[PRE REVIEW]: Longitudinal stability of brain and spinal cord quantitative MRI measures #15

roboneuro · 2023-06-14T17:28:48Z

Submitting author: @mathieuboudreau (Mathieu Boudreau)
Repository: https://github.com/courtois-neuromod/anat-processing-paper
Branch with paper.md (empty if default branch): main
Version: v1.0.0
Editor: @agahkarakuzu
Reviewers: @agahkarakuzu
Managing EiC: Agah Karakuzu

Status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/d31d64b266bc2759d7c793347c2f547d"><img src="https://neurolibre.org/papers/d31d64b266bc2759d7c793347c2f547d/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/d31d64b266bc2759d7c793347c2f547d/status.svg)](https://neurolibre.org/papers/d31d64b266bc2759d7c793347c2f547d)

Author instructions

Thanks for submitting your paper to NeuroLibre @mathieuboudreau. Currently, there isn't a NeuroLibre editor assigned to your paper.

The AEiC suggestion for the handling editor is @pbellec.

@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

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The text was updated successfully, but these errors were encountered:

agahkarakuzu · 2023-06-14T17:29:16Z

@roboneuro commands

roboneuro · 2023-06-14T17:29:19Z

Hello @agahkarakuzu, here are the things you can ask me to do:


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@roboneuro add @username as reviewer

# Remove from this issue's reviewers list
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@roboneuro list editors

# Assign a user as the editor of this submission
@roboneuro assign @username as editor

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agahkarakuzu · 2023-06-14T17:29:36Z

@roboneuro generate pdf

roboneuro · 2023-06-14T17:31:38Z

⚠️ An error happened when generating the pdf.

agahkarakuzu · 2023-06-14T17:36:24Z

@mathieuboudreau

Kiril Zelenkovski, perhaps the affiliations index need quoting? (Theoj::Error)

Reason is that affiliation 4 is not listed:

affiliations:
 - name: Lyman Spitzer, Jr. Fellow, Princeton University, USA
   index: 1
 - name: Institution Name, Country
   index: 2
 - name: Independent Researcher, Country
   index: 3

The same goes for the other affilitations 4-7.

mathieuboudreau · 2023-06-14T17:52:55Z

Woops - I forgot the affiliations, my bad. Adding them now!

mathieuboudreau · 2023-06-14T17:55:04Z

@roboneuro generate pdf

roboneuro · 2023-06-14T17:56:12Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

agahkarakuzu · 2023-06-14T17:59:16Z

Thanks @mathieuboudreau !

Another major issue has to do with how the repository is organized. NeuroLibre expects binder and content folders for runtime/data requirements and executable content, respectively.

Unless the repo follows this structure, we are not going to be able to proceed.

mathieuboudreau · 2023-06-14T18:00:20Z

Sorry @agahkarakuzu ! You're right - I forgot because I knew I did it for the T1 mapping challenge one, and for some reason thought I had also done if for this one. I will update and let you know when it's done

mathieuboudreau · 2023-06-14T18:03:42Z

@roboneuro check repository

roboneuro · 2023-06-14T18:03:46Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (609.2 files/s, 89653.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2             20              0             72
Jupyter Notebook                 1              0            672             54
YAML                             3             10             17             38
-------------------------------------------------------------------------------
SUM:                             6             30            689            164
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

roboneuro · 2023-06-14T18:03:48Z

Wordcount for paper.md is 735

roboneuro · 2023-06-14T18:03:48Z

Failed to discover a valid open source license

roboneuro · 2023-06-14T18:03:49Z

Failed to discover a Statement of need section in paper

agahkarakuzu · 2023-06-14T18:06:22Z

@mathieuboudreau just a heads up, the command you've just run has not been tailored for neurolibre specific checks yet.

mathieuboudreau · 2023-06-14T18:10:17Z

Ok! Thanks! I've made the changes, would @roboneuro build book work to test it?

mathieuboudreau · 2023-06-14T18:10:20Z

@roboneuro build book

roboneuro · 2023-06-14T18:10:21Z

Can't perform this without reviewers

agahkarakuzu · 2023-06-14T19:49:13Z

Please wait for me to assign a reviewer, then we'll go through boom build in the review issue.

