[REVIEW]: Testing the new submission system

neurolibre / neurolibre-reviews-testing

To test moderation and screening process

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[REVIEW]: Testing the new submission system #3

Open roboneuro opened 1 year ago

roboneuro commented 1 year ago

Submitting author: !--author-handle-->@agahkarakuzu@pbellec@mathieuboudreau<!--end-reviewers-list-- Reproducible preprint: Pending Repository archive: Pending Data archive: Pending Book archive: Pending Docker archive: Pending

Status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/b17407d40bbb47b3c42fdde8bc08ff00"><img src="https://neurolibre.org/papers/b17407d40bbb47b3c42fdde8bc08ff00/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/b17407d40bbb47b3c42fdde8bc08ff00/status.svg)](https://neurolibre.org/papers/b17407d40bbb47b3c42fdde8bc08ff00)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@mathieuboudreau, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@roboneuro generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @pbellec know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

@mathieuboudreau, please create your checklist typing: @roboneuro generate my checklist

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like watching a brilliant mind do a magic trick - impressive, entertaining, and left me wondering, 'how did they do that?'"

roboneuro commented 1 year ago

🥀 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/repo2dockeri0s5tw2g'...
HEAD is now at f303eaf Update requirements.txt
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/51 : FROM buildpack-deps:bionic
 ---> c03c2660fd46
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> a8c80c3f0dac
Step 3/51 : 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
 ---> 34ed66d0510e
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 0d37a316735b
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> dcbe3e3d1164
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> eb58b8a4ea16
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> 194f59b0df41
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 905839bf4324
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 5874a4fb097b
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> 754c7cb7cd4a
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 688069fd1ee8
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 3e0afae66d0c
Step 13/51 : 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
 ---> 41c9a316b358
Step 14/51 : 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
 ---> 1bf5d1cd5e7e
Step 15/51 : 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
 ---> 7bd5bb9be06b
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> b85008f1910f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> f6f181d7740a
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> cd9e94bf32d5
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 48828d1209bb
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 7c90687f6468
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 48eac6d39b1b
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 38af96404ca1
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 6f498f564758
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> b3cc95810f35
Step 25/51 : 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
 ---> 9a226f872be4
Step 26/51 : 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
 ---> 714955abf576
Step 27/51 : 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
 ---> 5097a420c3f9
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 073bc47bc25b
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 68ad00ae82af
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 9319c36ea212
Step 31/51 : USER root
 ---> Using cache
 ---> 6b2dcc399b7c
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> ec4d4c641769
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 24cacfe742d1
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 995e218f06ec
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 2926cfd1e643
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 3efce130000e
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 98a8c58e9b2f
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 6af0270d92f9
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 51f41bcc669d
Step 40/51 : USER ${NB_USER}
 ---> Using cache
 ---> bbc65a2088d5
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in c979f8fc1685
Collecting numpy==1.18.4
  Downloading numpy-1.18.4-cp37-cp37m-manylinux1_x86_64.whl (20.2 MB)
Collecting scipy==1.5.4
  Downloading scipy-1.5.4-cp37-cp37m-manylinux1_x86_64.whl (25.9 MB)
Collecting plotly==4.14.0
  Downloading plotly-4.14.0-py2.py3-none-any.whl (13.2 MB)
Collecting nilearn==0.7.1
  Downloading nilearn-0.7.1-py3-none-any.whl (3.0 MB)
Collecting repo2data>=2.6.0
  Downloading repo2data-2.7.0-py3-none-any.whl (7.1 kB)
[91mERROR: Could not find a version that satisfies the requirement jupyterbook (from versions: none)
ERROR: No matching distribution found for jupyterbook
[0mRemoving intermediate container c979f8fc1685
The command '/bin/sh -c ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"' returned a non-zero code: 1Built image, launching...

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

Jupyter Book build log



  
    NeuroLibre
    
    
  
  
    
      Oops!
      
        
    
      The reproducible preprint you are looking for does not exist.
      But it could!
      Visit our documentation below to prepare and submit a NeuroLibre preprint.
      NeuroLibre Docs

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"If coding was an art form, this paper would be the Mona Lisa of Python programming."

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like receiving a mental massage from a genius barber."

roboneuro commented 1 year ago

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

BinderHub build log


409 Conflict
Conflict
https://test.conp.cloud/v2/gh/agahkarakuzu/template/b5a0ae9d7f13d8322e61c24f76600bcebdf8535c

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

Jupyter Book build log

Because the Binder build failed, the book build was not triggered.

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like having a conversation with a brilliant mind, except I didn't have to interrupt to Google anything."

roboneuro commented 1 year ago

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

BinderHub build log

Found built image, launching...
Launching server...
Server requested
2023-05-04T02:18:43.290174Z [Normal] Successfully assigned binderhub/jupyter-agahkarakuzu-2dtemplate-2dmhwd5gqb to neurolibre-node1
2023-05-04T02:18:51Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-04T02:18:53Z [Normal] Created container block-cloud-metadata
2023-05-04T02:18:53Z [Normal] Started container block-cloud-metadata
2023-05-04T02:18:54Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:b5a0ae9d7f13d8322e61c24f76600bcebdf8535c" already present on machine
2023-05-04T02:18:57Z [Normal] Created container notebook
2023-05-04T02:18:58Z [Normal] Started container notebook
Server ready at /jupyter/user/agahkarakuzu-template-mhwd5gqb/
server running at https://test.conp.cloud/jupyter/user/agahkarakuzu-template-mhwd5gqb/

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

Jupyter Book build log

Running Jupyter-Book v0.15.1
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 242, in build
    parse_toc_yaml(toc)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx_external_toc/parsing.py", line 90, in parse_toc_yaml
    return parse_toc_data(data)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx_external_toc/parsing.py", line 100, in parse_toc_data
    raise MalformedError(f"toc is not a mapping: {type(data)}")
sphinx_external_toc.parsing.MalformedError: toc is not a mapping: 

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 245, in build
    f"The Table of Contents file is malformed: {exc}\n"
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/utils.py", line 48, in _error
    raise kind(box)
RuntimeError: 
[91m===============================================================================[0m

The Table of Contents file is malformed: toc is not a mapping: 
You may need to migrate from the old format, using:

    jupyter-book toc migrate /home/jovyan/content/_toc.yml -o /home/jovyan/content/_toc.yml

[91m===============================================================================[0m

Jupyter-book exit code: 1
Jupyter-book build failed!

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like having a conversation with a witty and brilliant mind. I only wish I could keep up!"

roboneuro commented 1 year ago

🥀 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/repo2dockervj5mr571'...
HEAD is now at d5e61aa Update toc
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/51 : FROM buildpack-deps:bionic
 ---> c03c2660fd46
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> a8c80c3f0dac
Step 3/51 : 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
 ---> 34ed66d0510e
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 0d37a316735b
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> dcbe3e3d1164
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> eb58b8a4ea16
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> 194f59b0df41
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 905839bf4324
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 5874a4fb097b
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> 754c7cb7cd4a
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 688069fd1ee8
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 3e0afae66d0c
Step 13/51 : 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
 ---> 41c9a316b358
Step 14/51 : 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
 ---> 1bf5d1cd5e7e
Step 15/51 : 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
 ---> 7bd5bb9be06b
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> b85008f1910f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> f6f181d7740a
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> cd9e94bf32d5
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 48828d1209bb
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 7c90687f6468
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 48eac6d39b1b
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 38af96404ca1
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 6f498f564758
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> b3cc95810f35
Step 25/51 : 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
 ---> 9a226f872be4
Step 26/51 : 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
 ---> 714955abf576
Step 27/51 : 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
 ---> 5097a420c3f9
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 073bc47bc25b
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 68ad00ae82af
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 9319c36ea212
Step 31/51 : USER root
 ---> Using cache
 ---> 6b2dcc399b7c
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> ec4d4c641769
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 24cacfe742d1
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 995e218f06ec
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 2926cfd1e643
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 3efce130000e
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 98a8c58e9b2f
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 6af0270d92f9
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> e85ddd916673
Step 40/51 : USER ${NB_USER}
 ---> Using cache
 ---> 60d81ecf8845
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> c606bc78e24c
Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> c10568cfded0
Step 43/51 : LABEL repo2docker.ref="d5e61aa41debd676e8c5dd7f5940000d57b6c31c"
 ---> Running in 0241e9564e47
Removing intermediate container 0241e9564e47
 ---> 23031f0c9089
Step 44/51 : LABEL repo2docker.repo="https://github.com/agahkarakuzu/template"
 ---> Running in a7864360ed2d
Removing intermediate container a7864360ed2d
 ---> d6af40341598
Step 45/51 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 93120ccddeed
Removing intermediate container 93120ccddeed
 ---> 1912e4bc6be7
Step 46/51 : USER ${NB_USER}
 ---> Running in 1f5307e69413
Removing intermediate container 1f5307e69413
 ---> 8e97b3912590
Step 47/51 : ENV PYTHONUNBUFFERED=1
 ---> Running in 8ca11ee14342
Removing intermediate container 8ca11ee14342
 ---> ae0ad3afe5cf
Step 48/51 : COPY /python3-login /usr/local/bin/python3-login
 ---> 867f80cff394
Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> ef235ead8707
Step 50/51 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in 8ef04cc3b545
Removing intermediate container 8ef04cc3b545
 ---> 38ee14fd607c
Step 51/51 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in 4fa22c8e0bc2
Removing intermediate container 4fa22c8e0bc2
 ---> 53d84a94002a
{"aux": {"ID": "sha256:53d84a94002a3565861243d8e21bdde61e1c199baea3d6dcce35ab8346863dd0"}}Successfully built 53d84a94002a
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:d5e61aa41debd676e8c5dd7f5940000d57b6c31c
Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:d5e61aa41debd676e8c5dd7f5940000d57b6c31cBuilt image, launching...
Launching server...
Server requested
2023-05-04T02:27:50.172312Z [Normal] Successfully assigned binderhub/jupyter-agahkarakuzu-2dtemplate-2d92pz1rd6 to neurolibre-node1
2023-05-04T02:27:58Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-04T02:28:01Z [Normal] Created container block-cloud-metadata
2023-05-04T02:28:02Z [Normal] Started container block-cloud-metadata
2023-05-04T02:28:05Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:d5e61aa41debd676e8c5dd7f5940000d57b6c31c" already present on machine
2023-05-04T02:28:09Z [Normal] Created container notebook
2023-05-04T02:28:13Z [Normal] Started container notebook
Server ready at /jupyter/user/agahkarakuzu-template-92pz1rd6/
server running at https://test.conp.cloud/jupyter/user/agahkarakuzu-template-92pz1rd6/

