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https://neurolibre.org
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[REVIEW]: Longitudinal stability of brain and spinal cord quantitative MRI measures #18

Closed roboneuro closed 1 year ago

roboneuro commented 1 year ago

Submitting author: !--author-handle-->@mathieuboudreau<!--end-author-handle-- (Mathieu Boudreau) Repository: https://github.com/courtois-neuromod/anat-processing-paper Branch with paper.md (empty if default branch): main Version: v1.0.0 Editor: !--editor-->@agahkarakuzu<!--end-editor-- Reviewers: !--reviewers-list-->@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00018 Repository archive: 10.5281/zenodo.10038872 Data archive: 10.5281/zenodo.10038874 Book archive: 10.5281/zenodo.10038870 Docker archive: 10.5281/zenodo.10038876

Status

status

Status badge code:

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

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

roboneuro commented 1 year ago

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:

@roboneuro generate pdf
roboneuro commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (995.4 files/s, 102521.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Markdown                          2             20              0             72
Jupyter Notebook                  1              0            685             67
YAML                              4             10             17             49
JSON                              1              0              0              5
Bourne Again Shell                1              0              0              2
--------------------------------------------------------------------------------
SUM:                              9             30            702            195
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
roboneuro commented 1 year ago

Wordcount for paper.md is 735

roboneuro commented 1 year ago

Failed to discover a valid open source license

roboneuro commented 1 year ago

Failed to discover a Statement of need section in paper

roboneuro commented 1 year ago

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

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success ecd30221 Last updated: 2023-10-18 13:46:51 PDT

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors on their neurolibre reproducible preprint (NRP)! With the brain and spinal cord's longitudinal stability at the forefront, they've created an open-source masterpiece that's as slick as a myelin-coated quantitative MRI image.

: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.

agahkarakuzu commented 1 year ago

@mathieuboudreau I'll edit the references, can you lmk if the book looks ok?

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🔴 Binder build has failed 🥀

Status: Failed a437c612 Last updated: 2023-10-18 19:39:40 PDT

:information_source: See details 
The next comment will forward the logs
agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 9e2deb87 Last updated: 2023-10-18 19:36:39 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 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.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. 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.

  5. ♻️ 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 commented 1 year ago

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

BinderHub build log 
Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerahzvk26s'...
HEAD is now at 5b7f816 References, fix issues, customize etc
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
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Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
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Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
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Step 5/53 : ENV LC_ALL en_US.UTF-8
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Step 6/53 : ENV LANG en_US.UTF-8
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Step 7/53 : ENV LANGUAGE en_US.UTF-8
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Step 8/53 : ENV SHELL /bin/bash
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Step 9/53 : ARG NB_USER
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Step 10/53 : ARG NB_UID
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Step 11/53 : ENV USER ${NB_USER}
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Step 12/53 : ENV HOME /home/${NB_USER}
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Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
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Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
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Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
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Step 16/53 : EXPOSE 8888
 ---> Using cache
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Step 17/53 : ENV APP_BASE /srv
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Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
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Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
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Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
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Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
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Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
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Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
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Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
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Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
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Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock
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Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
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Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
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Step 29/53 : USER ${NB_USER}
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Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
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Step 31/53 : USER root
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Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
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Step 33/53 : ARG REPO_DIR=${HOME}
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Step 34/53 : ENV REPO_DIR ${REPO_DIR}
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Step 35/53 : WORKDIR ${REPO_DIR}
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Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
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Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
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Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
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Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
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Step 40/53 : USER ${NB_USER}
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Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
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Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 184dea77d11b
Step 43/53 : LABEL repo2docker.ref="5b7f8161c1a119b9373d2b21d146c72127952c84"
 ---> Running in 2f00b4ce1435
Removing intermediate container 2f00b4ce1435
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Step 44/53 : LABEL repo2docker.repo="https://github.com/courtois-neuromod/anat-processing-paper"
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Step 45/53 : LABEL repo2docker.version="2021.08.0"
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Step 46/53 : USER ${NB_USER}
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Removing intermediate container 854019eb09c8
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Step 47/53 : RUN chmod +x binder/postBuild
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Removing intermediate container d3f733a6513e
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Step 48/53 : RUN ./binder/postBuild
 ---> Running in 84326b80083d
Cloning into 'content/analysis'...
Removing intermediate container 84326b80083d
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Step 49/53 : ENV PYTHONUNBUFFERED=1
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Removing intermediate container b12caab5d53d
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Step 50/53 : COPY /python3-login /usr/local/bin/python3-login
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Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> ec94c93fb1ed
Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in 9e7cc39326f7
Removing intermediate container 9e7cc39326f7
 ---> 1ca7266a67b1
Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in ea447b505dc6
Removing intermediate container ea447b505dc6
 ---> 082624f10ec1
{"aux": {"ID": "sha256:082624f10ec13960765b1477ad6a206de9962b009a054717c8b93470d6a08a8a"}}Successfully built 082624f10ec1
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-courtois-2dneuromod-2danat-2dprocessing-2dpaper-81fe86:5b7f8161c1a119b9373d2b21d146c72127952c84
Pushing image
Pushing image
Pushing image
Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-courtois-2dneuromod-2danat-2dprocessing-2dpaper-81fe86:5b7f8161c1a119b9373d2b21d146c72127952c84Built image, launching...
Launching server...
Server requested
2023-10-19T02:37:16.781586Z [Normal] Successfully assigned binderhub/jupyter-courtois-2dneurom-2drocessing-2dpaper-2d7yluryy8 to neurolibre-master
2023-10-19T02:37:27Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-10-19T02:37:32Z [Normal] Created container block-cloud-metadata
2023-10-19T02:37:34Z [Normal] Started container block-cloud-metadata
2023-10-19T02:37:36Z [Normal] Pulling image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-courtois-2dneuromod-2danat-2dprocessing-2dpaper-81fe86:5b7f8161c1a119b9373d2b21d146c72127952c84"
2023-10-19T02:38:06Z [Normal] Successfully pulled image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-courtois-2dneuromod-2danat-2dprocessing-2dpaper-81fe86:5b7f8161c1a119b9373d2b21d146c72127952c84" in 29.994315459s
2023-10-19T02:38:09Z [Normal] Created container notebook
2023-10-19T02:38:13Z [Normal] Started container notebook
Server ready at /jupyter/user/courtois-neurom-rocessing-paper-7yluryy8/
server running at https://test.conp.cloud/jupyter/user/courtois-neurom-rocessing-paper-7yluryy8/

