[REVIEW]: Quantitative T1 MRI

Submitting author: !--author-handle-->@mathieuboudreau@agahkarakuzu@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00019 Repository archive: 10.5281/zenodo.10067639 Data archive: 10.5281/zenodo.10067641 Book archive: 10.5281/zenodo.10067637 Docker archive: 10.5281/zenodo.10067643

Status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/27b301e98ed8df3437844f3f582b7e55"><img src="https://neurolibre.org/papers/27b301e98ed8df3437844f3f582b7e55/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/27b301e98ed8df3437844f3f582b7e55/status.svg)](https://neurolibre.org/papers/27b301e98ed8df3437844f3f582b7e55)

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

@agahkarakuzu, 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 @agahkarakuzu 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

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

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

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

@roboneuro commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (336.0 files/s, 99104.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              4              4           3436
Jupyter Notebook                 5              0            986           1516
TeX                              1             40              0            454
Markdown                         9             61              0            182
YAML                             2             10              1             68
CSS                              1              1              0             17
JSON                             1              0              0              4
-------------------------------------------------------------------------------
SUM:                            23            116            991           5677
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

Wordcount for paper.md is 125

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/B978-0-12-817057-1.00004-4 is OK
- 10.21105/joss.02343 is OK
- 10.55458/neurolibre.00014 is OK
- 10.1002/mrm.25135 is OK
- 10.1201/9780429493867 is OK
- 10.1002/mrm.22497 is OK
- 10.1088/0031-9155/28/6/012 is OK
- 10.1002/jmri.1880040511 is OK
- 10.1088/0031-9155/23/5/012 is OK
- 10.1186/1532-429X-12-69 is OK
- 10.1002/mrm.20110 is OK
- 10.1063/1.1684482 is OK
- 10.1103/PhysRev.76.145 is OK
- 10.1002/mrm.24251 is OK
- 10.1088/0370-1298/62/5/306 is OK
- 10.1002/mrm.26979 is OK
- 10.1016/b978-0-12-092861-3.x5000-6 is OK
- 10.1002/jmri.25692 is OK
- 10.1016/j.neuroimage.2005.04.031 is OK
- 10.1002/mrm.21669 is OK
- 10.1371/journal.pone.0015710 is OK
- 10.1063/1.1719961 is OK
- 10.1016/0730-725x(87)90021-x is OK
- 10.1016/0022-2364(77)90138-x is OK
- 10.1016/0022-2364(85)90318-x is OK
- 10.3389/fnins.2017.00106 is OK
- 10.1002/jmri.24373 is OK
- 10.1088/1361-6560/aad519 is OK
- 10.1016/j.mri.2005.10.025 is OK
- 10.1088/0031-9155/54/1/n01 is OK
- 10.1109/42.730409 is OK
- 10.1002/jmri.23996 is OK
- 10.1002/mrm.20377 is OK
- 10.1002/mrm.22394 is OK
- 10.1002/mrm.10120 is OK
- 10.3978/j.issn.2223-4292.2012.11.04 is OK
- 10.1002/mrm.1910210210 is OK
- 10.1002/mrm.10407 is OK

MISSING DOIs

- 10.1021/j100612a022 may be a valid DOI for title: Optimal determination of relaxation times of Fourier transform nuclear magnetic resonance. Determination of spin-lattice relaxation times in chemically polarized species

INVALID DOIs

- None

Failed to discover a Statement of need section in paper

@roboneuro build book

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

🔴 Binder build has failed 🥀

Status: Failed c3651104 Last updated: 2023-10-27 14:00:29 PDT

:information_source: See details

The next comment will forward the logs

@roboneuro build extended pdf

🔴 Extended PDF - Build draft

Status: Failed 025d440f Last updated: 2023-10-27 13:52:59 PDT

:information_source: See details

'NoneType' object has no attribute 'strip'

