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[REVIEW]: The quest for measuring myelin with MRI - An interactive meta-analysis #4

Closed roboneuro closed 2 years ago

roboneuro commented 2 years ago

Submitting author: @agahkarakuzu (Agah Karakuzu) Repository: https://github.com/Notebook-Factory/myelin-meta-analysis Editor: @emdupre Reviewer: @ltetrel Jupyter Book: http://neurolibre-data-prod.conp.cloud/book-artifacts/roboneurolibre/github.com/myelin-meta-analysis/68ae71f025a2f2a506c72525730f8c44f6a2705d/_build/html/ Repository archive: 10.5281/zenodo.6463433 Data archive: 10.5281/zenodo.6463435 Book archive: 10.5281/zenodo.6463431 Docker archive: 10.5281/zenodo.6463437

Status

status

Status badge code:

HTML: <a href="http://neurolibre.herokuapp.com/papers/eceea8a92584feae6cb1ac67d5eb2a01"><img src="http://neurolibre.herokuapp.com/papers/eceea8a92584feae6cb1ac67d5eb2a01/status.svg"></a>
Markdown: [![status](http://neurolibre.herokuapp.com/papers/eceea8a92584feae6cb1ac67d5eb2a01/status.svg)](http://neurolibre.herokuapp.com/papers/eceea8a92584feae6cb1ac67d5eb2a01)

Testers 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.)

Tester instructions & questions

@ltetrel, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @ltetrel

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ltetrel commented 2 years ago

Which commit are we talking ?

agahkarakuzu commented 2 years ago

The one hyperlinked.

ltetrel commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

roboneuro commented 2 years ago

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

ltetrel commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

roboneuro commented 2 years ago

We ran into a problem building your book. :(

Click here to see build log 

      ["Cloning into '/tmp/repo2dockerd4ody_4k'...\\n", "HEAD is now at bda67f2 Try weird toc paths for book linkings\\n", "Using RBuildPack builder\\n", "Step 1/70 : FROM buildpack-deps:bionic", "\\n", "Fetching base image...\\r", "Fetching base image...\\r", "Fetching base image...\\r", "Fetching base image...\\r", "Fetching base image...\\r", "Fetching base image...\\r", "Fetching base image...\\r", "Fetching base image...\\r", " ---> cb3fc72df6ea\\n", "Step 2/70 : ENV DEBIAN_FRONTEND=noninteractive", "\\n", " ---> Running in 0c3e25873e08\\n", "Removing intermediate container 0c3e25873e08\\n", " ---> fc32fdbb6b0d\\n", "Step 3/70 : 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/*", "\\n", " ---> Running in e6fefb5cf588\\n", "\\u001b[91mdebconf: delaying package configuration, since apt-utils is not installed\\n\\u001b[0m", "Removing intermediate container e6fefb5cf588\\n", " ---> 2f9c625bacae\\n", "Step 4/70 : RUN echo \\\"en_US.UTF-8 UTF-8\\\" > /etc/locale.gen &&     locale-gen", "\\n", " ---> Running in c2b72790fe5b\\n", "Generating locales (this might take a while)...\\n", "  en_US.UTF-8", "...", " done\\n", "Generation complete.\\n", "Removing intermediate container c2b72790fe5b\\n", " ---> 5cc3e57dbb8e\\n", "Step 5/70 : ENV LC_ALL en_US.UTF-8", "\\n", " ---> Running in c14f3c6b1d51\\n", "Removing intermediate container c14f3c6b1d51\\n", " ---> 349fcdd8e2cf\\n", "Step 6/70 : ENV LANG en_US.UTF-8", "\\n", " ---> Running in bf20f4d93a23\\n", "Removing intermediate container bf20f4d93a23\\n", " ---> 736e0440ef9b\\n", "Step 7/70 : ENV LANGUAGE en_US.UTF-8", "\\n", "No such image: sha256:736e0440ef9b0fa28021e519894450bab6417b1b92ffbfa9614f66b7296bc66c", "Built image, launching...\\n"]
agahkarakuzu commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

ltetrel commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

roboneuro commented 2 years ago

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

ltetrel commented 2 years ago

Almost here, not sure why but I am not able to catch book build errors, so it thinks build was successfull:

if jupyter-book build --all --verbose --path-output ${BOOK_DST_PATH} content 2>&1 | tee -a ${BOOK_BUILD_LOG}; then
  echo "Taring book build artifacts..."
  if tar -zcvf ${BOOK_DST_PATH}".tar.gz" ${BOOK_DST_PATH} 2>&1 | tee -a ${BOOK_BUILD_LOG}; then
    touch ${BOOK_BUILT_FLAG}
  fi
ltetrel commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

roboneuro commented 2 years ago

We ran into a problem building your book. :(

Click here to see build log 

      ["Found built imag", "server running at https://binder.conp.cloud/jupyter/user/notebook-factor-n-meta-analysis-mziv35ow/\\n\", \"image\": \"binder-registry.conp.cloud/binder-registry.conp.cloud/binder-notebook-2dfactory-2dmyelin-2dmeta-2danalysis-a6e591:bda67f2462b2b14cb00c70ea949ba2d64fdba6b3\", \"repo_url\": \"https://github.com/Notebook-Factory/myelin-meta-analysis\", \"token\": \"x9gdKmtDTsmpGcQEO1tgLw\", \"binder_ref_url\": \"https://github.com/Notebook-Factory/myelin-meta-analysis/tree/bda67f2462b2b14cb00c70ea949ba2d64fdba6b3\", \"binder_launch_host\": \"https://binder.conp.cloud/\", \"binder_request\": \"v2/gh/Notebook-Factory/myelin-meta-analysis.git/bda67f2462b2b14cb00c70ea949ba2d64fdba6b3\", \"binder_persistent_request\": \"v2/gh/Notebook-Factory/myelin-meta-analysis/bda67f2462b2b14cb00c70ea949ba2d64fdba6b3"]
ltetrel commented 2 years ago