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

Jupyter Book build log

Running Jupyter-Book v0.15.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/html
[01mRunning Sphinx v5.0.2[39;49;00m
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
[01mmaking output directory... [39;49;00mdone
[etoc] Changing master_doc to '00-simple_markdown'
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mmyst v0.18.1:[39;49;00m MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], disable_syntax=[], all_links_external=False, url_schemes=['mailto', 'http', 'https'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
[01mmyst-nb v0.17.2:[39;49;00m NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='cache', execution_cache_path='/mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/.jupyter_cache', execution_excludepatterns=[], execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/.jupyter_cache
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mbuilding [mo]: [39;49;00mtargets for 0 po files that are out of date
[01mbuilding [html]: [39;49;00mtargets for 3 source files that are out of date
[01mupdating environment: [39;49;00mlocale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[new config] 3 added, 0 changed, 0 removed
[01mreading sources... [39;49;00m[ 33%] [35m00-simple_markdown[39;49;00m
[01mreading sources... [39;49;00m[ 66%] [35m01-simple_notebook[39;49;00m
/home/jovyan/content/01-simple_notebook.ipynb: Executing notebook using local CWD [mystnb]
[01mreading sources... [39;49;00m[100%] [35m02-simple-myst[39;49;00m
/home/jovyan/content/02-simple-myst.md: Executing notebook using local CWD [mystnb]

[91m/home/jovyan/content/00-simple_markdown.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/00-simple_markdown.md:8: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/00-simple_markdown.md:: WARNING: toctree contains reference to nonexisting document '02-simple_myst' [etoc.ref][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb:30002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb: WARNING: Notebook exception traceback saved in: /mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/html/reports/01-simple_notebook.err.log [mystnb.exec][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:12: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:18: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:39: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md: WARNING: Notebook exception traceback saved in: /mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/html/reports/02-simple-myst.err.log [mystnb.exec][39;49;00m
[01mlooking for now-outdated files... [39;49;00mnone found
[01mpickling environment... [39;49;00mdone
[01mchecking consistency... [39;49;00m[91m/home/jovyan/content/02-simple-myst.md: WARNING: document isn't included in any toctree[39;49;00m
done
[01mpreparing documents... [39;49;00mdone
[01mwriting output... [39;49;00m[ 33%] [32m00-simple_markdown[39;49;00m

[91mExtension error (pydata_sphinx_theme):[39;49;00m
Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 241, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 236, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/theme/pydata_sphinx_theme/components/navbar-logo.html", line 13, in top-level template code
    {% set is_logo = "light" in theme_logo["image_relative"] %}
jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'image_relative'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 290, in build_update
    len(to_build))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 649, in write_doc
    self.handle_page(docname, ctx, event_arg=doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 1052, in handle_page
    templatename, ctx, event_arg)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 458, in emit_firstresult
    allowed_exceptions=allowed_exceptions)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 112, in emit_firstresult
    for result in self.emit(name, *args, allowed_exceptions=allowed_exceptions):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 103, in emit
    (listener.handler, name), exc, modname=modname) from exc
sphinx.errors.ExtensionError: Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 318, in build
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError: 
[91m===============================================================================[0m

There was an error in building your book. Look above for the cause.

[91m===============================================================================[0m

Jupyter-book exit code: 1
Jupyter-book build failed!

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like eating a delicious piece of cake - informative, satisfying and leaves you wanting more!"

roboneuro commented 1 year ago

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

BinderHub build log

Found built image, launching...
Launching server...
Server requested
2023-05-04T02:56:54.950997Z [Normal] Successfully assigned binderhub/jupyter-agahkarakuzu-2dtemplate-2dcdmbken6 to neurolibre-node1
2023-05-04T02:57:01Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-04T02:57:05Z [Normal] Created container block-cloud-metadata
2023-05-04T02:57:07Z [Normal] Started container block-cloud-metadata
2023-05-04T02:57:08Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:d5e61aa41debd676e8c5dd7f5940000d57b6c31c" already present on machine
2023-05-04T02:57:12Z [Normal] Created container notebook
2023-05-04T02:57:13Z [Normal] Started container notebook
Server ready at /jupyter/user/agahkarakuzu-template-cdmbken6/
server running at https://test.conp.cloud/jupyter/user/agahkarakuzu-template-cdmbken6/

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

Jupyter Book build log

Checking if jupyter book build will be done...
     content/_config.yml exists.
     /mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/successfully_built not found.
     Detecting user submission, changing launch_button config to test https://test.conp.cloud and adding jb cache execution.
detect existing binderhub_url

Building jupyter-book for agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c

Running Jupyter-Book v0.15.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/html
[01mRunning Sphinx v5.0.2[39;49;00m
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
[etoc] Changing master_doc to '00-simple_markdown'
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mmyst v0.18.1:[39;49;00m MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], disable_syntax=[], all_links_external=False, url_schemes=['mailto', 'http', 'https'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
[01mmyst-nb v0.17.2:[39;49;00m NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='cache', execution_cache_path='/mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/.jupyter_cache', execution_excludepatterns=[], execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/.jupyter_cache
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mbuilding [mo]: [39;49;00mtargets for 0 po files that are out of date
[01mbuilding [html]: [39;49;00mtargets for 3 source files that are out of date
[01mupdating environment: [39;49;00mlocale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[new config] 3 added, 0 changed, 0 removed
[01mreading sources... [39;49;00m[ 33%] [35m00-simple_markdown[39;49;00m
[01mreading sources... [39;49;00m[ 66%] [35m01-simple_notebook[39;49;00m
/home/jovyan/content/01-simple_notebook.ipynb: Executing notebook using local CWD [mystnb]
[01mreading sources... [39;49;00m[100%] [35m02-simple-myst[39;49;00m
/home/jovyan/content/02-simple-myst.md: Executing notebook using local CWD [mystnb]

[91m/home/jovyan/content/00-simple_markdown.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/00-simple_markdown.md:8: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/00-simple_markdown.md:: WARNING: toctree contains reference to nonexisting document '02-simple_myst' [etoc.ref][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb:30002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb: WARNING: Notebook exception traceback saved in: /mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/html/reports/01-simple_notebook.err.log [mystnb.exec][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:12: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:18: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:39: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md: WARNING: Notebook exception traceback saved in: /mnt/books/agahkarakuzu/github.com/template/d5e61aa41debd676e8c5dd7f5940000d57b6c31c/_build/html/reports/02-simple-myst.err.log [mystnb.exec][39;49;00m
[01mlooking for now-outdated files... [39;49;00mnone found
[01mpickling environment... [39;49;00mdone
[01mchecking consistency... [39;49;00m[91m/home/jovyan/content/02-simple-myst.md: WARNING: document isn't included in any toctree[39;49;00m
done
[01mpreparing documents... [39;49;00mdone
[01mwriting output... [39;49;00m[ 33%] [32m00-simple_markdown[39;49;00m

[91mExtension error (pydata_sphinx_theme):[39;49;00m
Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 241, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 236, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/theme/pydata_sphinx_theme/components/navbar-logo.html", line 13, in top-level template code
    {% set is_logo = "light" in theme_logo["image_relative"] %}
jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'image_relative'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 290, in build_update
    len(to_build))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 649, in write_doc
    self.handle_page(docname, ctx, event_arg=doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 1052, in handle_page
    templatename, ctx, event_arg)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 458, in emit_firstresult
    allowed_exceptions=allowed_exceptions)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 112, in emit_firstresult
    for result in self.emit(name, *args, allowed_exceptions=allowed_exceptions):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 103, in emit
    (listener.handler, name), exc, modname=modname) from exc
sphinx.errors.ExtensionError: Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 318, in build
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError: 
[91m===============================================================================[0m

There was an error in building your book. Look above for the cause.

[91m===============================================================================[0m

Jupyter-book exit code: 1
Jupyter-book build failed!

Execution error log for 01-simple_notebook.err notebook (01-simple_notebook.err.ipynb) or MyST (01-simple_notebook.err.md)).

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_cache/executors/utils.py", line 64, in single_nb_execution
    **kwargs,
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 1112, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/util.py", line 74, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/util.py", line 53, in just_run
    return loop.run_until_complete(coro)
  File "/srv/conda/envs/notebook/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
    return future.result()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 554, in async_execute
    cell, index, execution_count=self.code_cells_executed + 1
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 857, in async_execute_cell
    self._check_raise_for_error(cell, exec_reply)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 760, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
import plotly.express as px
from plotly.offline import plot

# Example dataset 
df = px.data.gapminder()

# Scatter plot with slider
fig = px.scatter(df.query("year==2007"), x="gdpPercap", y="lifeExp", size="pop", color="continent",
           hover_name="country", log_x=True, size_max=60)

# fig.show() # You can use this command for inline rendering as you are developing your notebook.

plot(fig, filename = 'example_figure.html')
display(HTML('example_figure.html'))
------------------

[0;31m---------------------------------------------------------------------------[0m
[0;31mNameError[0m                                 Traceback (most recent call last)
[0;32m[0m in [0;36m[0;34m[0m
[1;32m     12[0m [0;34m[0m[0m
[1;32m     13[0m [0mplot[0m[0;34m([0m[0mfig[0m[0;34m,[0m [0mfilename[0m [0;34m=[0m [0;34m'example_figure.html'[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
[0;32m---> 14[0;31m [0mdisplay[0m[0;34m([0m[0mHTML[0m[0;34m([0m[0;34m'example_figure.html'[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
[0m
[0;31mNameError[0m: name 'HTML' is not defined
NameError: name 'HTML' is not defined

Execution error log for 02-simple-myst.err notebook (02-simple-myst.err.ipynb) or MyST (02-simple-myst.err.md)).