🥀 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/repo2dockerrbx9h8cd'...
HEAD is now at 3fdeff4 Master edit
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/51 : FROM buildpack-deps:bionic
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Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
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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/*
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Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
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Step 5/51 : ENV LC_ALL en_US.UTF-8
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Step 6/51 : ENV LANG en_US.UTF-8
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Step 7/51 : ENV LANGUAGE en_US.UTF-8
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Step 8/51 : ENV SHELL /bin/bash
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Step 9/51 : ARG NB_USER
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Step 10/51 : ARG NB_UID
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Step 11/51 : ENV USER ${NB_USER}
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Step 12/51 : ENV HOME /home/${NB_USER}
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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}
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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
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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/*
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Step 16/51 : EXPOSE 8888
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Step 17/51 : ENV APP_BASE /srv
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Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
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Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
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Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
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Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
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Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
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Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
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Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
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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
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Step 26/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
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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
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Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
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Step 29/51 : USER ${NB_USER}
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Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
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Step 31/51 : USER root
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Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
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Step 33/51 : ARG REPO_DIR=${HOME}
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Step 34/51 : ENV REPO_DIR ${REPO_DIR}
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Step 35/51 : WORKDIR ${REPO_DIR}
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Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
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Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
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Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
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Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
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Step 40/51 : USER ${NB_USER}
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Removing intermediate container 0b00a82fc830
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Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
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Collecting wget
  Downloading wget-3.2.zip (10 kB)
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=98bd5c74bcf961c407d6774eb6290cbbe3dab822509b604e943ceb7adbdf5c72
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Successfully built wget
Installing collected packages: pygments, mdurl, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, more-itertools, markdown-it-py, latexcodec, jmespath, jeepney, importlib-metadata, imagesize, docutils, alabaster, typing-extensions, tabulate, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, mdit-py-plugins, jaraco.classes, importlib-resources, click, botocore, beautifulsoup4, accessible-pygments, wget, uc-micro-py, tqdm, tenacity, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, patool, numpy, myst-parser, msgpack, looseversion, keyrings.alt, keyring, jupyter-cache, iso8601, humanize, filelock, fasteners, distro, colorama, boto, annexremote, zenodo-get, sphinxcontrib-bibtex, sphinx-togglebutton, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, retrying, plotly, pillow, osfclient, myst-nb, linkify-it-py, kiwisolver, gdown, fonttools, datalad, cycler, contourpy, awscli, scipy, repo2data, matplotlib, jupyter-book, chart-studio
  Attempting uninstall: pygments
    Found existing installation: Pygments 2.9.0
    Uninstalling Pygments-2.9.0:
      Successfully uninstalled Pygments-2.9.0
  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
Successfully installed SecretStorage-3.3.3 accessible-pygments-0.0.4 alabaster-0.7.13 annexremote-1.6.3 awscli-1.29.73 beautifulsoup4-4.12.2 boto-2.49.0 botocore-1.31.73 chart-studio-1.1.0 click-8.1.7 colorama-0.4.4 contourpy-1.1.1 cycler-0.12.1 datalad-0.19.3 distro-1.8.0 docutils-0.16 fasteners-0.19 filelock-3.13.0 fonttools-4.43.1 gdown-4.7.1 humanize-4.8.0 imagesize-1.4.1 importlib-metadata-6.8.0 importlib-resources-6.1.0 iso8601-2.1.0 jaraco.classes-3.3.0 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.15.1 jupyter-cache-0.6.1 keyring-24.2.0 keyrings.alt-5.0.0 kiwisolver-1.4.5 latexcodec-2.0.1 linkify-it-py-2.0.2 looseversion-1.3.0 markdown-it-py-2.2.0 matplotlib-3.7.3 mdit-py-plugins-0.3.5 mdurl-0.1.2 more-itertools-10.1.0 msgpack-1.0.7 myst-nb-0.17.2 myst-parser-0.18.1 numpy-1.24.4 osfclient-0.0.5 patool-1.12 pillow-10.1.0 platformdirs-3.11.0 plotly-5.18.0 pyasn1-0.5.0 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.14.2 pygments-2.16.1 python-gitlab-3.15.0 pyyaml-6.0.1 repo2data-2.9.1 requests-toolbelt-1.0.0 retrying-1.3.4 rsa-4.7.2 s3transfer-0.7.0 scipy-1.10.1 snowballstemmer-2.2.0 soupsieve-2.5 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-1.0.4 sphinxcontrib-bibtex-2.5.0 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 tabulate-0.9.0 tenacity-8.2.3 tqdm-4.66.1 typing-extensions-4.8.0 uc-micro-py-1.0.2 wget-3.2 zenodo-get-1.5.0
Removing intermediate container dac7800d875e
 ---> 6b42ae64c460
Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 6be0ae4eff2d
Step 43/51 : LABEL repo2docker.ref="3fdeff47bc9826f80d5b4b29d966f83f56b16300"
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Removing intermediate container 965ca1d4c71c
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Step 44/51 : LABEL repo2docker.repo="https://github.com/qMRLab/t1-book-neurolibre"
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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
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Step 48/51 : COPY /python3-login /usr/local/bin/python3-login
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Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
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Step 50/51 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
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Step 51/51 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
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Removing intermediate container 7ebffe1d41bc
 ---> a7333579227b
{"aux": {"ID": "sha256:a7333579227ba31b64712c353b296e0f64494207b7134ceff3016e5a8d514fb9"}}Successfully built a7333579227b
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-qmrlab-2dt1-2dbook-2dneurolibre-efea62:3fdeff47bc9826f80d5b4b29d966f83f56b16300
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Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-qmrlab-2dt1-2dbook-2dneurolibre-efea62:3fdeff47bc9826f80d5b4b29d966f83f56b16300Built image, launching...
Launching server...
Server requested
2023-10-27T20:56:57Z [Normal] Successfully assigned binderhub/jupyter-qmrlab-2dt1-2dbook-2dneurolibre-2dm4wdck90 to neurolibre-master
2023-10-27T20:57:13Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-10-27T20:57:21Z [Normal] Created container block-cloud-metadata
2023-10-27T20:57:28Z [Normal] Started container block-cloud-metadata
2023-10-27T20:57:29Z [Normal] Pulling image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-qmrlab-2dt1-2dbook-2dneurolibre-efea62:3fdeff47bc9826f80d5b4b29d966f83f56b16300"
2023-10-27T20:58:04Z [Normal] Successfully pulled image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-qmrlab-2dt1-2dbook-2dneurolibre-efea62:3fdeff47bc9826f80d5b4b29d966f83f56b16300" in 34.305688224s
2023-10-27T20:58:21Z [Normal] Created container notebook
2023-10-27T20:58:26Z [Normal] Started container notebook
Server ready at /jupyter/user/qmrlab-t1-book-neurolibre-m4wdck90/
server running at https://test.conp.cloud/jupyter/user/qmrlab-t1-book-neurolibre-m4wdck90/

