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[PRE REVIEW]: Quantitative T1 MRI #2

Closed roboneuro closed 1 year ago

roboneuro commented 3 years ago

Submitting author: !--author-handle-->@mathieuboudreau<!--end-author-handle-- (Mathieu Boudreau) Repository: https://github.com/qMRLab/t1-book-neurolibre Branch with paper.md (empty if default branch): main Version: v1.0.0 Editor: !--editor-->@agahkarakuzu<!--end-editor-- Reviewers: !--reviewers-list-->@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: Pending Repository archive: Pending Data archive: Pending Book archive: Pending Docker archive: Pending

Author instructions

Thanks for submitting your paper to NeuroLibre @mathieuboudreau.

@mathieuboudreau if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for NeuroLibre and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The NeuroLibre submission bot @roboneuro is here to help you find and assign reviewers and start the main review. To find out what @roboneuro can do for you type:

@roboneuro commands
roboneuro commented 3 years ago

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

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

@roboneuro commands
roboneuro commented 3 years ago

PDF failed to compile for issue #2 with the following error:

Can't find any papers to compile :-(

emdupre commented 3 years ago

@roboneuro list commands

roboneuro commented 3 years ago

I'm sorry dear human, I don't understand that. You can see what commands I support by typing:

@roboneuro commands
emdupre commented 3 years ago

@roboneuro commands

roboneuro commented 3 years ago

Here are some things you can ask me to do:

# List all of RoboNeuro's capabilities
@roboneuro commands

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

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

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@roboneuro re-invite @username as reviewer

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@roboneuro remove @username as reviewer

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@roboneuro list editors

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@roboneuro set 10.0000/zenodo.00000 as archive

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emdupre commented 3 years ago

@roboneuro generate pdf from branch neurolibre

roboneuro commented 3 years ago 
Attempting PDF compilation from custom branch neurolibre. Reticulating splines etc...
roboneuro commented 3 years ago

PDF failed to compile for issue #2 with the following error:

/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-364ded062842/lib/whedon.rb:145:in check_fields': Paper YAML header is missing expected fields: bibliography (RuntimeError) from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-364ded062842/lib/whedon.rb:87:ininitialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-364ded062842/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-364ded062842/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-364ded062842/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-364ded062842/bin/whedon:119:in<top (required)>' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in

'

emdupre commented 3 years ago

@roboneuro check repository

roboneuro commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.76 s (192.2 files/s, 26853.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              7              4              5           3456
Sass                            59            950            421           3092
Markdown                        17            654              0           3072
Jupyter Notebook                13              0           2424           2198
TeX                              1             50             12           1573
HTML                            20            121             26            747
Python                           8            121            109            512
JavaScript                       8             29             68            246
YAML                             5             48             95            190
Dockerfile                       1              6              0             74
JSON                             3              0              0             46
make                             1              9              0             25
CSS                              3              0              7              5
-------------------------------------------------------------------------------
SUM:                           146           1992           3167          15236
-------------------------------------------------------------------------------

Statistical information for the repository '2' was gathered on 2021/09/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Mathieu Boudreau                11          1696            698          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Mathieu Boudreau           1085           64.0          0.1               15.76
emdupre commented 3 years ago

@roboneuro assign @pbellec as editor

pbellec commented 3 years ago

@mathieuboudreau I am a bit confused. I am looking at https://github.com/qmrlab/t1_book

I believe you are missing paper.md entirely, as well as the binder folder. It looks like you did not use the neurolibre template to prepare this submission, unless I am not looking at the right thing.

We can try to iterate and add the missing components from the template: https://github.com/neurolibre/template/ Or you may find it simpler to start from the template and move your book content.

mathieuboudreau commented 3 years ago

Hi @pbellec,

I left a note to the editor in my submission saying that the book for the NeuroLibre submission is in the neurolibre branch: https://github.com/qmrlab/t1_book/tree/neurolibre

RoboNeuro allows you to test on branches (see here: https://roboneuro.herokuapp.com, i.e. "git reference"), so I assumed submissions would also be allowed this way.

I needed to use a branch and not master because master is the Book that we hosed on qmrlab.org, https://qmrlab.org/t1_book/intro, which I don't want to break for the NeuroLibre submission.

mathieuboudreau commented 3 years ago

Also see here for the book built using RoboNeuro: http://neurolibre-data.conp.cloud/book-artifacts/qMRLab/github.com/t1_book/7b98a2d3cc8f5e130c8d9f0570202a0a96740e88/_build/html/intro.html

pbellec commented 3 years ago

I see. Based on the original error of roboneuro, I believe it tried to build from your main branch and not neurolibre.

