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[PRE REVIEW]: Ising_OPV v4.0: Experimental Tomography Data Import, Interpretation, and Analysis #1011

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @MikeHeiber (Michael Heiber) Repository: https://github.com/MikeHeiber/Ising_OPV Version: v4.0.0-rc.2 Editor: @katyhuff Reviewers: @myousefi2016, @stuartcampbell, @mdoucet

Author instructions

Thanks for submitting your paper to JOSS @MikeHeiber. 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.

@MikeHeiber 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 commented 5 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @labarba 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
whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
arfon commented 5 years ago

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

whedon commented 5 years ago

PDF failed to compile for issue #1011 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 0 167 0 --:--:-- --:--:-- --:--:-- 168 pandoc-citeproc: reference pfannmoeller2013ees not found pandoc-citeproc: reference vanbavel2009nl not found pandoc-citeproc: reference pfannmoeller2013ees not found pandoc-citeproc: reference proudian2018arXiv not found pandoc-citeproc: reference heiber2018ising4 not found Error producing PDF. ! Missing $ inserted.

$ l.265 ...{Acknowledgments}\label{acknowledgments}} Looks like we failed to compile the PDF
MikeHeiber commented 5 years ago

@whedon commands

whedon commented 5 years ago

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

šŸš§ šŸš§ šŸš§ Experimental Whedon features šŸš§ šŸš§ šŸš§

# Compile the paper from a custom git branch
@whedon generate pdf from branch custom-branch-name
MikeHeiber commented 5 years ago

I would suggest @stuartcampbell as a potential reviewer that is knowledgeable about C++ and materials science.

MikeHeiber commented 5 years ago

@whedon generate pdf from branch joss-edits

whedon commented 5 years ago 
Attempting PDF compilation from custom branch joss-edits. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1011 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 0 180 0 --:--:-- --:--:-- --:--:-- 180 Error producing PDF. ! Missing $ inserted.

$ l.266 ...{Acknowledgments}\label{acknowledgments}} Looks like we failed to compile the PDF
MikeHeiber commented 5 years ago

@whedon generate pdf from branch joss-edits

whedon commented 5 years ago 
Attempting PDF compilation from custom branch joss-edits. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1011 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 0 139 0 --:--:-- --:--:-- --:--:-- 140 Error producing PDF. ! Missing $ inserted.

$ l.279 Looks like we failed to compile the PDF
MikeHeiber commented 5 years ago

@whedon generate pdf from branch joss-edits

whedon commented 5 years ago 
Attempting PDF compilation from custom branch joss-edits. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1011 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 90 0 --:--:-- --:--:-- --:--:-- 90 Error producing PDF. ! Missing $ inserted.

$ l.280 Looks like we failed to compile the PDF
MikeHeiber commented 5 years ago

@arfon @labarba Any idea why the PDF is not compiling? I am not using any math in the document, so I can't figure out why latex is complaining.

arfon commented 5 years ago

I think the issue is actually with the underscore in the title. This pull request should fix the paper: https://github.com/MikeHeiber/Ising_OPV/pull/8

MikeHeiber commented 5 years ago

@arfon I tried that as well, and it didn't seem to fix the problem. See the joss-edits branch for my latest edited version.

arfon commented 5 years ago

@whedon commands

whedon commented 5 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

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

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

# Compile the paper
@whedon generate pdf

šŸš§ šŸš§ šŸš§ Experimental Whedon features šŸš§ šŸš§ šŸš§

# Compile the paper from a custom git branch
@whedon generate pdf from branch custom-branch-name
arfon commented 5 years ago

@whedon generate pdf from branch joss-edits

whedon commented 5 years ago 
Attempting PDF compilation from custom branch joss-edits. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1011 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 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 15 0 15 0 0 127 0 --:--:-- --:--:-- --:--:-- 127 Error producing PDF. ! Missing $ inserted.

$ l.280 Looks like we failed to compile the PDF
arfon commented 5 years ago

@MikeHeiber - I'm not sure what's going on here. I can compile your paper fine with the edits in your joss-edits branch: 10.21105.joss.01011.pdf

MikeHeiber commented 5 years ago

@arfon Hmm... Well thanks for providing the compiled PDF. Based on how that compiled, I've made a few more minor corrections/modifications to the joss-edits branch.