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_cache/executors/utils.py", line 64, in single_nb_execution
    **kwargs,
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 1112, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/util.py", line 74, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/util.py", line 53, in just_run
    return loop.run_until_complete(coro)
  File "/srv/conda/envs/notebook/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
    return future.result()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 554, in async_execute
    cell, index, execution_count=self.code_cells_executed + 1
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 857, in async_execute_cell
    self._check_raise_for_error(cell, exec_reply)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/nbclient/client.py", line 760, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
import plotly.express as px
from plotly.offline import plot

# Example dataset 
df = px.data.gapminder()

# Scatter plot with slider
fig = px.scatter(df.query("year==2007"), x="gdpPercap", y="lifeExp", size="pop", color="continent",
           hover_name="country", log_x=True, size_max=60)

# fig.show() # You can use this command for inline rendering as you are developing your notebook.

plot(fig, filename = 'example_figure.html')
display(HTML('example_figure.html'))

------------------

[0;31m---------------------------------------------------------------------------[0m
[0;31mNameError[0m                                 Traceback (most recent call last)
[0;32m[0m in [0;36m[0;34m[0m
[1;32m     12[0m [0;34m[0m[0m
[1;32m     13[0m [0mplot[0m[0;34m([0m[0mfig[0m[0;34m,[0m [0mfilename[0m [0;34m=[0m [0;34m'example_figure.html'[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
[0;32m---> 14[0;31m [0mdisplay[0m[0;34m([0m[0mHTML[0m[0;34m([0m[0;34m'example_figure.html'[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
[0m
[0;31mNameError[0m: name 'HTML' is not defined
NameError: name 'HTML' is not defined

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like taking a ride on a unicorn - magical and enlightening!"

roboneuro commented 1 year ago

🥀 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/repo2docker3e3z74py'...
HEAD is now at 6d8cd3b cleanup
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/51 : FROM buildpack-deps:bionic
 ---> c03c2660fd46
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> a8c80c3f0dac
Step 3/51 : 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
 ---> 34ed66d0510e
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 0d37a316735b
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> dcbe3e3d1164
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> eb58b8a4ea16
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> 194f59b0df41
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 905839bf4324
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 5874a4fb097b
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> 754c7cb7cd4a
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 688069fd1ee8
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 3e0afae66d0c
Step 13/51 : 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
 ---> 41c9a316b358
Step 14/51 : 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
 ---> 1bf5d1cd5e7e
Step 15/51 : 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
 ---> 7bd5bb9be06b
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> b85008f1910f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> f6f181d7740a
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> cd9e94bf32d5
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 48828d1209bb
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 7c90687f6468
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 48eac6d39b1b
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 38af96404ca1
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 6f498f564758
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> b3cc95810f35
Step 25/51 : 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
 ---> 9a226f872be4
Step 26/51 : 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
 ---> 714955abf576
Step 27/51 : 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
 ---> 5097a420c3f9
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 073bc47bc25b
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 68ad00ae82af
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 9319c36ea212
Step 31/51 : USER root
 ---> Using cache
 ---> 6b2dcc399b7c
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> ec4d4c641769
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 24cacfe742d1
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 995e218f06ec
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 2926cfd1e643
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 3efce130000e
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 98a8c58e9b2f
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 6af0270d92f9
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> 5cbeaf7ef20b
Step 40/51 : USER ${NB_USER}
 ---> Running in 39a9799569d5
Removing intermediate container 39a9799569d5
 ---> fce94f4b59ce
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in c7f9ee4bfb03
Collecting plotly
  Downloading plotly-5.14.1-py2.py3-none-any.whl (15.3 MB)
Collecting plotly-express
  Downloading plotly_express-0.4.1-py2.py3-none-any.whl (2.9 kB)
Collecting repo2data>=2.6.0
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  Downloading jupyter_book-0.15.1-py3-none-any.whl (43 kB)
Requirement already satisfied: packaging in /srv/conda/envs/notebook/lib/python3.7/site-packages (from plotly->-r binder/requirements.txt (line 1)) (21.0)
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Requirement already satisfied: jsonschema<5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jupyter-book->-r binder/requirements.txt (line 4)) (3.2.0)
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Requirement already satisfied: attrs>=17.4.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jsonschema<5->jupyter-book->-r binder/requirements.txt (line 4)) (21.2.0)
Requirement already satisfied: six>=1.11.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jsonschema<5->jupyter-book->-r binder/requirements.txt (line 4)) (1.16.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jsonschema<5->jupyter-book->-r binder/requirements.txt (line 4)) (0.17.3)
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Requirement already satisfied: sqlalchemy<1.5,>=1.3.12 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jupyter-cache<0.7,>=0.5->myst-nb~=0.17.1->jupyter-book->-r binder/requirements.txt (line 4)) (1.4.22)
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Requirement already satisfied: wheel in /srv/conda/envs/notebook/lib/python3.7/site-packages (from sphinx_togglebutton->jupyter-book->-r binder/requirements.txt (line 4)) (0.36.2)
Building wheels for collected packages: wget
  Building wheel for wget (setup.py): started
  Building wheel for wget (setup.py): finished with status 'done'
  Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9680 sha256=b0da23d3b32bec4e0e743e64ae57c998cf0655a45280949fede51dac7be2bf13
  Stored in directory: /tmp/pip-ephem-wheel-cache-a0zn3bcj/wheels/a1/b6/7c/0e63e34eb06634181c63adacca38b79ff8f35c37e3c13e3c02
Successfully built wget
Installing collected packages: typing-extensions, importlib-metadata, mdurl, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, Pygments, packaging, more-itertools, markdown-it-py, latexcodec, jmespath, jeepney, imagesize, docutils, alabaster, tabulate, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, numpy, mdit-py-plugins, jaraco.classes, importlib-resources, click, botocore, beautifulsoup4, accessible-pygments, wget, uc-micro-py, tqdm, tenacity, scipy, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, patsy, patool, pandas, myst-parser, msgpack, looseversion, keyrings.alt, keyring, jupyter-cache, iso8601, humanize, filelock, fasteners, colorama, boto, annexremote, zenodo-get, statsmodels, sphinxcontrib-bibtex, sphinx-togglebutton, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, plotly, osfclient, myst-nb, linkify-it-py, gdown, datalad, awscli, repo2data, plotly-express, jupyter-book
  Attempting uninstall: typing-extensions
    Found existing installation: typing-extensions 3.10.0.0
    Uninstalling typing-extensions-3.10.0.0:
      Successfully uninstalled typing-extensions-3.10.0.0
  Attempting uninstall: importlib-metadata
    Found existing installation: importlib-metadata 4.6.3
    Uninstalling importlib-metadata-4.6.3:
      Successfully uninstalled importlib-metadata-4.6.3
  Attempting uninstall: Pygments
    Found existing installation: Pygments 2.9.0
    Uninstalling Pygments-2.9.0:
      Successfully uninstalled Pygments-2.9.0
  Attempting uninstall: packaging
    Found existing installation: packaging 21.0
    Uninstalling packaging-21.0:
      Successfully uninstalled packaging-21.0
Successfully installed Pygments-2.15.1 SecretStorage-3.3.3 accessible-pygments-0.0.4 alabaster-0.7.13 annexremote-1.6.0 awscli-1.27.127 beautifulsoup4-4.12.2 boto-2.49.0 botocore-1.29.127 click-8.1.3 colorama-0.4.4 datalad-0.18.3 docutils-0.16 fasteners-0.18 filelock-3.12.0 gdown-4.7.1 humanize-4.6.0 imagesize-1.4.1 importlib-metadata-6.6.0 importlib-resources-5.12.0 iso8601-1.1.0 jaraco.classes-3.2.3 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.15.1 jupyter-cache-0.5.0 keyring-23.13.1 keyrings.alt-4.2.0 latexcodec-2.0.1 linkify-it-py-2.0.2 looseversion-1.1.2 markdown-it-py-2.2.0 mdit-py-plugins-0.3.5 mdurl-0.1.2 more-itertools-9.1.0 msgpack-1.0.5 myst-nb-0.17.2 myst-parser-0.18.1 numpy-1.21.6 osfclient-0.0.5 packaging-23.1 pandas-1.3.5 patool-1.12 patsy-0.5.3 platformdirs-3.5.0 plotly-5.14.1 plotly-express-0.4.1 pyasn1-0.5.0 pybtex-0.24.0 pybtex-docutils-1.0.2 pydata-sphinx-theme-0.13.3 python-gitlab-3.14.0 pyyaml-5.4.1 repo2data-2.7.0 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.6.1 scipy-1.7.3 snowballstemmer-2.2.0 soupsieve-2.4.1 sphinx-5.0.2 sphinx-book-theme-1.0.1 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.3.0 sphinx-external-toc-0.3.1 sphinx-jupyterbook-latex-0.5.2 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.2.1 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 statsmodels-0.13.5 tabulate-0.9.0 tenacity-8.2.2 tqdm-4.65.0 typing-extensions-4.5.0 uc-micro-py-1.0.2 wget-3.2 zenodo-get-1.3.4
Removing intermediate container c7f9ee4bfb03
 ---> a88f4744df44
Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 5a9926dd7225
Step 43/51 : LABEL repo2docker.ref="6d8cd3b832992b8054fdd3450a6ac44776242442"
 ---> Running in c0498ad9e261
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 ---> 7f65bb236770
Step 44/51 : LABEL repo2docker.repo="https://github.com/agahkarakuzu/template"
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 ---> b790752d7947
Step 45/51 : LABEL repo2docker.version="2021.08.0"
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Step 46/51 : USER ${NB_USER}
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Step 47/51 : ENV PYTHONUNBUFFERED=1
 ---> Running in 68685bd2821d
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 ---> b7d1485982f6
Step 48/51 : COPY /python3-login /usr/local/bin/python3-login
 ---> 8afbdfcf4f5b
Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> cdd232b8319f
Step 50/51 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in 7bb112c0fabe
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 ---> 996a16564246
Step 51/51 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in 669d3008d4b6
Removing intermediate container 669d3008d4b6
 ---> 3a3f8e792a07
{"aux": {"ID": "sha256:3a3f8e792a07185b290495b5b61e96044f2323564b2a2fcf908c00184e171d87"}}Successfully built 3a3f8e792a07
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:6d8cd3b832992b8054fdd3450a6ac44776242442
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Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:6d8cd3b832992b8054fdd3450a6ac44776242442Built image, launching...
Launching server...
Server requested
2023-05-04T22:05:49.411671Z [Normal] Successfully assigned binderhub/jupyter-agahkarakuzu-2dtemplate-2dotn393yq to neurolibre-node1
2023-05-04T22:05:53Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-04T22:05:55Z [Normal] Created container block-cloud-metadata
2023-05-04T22:05:56Z [Normal] Started container block-cloud-metadata
2023-05-04T22:05:57Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:6d8cd3b832992b8054fdd3450a6ac44776242442" already present on machine
2023-05-04T22:05:58Z [Normal] Created container notebook
2023-05-04T22:05:59Z [Normal] Started container notebook
Server ready at /jupyter/user/agahkarakuzu-template-otn393yq/
server running at https://test.conp.cloud/jupyter/user/agahkarakuzu-template-otn393yq/