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/qMRLab/github.com/t1-book-neurolibre/3fdeff47bc9826f80d5b4b29d966f83f56b16300/_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 'intro'
[etoc] Excluded 3 extra file(s) not in toc
checking bibtex cache... out of date
parsing bibtex file /home/jovyan/paper.bib... parsed 40 entries
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=['html_image', 'amsmath', 'colon_fence', 'deflist', 'dollarmath', 'html_admonition', 'linkify', 'replacements', 'smartquotes', 'substitution'], 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/qMRLab/github.com/t1-book-neurolibre/3fdeff47bc9826f80d5b4b29d966f83f56b16300/_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/qMRLab/github.com/t1-book-neurolibre/3fdeff47bc9826f80d5b4b29d966f83f56b16300/_build/.jupyter_cache
[91mWARNING: The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file.Be aware that `navigation_with_keys = True` has negative accessibility implications:https://github.com/pydata/pydata-sphinx-theme/issues/1492[39;49;00m
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 10 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] 10 added, 0 changed, 0 removed
[01mreading sources... [39;49;00m[ 10%] [35m01/IR_BenefitsAndPitfalls[39;49;00m
/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb: Executed notebook in 2.82 seconds [mystnb]
/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb: Cached executed notebook: ID=1 [mystnb]
[01mreading sources... [39;49;00m[ 20%] [35m01/IR_DataFitting[39;49;00m
/home/jovyan/content/01/IR_DataFitting.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01/IR_DataFitting.ipynb: Executed notebook in 2.25 seconds [mystnb]
/home/jovyan/content/01/IR_DataFitting.ipynb: Cached executed notebook: ID=2 [mystnb]
[01mreading sources... [39;49;00m[ 30%] [35m01/IR_Introduction[39;49;00m
[01mreading sources... [39;49;00m[ 40%] [35m01/IR_OtherMethods[39;49;00m
[01mreading sources... [39;49;00m[ 50%] [35m01/IR_SignalModelling[39;49;00m
/home/jovyan/content/01/IR_SignalModelling.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01/IR_SignalModelling.ipynb: Executed notebook in 3.02 seconds [mystnb]
/home/jovyan/content/01/IR_SignalModelling.ipynb: Cached executed notebook: ID=3 [mystnb]
[01mreading sources... [39;49;00m[ 60%] [35m02/VFA_BenefitsAndPitfalls[39;49;00m
[01mreading sources... [39;49;00m[ 70%] [35m02/VFA_DataFitting[39;49;00m
/home/jovyan/content/02/VFA_DataFitting.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/02/VFA_DataFitting.ipynb: Executed notebook in 2.21 seconds [mystnb]
/home/jovyan/content/02/VFA_DataFitting.ipynb: Cached executed notebook: ID=4 [mystnb]
[01mreading sources... [39;49;00m[ 80%] [35m02/VFA_Introduction[39;49;00m
[01mreading sources... [39;49;00m[ 90%] [35m02/VFA_SignalModelling[39;49;00m
/home/jovyan/content/02/VFA_SignalModelling.ipynb: Executing notebook using local CWD [mystnb]
[01mreading sources... [39;49;00m[100%] [35mintro[39;49;00m

[91m/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_SignalModelling.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec][39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb: WARNING: Notebook exception traceback saved in: /mnt/books/qMRLab/github.com/t1-book-neurolibre/3fdeff47bc9826f80d5b4b29d966f83f56b16300/_build/html/reports/02/VFA_SignalModelling.err.log [mystnb.exec][39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:90005: WARNING: duplicate label "1" for keys "Boudreau2023" and "Barral2010-qm"[39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:90005: WARNING: duplicate citation for key "Fukushima1981"[39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:90005: WARNING: duplicate label "3" for keys "Stikov2015" and "Pykett1983"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate label "1" for keys "Boudreau2023" and "Drain1949"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate label "2" for keys "Fukushima1981" and "Hahn1949"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate label "3" for keys "Stikov2015" and "Messroghli2004"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate citation for key "Stikov2015"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "1" for keys "Boudreau2023" and "Gai2013"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "2" for keys "Fukushima1981" and "Look1970"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate citation for key "Messroghli2004"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "3" for keys "Stikov2015" and "Messroghli2004"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate citation for key "Piechnik2010"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate citation for key "Stikov2015"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "5" for keys "Pykett1978" and "Stikov2015"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "1" for keys "Boudreau2023" and "Baudrexel2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "2" for keys "Fukushima1981" and "Boudreau2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "3" for keys "Stikov2015" and "Cercignani2005"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "4" for keys "Piechnik2010" and "Lee2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "5" for keys "Pykett1978" and "Li2018"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "6" for keys "Steen1994" and "Liberman2013"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "7" for keys "Stikov2015" and "Lutti2013"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate citation for key "Stikov2015"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "1" for keys "Boudreau2023" and "Chang2008"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "2" for keys "Fukushima1981" and "Deoni2003"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "3" for keys "Stikov2015" and "Gupta1977"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "4" for keys "Piechnik2010" and "Schabel2008"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "5" for keys "Pykett1978" and "Sled1998"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Boudreau2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "1" for keys "Boudreau2023" and "Boudreau2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "2" for keys "Fukushima1981" and "Christensen1974"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Deoni2003"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "3" for keys "Stikov2015" and "Deoni2003"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "4" for keys "Piechnik2010" and "Fram1987"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Gupta1977"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "5" for keys "Pykett1978" and "Gupta1977"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "6" for keys "Steen1994" and "Homer1985"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Lee2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "7" for keys "Stikov2015" and "Lee2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Sled1998"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "8" for keys "Samson2006" and "Sled1998"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "1" for keys "Boudreau2023" and "Handbook2004"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "2" for keys "Fukushima1981" and "Ernst1966"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "3" for keys "Stikov2015" and "Yarnykh2010"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "4" for keys "Piechnik2010" and "Zur1991"[39;49;00m
[91m/home/jovyan/content/intro.md:19: WARNING: duplicate label "1" for keys "Boudreau2023" and "Karakuzu2020-ul"[39;49;00m
[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[ 10%] [32m01/IR_BenefitsAndPitfalls[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/python3.8/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/pydata_sphinx_theme/__init__.py", line 236, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/pydata_sphinx_theme/__init__.py", line 231, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.8/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/python3.8/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 288, in build_update
    self.build(to_build,
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.8/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/python3.8/site-packages/sphinx/builders/html/__init__.py", line 1051, in handle_page
    newtmpl = self.app.emit_firstresult('html-page-context', pagename,
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/application.py", line 457, in emit_firstresult
    return self.events.emit_firstresult(event, *args,
  File "/srv/conda/envs/notebook/lib/python3.8/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/python3.8/site-packages/sphinx/events.py", line 102, in emit
    raise ExtensionError(__("Handler %r for event %r threw an exception") %
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/python3.8/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jupyter_book/cli/main.py", line 317, in build
    builder_specific_actions(
  File "/srv/conda/envs/notebook/lib/python3.8/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.