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

Jupyter Book build log 

Customized book build: traditional paper layout based on index.ipynb
Running Jupyter-Book v0.13.0
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/courtois-neuromod/github.com/anat-processing-paper/5b7f8161c1a119b9373d2b21d146c72127952c84/_build/_page/index/singlehtml
Running Sphinx v4.5.0
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/jovyan/paper.bib... parsed 87 entries
myst v0.15.2: MdParserConfig(renderer='sphinx', commonmark_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], 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', disable_syntax=[], url_schemes=['mailto', 'http', 'https'], heading_anchors=None, heading_slug_func=None, html_meta=[], footnote_transition=True, substitutions=[], sub_delimiters=['{', '}'], words_per_minute=200)
MyST-NB: Excluded Paths: set()
updating environment: MyST-NB: Potential docnames to execute: ['index']
executing outdated notebooks... Executing: /home/jovyan/content/index.ipynb
Execution Succeeded: /home/jovyan/content/index.ipynb
done
[new config] 1 added, 0 changed, 0 removed
reading sources... [100%] index
Merged cached outputs into content/index.ipynb
/home/jovyan/content/index.ipynb:210010: ERROR: Unknown interpreted text role "cite:".

Extension error (sphinxcontrib.bibtex.domain):
Handler  for event 'env-updated' threw an exception (exception: 'Style' object has no attribute 'format_patent')
Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pybtex/style/formatting/__init__.py", line 67, in format_entry
    get_template = getattr(self, 'get_{}_template'.format(entry.type))
AttributeError: 'Style' object has no attribute 'get_patent_template'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinxcontrib/bibtex/domain.py", line 218, in env_updated
    return domain.env_updated()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinxcontrib/bibtex/domain.py", line 343, in env_updated
    self.env.app.config.bibtex_tooltips_style):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinxcontrib/bibtex/domain.py", line 517, in get_formatted_entries
    bibliography.labelprefix + label, entry),
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/pybtex/style/formatting/__init__.py", line 69, in format_entry
    format_method = getattr(self, "format_" + entry.type)
AttributeError: 'Style' object has no attribute 'format_patent'

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

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 163, in build_sphinx
    app.builder.read()
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 413, in read
    for retval in self.events.emit('env-updated', self.env):
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/events.py", line 103, in emit
    (listener.handler, name), exc, modname=modname) from exc
sphinx.errors.ExtensionError: Handler  for event 'env-updated' threw an exception (exception: 'Style' object has no attribute 'format_patent')

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

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 324, in build
    result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 531, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError:
===============================================================================

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

===============================================================================

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.