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

Jupyter Book build log

Running Jupyter-Book v0.15.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/agahkarakuzu/github.com/template/6d8cd3b832992b8054fdd3450a6ac44776242442/_build/html
[01mRunning Sphinx v5.0.2[39;49;00m
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
[01mmaking output directory... [39;49;00mdone
[etoc] Changing master_doc to '00-simple_markdown'
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mmyst v0.18.1:[39;49;00m MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], disable_syntax=[], all_links_external=False, url_schemes=['mailto', 'http', 'https'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
[01mmyst-nb v0.17.2:[39;49;00m NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='cache', execution_cache_path='/mnt/books/agahkarakuzu/github.com/template/6d8cd3b832992b8054fdd3450a6ac44776242442/_build/.jupyter_cache', execution_excludepatterns=[], execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /mnt/books/agahkarakuzu/github.com/template/6d8cd3b832992b8054fdd3450a6ac44776242442/_build/.jupyter_cache
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mbuilding [mo]: [39;49;00mtargets for 0 po files that are out of date
[01mbuilding [html]: [39;49;00mtargets for 3 source files that are out of date
[01mupdating environment: [39;49;00mlocale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[new config] 3 added, 0 changed, 0 removed
[01mreading sources... [39;49;00m[ 33%] [35m00-simple_markdown[39;49;00m
[01mreading sources... [39;49;00m[ 66%] [35m01-simple_notebook[39;49;00m
/home/jovyan/content/01-simple_notebook.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01-simple_notebook.ipynb: Executed notebook in 3.05 seconds [mystnb]
/home/jovyan/content/01-simple_notebook.ipynb: Cached executed notebook: ID=1 [mystnb]
[01mreading sources... [39;49;00m[100%] [35m02-simple-myst[39;49;00m
/home/jovyan/content/02-simple-myst.md: Executing notebook using local CWD [mystnb]
/home/jovyan/content/02-simple-myst.md: Executed notebook in 1.84 seconds [mystnb]
/home/jovyan/content/02-simple-myst.md: Cached executed notebook: ID=2 [mystnb]

[91m/home/jovyan/content/00-simple_markdown.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/00-simple_markdown.md:8: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/00-simple_markdown.md:: WARNING: toctree contains reference to nonexisting document '02-simple_myst' [etoc.ref][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb:30002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:12: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:18: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:39: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[01mlooking for now-outdated files... [39;49;00mnone found
[01mpickling environment... [39;49;00mdone
[01mchecking consistency... [39;49;00m[91m/home/jovyan/content/02-simple-myst.md: WARNING: document isn't included in any toctree[39;49;00m
done
[01mpreparing documents... [39;49;00mdone
[01mwriting output... [39;49;00m[ 33%] [32m00-simple_markdown[39;49;00m

[91mExtension error (pydata_sphinx_theme):[39;49;00m
Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 241, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 236, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/theme/pydata_sphinx_theme/components/navbar-logo.html", line 13, in top-level template code
    {% set is_logo = "light" in theme_logo["image_relative"] %}
jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'image_relative'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 290, in build_update
    len(to_build))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 649, in write_doc
    self.handle_page(docname, ctx, event_arg=doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 1052, in handle_page
    templatename, ctx, event_arg)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 458, in emit_firstresult
    allowed_exceptions=allowed_exceptions)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 112, in emit_firstresult
    for result in self.emit(name, *args, allowed_exceptions=allowed_exceptions):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 103, in emit
    (listener.handler, name), exc, modname=modname) from exc
sphinx.errors.ExtensionError: Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 318, in build
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError: 
[91m===============================================================================[0m

There was an error in building your book. Look above for the cause.

[91m===============================================================================[0m

Jupyter-book exit code: 1
Jupyter-book build failed!

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper is like having a conversation with a brilliant mind, but without the awkward pauses and stuttering."

roboneuro commented 1 year ago

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

BinderHub build log

Waiting for build to start...
 ---> Using cache
 ---> 1bf5d1cd5e7e
Step 15/51 : 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
 ---> 7bd5bb9be06b
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> b85008f1910f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> f6f181d7740a
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> cd9e94bf32d5
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 48828d1209bb
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 7c90687f6468
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 48eac6d39b1b
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 38af96404ca1
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 6f498f564758
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> b3cc95810f35
Step 25/51 : 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
 ---> 9a226f872be4
Step 26/51 : 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
 ---> 714955abf576
Step 27/51 : 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
 ---> 5097a420c3f9
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 073bc47bc25b
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 68ad00ae82af
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 9319c36ea212
Step 31/51 : USER root
 ---> Using cache
 ---> 6b2dcc399b7c
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> ec4d4c641769
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 24cacfe742d1
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 995e218f06ec
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 2926cfd1e643
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 3efce130000e
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 98a8c58e9b2f
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 6af0270d92f9
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> 722870c360e6
Step 40/51 : USER ${NB_USER}
 ---> Running in ca343bdb5e01
Removing intermediate container ca343bdb5e01
 ---> ebc291845c70
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in b6baafd12531
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Collecting filelock
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Collecting more-itertools
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Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from requests>=2.5.0->sphinx<6,>=4->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (1.7.1)
Requirement already satisfied: wheel in /srv/conda/envs/notebook/lib/python3.7/site-packages (from sphinx_togglebutton->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.36.2)
Building wheels for collected packages: wget
  Building wheel for wget (setup.py): started
  Building wheel for wget (setup.py): finished with status 'done'
  Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9680 sha256=90cbda5396106e7304ecdede2578ad4c5bcef171177d4d2e56a79964ec62a726
  Stored in directory: /tmp/pip-ephem-wheel-cache-wqsuo1ca/wheels/a1/b6/7c/0e63e34eb06634181c63adacca38b79ff8f35c37e3c13e3c02
Successfully built wget
Installing collected packages: typing-extensions, importlib-metadata, mdurl, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, Pygments, packaging, more-itertools, markdown-it-py, latexcodec, jmespath, jeepney, imagesize, docutils, alabaster, tabulate, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, numpy, mdit-py-plugins, jaraco.classes, importlib-resources, click, botocore, beautifulsoup4, accessible-pygments, wget, uc-micro-py, tqdm, tenacity, scipy, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, patsy, patool, pandas, myst-parser, msgpack, looseversion, keyrings.alt, keyring, jupyter-cache, iso8601, humanize, filelock, fasteners, colorama, boto, annexremote, zenodo-get, statsmodels, sphinxcontrib-bibtex, sphinx-togglebutton, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, plotly, osfclient, myst-nb, linkify-it-py, gdown, datalad, awscli, repo2data, plotly-express, jupyter-book
  Attempting uninstall: typing-extensions
    Found existing installation: typing-extensions 3.10.0.0
    Uninstalling typing-extensions-3.10.0.0:
      Successfully uninstalled typing-extensions-3.10.0.0
  Attempting uninstall: importlib-metadata
    Found existing installation: importlib-metadata 4.6.3
    Uninstalling importlib-metadata-4.6.3:
      Successfully uninstalled importlib-metadata-4.6.3
  Attempting uninstall: Pygments
    Found existing installation: Pygments 2.9.0
    Uninstalling Pygments-2.9.0:
      Successfully uninstalled Pygments-2.9.0
  Attempting uninstall: packaging
    Found existing installation: packaging 21.0
    Uninstalling packaging-21.0:
      Successfully uninstalled packaging-21.0
Successfully installed Pygments-2.15.1 SecretStorage-3.3.3 accessible-pygments-0.0.4 alabaster-0.7.13 annexremote-1.6.0 awscli-1.27.127 beautifulsoup4-4.12.2 boto-2.49.0 botocore-1.29.127 click-8.1.3 colorama-0.4.4 datalad-0.18.3 docutils-0.16 fasteners-0.18 filelock-3.12.0 gdown-4.7.1 humanize-4.6.0 imagesize-1.4.1 importlib-metadata-6.6.0 importlib-resources-5.12.0 iso8601-1.1.0 jaraco.classes-3.2.3 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.15.1 jupyter-cache-0.5.0 keyring-23.13.1 keyrings.alt-4.2.0 latexcodec-2.0.1 linkify-it-py-2.0.2 looseversion-1.1.2 markdown-it-py-2.2.0 mdit-py-plugins-0.3.5 mdurl-0.1.2 more-itertools-9.1.0 msgpack-1.0.5 myst-nb-0.17.2 myst-parser-0.18.1 numpy-1.21.6 osfclient-0.0.5 packaging-23.1 pandas-1.3.5 patool-1.12 patsy-0.5.3 platformdirs-3.5.0 plotly-5.14.1 plotly-express-0.4.1 pyasn1-0.5.0 pybtex-0.24.0 pybtex-docutils-1.0.2 pydata-sphinx-theme-0.13.3 python-gitlab-3.14.0 pyyaml-5.4.1 repo2data-2.7.0 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.6.1 scipy-1.7.3 snowballstemmer-2.2.0 soupsieve-2.4.1 sphinx-5.0.2 sphinx-book-theme-1.0.1 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.3.0 sphinx-external-toc-0.3.1 sphinx-jupyterbook-latex-0.5.2 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.2.1 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 statsmodels-0.13.5 tabulate-0.9.0 tenacity-8.2.2 tqdm-4.65.0 typing-extensions-4.5.0 uc-micro-py-1.0.2 wget-3.2 zenodo-get-1.3.4
Removing intermediate container b6baafd12531
 ---> 589a88b768dc
Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 0acd977d120d
Step 43/51 : LABEL repo2docker.ref="833b959666808b53e4876ac858622893187df94c"
 ---> Running in 473e3bd508b6
Removing intermediate container 473e3bd508b6
 ---> 1cb51c93b067
Step 44/51 : LABEL repo2docker.repo="https://github.com/agahkarakuzu/template"
 ---> Running in de2ef469c2a5
Removing intermediate container de2ef469c2a5
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Step 45/51 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 7897124036d9
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Step 46/51 : USER ${NB_USER}
 ---> Running in fcc9ee416534
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Step 47/51 : ENV PYTHONUNBUFFERED=1
 ---> Running in 246b1c915d18
Removing intermediate container 246b1c915d18
 ---> 8461f696cd89
Step 48/51 : COPY /python3-login /usr/local/bin/python3-login
 ---> 7bfe21673bc0
Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> d0adf5267df0
Step 50/51 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in ca37d0e72516
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Step 51/51 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in 780fc2d647b6
Removing intermediate container 780fc2d647b6
 ---> 1ef3ad6f7de9
{"aux": {"ID": "sha256:1ef3ad6f7de9b19f2e499e38469a5b7ef8f5ce26b9fdc9e33c31047e889bc7b7"}}Successfully built 1ef3ad6f7de9
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:833b959666808b53e4876ac858622893187df94c
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Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:833b959666808b53e4876ac858622893187df94cBuilt image, launching...
Launching server...
Server requested
2023-05-04T22:24:05.971294Z [Normal] Successfully assigned binderhub/jupyter-agahkarakuzu-2dtemplate-2dkculnsq0 to neurolibre-node1
2023-05-04T22:24:09Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-04T22:24:10Z [Normal] Created container block-cloud-metadata
2023-05-04T22:24:11Z [Normal] Started container block-cloud-metadata
2023-05-04T22:24:12Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:833b959666808b53e4876ac858622893187df94c" already present on machine
2023-05-04T22:24:14Z [Normal] Created container notebook
2023-05-04T22:24:14Z [Normal] Started container notebook
Server ready at /jupyter/user/agahkarakuzu-template-kculnsq0/
server running at https://test.conp.cloud/jupyter/user/agahkarakuzu-template-kculnsq0/