mathieuboudreau · 2023-06-14T22:59:06Z

Sorry about that @agahkarakuzu ! I wanted to test that I got the repository directory structure correct, so I checked the documentation https://docs.neurolibre.org/en/latest/TEST_SUBMISSION.html#testing-on-neurolibre-servers but the roboneuro preview service that's linked there (https://roboneuro.herokuapp.com) appears to be down, so I thought trying that command here might of tested the same thing. I'll wait for further instructions

mathieuboudreau · 2023-06-27T15:16:17Z

@agahkarakuzu following up on your comment #14 (comment) in my other submission, I've pre-emptively updated the repo for this submission to adhere to your requests (removed the duplicate requirements.txt, archived the data in a zip file, used repo2data to load it, and added a postBuild to clone the code repo I need)

agahkarakuzu · 2023-06-27T16:08:21Z

That's great, thank you so much @mathieuboudreau! I am working on some OHBM video submissions today, I'll get to this once I am done with that :)

agahkarakuzu · 2023-09-07T13:44:19Z

@mathieuboudreau can you add content/_neurolibre.yml to this repository as well?

mathieuboudreau · 2023-09-08T10:41:18Z

Done ✅

agahkarakuzu · 2023-09-08T10:42:32Z

@roboneuro commands

roboneuro · 2023-09-08T10:42:35Z

Hello @agahkarakuzu, here are the things you can ask me to do:


# List all available commands
@roboneuro commands

# Add to this issue's reviewers list
@roboneuro add @username as reviewer

# Remove from this issue's reviewers list
@roboneuro remove @username from reviewers

# Get a list of all editors's GitHub handles
@roboneuro list editors

# Assign a user as the editor of this submission
@roboneuro assign @username as editor

# Remove the editor assigned to this submission
@roboneuro remove editor

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

# Check the references of the PDF for missing DOIs
@roboneuro check references

# Perform checks on the repository
@roboneuro check repository

# Adds a checklist for the reviewer using this command
@roboneuro generate my checklist

# Set a value for version
@roboneuro set v1.0.0 as version

# Set a value for branch
@roboneuro set neurolibre-paper as branch

# Set a value for repository
@roboneuro set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@roboneuro set set 10.5281/zenodo.6861996 as archive

# Set a value for the (data/book/repository/docker) archive DOI.
@roboneuro set 10.5281/zenodo.6861996 as data archive

# Set executable book URI for the preprint.
@roboneuro set book uri

# Mention the EiCs for the correct track
@roboneuro ping track-eic

# Reject paper
@roboneuro reject

# Withdraw paper
@roboneuro withdraw

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

# Generates the pdf paper
@roboneuro generate pdf

# Recommends the submission for acceptance
@roboneuro recommend-accept

# Accept and publish the paper
@roboneuro accept

# Update data on an accepted/published paper
@roboneuro reaccept

# Generates a LaTeX preprint file
@roboneuro generate preprint

# Flag submission with questionable scope
@roboneuro query scope

# Get a link to the complete list of reviewers
@roboneuro list reviewers

# Creates a post-review checklist with editor and authors tasks
@roboneuro create post-review checklist

# Open the review issue
@roboneuro start review

# Check the status of the NeuroLibre preview server.
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# Check the status of the NeuroLibre preprint (production) server.
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# Build a NeuroLibre reproducible preprint for technical screening.
@roboneuro build book

# After screening, build book from the forked reository.
@roboneuro production build book

# Transfer data from preview to the preprint (production) server.
@roboneuro production sync data

# Transfer the final preprint (forked repo) to the preprint (production) server (DOI URL).
@roboneuro production sync book

# Start the production process by forking repository and configuring it.
@roboneuro production start

# Creates Zenodo deposits (a.k.a buckets) for archiving reproducibility assets.
@roboneuro zenodo create buckets

# Status check for the archival of the reproducibility assets.
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# Copy summary PDF from the preprints repository to the NeuroLibre production server.
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# Upload the latest Jupyter Book to Zenodo for archival.
@roboneuro zenodo upload book

# Upload the latest version of the book repository to Zenodo for archival.
@roboneuro zenodo upload repository

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@roboneuro zenodo upload docker