However the latest error message only complains about paper.bib missing. Could you try to add paper.bib (even if empty) and add the corresponding bibliography line in the header of paper.md (l. 21 of https://github.com/neurolibre/template/edit/main/paper.md ). It seems that this missing config line is triggering the error.

pbellec commented 3 years ago

Also by the way, I don't see the note you attached to the submission, neither in this thread or on the neurolibre website. I'll have to investigate where this information can be accessed, if possible at all.

mathieuboudreau commented 3 years ago

So reading the doc again, it's not clear to me what's supposed to be in papers.bib. Am I supposed to include the list of references that I cite in my book? It might take me a little while to make the file, as I have a lot and didn't have them in the latex bibliography format beforehand. They're all in my book already though, https://qmrlab.org/t1_book/01/ir_blog/IR_References.html and https://qmrlab.org/t1_book/01/vfa_blog/VFA_References.html

mathieuboudreau commented 3 years ago

I created a blank papers.bib and added it to paper.md as a placeholder for now, not sure if testing the build will work with an empty *.bib file.

pbellec commented 3 years ago

@roboneuro generate pdf from branch neurolibre

roboneuro commented 3 years ago 
Attempting PDF compilation from custom branch neurolibre. Reticulating splines etc...
roboneuro commented 3 years ago

PDF failed to compile for issue #2 with the following error:

pandoc: /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-364ded062842/resources/NeuroLibre/latex.template: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

pbellec commented 3 years ago

@mathieuboudreau those are the references for the pdf summary of the book. This pdf summary will be displayed on the neurolibre website. You may want to add at least one bibtex reference, to check if that's what is causing the failure. I don't think that our testing workflow actually looks at the paper summary.

agahkarakuzu commented 3 years ago

There was a bug with the build that I fixed for the roboneuro page entrypoint, may require a fix for this comment as well. I will look into this once I am in Montreal.

emdupre commented 3 years ago

In general it would be a better test to build a non-empty PDF, assuming that the PDF will be retained as part of the submission workflow.

mathieuboudreau commented 3 years ago

Ok, created a very basic PDF and it converted correctly: http://res.cloudinary.com/houcseodx/image/upload/v1632272379/m6opnjbyqlcm1bcjtcsv.pdf

mathieuboudreau commented 3 years ago

@roboneuro generate pdf from branch neurolibre

roboneuro commented 3 years ago 
Attempting PDF compilation from custom branch neurolibre. Reticulating splines etc...
roboneuro commented 3 years ago

PDF failed to compile for issue #2 with the following error:

pandoc: /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-364ded062842/resources/NeuroLibre/latex.template: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

mathieuboudreau commented 3 years ago

Hum, it worked on RoboNeuro.

pbellec commented 3 years ago

@mathieuboudreau From what Agah said earlier, it's a known bug he did fix on the test workflow, but has not been applied to the production workflow. We're going to have to wait for him to be back.

mathieuboudreau commented 3 years ago

Ah gotcha. Ok!

mathieuboudreau commented 3 years ago

@roboneuro generate pdf from branch neurolibre

agahkarakuzu commented 3 years ago

@roboneuro generate pdf from branch neurolibre

roboneuro commented 3 years ago 
Attempting PDF compilation from custom branch neurolibre. Reticulating splines etc...
mathieuboudreau commented 3 years ago

@roboneuro generate pdf from branch neurolibre

roboneuro commented 3 years ago 
Attempting PDF compilation from custom branch neurolibre. Reticulating splines etc...
mathieuboudreau commented 3 years ago

The PDF builds fine on RoboNeuro, but seems to hang here on GitHub actions

emdupre commented 3 years ago

The PDF builds fine on RoboNeuro, but seems to hang here on GitHub actions

Working on it :woman_technologist:

emdupre commented 3 years ago

@roboneuro generate pdf from branch neurolibre

roboneuro commented 3 years ago 
Attempting PDF compilation from custom branch neurolibre. Reticulating splines etc...
roboneuro commented 3 years ago

PDF failed to compile for issue #2 with the following error:

[WARNING] Could not deduce format from file extension Defaulting to html Could not find data file templates/latex.template

emdupre commented 3 years ago

@roboneuro generate pdf from branch neurolibre

roboneuro commented 3 years ago 
Attempting PDF compilation from custom branch neurolibre. Reticulating splines etc...
roboneuro commented 3 years ago

PDF failed to compile for issue #2 with the following error:

[WARNING] Could not deduce format from file extension Defaulting to html pandoc: Bellec: openBinaryFile: does not exist (No such file or directory)

emdupre commented 3 years ago

@roboneuro generate pdf from branch neurolibre

roboneuro commented 3 years ago 
Attempting PDF compilation from custom branch neurolibre. Reticulating splines etc...
roboneuro commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

emdupre commented 3 years ago

@roboneuro generate pdf from branch neurolibre

roboneuro commented 3 years ago 
Attempting PDF compilation from custom branch neurolibre. Reticulating splines etc...