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

Jupyter Book build log

Running Jupyter-Book v0.15.1
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 242, in build
    parse_toc_yaml(toc)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx_external_toc/parsing.py", line 90, in parse_toc_yaml
    return parse_toc_data(data)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx_external_toc/parsing.py", line 116, in parse_toc_data
    data, defaults, "/", depth=0, is_root=True, file_format=file_format
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx_external_toc/parsing.py", line 172, in _parse_doc_item
    f"Unknown keys found: {unknown_keys!r}, allowed: {allowed_keys!r} @ '{path}'"
sphinx_external_toc.parsing.MalformedError: Unknown keys found: {'parts'}, allowed: {'meta', 'root', 'subtrees', 'defaults', 'format', 'sections', 'title', 'options'} @ '/'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 245, in build
    f"The Table of Contents file is malformed: {exc}\n"
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/utils.py", line 48, in _error
    raise kind(box)
RuntimeError: 
[91m===============================================================================[0m

The Table of Contents file is malformed: Unknown keys found: {'parts'}, allowed: {'meta', 'root', 'subtrees', 'defaults', 'format', 'sections', 'title', 'options'} @ '/'
You may need to migrate from the old format, using:

    jupyter-book toc migrate /home/jovyan/content/_toc.yml -o /home/jovyan/content/_toc.yml

[91m===============================================================================[0m

Jupyter-book exit code: 1
Jupyter-book build failed!

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like a rollercoaster ride, but without the nausea and with a lot more knowledge gained."

roboneuro commented 1 year ago

🥀 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/repo2dockerzpt42lyh'...
HEAD is now at 9af5315 fix toc
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/51 : FROM buildpack-deps:bionic
 ---> c03c2660fd46
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> a8c80c3f0dac
Step 3/51 : 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
 ---> 34ed66d0510e
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 0d37a316735b
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> dcbe3e3d1164
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> eb58b8a4ea16
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> 194f59b0df41
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 905839bf4324
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 5874a4fb097b
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> 754c7cb7cd4a
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 688069fd1ee8
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 3e0afae66d0c
Step 13/51 : 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
 ---> 41c9a316b358
Step 14/51 : 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
 ---> 1bf5d1cd5e7e
Step 15/51 : 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
 ---> 7bd5bb9be06b
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> b85008f1910f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> f6f181d7740a
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> cd9e94bf32d5
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 48828d1209bb
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 7c90687f6468
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 48eac6d39b1b
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 38af96404ca1
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 6f498f564758
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> b3cc95810f35
Step 25/51 : 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
 ---> 9a226f872be4
Step 26/51 : 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
 ---> 714955abf576
Step 27/51 : 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
 ---> 5097a420c3f9
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 073bc47bc25b
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 68ad00ae82af
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 9319c36ea212
Step 31/51 : USER root
 ---> Using cache
 ---> 6b2dcc399b7c
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> ec4d4c641769
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 24cacfe742d1
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 995e218f06ec
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 2926cfd1e643
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 3efce130000e
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 98a8c58e9b2f
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 6af0270d92f9
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 722870c360e6
Step 40/51 : USER ${NB_USER}
 ---> Using cache
 ---> ebc291845c70
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> 589a88b768dc
Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 096d73ca560f
Step 43/51 : LABEL repo2docker.ref="9af53150075fb1ab05340a0a14ee389f7592b043"
 ---> Running in 4b518139e0d1
Removing intermediate container 4b518139e0d1
 ---> 22c3bd3ee1fb
Step 44/51 : LABEL repo2docker.repo="https://github.com/agahkarakuzu/template"
 ---> Running in caa703029c73
Removing intermediate container caa703029c73
 ---> 55a677badb6f
Step 45/51 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 7264747862fb
Removing intermediate container 7264747862fb
 ---> 87570ce0ba97
Step 46/51 : USER ${NB_USER}
 ---> Running in 7300019fd855
Removing intermediate container 7300019fd855
 ---> 3a14a957e5dc
Step 47/51 : ENV PYTHONUNBUFFERED=1
 ---> Running in b7fa8f4cdf42
Removing intermediate container b7fa8f4cdf42
 ---> c0c438cf3414
Step 48/51 : COPY /python3-login /usr/local/bin/python3-login
 ---> 88d9487ef400
Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> 223fe190dab2
Step 50/51 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in eedee87f1e8c
Removing intermediate container eedee87f1e8c
 ---> 5c265715f336
Step 51/51 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in 974560a20588
Removing intermediate container 974560a20588
 ---> 0c9c3ee83e5b
{"aux": {"ID": "sha256:0c9c3ee83e5bb20be5d2ad133bbe0e0f2d9f56252fc02cf701e9fe6dd6ed31c5"}}Successfully built 0c9c3ee83e5b
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:9af53150075fb1ab05340a0a14ee389f7592b043
Pushing image
Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:9af53150075fb1ab05340a0a14ee389f7592b043Built image, launching...
Launching server...
Server requested
2023-05-04T22:35:05.090222Z [Normal] Successfully assigned binderhub/jupyter-agahkarakuzu-2dtemplate-2dtnwdgswv to neurolibre-node1
2023-05-04T22:35:09Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-04T22:35:11Z [Normal] Created container block-cloud-metadata
2023-05-04T22:35:12Z [Normal] Started container block-cloud-metadata
2023-05-04T22:35:13Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:9af53150075fb1ab05340a0a14ee389f7592b043" already present on machine
2023-05-04T22:35:15Z [Normal] Created container notebook
2023-05-04T22:35:15Z [Normal] Started container notebook
Server ready at /jupyter/user/agahkarakuzu-template-tnwdgswv/
server running at https://test.conp.cloud/jupyter/user/agahkarakuzu-template-tnwdgswv/

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

Jupyter Book build log

Running Jupyter-Book v0.15.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/agahkarakuzu/github.com/template/9af53150075fb1ab05340a0a14ee389f7592b043/_build/html
[01mRunning Sphinx v5.0.2[39;49;00m
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
[01mmaking output directory... [39;49;00mdone
[etoc] Changing master_doc to '00-simple_markdown'
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mmyst v0.18.1:[39;49;00m MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], disable_syntax=[], all_links_external=False, url_schemes=['mailto', 'http', 'https'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
[01mmyst-nb v0.17.2:[39;49;00m NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='cache', execution_cache_path='/mnt/books/agahkarakuzu/github.com/template/9af53150075fb1ab05340a0a14ee389f7592b043/_build/.jupyter_cache', execution_excludepatterns=[], execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /mnt/books/agahkarakuzu/github.com/template/9af53150075fb1ab05340a0a14ee389f7592b043/_build/.jupyter_cache
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mbuilding [mo]: [39;49;00mtargets for 0 po files that are out of date
[01mbuilding [html]: [39;49;00mtargets for 3 source files that are out of date
[01mupdating environment: [39;49;00mlocale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[new config] 3 added, 0 changed, 0 removed
[01mreading sources... [39;49;00m[ 33%] [35m00-simple_markdown[39;49;00m
[01mreading sources... [39;49;00m[ 66%] [35m01-simple_notebook[39;49;00m
/home/jovyan/content/01-simple_notebook.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01-simple_notebook.ipynb: Executed notebook in 3.05 seconds [mystnb]
/home/jovyan/content/01-simple_notebook.ipynb: Cached executed notebook: ID=1 [mystnb]
[01mreading sources... [39;49;00m[100%] [35m02-simple-myst[39;49;00m
/home/jovyan/content/02-simple-myst.md: Executing notebook using local CWD [mystnb]
/home/jovyan/content/02-simple-myst.md: Executed notebook in 1.90 seconds [mystnb]
/home/jovyan/content/02-simple-myst.md: Cached executed notebook: ID=2 [mystnb]