# Publish reproducibility assets on Zenodo. Sets DOIs if successful.
@roboneuro zenodo publish

roboneuro · 2023-09-08T14:28:08Z

🔴 Binder build has failed 🥀

Status: Failed 3e3f3659
Last updated: 2023-09-08 07:30:22 PDT

ℹ️ See details

The next comment will forward the logs

roboneuro · 2023-09-08T14:30:24Z

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerddniqp65'...
HEAD is now at d235166 Update postBuild
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 4b304d0760ef
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 7f1b7259e459
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 7bb3d08f1de8
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 809b33e2cf15
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 4d00855d4ac4
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> e0eb756531cb
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> e08d1a12464e
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> a62ae68913e8
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 93b9c163c81a
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 97d1693ed76c
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 8daf0d2d790c
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 4eda22e52ebf
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 4a0588a11031
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3916bc471288
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> f3bda1e3877d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 86a774284ed1
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> d5211a98f273
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e2f328dd7a4e
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> e3a9180d2511
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 3954f09301c7
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5ea52513ec0f
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 995ff224d88d
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 9b184daf53f4
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b270ac4976f5
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock
 ---> Using cache
 ---> ed873e6441d2
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> da30a1b72e0b
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> ef27c8a49dad
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> a9f85c7d37a1
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> f274f300476c
Step 31/53 : USER root
 ---> Using cache
 ---> 7b42dc98661c
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 42ca71538059
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> a1b039334dfa
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 31d69548572e
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> dcdb29a9cee8
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 16c18409c840
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> d0c06d5cbb57
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 134129bb05e6
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 5896de11c6a8
Step 40/53 : USER ${NB_USER}
 ---> Using cache
 ---> 543109298af8
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> ad5c8b7b7b60
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 8e1fdb2e236e
Step 43/53 : LABEL repo2docker.ref="d2351668b1f74462387ef85c0baa7bb6057efa3e"
 ---> Running in 70c1a9d24d19
Removing intermediate container 70c1a9d24d19
 ---> 3a386f860dc4
Step 44/53 : LABEL repo2docker.repo="https://github.com/courtois-neuromod/anat-processing-paper"
 ---> Running in a76c1c4bd14e
Removing intermediate container a76c1c4bd14e
 ---> 10e2d4f88be8
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 8a2d9f40bf5a
Removing intermediate container 8a2d9f40bf5a
 ---> e132efc34bba
Step 46/53 : USER ${NB_USER}
 ---> Running in adff5c74a2f8
Removing intermediate container adff5c74a2f8
 ---> 2392d06e5b07
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in bb65464cc5fc
Removing intermediate container bb65464cc5fc
 ---> 0e331dfaaf6f
Step 48/53 : RUN ./binder/postBuild
 ---> Running in c5f88466da3f
�[91mCloning into 'content/analysis'...
�[0mbinder
content
figure1.png
paper.md
README.md
jovyan
�[91m./binder/postBuild: line 5: ../../: Is a directory
�[0m�[91mls: cannot access '../data': No such file or directory
�[0m�[91mls: cannot access '../data/courtois-anat-neurolibre/': No such file or directory
�[0m�[91mcp: cannot stat '../data/courtois-anat-neurolibre/courtois-anat-neurolibre': No such file or directory
�[0mRemoving intermediate container c5f88466da3f
The command '/bin/sh -c ./binder/postBuild' returned a non-zero code: 1Built image, launching...

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for courtois-neuromod/anat-processing-paper at d2351668b1f74462387ef85c0baa7bb6057efa3e

