[PRE REVIEW]: Quantitative T1 MRI

roboneuro commented 3 years ago

Submitting author: !--author-handle-->@mathieuboudreau@agahkarakuzu@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

: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...

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 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

# Re-invite a reviewer (if they can't update checklists)
@roboneuro re-invite @username as reviewer

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

# List of editor GitHub usernames
@roboneuro list editors

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

# Change editorial assignment
@roboneuro assign @username as editor

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

# Set the software version at the top of the issue e.g.
@roboneuro set v1.0.1 as version

# Open the review issue
@roboneuro start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

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

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@roboneuro remind @reviewer in 2 days

# Ask RoboNeuro to do a dry run of accepting the paper and depositing with Crossref
@roboneuro accept

# Ask RoboNeuro to check the references for missing DOIs
@roboneuro check references

# Ask RoboNeuro to check repository statistics for the submitted software
@roboneuro check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@roboneuro invite @editor as editor

# Reject a paper
@roboneuro reject

# Withdraw a paper
@roboneuro withdraw

# Ask RoboNeuro to actually accept the paper and deposit with Crossref
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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...

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:

pbellec commented 3 years ago

@roboneuro generate html from branch neurolibre

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

pbellec commented 3 years ago

@roboneuro build jupyter-book

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

# Re-invite a reviewer (if they can't update checklists)
@roboneuro re-invite @username as reviewer

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

# List of editor GitHub usernames
@roboneuro list editors

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

# Change editorial assignment
@roboneuro assign @username as editor

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

# Set the software version at the top of the issue e.g.
@roboneuro set v1.0.1 as version

# Open the review issue
@roboneuro start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@roboneuro generate pdf

# Compile the paper from alternative branch
@roboneuro generate pdf from branch custom-branch-name

# Compile the NeuroLibre notebook
@roboneuro generate nl-notebook

# Compile the NeuroLibre notebook from alternative branch
@roboneuro generate nl-notebook from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@roboneuro remind @reviewer in 2 days

# Ask RoboNeuro to do a dry run of accepting the paper and depositing with Crossref
@roboneuro accept

# Ask RoboNeuro to check the references for missing DOIs
@roboneuro check references

# Ask RoboNeuro to check repository statistics for the submitted software
@roboneuro check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@roboneuro invite @editor as editor

# Reject a paper
@roboneuro reject

# Withdraw a paper
@roboneuro withdraw

# Ask RoboNeuro to actually accept the paper and deposit with Crossref
@roboneuro accept deposit=true

emdupre commented 3 years ago

@roboneuro generate nl-notebook

roboneuro commented 3 years ago

Missing 'binder' or 'content' folder for https://github.com/qmrlab/t1_book

emdupre commented 3 years ago

@roboneuro generate nl-notebook from branch neurolibre

roboneuro commented 3 years ago

Attempting NeuroLibre notebook compilation from custom branch neurolibre. Reticulating splines etc...

roboneuro commented 3 years ago

:seedling: We are currently building your NeuroLibre notebook! Good things take time :seedling:

pbellec commented 3 years ago

@ltetrel any idea why roboneuro is stuck?

emdupre commented 3 years ago

@ltetrel any idea why roboneuro is stuck?

@pbellec it's in the push-to-GH step -- you can see the exact error here. Unfortunately I can only work on this on off-hours, but I'll get something pushed for this soon.

ltetrel commented 3 years ago

The latest entry in the cluster says that the jupyter book build already exists for commit 93466a31. Unfortunately as for RoboNeuro I cannot help :(

[I 2021-09-28 01:20:24.596 JupyterHub log:181] 201 POST /jupyter/hub/api/users/qmrlab-t1_book-avzdxp9t (binder@206.12.88.157) 431.14ms
Getting data requirements from https://raw.githubusercontent.com/qmrlab/t1_book/93466a316bfdb86ae2b0b03afe9d160230b417f1/
https://raw.githubusercontent.com/qmrlab/t1_book/93466a316bfdb86ae2b0b03afe9d160230b417f1/binder/data_requirement.json not found
/srv/jupyterhub/data/book-artifacts/qmrlab/github.com/t1_book/93466a316bfdb86ae2b0b03afe9d160230b417f1/successfully_built exists, skipping book build
[I 2021-09-28 01:20:25.905 JupyterHub log:181] 202 POST /jupyter/hub/api/users/qmrlab-t1_book-avzdxp9t/servers/ (binder@206.12.88.157) 1284.88ms
[W 2021-09-28 01:20:25.908 JupyterHub spawner:2182] Ignoring unrecognized KubeSpawner user_options: binder_launch_host, binder_persistent_request, binder_ref_url, binder_request, image, repo_url, token
[I 2021-09-28 01:20:25.917 JupyterHub spawner:1840] Attempting to create pod jupyter-qmrlab-2dt1-5fbook-2davzdxp9t, with timeout 3
[I 2021-09-28 01:20:25.964 JupyterHub log:181] 200 GET /jupyter/hub/api/users/qmrlab-t1_book-avzdxp9t (binder@206.12.88.157) 41.52ms
[I 2021-09-28 01:20:27.004 JupyterHub log:181] 200 GET /jupyter/hub/api/users/qmrlab-t1_book-avzdxp9t (binder@206.12.88.157) 18.72ms
[I 2021-09-28 01:20:28.445 JupyterHub log:181] 200 GET /jupyter/hub/api/users/qmrlab-t1_book-avzdxp9t (binder@206.12.88.157) 18.68ms
[I 2021-09-28 01:20:30.444 JupyterHub log:181] 200 GET /jupyter/hub/api/users/qmrlab-t1_book-avzdxp9t (binder@206.12.88.157) 20.38ms
[I 2021-09-28 01:20:33.233 JupyterHub log:181] 200 GET /jupyter/hub/api/users/qmrlab-t1_book-avzdxp9t (binder@206.12.88.157) 19.07ms
[W 2021-09-28 01:20:34.759 JupyterHub _version:41] Single-user server has no version header, which means it is likely < 0.8. Expected 1.3.0
[I 2021-09-28 01:20:34.759 JupyterHub base:904] User qmrlab-t1_book-avzdxp9t took 10.112 seconds to start