[91m/home/jovyan/content/00-simple_markdown.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/00-simple_markdown.md:8: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/00-simple_markdown.md:: WARNING: toctree contains reference to nonexisting document '02-simple_myst' [etoc.ref][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01-simple_notebook.ipynb:30002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:12: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:18: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02-simple-myst.md:39: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[01mlooking for now-outdated files... [39;49;00mnone found
[01mpickling environment... [39;49;00mdone
[01mchecking consistency... [39;49;00m[91m/home/jovyan/content/02-simple-myst.md: WARNING: document isn't included in any toctree[39;49;00m
done
[01mpreparing documents... [39;49;00mdone
[01mwriting output... [39;49;00m[ 33%] [32m00-simple_markdown[39;49;00m

[91mExtension error (pydata_sphinx_theme):[39;49;00m
Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 241, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 236, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/theme/pydata_sphinx_theme/components/navbar-logo.html", line 13, in top-level template code
    {% set is_logo = "light" in theme_logo["image_relative"] %}
jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'image_relative'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 290, in build_update
    len(to_build))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 649, in write_doc
    self.handle_page(docname, ctx, event_arg=doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 1052, in handle_page
    templatename, ctx, event_arg)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 458, in emit_firstresult
    allowed_exceptions=allowed_exceptions)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 112, in emit_firstresult
    for result in self.emit(name, *args, allowed_exceptions=allowed_exceptions):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 103, in emit
    (listener.handler, name), exc, modname=modname) from exc
sphinx.errors.ExtensionError: Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 318, in build
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError: 
[91m===============================================================================[0m

There was an error in building your book. Look above for the cause.

[91m===============================================================================[0m

Jupyter-book exit code: 1
Jupyter-book build failed!

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like watching a magician perform - I couldn't believe how seamlessly the author made complex concepts disappear!"

roboneuro commented 1 year ago

🥀 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/repo2dockern1lbs86s'...
HEAD is now at 276c28c Cleanup some formatting
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/51 : FROM buildpack-deps:bionic
 ---> c03c2660fd46
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> a8c80c3f0dac
Step 3/51 : 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
 ---> 34ed66d0510e
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 0d37a316735b
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> dcbe3e3d1164
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> eb58b8a4ea16
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> 194f59b0df41
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 905839bf4324
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 5874a4fb097b
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> 754c7cb7cd4a
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 688069fd1ee8
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 3e0afae66d0c
Step 13/51 : 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
 ---> 41c9a316b358
Step 14/51 : 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
 ---> 1bf5d1cd5e7e
Step 15/51 : 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
 ---> 7bd5bb9be06b
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> b85008f1910f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> f6f181d7740a
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> cd9e94bf32d5
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 48828d1209bb
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 7c90687f6468
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 48eac6d39b1b
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 38af96404ca1
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 6f498f564758
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> b3cc95810f35
Step 25/51 : 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
 ---> 9a226f872be4
Step 26/51 : 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
 ---> 714955abf576
Step 27/51 : 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
 ---> 5097a420c3f9
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 073bc47bc25b
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 68ad00ae82af
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 9319c36ea212
Step 31/51 : USER root
 ---> Using cache
 ---> 6b2dcc399b7c
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> ec4d4c641769
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 24cacfe742d1
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 995e218f06ec
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 2926cfd1e643
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 3efce130000e
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 98a8c58e9b2f
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 6af0270d92f9
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 722870c360e6
Step 40/51 : USER ${NB_USER}
 ---> Using cache
 ---> ebc291845c70
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> 589a88b768dc
Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> d15d6ec14c6e
Step 43/51 : LABEL repo2docker.ref="276c28ced244e420032015c8112e5e5f92431eec"
 ---> Running in b21cd39c2d4e
Removing intermediate container b21cd39c2d4e
 ---> c1116b7993f1
Step 44/51 : LABEL repo2docker.repo="https://github.com/agahkarakuzu/template"
 ---> Running in ac9c4b6cfd15
Removing intermediate container ac9c4b6cfd15
 ---> 9e52402e8f26
Step 45/51 : LABEL repo2docker.version="2021.08.0"
 ---> Running in a670c1d946d7
Removing intermediate container a670c1d946d7
 ---> 3794ff3badd5
Step 46/51 : USER ${NB_USER}
 ---> Running in 30292bd69330
Removing intermediate container 30292bd69330
 ---> d80a01844b44
Step 47/51 : ENV PYTHONUNBUFFERED=1
 ---> Running in 64f1bb7e4a0b
Removing intermediate container 64f1bb7e4a0b
 ---> b3bb31908c0f
Step 48/51 : COPY /python3-login /usr/local/bin/python3-login
 ---> 90c5f925d03f
Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> 171627c8561f
Step 50/51 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in b332ec9ada6f
Removing intermediate container b332ec9ada6f
 ---> 0b95759e179c
Step 51/51 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in e8e0bd57f513
Removing intermediate container e8e0bd57f513
 ---> 67a13e6b03a4
{"aux": {"ID": "sha256:67a13e6b03a4785e10730c6b7c86b127b05a98a74bd2736995a570ff26e392ed"}}Successfully built 67a13e6b03a4
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:276c28ced244e420032015c8112e5e5f92431eec
Pushing image
Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:276c28ced244e420032015c8112e5e5f92431eecBuilt image, launching...
Launching server...
Server requested
2023-05-04T23:29:46.265420Z [Normal] Successfully assigned binderhub/jupyter-agahkarakuzu-2dtemplate-2d6dj23gsj to neurolibre-master
2023-05-04T23:29:53Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-04T23:29:57Z [Normal] Created container block-cloud-metadata
2023-05-04T23:29:59Z [Normal] Started container block-cloud-metadata
2023-05-04T23:30:00Z [Normal] Pulling image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:276c28ced244e420032015c8112e5e5f92431eec"
2023-05-04T23:30:38Z [Normal] Successfully pulled image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:276c28ced244e420032015c8112e5e5f92431eec" in 38.145379191s
2023-05-04T23:30:50Z [Normal] Created container notebook
2023-05-04T23:30:51Z [Normal] Started container notebook
Server ready at /jupyter/user/agahkarakuzu-template-6dj23gsj/
server running at https://test.conp.cloud/jupyter/user/agahkarakuzu-template-6dj23gsj/

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

Jupyter Book build log

Running Jupyter-Book v0.15.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/agahkarakuzu/github.com/template/276c28ced244e420032015c8112e5e5f92431eec/_build/html
[01mRunning Sphinx v5.0.2[39;49;00m
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
[01mmaking output directory... [39;49;00mdone
[etoc] Changing master_doc to '00-simple_markdown'
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mmyst v0.18.1:[39;49;00m MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], disable_syntax=[], all_links_external=False, url_schemes=['mailto', 'http', 'https'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
[01mmyst-nb v0.17.2:[39;49;00m NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='cache', execution_cache_path='/mnt/books/agahkarakuzu/github.com/template/276c28ced244e420032015c8112e5e5f92431eec/_build/.jupyter_cache', execution_excludepatterns=[], execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /mnt/books/agahkarakuzu/github.com/template/276c28ced244e420032015c8112e5e5f92431eec/_build/.jupyter_cache
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mbuilding [mo]: [39;49;00mtargets for 0 po files that are out of date
[01mbuilding [html]: [39;49;00mtargets for 3 source files that are out of date
[01mupdating environment: [39;49;00mlocale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[new config] 3 added, 0 changed, 0 removed
[01mreading sources... [39;49;00m[ 33%] [35m00-simple_markdown[39;49;00m
[01mreading sources... [39;49;00m[ 66%] [35m01-simple_notebook[39;49;00m
/home/jovyan/content/01-simple_notebook.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01-simple_notebook.ipynb: Executed notebook in 3.05 seconds [mystnb]
/home/jovyan/content/01-simple_notebook.ipynb: Cached executed notebook: ID=1 [mystnb]
[01mreading sources... [39;49;00m[100%] [35m02-simple-myst[39;49;00m
/home/jovyan/content/02-simple-myst.md: Executing notebook using local CWD [mystnb]
/home/jovyan/content/02-simple-myst.md: Executed notebook in 2.28 seconds [mystnb]
/home/jovyan/content/02-simple-myst.md: Cached executed notebook: ID=2 [mystnb]

[01mlooking for now-outdated files... [39;49;00mnone found
[01mpickling environment... [39;49;00mdone
[01mchecking consistency... [39;49;00mdone
[01mpreparing documents... [39;49;00mdone
[01mwriting output... [39;49;00m[ 33%] [32m00-simple_markdown[39;49;00m

[91mExtension error (pydata_sphinx_theme):[39;49;00m
Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 241, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 236, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/theme/pydata_sphinx_theme/components/navbar-logo.html", line 13, in top-level template code
    {% set is_logo = "light" in theme_logo["image_relative"] %}
jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'image_relative'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 290, in build_update
    len(to_build))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 649, in write_doc
    self.handle_page(docname, ctx, event_arg=doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 1052, in handle_page
    templatename, ctx, event_arg)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 458, in emit_firstresult
    allowed_exceptions=allowed_exceptions)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 112, in emit_firstresult
    for result in self.emit(name, *args, allowed_exceptions=allowed_exceptions):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 103, in emit
    (listener.handler, name), exc, modname=modname) from exc
sphinx.errors.ExtensionError: Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 318, in build
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError: 
[91m===============================================================================[0m

There was an error in building your book. Look above for the cause.