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

mathieuboudreau · 2023-09-08T14:41:26Z

@roboneuro build book

roboneuro · 2023-09-08T14:41:29Z

🔴 Binder build has failed 🥀

Status: Failed cf440e91
Last updated: 2023-09-08 07:43:45 PDT

ℹ️ See details

The next comment will forward the logs

roboneuro · 2023-09-08T14:43:47Z

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerolndz7t4'...
HEAD is now at faefd2e Update postBuild
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 4b304d0760ef
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 7f1b7259e459
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 7bb3d08f1de8
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 809b33e2cf15
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 4d00855d4ac4
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> e0eb756531cb
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> e08d1a12464e
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> a62ae68913e8
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 93b9c163c81a
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 97d1693ed76c
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 8daf0d2d790c
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 4eda22e52ebf
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 4a0588a11031
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3916bc471288
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> f3bda1e3877d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 86a774284ed1
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> d5211a98f273
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e2f328dd7a4e
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> e3a9180d2511
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 3954f09301c7
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5ea52513ec0f
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 995ff224d88d
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 9b184daf53f4
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b270ac4976f5
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock
 ---> Using cache
 ---> ed873e6441d2
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> da30a1b72e0b
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> ef27c8a49dad
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> a9f85c7d37a1
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> f274f300476c
Step 31/53 : USER root
 ---> Using cache
 ---> 7b42dc98661c
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 42ca71538059
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> a1b039334dfa
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 31d69548572e
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> dcdb29a9cee8
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 16c18409c840
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> d0c06d5cbb57
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 134129bb05e6
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 5896de11c6a8
Step 40/53 : USER ${NB_USER}
 ---> Using cache
 ---> 543109298af8
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> ad5c8b7b7b60
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 508cd1bd3d02
Step 43/53 : LABEL repo2docker.ref="faefd2e345d1b84aee01b1f71f61441f17848d34"
 ---> Running in 95e56d102372
Removing intermediate container 95e56d102372
 ---> cc84be28fa40
Step 44/53 : LABEL repo2docker.repo="https://github.com/courtois-neuromod/anat-processing-paper"
 ---> Running in b6ab0dcc305d
Removing intermediate container b6ab0dcc305d
 ---> ba582be2962d
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 995d9a664362
Removing intermediate container 995d9a664362
 ---> 4c4038910d0a
Step 46/53 : USER ${NB_USER}
 ---> Running in 9dc80db8c1b0
Removing intermediate container 9dc80db8c1b0
 ---> 146e1f0b4d83
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in 0fafae162c47
Removing intermediate container 0fafae162c47
 ---> 9a6b79fec908
Step 48/53 : RUN ./binder/postBuild
 ---> Running in 3f26365fff07
�[91mCloning into 'content/analysis'...
�[0mbinder
content
figure1.png
paper.md
README.md
jovyan
bin
boot
dev
etc
home
lib
lib64
media
mnt
opt
proc
root
run
sbin
srv
sys
tmp
usr
var
�[91mls: cannot access '../data': No such file or directory
�[0m�[91mls: cannot access '../data/courtois-anat-neurolibre/': No such file or directory
�[0m�[91mcp: cannot stat '../data/courtois-anat-neurolibre/courtois-anat-neurolibre': No such file or directory
�[0mRemoving intermediate container 3f26365fff07
The command '/bin/sh -c ./binder/postBuild' returned a non-zero code: 1Built image, launching...

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for courtois-neuromod/anat-processing-paper at faefd2e345d1b84aee01b1f71f61441f17848d34

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

mathieuboudreau · 2023-09-08T16:24:14Z

I should have access to the downloaded repo2data "data" folder during the postbuild stage though right?

I can't seem to find it - can you confirm @agahkarakuzu ?