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

For guidelines, please see the relevant documentation.

@roboneuro build book

🔴 Binder build has failed 🥀

Status: Failed d467b4aa Last updated: 2023-10-27 14:20:47 PDT

:information_source: See details

The next comment will forward the logs

🥀 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/repo2dockerznwgguyt'...
HEAD is now at 83b2636 Fix theme version
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/51 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> ae378de4f5b9
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
 ---> 08a78cfb4049
Step 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> fbceb2a67733
Step 5/51 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 3cf70612d1fc
Step 6/51 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 54727b822f5d
Step 7/51 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> dc588c857c02
Step 8/51 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 5e06214b4b44
Step 9/51 : ARG NB_USER
 ---> Using cache
 ---> 42ff2be77138
Step 10/51 : ARG NB_UID
 ---> Using cache
 ---> bd417f3d3dd4
Step 11/51 : ENV USER ${NB_USER}
 ---> Using cache
 ---> b60430c82d10
Step 12/51 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 5e458aff2510
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
 ---> a438632f3dc3
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
 ---> 0942e47ae895
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
 ---> bad1e96f449e
Step 16/51 : EXPOSE 8888
 ---> Using cache
 ---> 73090ab9c46f
Step 17/51 : ENV APP_BASE /srv
 ---> Using cache
 ---> 3a4d18f1d969
Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 0475c612f284
Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 4a2d8b0fcc6c
Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> d1a029699546
Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> b14a9e7011ae
Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 7bb964d87d10
Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 56b69ac27d81
Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 55a865e1b0ca
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
 ---> d82b4d87d277
Step 26/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
 ---> Using cache
 ---> d3f1fef730ce
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
 ---> 9ba1874bc4c7
Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 9152c383d252
Step 29/51 : USER ${NB_USER}
 ---> Using cache
 ---> 51d7e1747282
Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 22ddec68b188
Step 31/51 : USER root
 ---> Using cache
 ---> d5972cb0f670
Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 33c7bdbe312e
Step 33/51 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 479614e3035e
Step 34/51 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 4f3657da5f62
Step 35/51 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 9f85fe4764c0
Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 932d4b31c401
Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 981d892d58f3
Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 75c1ad851985
Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> ee0db23d6b57
Step 40/51 : USER ${NB_USER}
 ---> Running in 615b3a270547
Removing intermediate container 615b3a270547
 ---> da5c76310134
Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in a214f523d6ee
Collecting repo2data==2.9.1
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Requirement already satisfied: Babel in /srv/conda/envs/notebook/lib/python3.8/site-packages (from pydata-sphinx-theme==0.14.2->-r binder/requirements.txt (line 10)) (2.9.1)
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Requirement already satisfied: packaging in /srv/conda/envs/notebook/lib/python3.8/site-packages (from pydata-sphinx-theme==0.14.2->-r binder/requirements.txt (line 10)) (21.0)
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Requirement already satisfied: six in /srv/conda/envs/notebook/lib/python3.8/site-packages (from chart_studio->-r binder/requirements.txt (line 5)) (1.16.0)
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Requirement already satisfied: python-dateutil>=2.7 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from matplotlib->-r binder/requirements.txt (line 8)) (2.8.2)
Collecting contourpy>=1.0.1
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Collecting importlib-resources>=3.2.0
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Collecting pillow>=6.2.0
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Collecting fonttools>=4.22.0
  Downloading fonttools-4.43.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.4.5-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.2 MB)
Requirement already satisfied: zipp>=3.1.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from importlib-resources>=3.2.0->matplotlib->-r binder/requirements.txt (line 8)) (3.5.0)
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Collecting uc-micro-py
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Installing collected packages: pygments, mdurl, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, more-itertools, markdown-it-py, latexcodec, jmespath, jeepney, importlib-metadata, imagesize, docutils, alabaster, typing-extensions, tabulate, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, mdit-py-plugins, jaraco.classes, importlib-resources, click, botocore, beautifulsoup4, accessible-pygments, wget, uc-micro-py, tqdm, tenacity, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, patool, numpy, myst-parser, msgpack, looseversion, keyrings.alt, keyring, jupyter-cache, iso8601, humanize, filelock, fasteners, distro, colorama, boto, annexremote, zenodo-get, sphinxcontrib-bibtex, sphinx-togglebutton, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, retrying, plotly, pillow, osfclient, myst-nb, linkify-it-py, kiwisolver, gdown, fonttools, datalad, cycler, contourpy, awscli, scipy, repo2data, matplotlib, jupyter-book, chart-studio
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Successfully installed SecretStorage-3.3.3 accessible-pygments-0.0.4 alabaster-0.7.13 annexremote-1.6.3 awscli-1.29.73 beautifulsoup4-4.12.2 boto-2.49.0 botocore-1.31.73 chart-studio-1.1.0 click-8.1.7 colorama-0.4.4 contourpy-1.1.1 cycler-0.12.1 datalad-0.19.3 distro-1.8.0 docutils-0.16 fasteners-0.19 filelock-3.13.0 fonttools-4.43.1 gdown-4.7.1 humanize-4.8.0 imagesize-1.4.1 importlib-metadata-6.8.0 importlib-resources-6.1.0 iso8601-2.1.0 jaraco.classes-3.3.0 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.15.1 jupyter-cache-0.6.1 keyring-24.2.0 keyrings.alt-5.0.0 kiwisolver-1.4.5 latexcodec-2.0.1 linkify-it-py-2.0.2 looseversion-1.3.0 markdown-it-py-2.2.0 matplotlib-3.7.3 mdit-py-plugins-0.3.5 mdurl-0.1.2 more-itertools-10.1.0 msgpack-1.0.7 myst-nb-0.17.2 myst-parser-0.18.1 numpy-1.24.4 osfclient-0.0.5 patool-1.12 pillow-10.1.0 platformdirs-3.11.0 plotly-5.18.0 pyasn1-0.5.0 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.14.2 pygments-2.16.1 python-gitlab-3.15.0 pyyaml-6.0.1 repo2data-2.9.1 requests-toolbelt-1.0.0 retrying-1.3.4 rsa-4.7.2 s3transfer-0.7.0 scipy-1.10.1 snowballstemmer-2.2.0 soupsieve-2.5 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-1.0.4 sphinxcontrib-bibtex-2.5.0 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 tabulate-0.9.0 tenacity-8.2.3 tqdm-4.66.1 typing-extensions-4.8.0 uc-micro-py-1.0.2 wget-3.2 zenodo-get-1.5.0
Removing intermediate container a214f523d6ee
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Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}
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Step 43/51 : LABEL repo2docker.ref="83b26362ed02cc06d8748f6daa8fdb1fec553734"
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{"aux": {"ID": "sha256:fbdefb03e19f0c809ab352f5761bc2b38c31b7a2486909515194a3eb86226eaf"}}Successfully built fbdefb03e19f
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-qmrlab-2dt1-2dbook-2dneurolibre-efea62:83b26362ed02cc06d8748f6daa8fdb1fec553734
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Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-qmrlab-2dt1-2dbook-2dneurolibre-efea62:83b26362ed02cc06d8748f6daa8fdb1fec553734Built image, launching...
Launching server...
Server requested
2023-10-27T21:16:52Z [Normal] Successfully assigned binderhub/jupyter-qmrlab-2dt1-2dbook-2dneurolibre-2dss7iit2m to neurolibre-master
2023-10-27T21:17:13Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-10-27T21:17:19Z [Normal] Created container block-cloud-metadata
2023-10-27T21:17:29Z [Normal] Started container block-cloud-metadata
2023-10-27T21:17:30Z [Normal] Pulling image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-qmrlab-2dt1-2dbook-2dneurolibre-efea62:83b26362ed02cc06d8748f6daa8fdb1fec553734"
2023-10-27T21:18:24Z [Normal] Successfully pulled image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-qmrlab-2dt1-2dbook-2dneurolibre-efea62:83b26362ed02cc06d8748f6daa8fdb1fec553734" in 53.884724159s
2023-10-27T21:18:39Z [Normal] Created container notebook
2023-10-27T21:18:42Z [Normal] Started container notebook
Server ready at /jupyter/user/qmrlab-t1-book-neurolibre-ss7iit2m/
server running at https://test.conp.cloud/jupyter/user/qmrlab-t1-book-neurolibre-ss7iit2m/