agahkarakuzu commented 3 years ago

I can push a commit to deal with that when @emdupre gives green light.

emdupre commented 3 years ago

I can push a commit to deal with that when @emdupre gives green light.

Sorry, are you planning a commit for the cluster or RoboNeuro ? So long as the artifact persists at least another 24 hours on the cluster, it's fine for me -- I just need to be able to grab those artifacts through a REST call and test pushing the folder with OctoKit.

agahkarakuzu commented 3 years ago

Oh, I meant a commit to this repo under review.

emdupre commented 3 years ago

Oh that shouldn't interact ! And a good test, really. Go for it 🚀.

agahkarakuzu commented 3 years ago

Done! The artifacts should be there for 24 hrs for 🐙

mathieuboudreau commented 3 years ago

Could someone ELI5 (explain like I'm 5) the current status of the submission?

pbellec commented 3 years ago

There is development needed on roboneuro. Current conversation happening here: https://github.com/neurolibre/roboneuro/issues/10 Also in the process of recruiting first neurolibre tester, so I have someone to tag when there is a book to review.

ltetrel commented 3 years ago

@pbellec I think you want to refer https://github.com/neurolibre/roboneuro/pull/9#issuecomment-930354531 instead. The current discussion in neurolibre/roboneuro#10 is a change proposal for the jupyter book build workflow, the current behaviour should not be an issue.

emdupre commented 3 years ago

@roboneuro generate nl-notebook from branch neurolibre

roboneuro commented 3 years ago

Attempting NeuroLibre notebook compilation from custom branch neurolibre. Reticulating splines etc...

roboneuro commented 3 years ago

:point_right::page_facing_up: View built NeuroLibre Notebook :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...

roboneuro commented 3 years ago

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

Error producing PDF. ! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ...

l.1 4

emdupre commented 3 years ago

Successfully replicating the test server behavior :

Screenshot from 2021-09-30 13-37-22

agahkarakuzu commented 3 years ago

@roboneuro generate nl-notebook from branch neurolibre

roboneuro commented 3 years ago

Attempting NeuroLibre notebook compilation from custom branch neurolibre. Reticulating splines etc...

roboneuro commented 3 years ago

:point_right::page_facing_up: View built NeuroLibre Notebook :page_facing_up::point_left:

agahkarakuzu commented 3 years ago

Cool! This also mirrors the roboneuro page functionality, returning the book if it already exists for the latest commit! Now I will change something small, then call another build.

agahkarakuzu commented 3 years ago

@roboneuro generate nl-notebook from branch neurolibre

roboneuro commented 3 years ago

Attempting NeuroLibre notebook compilation from custom branch neurolibre. Reticulating splines etc...

roboneuro commented 3 years ago

:seedling: We are currently building your NeuroLibre notebook! Good things take time :seedling:

roboneuro commented 3 years ago

:point_right::page_facing_up: View built NeuroLibre Notebook :page_facing_up::point_left:

agahkarakuzu commented 3 years ago

Interesting, the book address has the latest commit 90dc3, but the changes I made there are not rendered on the Introduction page.

emdupre commented 3 years ago

Interesting, the book address has the latest commit 90dc3, but the changes I made there are not rendered on the Introduction page.

Can replicate, though I'm not yet sure where this behavior is being introduced .... Can you make another commit and build it first through the preview page to confirm that it shows the correct behavior there ?

mathieuboudreau commented 3 years ago

Interesting, the book address has the latest commit 90dc3, but the changes I made there are not rendered on the Introduction page.

Did you modify the Dockerfile (e.g. add a space) to force a rebuild?

agahkarakuzu commented 3 years ago

I changed the intro.md, you can click the link to see changes. Now I pushed another commit 7b4e6e1 for which I started a book build on roboneuro page as @emdupre suggested.

agahkarakuzu commented 3 years ago

@emdupre the result was the same when I built after commit 7b4e6e1.

In the new intro.md these are the changes:

MyBinder --> Neurolibre's BinderHub
Thebelab --> executablebooks/thebe

neurolibre / neurolibre-reviews

[PRE REVIEW]: Quantitative T1 MRI #2