mathieuboudreau · 2023-09-08T16:25:28Z

@roboneuro build book

roboneuro · 2023-09-08T16:25:32Z

🔴 Binder build has failed 🥀

Status: Failed 31e7feba
Last updated: 2023-09-08 09:28:28 PDT

ℹ️ See details

The next comment will forward the logs

roboneuro · 2023-09-08T16:28:30Z

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerd_p6vkaj'...
HEAD is now at 4c64985 Update postBuild
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 4b304d0760ef
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 7f1b7259e459
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 7bb3d08f1de8
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 809b33e2cf15
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 4d00855d4ac4
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> e0eb756531cb
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> e08d1a12464e
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> a62ae68913e8
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 93b9c163c81a
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 97d1693ed76c
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 8daf0d2d790c
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 4eda22e52ebf
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 4a0588a11031
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3916bc471288
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> f3bda1e3877d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 86a774284ed1
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> d5211a98f273
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e2f328dd7a4e
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> e3a9180d2511
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 3954f09301c7
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5ea52513ec0f
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 995ff224d88d
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 9b184daf53f4
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b270ac4976f5
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock
 ---> Using cache
 ---> ed873e6441d2
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> da30a1b72e0b
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> ef27c8a49dad
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> a9f85c7d37a1
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> f274f300476c
Step 31/53 : USER root
 ---> Using cache
 ---> 7b42dc98661c
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 42ca71538059
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> a1b039334dfa
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 31d69548572e
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> dcdb29a9cee8
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 16c18409c840
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> d0c06d5cbb57
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 134129bb05e6
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 5896de11c6a8
Step 40/53 : USER ${NB_USER}
 ---> Using cache
 ---> 543109298af8
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> ad5c8b7b7b60
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 426c2ce5a073
Step 43/53 : LABEL repo2docker.ref="4c64985dcd074012c8dad8c57f6fbdd4189947a0"
 ---> Running in 5d1ec3710306
Removing intermediate container 5d1ec3710306
 ---> aebbdbf22d06
Step 44/53 : LABEL repo2docker.repo="https://github.com/courtois-neuromod/anat-processing-paper"
 ---> Running in d4284b7e3518
Removing intermediate container d4284b7e3518
 ---> ca3ac5233910
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in d5c453b35968
Removing intermediate container d5c453b35968
 ---> 4c4afffc951d
Step 46/53 : USER ${NB_USER}
 ---> Running in 99920ee3480e
Removing intermediate container 99920ee3480e
 ---> b2247a3c521a
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in 2ebd0ed1a3f5
Removing intermediate container 2ebd0ed1a3f5
 ---> 1908dea1a45a
Step 48/53 : RUN ./binder/postBuild
 ---> Running in d65ffe1e0ae9
�[91mCloning into 'content/analysis'...
�[0mbinder
content
figure1.png
paper.md
README.md
jovyan
bin
boot
dev
etc
home
lib
lib64
media
mnt
opt
proc
root
run
sbin
srv
sys
tmp
usr
var
�[91mls: cannot access '../data': No such file or directory
�[0m�[91mls: cannot access '../data/courtois-anat-neurolibre/'�[0m�[91m: No such file or directory
�[0m�[91mfind: ‘/var/cache/apt/archives/partial’: Permission denied
�[0m�[91mfind: ‘/var/cache/ldconfig’: Permission denied
�[0m�[91mfind: ‘/proc/tty/driver’: Permission denied
�[0m�[91mfind: ‘/root’: Permission denied
�[0m�[91mfind: ‘/etc/ssl/private’: Permission denied
�[0m�[91mcp: cannot stat '../data/courtois-anat-neurolibre/courtois-anat-neurolibre': No such file or directory
�[0mRemoving intermediate container d65ffe1e0ae9
The command '/bin/sh -c ./binder/postBuild' returned a non-zero code: 1Built image, launching...

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for courtois-neuromod/anat-processing-paper at 4c64985dcd074012c8dad8c57f6fbdd4189947a0

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

agahkarakuzu · 2023-09-08T19:35:10Z

This one probably needs /home/jovyan/data/... (abs path) as the postBuild is attempting to use root dir otherwise.