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success df12644e Last updated: 2023-10-18 19:43:55 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 2cfc201d Last updated: 2023-10-18 19:49:23 PDT

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 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.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. 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.

  5. ♻️ 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 commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for constructing the neurolibre reproducible preprint (NRP)! Their work not only demonstrates the longitudinal stability of quantitative MRI measures, but also opens the "myelin" of open-source possibilities for future neuroimaging research.

: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.

mathieuboudreau commented 1 year ago

@mathieuboudreau I'll edit the references, can you lmk if the book looks ok?

At a quick glance, it the build NeuroLibre book appears to be exactly or very close to the book built by our GitHub Actions CI in that repo!

mathieuboudreau commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 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.
  2. ⬇️ Download the updated paper.md.
  3. ⬇️ Download the updated paper.bib.
  4. 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.
  1. ♻️ 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.

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

Should I ignore this at the moment - ie are you debugging some stuff? (the references don't appear) If so, I'll wait to hear when it's ready for me to do the checklist later

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 485317e3 Last updated: 2023-10-19 05:53:27 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 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.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. 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.

  5. ♻️ 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.

agahkarakuzu commented 1 year ago

Should I ignore this at the moment - ie are you debugging some stuff? (the references don't appear) If so, I'll wait to hear when it's ready for me to do the checklist later

@mathieuboudreau you can ignore them for now. I'll add a "draft" option to that task so that it is not verbose on every request. In the latest one the references are rendered, paper.md was missing paper.bib link.

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success ddabfb62 Last updated: 2023-10-19 10:10:23 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 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.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. 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.

  5. ♻️ 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.

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 9d7ba7d0 Last updated: 2023-10-19 14:07:20 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 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.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. 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.

  5. ♻️ 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.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success e4aa9bb8 Last updated: 2023-10-19 14:46:39 PDT

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for constructing the neurolibre reproducible preprint! With brain and spinal cord quantitative MRI measures in their repertoire, their work is a myelin marvel that brings open-source accessibility to the forefront of neuroscience.

: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.

pbellec commented 1 year ago

still spotted a broken citation, in the section "stability of qMRI measures"

[:cite::`Cohen-Adad2021-so`](https://preview.neurolibre.org/book-artifacts/courtois-neuromod/github.com/anat-processing-paper/23c2c00f0cd3ec8bff1119b5f3ff08ebb5469cd4/_build/_page/index/singlehtml/#id36)
agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 64aa00b3 Last updated: 2023-10-20 07:22:11 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 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.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. 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.

  5. ♻️ 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.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 082cc4ac Last updated: 2023-10-20 07:31:30 PDT

:information_source: See details 
:confetti_ball: Roboneuro will send you the book URL.
roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for constructing the ultimate neuro-travel guide! With their neurolibre reproducible preprint (NRP), they have crafted a brainy roadmap that ensures the longitudinal stability of our neural highways, all while embracing the open-source spirit and unlocking the secrets of myelin relaxation.

: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.

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success d6d298fb Last updated: 2023-10-20 07:35:14 PDT

:information_source: See details 
Roboneuro will post a new comment to share the results and provide an explanation of the next steps.
roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

  1. 👀 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.

  2. ⬇️ Download the updated paper.md.

  3. ⬇️ Download the updated paper.bib.

  4. 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.

  5. ♻️ 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.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

:eyes: Looks like the reproducible preprint you requested has been already built: 

[{"time_added":"2023-10-20 14:30:23 +0000","book_url":"https://preview.neurolibre.org/book-artifacts/courtois-neuromod/github.com/anat-processing-paper/2cc73acc1ade358c0120ecf147cf6d0f3c7dda21/_build/_page/index/singlehtml/","download_url":null}]
agahkarakuzu commented 1 year ago

@pbellec I've fixed that broken reference and also changed the endpoint so that the all narrative content is included. Now the PDF renders footnotes as well.

There are missing DOIs in the bibliography, I will add them. In the meantime, @mathieuboudreau can you proofread and lmk if there is anything you'd like to correct.