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/qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734/_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 'intro'
[etoc] Excluded 3 extra file(s) not in toc
checking bibtex cache... out of date
parsing bibtex file /home/jovyan/paper.bib... parsed 40 entries
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=['html_image', 'amsmath', 'colon_fence', 'deflist', 'dollarmath', 'html_admonition', 'linkify', 'replacements', 'smartquotes', 'substitution'], 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/qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734/_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/qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734/_build/.jupyter_cache
[91mWARNING: The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file.Be aware that `navigation_with_keys = True` has negative accessibility implications:https://github.com/pydata/pydata-sphinx-theme/issues/1492[39;49;00m
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 10 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] 10 added, 0 changed, 0 removed
[01mreading sources... [39;49;00m[ 10%] [35m01/IR_BenefitsAndPitfalls[39;49;00m
/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb: Executed notebook in 3.04 seconds [mystnb]
/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb: Cached executed notebook: ID=1 [mystnb]
[01mreading sources... [39;49;00m[ 20%] [35m01/IR_DataFitting[39;49;00m
/home/jovyan/content/01/IR_DataFitting.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01/IR_DataFitting.ipynb: Executed notebook in 2.39 seconds [mystnb]
/home/jovyan/content/01/IR_DataFitting.ipynb: Cached executed notebook: ID=2 [mystnb]
[01mreading sources... [39;49;00m[ 30%] [35m01/IR_Introduction[39;49;00m
[01mreading sources... [39;49;00m[ 40%] [35m01/IR_OtherMethods[39;49;00m
[01mreading sources... [39;49;00m[ 50%] [35m01/IR_SignalModelling[39;49;00m
/home/jovyan/content/01/IR_SignalModelling.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/01/IR_SignalModelling.ipynb: Executed notebook in 2.51 seconds [mystnb]
/home/jovyan/content/01/IR_SignalModelling.ipynb: Cached executed notebook: ID=3 [mystnb]
[01mreading sources... [39;49;00m[ 60%] [35m02/VFA_BenefitsAndPitfalls[39;49;00m
[01mreading sources... [39;49;00m[ 70%] [35m02/VFA_DataFitting[39;49;00m
/home/jovyan/content/02/VFA_DataFitting.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/02/VFA_DataFitting.ipynb: Executed notebook in 2.25 seconds [mystnb]
/home/jovyan/content/02/VFA_DataFitting.ipynb: Cached executed notebook: ID=4 [mystnb]
[01mreading sources... [39;49;00m[ 80%] [35m02/VFA_Introduction[39;49;00m
[01mreading sources... [39;49;00m[ 90%] [35m02/VFA_SignalModelling[39;49;00m
/home/jovyan/content/02/VFA_SignalModelling.ipynb: Executing notebook using local CWD [mystnb]
[01mreading sources... [39;49;00m[100%] [35mintro[39;49;00m