mathieuboudreau · 2023-09-14T13:36:01Z

@roboneuro build book

roboneuro · 2023-09-14T13:36:04Z

🔴 Binder build has failed 🥀

Status: Failed 6e670a12
Last updated: 2023-09-14 06:40:11 PDT

ℹ️ See details

The next comment will forward the logs

roboneuro · 2023-09-14T13:40:13Z

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker96_8fbah'...
HEAD is now at 9836694 Update postBuild
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> ae378de4f5b9
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 08a78cfb4049
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> fbceb2a67733
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 3cf70612d1fc
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 54727b822f5d
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> dc588c857c02
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 5e06214b4b44
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> 42ff2be77138
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> bd417f3d3dd4
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> b60430c82d10
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 5e458aff2510
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> a438632f3dc3
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 0942e47ae895
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> bad1e96f449e
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> 73090ab9c46f
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 3a4d18f1d969
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 0475c612f284
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 4a2d8b0fcc6c
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> d1a029699546
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> b14a9e7011ae
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 7bb964d87d10
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 56b69ac27d81
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 55a865e1b0ca
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> d82b4d87d277
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock
 ---> Using cache
 ---> 175f3c212aac
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> c1bcf5d3bbd2
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 1c2997e02be2
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 43da6d61d80f
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> a0eb3d6c7bde
Step 31/53 : USER root
 ---> Using cache
 ---> 3cddb7aebc76
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 1031221c3d3e
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 6ce4404a9fa0
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 040b57734c85
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> a22c4522f25b
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 487a0e882c0b
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 942a7191c6f5
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> a79741aa8269
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> 6df5ded3432c
Step 40/53 : USER ${NB_USER}
 ---> Running in f2980d7691a2
Removing intermediate container f2980d7691a2
 ---> 5466a4f69929
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in 0c87f7e36ff1
Collecting jupyter-book==0.13.0
  Downloading jupyter_book-0.13.0-py3-none-any.whl (43 kB)
Collecting plotly==5.7.0
  Downloading plotly-5.7.0-py2.py3-none-any.whl (28.8 MB)
Collecting matplotlib==3.5.1
  Downloading matplotlib-3.5.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
Collecting numpy==1.21.6
  Downloading numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
Collecting pandas==1.3.5
  Downloading pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
Collecting nibabel==3.2.2
  Downloading nibabel-3.2.2-py3-none-any.whl (3.3 MB)
Collecting scipy
  Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
Collecting markdown
  Downloading Markdown-3.4.4-py3-none-any.whl (94 kB)
Collecting wget
  Downloading wget-3.2.zip (10 kB)
Collecting repo2data
  Downloading repo2data-2.7.0-py3-none-any.whl (7.1 kB)
Collecting sphinx-comments
  Downloading sphinx_comments-0.0.3-py3-none-any.whl (4.6 kB)
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Building wheels for collected packages: wget
  Building wheel for wget (setup.py): started
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Installing collected packages: typing-extensions, importlib-metadata, smmap, gitdb, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, more-itertools, markdown-it-py, latexcodec, jupyter-server-mathjax, jmespath, jeepney, imagesize, GitPython, docutils, colorama, alabaster, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, nbdime, mdit-py-plugins, jaraco.classes, importlib-resources, botocore, beautifulsoup4, wget, uc-micro-py, tqdm, sphinx-togglebutton, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, patool, myst-parser, msgpack, looseversion, keyrings.alt, keyring, jupyter-sphinx, jupyter-cache, iso8601, humanize, filelock, fasteners, click, boto, annexremote, zenodo-get, tenacity, sphinxcontrib-bibtex, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, pillow, osfclient, numpy, myst-nb, linkify-it-py, kiwisolver, gdown, fonttools, datalad, cycler, awscli, scipy, repo2data, plotly, pandas, nibabel, matplotlib, markdown, jupyter-book
  Attempting uninstall: typing-extensions
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Successfully installed GitPython-3.1.36 SecretStorage-3.3.3 alabaster-0.7.13 annexremote-1.6.0 awscli-1.29.47 beautifulsoup4-4.12.2 boto-2.49.0 botocore-1.31.47 click-8.1.7 colorama-0.4.4 cycler-0.11.0 datalad-0.19.3 docutils-0.16 fasteners-0.18 filelock-3.12.2 fonttools-4.38.0 gdown-4.7.1 gitdb-4.0.10 humanize-4.6.0 imagesize-1.4.1 importlib-metadata-6.7.0 importlib-resources-5.12.0 iso8601-2.0.0 jaraco.classes-3.2.3 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.13.0 jupyter-cache-0.4.3 jupyter-server-mathjax-0.2.6 jupyter-sphinx-0.3.2 keyring-24.1.1 keyrings.alt-4.2.0 kiwisolver-1.4.5 latexcodec-2.0.1 linkify-it-py-1.0.3 looseversion-1.3.0 markdown-3.4.4 markdown-it-py-1.1.0 matplotlib-3.5.1 mdit-py-plugins-0.2.8 more-itertools-9.1.0 msgpack-1.0.5 myst-nb-0.13.2 myst-parser-0.15.2 nbdime-3.2.1 nibabel-3.2.2 numpy-1.21.6 osfclient-0.0.5 pandas-1.3.5 patool-1.12 pillow-9.5.0 platformdirs-3.10.0 plotly-5.7.0 pyasn1-0.5.0 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.8.1 python-gitlab-3.15.0 pyyaml-6.0.1 repo2data-2.7.0 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.6.2 scipy-1.7.3 smmap-5.0.0 snowballstemmer-2.2.0 soupsieve-2.4.1 sphinx-4.5.0 sphinx-book-theme-0.3.3 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.1.0 sphinx-external-toc-0.2.4 sphinx-jupyterbook-latex-0.4.7 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.1.2 sphinx-togglebutton-0.3.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-bibtex-2.5.0 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 tenacity-8.2.3 tqdm-4.66.1 typing-extensions-4.7.1 uc-micro-py-1.0.2 wget-3.2 zenodo-get-1.3.4
Removing intermediate container 0c87f7e36ff1
 ---> 4aa94e144413
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
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Step 47/53 : RUN chmod +x binder/postBuild
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Step 48/53 : RUN ./binder/postBuild
 ---> Running in d8ce58d31ba9
�[91mCloning into 'content/analysis'...
�[0mbinder
content
figure1.png
paper.md
README.md
jovyan
bin
boot
dev
etc
home
lib
lib64
media
mnt
opt
proc
root
run
sbin
srv
sys
tmp
usr
var
�[91mls: cannot access '../data': No such file or directory
�[0m�[91mls: cannot access '../data/courtois-anat-neurolibre/': No such file or directory
�[0m�[91mls: cannot access '/home/jovyan/data/'�[0m�[91m: No such file or directory
�[0m�[91mcp: cannot stat '/home/jovyan/data/courtois-anat-neurolibre/courtois-anat-neurolibre'�[0m�[91m: No such file or directory
�[0mRemoving intermediate container d8ce58d31ba9
The command '/bin/sh -c ./binder/postBuild' returned a non-zero code: 1Built image, launching...