[91m===============================================================================[0m

Jupyter-book exit code: 1
Jupyter-book build failed!

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like watching a perfectly executed dance routine, except instead of dancers it was words and instead of music it was science."

roboneuro commented 1 year ago

🥀 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/repo2dockerav_hvwks'...
HEAD is now at 882ccd3 Try fixing the theme bug
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/51 : FROM buildpack-deps:bionic
 ---> c03c2660fd46
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> a8c80c3f0dac
Step 3/51 : 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
 ---> 34ed66d0510e
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 0d37a316735b
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> dcbe3e3d1164
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> eb58b8a4ea16
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> 194f59b0df41
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 905839bf4324
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 5874a4fb097b
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> 754c7cb7cd4a
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 688069fd1ee8
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 3e0afae66d0c
Step 13/51 : 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
 ---> 41c9a316b358
Step 14/51 : 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
 ---> 1bf5d1cd5e7e
Step 15/51 : 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
 ---> 7bd5bb9be06b
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> b85008f1910f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> f6f181d7740a
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> cd9e94bf32d5
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 48828d1209bb
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 7c90687f6468
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 48eac6d39b1b
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 38af96404ca1
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 6f498f564758
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> b3cc95810f35
Step 25/51 : 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
 ---> 9a226f872be4
Step 26/51 : 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
 ---> 714955abf576
Step 27/51 : 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
 ---> 5097a420c3f9
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 073bc47bc25b
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 68ad00ae82af
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 9319c36ea212
Step 31/51 : USER root
 ---> Using cache
 ---> 6b2dcc399b7c
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> ec4d4c641769
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 24cacfe742d1
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 995e218f06ec
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 2926cfd1e643
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 3efce130000e
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 98a8c58e9b2f
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 6af0270d92f9
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> 36afb5ff9d0f
Step 40/51 : USER ${NB_USER}
 ---> Running in 176f79b05b0f
Removing intermediate container 176f79b05b0f
 ---> b2594f6ef27b
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in 4a698b74d840
Collecting plotly==5.14.1
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Requirement already satisfied: jsonschema<5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (3.2.0)
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Requirement already satisfied: Jinja2 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (3.0.1)
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  Downloading awscli-1.27.127-py3-none-any.whl (4.1 MB)
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  Downloading wget-3.2.zip (10 kB)
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  Downloading gdown-4.7.1-py3-none-any.whl (15 kB)
Requirement already satisfied: importlib-metadata in /srv/conda/envs/notebook/lib/python3.7/site-packages (from click<9,>=7.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (4.6.3)
Requirement already satisfied: six>=1.11.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jsonschema<5->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (1.16.0)
Requirement already satisfied: setuptools in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jsonschema<5->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (49.6.0.post20210108)
Requirement already satisfied: attrs>=17.4.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jsonschema<5->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (21.2.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jsonschema<5->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.17.3)
Collecting uc-micro-py
  Downloading uc_micro_py-1.0.2-py3-none-any.whl (6.2 kB)
Requirement already satisfied: nbformat~=5.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (5.1.3)
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  Downloading jupyter_cache-0.5.0-py3-none-any.whl (34 kB)
Requirement already satisfied: ipykernel in /srv/conda/envs/notebook/lib/python3.7/site-packages (from myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (5.5.5)
Requirement already satisfied: ipython in /srv/conda/envs/notebook/lib/python3.7/site-packages (from myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (7.26.0)
Requirement already satisfied: typing-extensions in /srv/conda/envs/notebook/lib/python3.7/site-packages (from myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (3.10.0.0)
Requirement already satisfied: nbclient in /srv/conda/envs/notebook/lib/python3.7/site-packages (from myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.5.3)
Collecting myst-parser~=0.18.0
  Downloading myst_parser-0.18.1-py3-none-any.whl (58 kB)
Collecting tabulate
  Downloading tabulate-0.9.0-py3-none-any.whl (35 kB)
Requirement already satisfied: sqlalchemy<1.5,>=1.3.12 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jupyter-cache<0.7,>=0.5->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (1.4.22)
Collecting mdit-py-plugins~=0.3.1
  Downloading mdit_py_plugins-0.3.5-py3-none-any.whl (52 kB)
Collecting markdown-it-py<3.0.0,>=1.0.0
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Collecting mdurl~=0.1
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Requirement already satisfied: traitlets>=4.2 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from nbclient->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (5.0.5)
Requirement already satisfied: async-generator in /srv/conda/envs/notebook/lib/python3.7/site-packages (from nbclient->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (1.10)
Requirement already satisfied: nest-asyncio in /srv/conda/envs/notebook/lib/python3.7/site-packages (from nbclient->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (1.5.1)
Requirement already satisfied: jupyter-client>=6.1.5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from nbclient->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (6.1.12)
Requirement already satisfied: tornado>=4.1 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jupyter-client>=6.1.5->nbclient->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (6.1)
Requirement already satisfied: jupyter-core>=4.6.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jupyter-client>=6.1.5->nbclient->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (4.7.1)
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Requirement already satisfied: pyzmq>=13 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jupyter-client>=6.1.5->nbclient->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (22.1.0)
Requirement already satisfied: ipython-genutils in /srv/conda/envs/notebook/lib/python3.7/site-packages (from nbformat~=5.0->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.2.0)
Requirement already satisfied: pytz>=2017.3 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pandas>=0.20.0->plotly-express==0.4.1->-r binder/requirements.txt (line 2)) (2021.1)
Collecting imagesize>=1.3
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting sphinxcontrib-applehelp
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Collecting snowballstemmer>=2.0
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Collecting alabaster<0.8,>=0.7
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Collecting sphinxcontrib-qthelp
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Requirement already satisfied: babel>=2.9 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from sphinx<6,>=4->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (2.9.1)
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Collecting filelock
  Downloading filelock-3.12.0-py3-none-any.whl (10 kB)
Requirement already satisfied: pexpect>4.3 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (4.8.0)
Requirement already satisfied: pickleshare in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.7.5)
Requirement already satisfied: matplotlib-inline in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.1.2)
Requirement already satisfied: backcall in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.2.0)
Requirement already satisfied: jedi>=0.16 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.18.0)
Requirement already satisfied: decorator in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (5.0.9)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (3.0.19)
Requirement already satisfied: parso<0.9.0,>=0.8.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from jedi>=0.16->ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.8.2)
Requirement already satisfied: ptyprocess>=0.5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from pexpect>4.3->ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.7.0)
Requirement already satisfied: wcwidth in /srv/conda/envs/notebook/lib/python3.7/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->myst-nb~=0.17.1->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.2.5)
Collecting more-itertools
  Downloading more_itertools-9.1.0-py3-none-any.whl (54 kB)
Collecting typing-extensions
  Downloading typing_extensions-4.5.0-py3-none-any.whl (27 kB)
Collecting requests-toolbelt>=0.10.1
  Downloading requests_toolbelt-1.0.0-py2.py3-none-any.whl (54 kB)
Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from requests>=2.5.0->sphinx<6,>=4->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (1.7.1)
Requirement already satisfied: wheel in /srv/conda/envs/notebook/lib/python3.7/site-packages (from sphinx_togglebutton->jupyter-book==0.15.1->-r binder/requirements.txt (line 4)) (0.36.2)
Building wheels for collected packages: wget
  Building wheel for wget (setup.py): started
  Building wheel for wget (setup.py): finished with status 'done'
  Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9680 sha256=e1d264a018647ff0bc9dbc395c5548d2be750641c6d7ada2d061d43da8fbe5bc
  Stored in directory: /tmp/pip-ephem-wheel-cache-06gb37_r/wheels/a1/b6/7c/0e63e34eb06634181c63adacca38b79ff8f35c37e3c13e3c02
Successfully built wget
Installing collected packages: typing-extensions, importlib-metadata, mdurl, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, Pygments, packaging, more-itertools, markdown-it-py, latexcodec, jmespath, jeepney, imagesize, docutils, alabaster, tabulate, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, numpy, mdit-py-plugins, jaraco.classes, importlib-resources, click, botocore, beautifulsoup4, accessible-pygments, wget, uc-micro-py, tqdm, tenacity, scipy, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, patsy, patool, pandas, myst-parser, msgpack, looseversion, keyrings.alt, keyring, jupyter-cache, iso8601, humanize, filelock, fasteners, colorama, boto, annexremote, zenodo-get, statsmodels, sphinxcontrib-bibtex, sphinx-togglebutton, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, plotly, osfclient, myst-nb, linkify-it-py, gdown, datalad, awscli, repo2data, plotly-express, jupyter-book
  Attempting uninstall: typing-extensions
    Found existing installation: typing-extensions 3.10.0.0
    Uninstalling typing-extensions-3.10.0.0:
      Successfully uninstalled typing-extensions-3.10.0.0
  Attempting uninstall: importlib-metadata
    Found existing installation: importlib-metadata 4.6.3
    Uninstalling importlib-metadata-4.6.3:
      Successfully uninstalled importlib-metadata-4.6.3
  Attempting uninstall: Pygments
    Found existing installation: Pygments 2.9.0
    Uninstalling Pygments-2.9.0:
      Successfully uninstalled Pygments-2.9.0
  Attempting uninstall: packaging
    Found existing installation: packaging 21.0
    Uninstalling packaging-21.0:
      Successfully uninstalled packaging-21.0
Successfully installed Pygments-2.15.1 SecretStorage-3.3.3 accessible-pygments-0.0.4 alabaster-0.7.13 annexremote-1.6.0 awscli-1.27.127 beautifulsoup4-4.12.2 boto-2.49.0 botocore-1.29.127 click-8.1.3 colorama-0.4.4 datalad-0.18.3 docutils-0.16 fasteners-0.18 filelock-3.12.0 gdown-4.7.1 humanize-4.6.0 imagesize-1.4.1 importlib-metadata-6.6.0 importlib-resources-5.12.0 iso8601-1.1.0 jaraco.classes-3.2.3 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.15.1 jupyter-cache-0.5.0 keyring-23.13.1 keyrings.alt-4.2.0 latexcodec-2.0.1 linkify-it-py-2.0.2 looseversion-1.1.2 markdown-it-py-2.2.0 mdit-py-plugins-0.3.5 mdurl-0.1.2 more-itertools-9.1.0 msgpack-1.0.5 myst-nb-0.17.2 myst-parser-0.18.1 numpy-1.21.6 osfclient-0.0.5 packaging-23.1 pandas-1.3.5 patool-1.12 patsy-0.5.3 platformdirs-3.5.0 plotly-5.14.1 plotly-express-0.4.1 pyasn1-0.5.0 pybtex-0.24.0 pybtex-docutils-1.0.2 pydata-sphinx-theme-0.13.3 python-gitlab-3.14.0 pyyaml-5.4.1 repo2data-2.7.0 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.6.1 scipy-1.7.3 snowballstemmer-2.2.0 soupsieve-2.4.1 sphinx-5.0.2 sphinx-book-theme-1.0.1 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.3.0 sphinx-external-toc-0.3.1 sphinx-jupyterbook-latex-0.5.2 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.2.1 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 statsmodels-0.13.5 tabulate-0.9.0 tenacity-8.2.2 tqdm-4.65.0 typing-extensions-4.5.0 uc-micro-py-1.0.2 wget-3.2 zenodo-get-1.3.4
Removing intermediate container 4a698b74d840
 ---> 9a94c8239dd4
Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> c1bdc2957952
Step 43/51 : LABEL repo2docker.ref="882ccd3886ff9ef98e8304c5c13908c4a5d96f8b"
 ---> Running in 7252ab3a4f49
Removing intermediate container 7252ab3a4f49
 ---> 138f2b36c090
Step 44/51 : LABEL repo2docker.repo="https://github.com/agahkarakuzu/template"
 ---> Running in 03201cf87d96
Removing intermediate container 03201cf87d96
 ---> 37287326c8cd
Step 45/51 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 447c74a46652
Removing intermediate container 447c74a46652
 ---> a23c0654bb61
Step 46/51 : USER ${NB_USER}
 ---> Running in c033edc0f0ce
Removing intermediate container c033edc0f0ce
 ---> 8876a7a06d4c
Step 47/51 : ENV PYTHONUNBUFFERED=1
 ---> Running in 44d4d1bfa965
Removing intermediate container 44d4d1bfa965
 ---> 5ab35b993175
Step 48/51 : COPY /python3-login /usr/local/bin/python3-login
 ---> 327f7d0f31e7
Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> 9ff674f42709
Step 50/51 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in ace72e8201ad
Removing intermediate container ace72e8201ad
 ---> 936a13d07384
Step 51/51 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in 1b4bac348e51
Removing intermediate container 1b4bac348e51
 ---> 22f85c34a0dc
{"aux": {"ID": "sha256:22f85c34a0dc66e2e2488bf25112fa60778e6e4f83e7a65f0c2fb74baa7bd268"}}Successfully built 22f85c34a0dc
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:882ccd3886ff9ef98e8304c5c13908c4a5d96f8b
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Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:882ccd3886ff9ef98e8304c5c13908c4a5d96f8bBuilt image, launching...
Launching server...
Server requested
2023-05-05T00:29:25.679512Z [Normal] Successfully assigned binderhub/jupyter-agahkarakuzu-2dtemplate-2dm1iczq34 to neurolibre-node1
2023-05-05T00:29:30Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-05T00:29:31Z [Normal] Created container block-cloud-metadata
2023-05-05T00:29:33Z [Normal] Started container block-cloud-metadata
2023-05-05T00:29:34Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:882ccd3886ff9ef98e8304c5c13908c4a5d96f8b" already present on machine
2023-05-05T00:29:35Z [Normal] Created container notebook
2023-05-05T00:29:36Z [Normal] Started container notebook
Server ready at /jupyter/user/agahkarakuzu-template-m1iczq34/
server running at https://test.conp.cloud/jupyter/user/agahkarakuzu-template-m1iczq34/