[91m/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_SignalModelling.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec][39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb: WARNING: Notebook exception traceback saved in: /mnt/books/qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734/_build/html/reports/02/VFA_SignalModelling.err.log [mystnb.exec][39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:90005: WARNING: duplicate label "1" for keys "Boudreau2023" and "Barral2010-qm"[39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:90005: WARNING: duplicate citation for key "Fukushima1981"[39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:90005: WARNING: duplicate label "3" for keys "Stikov2015" and "Pykett1983"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate label "1" for keys "Boudreau2023" and "Drain1949"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate label "2" for keys "Fukushima1981" and "Hahn1949"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate label "3" for keys "Stikov2015" and "Messroghli2004"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate citation for key "Stikov2015"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "1" for keys "Boudreau2023" and "Gai2013"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "2" for keys "Fukushima1981" and "Look1970"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate citation for key "Messroghli2004"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "3" for keys "Stikov2015" and "Messroghli2004"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate citation for key "Piechnik2010"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate citation for key "Stikov2015"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "5" for keys "Pykett1978" and "Stikov2015"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "1" for keys "Boudreau2023" and "Baudrexel2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "2" for keys "Fukushima1981" and "Boudreau2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "3" for keys "Stikov2015" and "Cercignani2005"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "4" for keys "Piechnik2010" and "Lee2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "5" for keys "Pykett1978" and "Li2018"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "6" for keys "Steen1994" and "Liberman2013"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "7" for keys "Stikov2015" and "Lutti2013"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate citation for key "Stikov2015"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "1" for keys "Boudreau2023" and "Chang2008"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "2" for keys "Fukushima1981" and "Deoni2003"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "3" for keys "Stikov2015" and "Gupta1977"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "4" for keys "Piechnik2010" and "Schabel2008"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "5" for keys "Pykett1978" and "Sled1998"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Boudreau2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "1" for keys "Boudreau2023" and "Boudreau2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "2" for keys "Fukushima1981" and "Christensen1974"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Deoni2003"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "3" for keys "Stikov2015" and "Deoni2003"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "4" for keys "Piechnik2010" and "Fram1987"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Gupta1977"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "5" for keys "Pykett1978" and "Gupta1977"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "6" for keys "Steen1994" and "Homer1985"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Lee2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "7" for keys "Stikov2015" and "Lee2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Sled1998"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "8" for keys "Samson2006" and "Sled1998"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "1" for keys "Boudreau2023" and "Handbook2004"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "2" for keys "Fukushima1981" and "Ernst1966"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "3" for keys "Stikov2015" and "Yarnykh2010"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "4" for keys "Piechnik2010" and "Zur1991"[39;49;00m
[91m/home/jovyan/content/intro.md:19: WARNING: duplicate label "1" for keys "Boudreau2023" and "Karakuzu2020-ul"[39;49;00m
[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[ 10%] [32m01/IR_BenefitsAndPitfalls[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/python3.8/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/pydata_sphinx_theme/__init__.py", line 236, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/pydata_sphinx_theme/__init__.py", line 231, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.8/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/python3.8/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 288, in build_update
    self.build(to_build,
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.8/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/python3.8/site-packages/sphinx/builders/html/__init__.py", line 1051, in handle_page
    newtmpl = self.app.emit_firstresult('html-page-context', pagename,
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/application.py", line 457, in emit_firstresult
    return self.events.emit_firstresult(event, *args,
  File "/srv/conda/envs/notebook/lib/python3.8/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/python3.8/site-packages/sphinx/events.py", line 102, in emit
    raise ExtensionError(__("Handler %r for event %r threw an exception") %
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/python3.8/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jupyter_book/cli/main.py", line 317, in build
    builder_specific_actions(
  File "/srv/conda/envs/notebook/lib/python3.8/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.

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

For guidelines, please see the relevant documentation.

@roboneuro build book

🔴 Binder build has failed 🥀

Status: Failed 4bb2dc3e Last updated: 2023-10-27 14:26:07 PDT

:information_source: See details

The next comment will forward the logs

🥀 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
2023-10-27T21:24:47Z [Normal] Successfully assigned binderhub/jupyter-qmrlab-2dt1-2dbook-2dneurolibre-2dyo8t3bap to neurolibre-master
2023-10-27T21:25:04Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-10-27T21:25:13Z [Normal] Created container block-cloud-metadata
2023-10-27T21:25:22Z [Normal] Started container block-cloud-metadata
2023-10-27T21:25:23Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-qmrlab-2dt1-2dbook-2dneurolibre-efea62:83b26362ed02cc06d8748f6daa8fdb1fec553734" already present on machine
2023-10-27T21:25:31Z [Normal] Created container notebook
2023-10-27T21:25:34Z [Normal] Started container notebook
Server ready at /jupyter/user/qmrlab-t1-book-neurolibre-yo8t3bap/
server running at https://test.conp.cloud/jupyter/user/qmrlab-t1-book-neurolibre-yo8t3bap/

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

Jupyter Book build log

Checking if the book will be built...
     content/_config.yml exists.
     /mnt/books/qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734/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