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

I could not find any book log for courtois-neuromod/anat-processing-paper at 9836694701c515c010bd76dc88aca08a52f1802e

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

mathieuboudreau · 2023-09-14T13:42:09Z

This one probably needs /home/jovyan/data/... (abs path) as the postBuild is attempting to use root dir otherwise.

From the report above, that absolute path doesn't appear to exist. I ls'd it, and it outputs:

�[0m�[91mls: cannot access '/home/jovyan/data/'�[0m�[91m: No such file or directory

mathieuboudreau · 2023-09-15T14:27:39Z

@agahkarakuzu any other ideas on how to access the neurolibre data in postbuild? Is it even possible? (I thought it should, but maybe I'm misunderstanding when the data is being mounted to the image)

agahkarakuzu · 2023-09-27T03:09:00Z

@roboneuro generate pdf

roboneuro · 2023-09-27T03:10:04Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

agahkarakuzu · 2023-10-06T13:22:53Z

Leaving this here as this command is trying to copy data before it becomes available:

cp -r /home/jovyan/data/courtois-anat-neurolibre/courtois-anat-neurolibre content/analysis/source/data

mathieuboudreau · 2023-10-06T14:15:45Z

So the data can't be available in either the Docker build stage or the postbuild stage? That means I would need to copy it inside the jupyter notebook after the image is running?

agahkarakuzu · 2023-10-06T14:21:12Z

Both build and postbuild stages are taking place in the build pod, and the data is mounted to the user pod that is spawn from the image built by the build pod :)

That means I would need to copy it inside the jupyter notebook after the image is running?

I'll see what we can do for that, but first I need to debug something with repo2data to download a file using python... The simplest thing you'd expect it would achieve.

mathieuboudreau · 2023-10-06T14:26:59Z

but first I need to debug something with repo2data to download a file using python... The simplest thing you'd expect it would achieve.

😅

agahkarakuzu · 2023-10-17T16:18:49Z

@roboneuro build book

roboneuro · 2023-10-17T16:18:52Z

🔴 Binder build has failed 🥀

Status: Failed 61181e4c
Last updated: 2023-10-17 09:28:17 PDT

ℹ️ See details

The next comment will forward the logs

agahkarakuzu · 2023-10-17T16:46:34Z

FileNotFoundError: [Errno 2] No such file or directory: 'analysis/source/data/brain/results-neuromod-anat-brain-qmri.csv'
FileNotFoundError: [Errno 2] No such file or directory: 'analysis/source/data/brain/results-neuromod-anat-brain-qmri.csv'

OK good, not I can deal with this in the review issue, I'll close the pre-review and start the review.

agahkarakuzu · 2023-10-17T16:46:56Z

@roboneuro start review

roboneuro · 2023-10-17T16:46:59Z

OK, I've started the review over in openjournals/joss-reviews#18.

mathieuboudreau · 2023-11-01T13:49:59Z

OK, I've started the review over in openjournals/joss-reviews#18.

Bug?

agahkarakuzu · 2023-11-01T13:55:01Z

It was, fixed though. Issue #10 should have shown the correct one on closure.

mathieuboudreau · 2023-11-01T13:59:05Z

Got it, just something I had just noticed haha. Thanks!

roboneuro added pre-review Track: 1 (executable) labels Jun 14, 2023

roboneuro added the Jupyter Notebook label Jun 14, 2023

roboneuro closed this as completed Oct 17, 2023

[PRE REVIEW]: Longitudinal stability of brain and spinal cord quantitative MRI measures #15

[PRE REVIEW]: Longitudinal stability of brain and spinal cord quantitative MRI measures #15

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🔴 Binder build has failed 🥀

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🔴 Binder build has failed 🥀

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