MikeHeiber commented 5 years ago

@whedon generate pdf from branch joss-edits

whedon commented 5 years ago 
Attempting PDF compilation from custom branch joss-edits. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1011 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 0 189 0 --:--:-- --:--:-- --:--:-- 189 Error producing PDF. ! Missing $ inserted.

$ l.279 Looks like we failed to compile the PDF
arfon commented 5 years ago

Compiled again locally 10.21105.joss.01011.pdf

MikeHeiber commented 5 years ago

The proof looks good to me!

MikeHeiber commented 5 years ago

@labarba @arfon Just wondering when reviewer(s) will be assigned so that we can move forward. Please let me know if you are waiting on me for anything. Thanks!

labarba commented 5 years ago

You should expect at least a period of two weeks for finding reviewers. Sometimes more. Editors and reviewers are volunteers and most often have latency before new tasks enter our queue. Right now, for example, I'm starting a trip, with two talks to give, and last week, another trip and another talk.

MikeHeiber commented 5 years ago

@arfon @labarba It's now been 4 weeks since submission. I understand that sometime things are busy, but it should not take so long to start assigning reviewers. Is there possibly another editor available that has time to handle this submission?

arfon commented 5 years ago

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

arfon commented 5 years ago

@arfon @labarba It's now been 4 weeks since submission. I understand that sometime things are busy, but it should not take so long to start assigning reviewers. Is there possibly another editor available that has time to handle this submission?

Hi @MikeHeiber - thanks for your patience here. I posit that your frustration here is a consequence of the extreme transparency of the JOSS review process. That is, if this were this a 'traditional' journal, the process of assignment of an editor would be complete opaque to you as the submitting author and as such a ~1 month delay would be very reasonable anywhere other than JOSS.

Thanks for your patience šŸ˜ƒ

MikeHeiber commented 5 years ago

@arfon Thank you for trying to move this along. With the traditional publishers that I submit to, most of the time is spent waiting for the reviewers to assess the technical aspects of the work and not on waiting for the editors to make initial editorial decisions and sending the manuscript out for review. I am happy to put in some more work to comb over the reviewer list again and suggest reviewers if it helps get things going. I could even suggest new JOSS reviewers that work in my field and are active Github users, if it would help.

katyhuff commented 5 years ago

@MikeHeiber This level of materials science is slightly beyond my wheelhouse, so I spent a few hours on the plane looking over your submission to understand the purpose. At this point, I think I grok it, and I'm certainly happy to help out in finding reviewers unless @labarba has an objection ( @labarba I know you're on travel and juggling more papers than most, but if you object to changing editors I'm happy to return this to your capable hands ).

katyhuff commented 5 years ago

@whedon assign @katyhuff as editor

whedon commented 5 years ago

OK, the editor is @katyhuff

katyhuff commented 5 years ago

Now, @MikeHeiber , let's ping a few fitting reviewers, with materials science, physics, and c or c++ expertise. We can start the review once two or three of them accept the request to review.

Dear reviewers,

Title: Ising_OPV v4.0: Experimental Tomography Data Import, Interpretation, and Analysis Summary: A C++ software tool for generating and analyzing model bulk heterojunction morphologies in a parallel computing environment Topic: Computational Materials Science Article Proof: https://github.com/openjournals/joss-reviews/files/2474390/10.21105.joss.01011.pdf Submitting author: @MikeHeiber (Michael Heiber) Repository: https://github.com/MikeHeiber/Ising_OPV Version: v4.0.0-rc.2

myousefi2016 commented 5 years ago

@katyhuff Hi, Iā€™m interested to review this software.

katyhuff commented 5 years ago

@myousefi2016 Excellent! Thank you for the prompt response. We'll get started as soon as a couple of folks volunteer.

stuartcampbell commented 5 years ago

@katyhuff yes I'm happy to help

katyhuff commented 5 years ago

Fabulous, thanks @stuartcampbell ! I'll give the other reviewers another few hours to volunteer if they're interested before we start the review. Three is always slightly better than two if folks are interested!

katyhuff commented 5 years ago

@whedon assign @myousefi2016 as reviewer

whedon commented 5 years ago

OK, the reviewer is @myousefi2016

katyhuff commented 5 years ago

@whedon add @stuartcampbell as reviewer

whedon commented 5 years ago

OK, @stuartcampbell is now a reviewer

mdoucet commented 5 years ago

@katyhuff Iā€™m happy to help