Build source: qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734

Running Jupyter-Book v0.15.1
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734/_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 'intro'
[etoc] Excluded 3 extra file(s) not in toc
checking bibtex cache... out of date
parsing bibtex file /home/jovyan/paper.bib... parsed 40 entries
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=['html_image', 'amsmath', 'colon_fence', 'deflist', 'dollarmath', 'html_admonition', 'linkify', 'replacements', 'smartquotes', 'substitution'], 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/qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734/_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/qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734/_build/.jupyter_cache
[91mWARNING: The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file.Be aware that `navigation_with_keys = True` has negative accessibility implications:https://github.com/pydata/pydata-sphinx-theme/issues/1492[39;49;00m
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 10 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] 10 added, 0 changed, 0 removed
[01mreading sources... [39;49;00m[ 10%] [35m01/IR_BenefitsAndPitfalls[39;49;00m
/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb: Using cached notebook: ID=1 [mystnb]
[01mreading sources... [39;49;00m[ 20%] [35m01/IR_DataFitting[39;49;00m
/home/jovyan/content/01/IR_DataFitting.ipynb: Using cached notebook: ID=2 [mystnb]
[01mreading sources... [39;49;00m[ 30%] [35m01/IR_Introduction[39;49;00m
[01mreading sources... [39;49;00m[ 40%] [35m01/IR_OtherMethods[39;49;00m
[01mreading sources... [39;49;00m[ 50%] [35m01/IR_SignalModelling[39;49;00m
/home/jovyan/content/01/IR_SignalModelling.ipynb: Using cached notebook: ID=3 [mystnb]
[01mreading sources... [39;49;00m[ 60%] [35m02/VFA_BenefitsAndPitfalls[39;49;00m
[01mreading sources... [39;49;00m[ 70%] [35m02/VFA_DataFitting[39;49;00m
/home/jovyan/content/02/VFA_DataFitting.ipynb: Using cached notebook: ID=4 [mystnb]
[01mreading sources... [39;49;00m[ 80%] [35m02/VFA_Introduction[39;49;00m
[01mreading sources... [39;49;00m[ 90%] [35m02/VFA_SignalModelling[39;49;00m
/home/jovyan/content/02/VFA_SignalModelling.ipynb: Executing notebook using local CWD [mystnb]
[01mreading sources... [39;49;00m[100%] [35mintro[39;49;00m

[91m/home/jovyan/content/01/IR_BenefitsAndPitfalls.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/01/IR_SignalModelling.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:1: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec][39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:10002: WARNING: Document headings start at H2, not H1 [myst.header][39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb: WARNING: Notebook exception traceback saved in: /mnt/books/qMRLab/github.com/t1-book-neurolibre/83b26362ed02cc06d8748f6daa8fdb1fec553734/_build/html/reports/02/VFA_SignalModelling.err.log [mystnb.exec][39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:90005: WARNING: duplicate label "1" for keys "Boudreau2023" and "Barral2010-qm"[39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:90005: WARNING: duplicate citation for key "Fukushima1981"[39;49;00m
[91m/home/jovyan/content/01/IR_DataFitting.ipynb:90005: WARNING: duplicate label "3" for keys "Stikov2015" and "Pykett1983"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate label "1" for keys "Boudreau2023" and "Drain1949"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate label "2" for keys "Fukushima1981" and "Hahn1949"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate label "3" for keys "Stikov2015" and "Messroghli2004"[39;49;00m
[91m/home/jovyan/content/01/IR_Introduction.md:27: WARNING: duplicate citation for key "Stikov2015"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "1" for keys "Boudreau2023" and "Gai2013"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "2" for keys "Fukushima1981" and "Look1970"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate citation for key "Messroghli2004"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "3" for keys "Stikov2015" and "Messroghli2004"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate citation for key "Piechnik2010"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate citation for key "Stikov2015"[39;49;00m
[91m/home/jovyan/content/01/IR_OtherMethods.md:10: WARNING: duplicate label "5" for keys "Pykett1978" and "Stikov2015"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "1" for keys "Boudreau2023" and "Baudrexel2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "2" for keys "Fukushima1981" and "Boudreau2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "3" for keys "Stikov2015" and "Cercignani2005"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "4" for keys "Piechnik2010" and "Lee2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "5" for keys "Pykett1978" and "Li2018"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "6" for keys "Steen1994" and "Liberman2013"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate label "7" for keys "Stikov2015" and "Lutti2013"[39;49;00m
[91m/home/jovyan/content/02/VFA_BenefitsAndPitfalls.md:10: WARNING: duplicate citation for key "Stikov2015"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "1" for keys "Boudreau2023" and "Chang2008"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "2" for keys "Fukushima1981" and "Deoni2003"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "3" for keys "Stikov2015" and "Gupta1977"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "4" for keys "Piechnik2010" and "Schabel2008"[39;49;00m
[91m/home/jovyan/content/02/VFA_DataFitting.ipynb:110005: WARNING: duplicate label "5" for keys "Pykett1978" and "Sled1998"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Boudreau2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "1" for keys "Boudreau2023" and "Boudreau2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "2" for keys "Fukushima1981" and "Christensen1974"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Deoni2003"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "3" for keys "Stikov2015" and "Deoni2003"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "4" for keys "Piechnik2010" and "Fram1987"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Gupta1977"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "5" for keys "Pykett1978" and "Gupta1977"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "6" for keys "Steen1994" and "Homer1985"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Lee2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "7" for keys "Stikov2015" and "Lee2017"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate citation for key "Sled1998"[39;49;00m
[91m/home/jovyan/content/02/VFA_Introduction.md:24: WARNING: duplicate label "8" for keys "Samson2006" and "Sled1998"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "1" for keys "Boudreau2023" and "Handbook2004"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "2" for keys "Fukushima1981" and "Ernst1966"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "3" for keys "Stikov2015" and "Yarnykh2010"[39;49;00m
[91m/home/jovyan/content/02/VFA_SignalModelling.ipynb:110005: WARNING: duplicate label "4" for keys "Piechnik2010" and "Zur1991"[39;49;00m
[91m/home/jovyan/content/intro.md:19: WARNING: duplicate label "1" for keys "Boudreau2023" and "Karakuzu2020-ul"[39;49;00m
[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[ 10%] [32m01/IR_BenefitsAndPitfalls[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/python3.8/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/pydata_sphinx_theme/__init__.py", line 236, in update_and_remove_templates
    context[section] = list(filter(_remove_empty_templates, context[section]))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/pydata_sphinx_theme/__init__.py", line 231, in _remove_empty_templates
    rendered = app.builder.templates.render(tname, context)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/jinja2glue.py", line 189, in render
    return self.environment.get_template(template).render(context)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/srv/conda/envs/notebook/lib/python3.8/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/python3.8/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/application.py", line 329, in build
    self.builder.build_update()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 288, in build_update
    self.build(to_build,
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 352, in build
    self.write(docnames, list(updated_docnames), method)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 544, in write
    self._write_serial(sorted(docnames))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 554, in _write_serial
    self.write_doc(docname, doctree)
  File "/srv/conda/envs/notebook/lib/python3.8/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/python3.8/site-packages/sphinx/builders/html/__init__.py", line 1051, in handle_page
    newtmpl = self.app.emit_firstresult('html-page-context', pagename,
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/sphinx/application.py", line 457, in emit_firstresult
    return self.events.emit_firstresult(event, *args,
  File "/srv/conda/envs/notebook/lib/python3.8/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/python3.8/site-packages/sphinx/events.py", line 102, in emit
    raise ExtensionError(__("Handler %r for event %r threw an exception") %
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/python3.8/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jupyter_book/cli/main.py", line 317, in build
    builder_specific_actions(
  File "/srv/conda/envs/notebook/lib/python3.8/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.