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

Jupyter Book build log

Running Jupyter-Book v0.15.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/agahkarakuzu/github.com/template/882ccd3886ff9ef98e8304c5c13908c4a5d96f8b/_build/html
[01mRunning Sphinx v5.0.2[39;49;00m
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
[01mmaking output directory... [39;49;00mdone
[etoc] Changing master_doc to '00-simple_markdown'
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mmyst v0.18.1:[39;49;00m MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], disable_syntax=[], all_links_external=False, url_schemes=['mailto', 'http', 'https'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
[01mmyst-nb v0.17.2:[39;49;00m NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='cache', execution_cache_path='/mnt/books/agahkarakuzu/github.com/template/882ccd3886ff9ef98e8304c5c13908c4a5d96f8b/_build/.jupyter_cache', execution_excludepatterns=[], execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /mnt/books/agahkarakuzu/github.com/template/882ccd3886ff9ef98e8304c5c13908c4a5d96f8b/_build/.jupyter_cache
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[01mbuilding [mo]: [39;49;00mtargets for 0 po files that are out of date
[01mbuilding [html]: [39;49;00mtargets for 3 source files that are out of date
[01mupdating environment: [39;49;00mlocale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[new config] 3 added, 0 changed, 0 removed
[01mreading sources... [39;49;00m[ 33%] [35m00-simple_markdown[39;49;00m
[01mreading sources... [39;49;00m[ 66%] [35m01-simple_notebook[39;49;00m
/home/jovyan/content/01-simple_notebook.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01-simple_notebook.ipynb: Executed notebook in 3.06 seconds [mystnb]
/home/jovyan/content/01-simple_notebook.ipynb: Cached executed notebook: ID=1 [mystnb]
[01mreading sources... [39;49;00m[100%] [35m02-simple-myst[39;49;00m
/home/jovyan/content/02-simple-myst.md: Executing notebook using local CWD [mystnb]
/home/jovyan/content/02-simple-myst.md: Executed notebook in 1.83 seconds [mystnb]
/home/jovyan/content/02-simple-myst.md: Cached executed notebook: ID=2 [mystnb]

[01mlooking for now-outdated files... [39;49;00mnone found
[01mpickling environment... [39;49;00mdone
[01mchecking consistency... [39;49;00mdone
[01mpreparing documents... [39;49;00mdone
[01mwriting output... [39;49;00m[ 33%] [32m00-simple_markdown[39;49;00m

[91mExtension error (pydata_sphinx_theme):[39;49;00m
Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 241, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/__init__.py", line 236, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pydata_sphinx_theme/theme/pydata_sphinx_theme/components/navbar-logo.html", line 13, in top-level template code
    {% set is_logo = "light" in theme_logo["image_relative"] %}
jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'image_relative'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 290, in build_update
    len(to_build))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 649, in write_doc
    self.handle_page(docname, ctx, event_arg=doctree)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/html/__init__.py", line 1052, in handle_page
    templatename, ctx, event_arg)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 458, in emit_firstresult
    allowed_exceptions=allowed_exceptions)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 112, in emit_firstresult
    for result in self.emit(name, *args, allowed_exceptions=allowed_exceptions):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 103, in emit
    (listener.handler, name), exc, modname=modname) from exc
sphinx.errors.ExtensionError: Handler  for event 'html-page-context' threw an exception (exception: 'dict object' has no attribute 'image_relative')

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 318, in build
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError: 
[91m===============================================================================[0m

There was an error in building your book. Look above for the cause.

[91m===============================================================================[0m

Jupyter-book exit code: 1
Jupyter-book build failed!

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

For guidelines, please see the relevant documentation.

agahkarakuzu commented 1 year ago

OK, opened an issue about this elsewhere: https://github.com/pydata/pydata-sphinx-theme/issues/1315

Moving forward, not really a neurolibre problem. I went into the pod and switched jupyter-book version to 0.14.0, which appears to complete book build. Now I'll push it on the target repo and annoy everyone subscribed to this issue once again.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like being tickled by a feather - informative, yet surprisingly delightful!"

agahkarakuzu commented 1 year ago

:hibiscus: Awesome news! :hibiscus:

Your build was successful and the latest version of your reproducible preprint is ready for you to check out :confetti_ball:

agahkarakuzu commented 1 year ago

@roboneuro commands

agahkarakuzu commented 1 year ago

@roboneuro commands

agahkarakuzu commented 1 year ago

@roboneuro commands

roboneuro commented 1 year ago

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

# 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.
@roboneuro preview server status

# Check the status of the NeuroLibre preprint (production) server.
@roboneuro preprint server status

# Build a NeuroLibre reproducible preprint for technical screening.
@roboneuro build book

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

agahkarakuzu commented 1 year ago

@roboneuro production sync data

agahkarakuzu commented 1 year ago

@roboneuro production sync data

roboneuro commented 1 year ago

⠀⠀ DATA TRANSFER (Preview --> Preprint) ⚪ Status: Request queued on NeuroLibre servers ⠀⠀ Last updated: 2023-05-08 20:11:42 PDT

agahkarakuzu commented 1 year ago

@roboneuro production sync data

agahkarakuzu commented 1 year ago

@roboneuro production sync data

roboneuro commented 1 year ago

⠀⠀ DATA TRANSFER (Preview --> Preprint) ⚪ Status: Request queued on NeuroLibre servers ⠀⠀ Last updated: 2023-05-08 20:32:19 PDT

agahkarakuzu commented 1 year ago

@roboneuro production sync data

roboneuro commented 1 year ago

⠀⠀ DATA TRANSFER (Preview --> Preprint) 🟠 Status: In progress 3e349f82 ⠀⠀ Last updated: 2023-05-08 20:39:32 PDT

agahkarakuzu commented 1 year ago

@roboneuro production sync data

roboneuro commented 1 year ago

⠀⠀ DATA TRANSFER (Preview --> Preprint) 🔴 Status: Failed c5251ef0 ⠀⠀ Last updated: 2023-05-08 21:00:15 PDT ⠀⠀ None

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