks like we failed to compile the PDF

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whedon commented Dec 6, 2017

PDF failed to compile for issue #484 with the following error: 

 pandoc-citeproc: Could not find paper.bib
CallStack (from HasCallStack):
  error, called at src/Text/CSL/Pandoc.hs:224:39 in pandoc-citeproc-0.10.4-BdOyQb33rzG2TMOLj4Fbp9:Text.CSL.Pandoc
pandoc: Error running filter pandoc-citeproc
Filter returned error status 1
Looks like we failed to compile the PDF

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👋 @sjspielman - it looks like you're paper.md file is referencing a bibtex file named paper.bib but there isn't a bibtex file with that name. Could you rename the bibtex file appropriately?

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arfon commented Dec 6, 2017

👋 @sjspielman - it looks like you're paper.md file is referencing a bibtex file named paper.bib but there isn't a bibtex file with that name. Could you rename the bibtex file appropriately?

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sjspielman Dec 6, 2017

Yes, my apologies! It was accidentally named bib.md. I have now renamed it to paper.bib and pushed the change.

sjspielman commented Dec 6, 2017

Yes, my apologies! It was accidentally named bib.md. I have now renamed it to paper.bib and pushed the change.

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@whedon generate pdf

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arfon commented Dec 6, 2017

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Dec 6, 2017

Attempting PDF compilation. Reticulating splines etc...
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https://github.com/openjournals/joss-papers/blob/joss.00484/joss.00484/10.21105.joss.00484.pdf
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whedon commented Dec 6, 2017

https://github.com/openjournals/joss-papers/blob/joss.00484/joss.00484/10.21105.joss.00484.pdf
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Yes, my apologies! It was accidentally named bib.md. I have now renamed it to paper.bib and pushed the change.

Great, that's looking much better. This was just a 'pre-flight' check on my part to make sure the paper was compiling OK. Don't expect much activity until one of the JOSS topic editors has volunteered to handle this submission :-)

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arfon commented Dec 6, 2017

Yes, my apologies! It was accidentally named bib.md. I have now renamed it to paper.bib and pushed the change.

Great, that's looking much better. This was just a 'pre-flight' check on my part to make sure the paper was compiling OK. Don't expect much activity until one of the JOSS topic editors has volunteered to handle this submission :-)

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arfon Dec 9, 2017

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@brainstorm @biorelated @mgymrek @pjotrp - would one of your be willing to edit this submission for JOSS?

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arfon commented Dec 9, 2017

@brainstorm @biorelated @mgymrek @pjotrp - would one of your be willing to edit this submission for JOSS?

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mgymrek commented Dec 12, 2017

@whedon assign @mgymrek as editor

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OK, the editor is @mgymrek

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whedon commented Dec 12, 2017

OK, the editor is @mgymrek

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mgymrek Dec 16, 2017

@krother @genomematt @luizirber @konrad @cbrueffer Would anyone like to review this submission?

mgymrek commented Dec 16, 2017

@krother @genomematt @luizirber @konrad @cbrueffer Would anyone like to review this submission?

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luizirber Dec 17, 2017

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I can review it

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luizirber commented Dec 17, 2017

I can review it

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mgymrek Dec 17, 2017

@whedon assign @luizirber as reviewer

mgymrek commented Dec 17, 2017

@whedon assign @luizirber as reviewer

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OK, the reviewer is @luizirber

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whedon commented Dec 17, 2017

OK, the reviewer is @luizirber

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mgymrek Dec 17, 2017

@whedon start review magic-word=bananas

mgymrek commented Dec 17, 2017

@whedon start review magic-word=bananas

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whedon Dec 17, 2017

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OK, I've started the review over in #514. Feel free to close this issue now!

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whedon commented Dec 17, 2017

OK, I've started the review over in #514. Feel free to close this issue now!

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