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

For guidelines, please see the relevant documentation.

@roboneuro build book

🟢 Successfully built

Status: Success 57212eb6 Last updated: 2023-10-27 14:37:08 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

These build errors are relevant to : https://github.com/pydata/pydata-sphinx-theme/issues/1315#issuecomment-1540862699

Trying to solve it. "It works on my machine" but I think OSX is installing different versions, not a replica of what is pulled in during repo2data.

From the build pod:

From Jinja2 3.0.1 --> 3.1.2 will hopefully resolve this issue.

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for creating a neurolibre masterpiece! With their quantitative T1 MRI reproducible preprint, they've taken the MRI field to new heights, leaving no relaxation behind.

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

@roboneuro build book

🟢 Successfully built

Status: Success f1f230e0 Last updated: 2023-10-27 14:46:22 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors on constructing the neurolibre reproducible preprint (NRP) that quantifies T1 relaxometry using MRI! Your work is truly a "neurolibre-tarian" delight, providing actionable insights with quantifiable precision.

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

@roboneuro build extended pdf

🔴 Extended PDF - Build draft

Status: Failed 1796f7fe Last updated: 2023-10-27 15:07:00 PDT

:information_source: See details

'NoneType' object has no attribute 'strip'

@roboneuro build extended pdf

🔴 Extended PDF - Build draft

Status: Failed 9e947a02 Last updated: 2023-10-27 15:24:12 PDT

:information_source: See details

'NoneType' object has no attribute 'strip'

@roboneuro build extended pdf

🔴 Extended PDF - Build draft

Status: Failed ed1796f8 Last updated: 2023-10-27 15:39:55 PDT

:information_source: See details

'NoneType' object has no attribute 'strip'

@roboneuro build extended pdf

🔴 Extended PDF - Build draft

Status: Failed aca99e5f Last updated: 2023-10-27 15:40:59 PDT

:information_source: See details

listdir: path should be string, bytes, os.PathLike, integer or None, not list

@roboneuro build extended pdf

🟢 Successfully built

Status: Success c822f412 Last updated: 2023-10-27 15:43:29 PDT

:information_source: See details

Roboneuro will post a new comment to share the results and provide an explanation of the next steps.

📑 Extended PDF has been compiled!

For the submitting author

👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.
⬇️ Download the updated paper.md.
⬇️ Download the updated paper.bib.
ℹ️ Please read and confirm the following:

[!IMPORTANT]
We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.
- [ ] I, the submitting author, confirm that I have read the note above.
♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

For the technical screener

Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

:warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

@roboneuro build extended pdf

🟢 Successfully built

Status: Success f37523b1 Last updated: 2023-10-27 15:50:57 PDT

:information_source: See details

Roboneuro will post a new comment to share the results and provide an explanation of the next steps.

📑 Extended PDF has been compiled!

For the submitting author

👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.
⬇️ Download the updated paper.md.
⬇️ Download the updated paper.bib.
ℹ️ Please read and confirm the following:

[!IMPORTANT]
We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.
- [ ] I, the submitting author, confirm that I have read the note above.
♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

For the technical screener

Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

:warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

@roboneuro build extended pdf

🟢 Successfully built

Status: Success 3ca9dfb1 Last updated: 2023-10-27 15:57:09 PDT

:information_source: See details

Roboneuro will post a new comment to share the results and provide an explanation of the next steps.

📑 Extended PDF has been compiled!

For the submitting author

👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.
⬇️ Download the updated paper.md.
⬇️ Download the updated paper.bib.
ℹ️ Please read and confirm the following:

[!IMPORTANT]
We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.
- [ ] I, the submitting author, confirm that I have read the note above.
♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

For the technical screener

Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

:warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

@roboneuro build book

🟢 Successfully built

Status: Success 34373b99 Last updated: 2023-10-30 15:39:18 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for magnetically capturing our attention with their innovative neurolibre reproducible preprint! Their quantitative T1 MRI approach is a neuroscientific masterpiece that will surely relax any doubts about reproducibility in the field.

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

@roboneuro build book

🟢 Successfully built

Status: Success 0b2615a6 Last updated: 2023-10-31 09:22:09 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for embracing the power of neurolibre reproducible preprints (NRPs) and embodying the true meaning of "MRI" - Making Reliable Information! Your quantitative T1 MRI research is undoubtedly a relaxing journey that will bring clarity to the field of neuroimaging.

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

@roboneuro build extended pdf

🟢 Successfully built

Status: Success 14d30e1e Last updated: 2023-10-31 14:18:12 PDT

:information_source: See details

Roboneuro will post a new comment to share the results and provide an explanation of the next steps.

📑 Extended PDF has been compiled!

For the submitting author

👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.
⬇️ Download the updated paper.md.
⬇️ Download the updated paper.bib.
ℹ️ Please read and confirm the following:

[!IMPORTANT]
We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.
- [ ] I, the submitting author, confirm that I have read the note above.
♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

For the technical screener

Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

:warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

neurolibre / neurolibre-reviews