Still some issue with RoboNeuro logs, but at least now it fails as intended! you should double check the build error @agahkarakuzu

agahkarakuzu commented 2 years ago

Hmm that's not even an error message. I'll push another commit and see what it gives!

agahkarakuzu commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

emdupre commented 2 years ago

Hmm that's not even an error message. I'll push another commit and see what it gives!

I think the error message is in the book log, so we'll need to update RoboNeuro to provide both. From a UX perspective it'd be nice to only provide the failing log, but I'm not sure if we have that fine grained reporting yet ?

On Fri., Oct. 29, 2021, 12:04 Agah, @.***> wrote:

Hmm that's not even an error message. I'll push another commit and see what it gives!

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/neurolibre/neurolibre-reviews/issues/4#issuecomment-954863198, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADSSJZZWAO4GZ33KYWX7VWLUJLAZPANCNFSM5GL4SAXQ .

roboneuro commented 2 years ago

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

agahkarakuzu commented 2 years ago

@emdupre indeed the failure was the book build, and I understand why. I was trying to deal with the issue that the _toc is not sitting at the base of the repo, so the links to the notebooks were relative to the content folder, as a result links were not resolving into the notebook path on JB.

I think seeing both logs when one of two things fail is completely OK, even better. So feeding the book log would be enough without much case handling.

ltetrel commented 2 years ago

Hmm that's not even an error message. I'll push another commit and see what it gives! I think the error message is in the book log, so we'll need to update RoboNeuro to provide both. From a UX perspective it'd be nice to only provide the failing log, but I'm not sure if we have that fine grained reporting yet ?

If binder build fails => No jb build log will exists since user does not spawn env. if binder build is ok => Maybe jb failed

So in short, check if jb build log exists.

agahkarakuzu commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

roboneuro commented 2 years ago

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

ltetrel commented 2 years ago

Still wrong path xD

agahkarakuzu commented 2 years ago

@emdupre do you have any idea how to solve this link issue?

The links of the BinderHub launcher look like:

lab/tree/02/closer_look.ipynb

It should be:

lab/tree/content/02/closer_look.ipynb

but in the _toc I cannot add that content, as that's the folder where these contents are. ♺

emdupre commented 2 years ago

Fixed in https://github.com/Notebook-Factory/myelin-meta-analysis/pull/9/files.

You were missing the path_to_book param in your _config file. I also updated your _toc to be compatible with the newest jupyter-book release in the same PR -- feel free to keep or discard that change !

agahkarakuzu commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

roboneuro commented 2 years ago

We ran into a problem building your book. :(

Click here to see build log 

      ["Cloning into '/tmp/repo2dockerxyr4rb02'...\\n", "HEAD is now at 518c8a5 Merge pull request #9 from emdupre/fix/toc-config\\n", "Using RBuildPack builder\\n", "Step 1/73 : FROM buildpack-deps:bionic", "\\n", " ---> cb3fc72df6ea\\n", "Step 2/73 : ENV DEBIAN_FRONTEND=noninteractive", "\\n", " ---> Using cache\\n", " ---> 72acdf6eec08\\n", "Step 3/73 : 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/*", "\\n", " ---> Using cache\\n", " ---> f214f4f3bf44\\n", "Step 4/73 : RUN echo \\\"en_US.UTF-8 UTF-8\\\" > /etc/locale.gen &&     locale-gen", "\\n", " ---> Using cache\\n", " ---> 272e81f97e82\\n", "Step 5/73 : ENV LC_ALL en_US.UTF-8", "\\n", " ---> Using cache\\n", " ---> 1d018c152688\\n", "Step 6/73 : ENV LANG en_US.UTF-8", "\\n", " ---> Using cache\\n", " ---> 6db3fe2db2c9\\n", "Step 7/73 : ENV LANGUAGE en_US.UTF-8", "\\n", " ---> Using cache\\n", " ---> a8006ae656a8\\n", "Step 8/73 : ENV SHELL /bin/bash", "\\n", " ---> Using cache\\n", " ---> c9c153c437dd\\n", "Step 9/73 : ARG NB_USER", "\\n", " ---> Using cache\\n", " ---> 5b3a4e779e3b\\n", "Step 10/73 : ARG NB_UID", "\\n", " ---> Using cache\\n", " ---> 3ac38dfe60a4\\n", "Step 11/73 : ENV USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> ecb84a25dfb6\\n", "Step 12/73 : ENV HOME /home/${NB_USER}", "\\n", " ---> Using cache\\n", " ---> 646007b142dd\\n", "Step 13/73 : 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}", "\\n", " ---> Using cache\\n", " ---> 1a6b5dec6d96\\n", "Step 14/73 : 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", "\\n", " ---> Using cache\\n", " ---> 32b750d70868\\n", "Step 15/73 : 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/*", "\\n", " ---> Using cache\\n", " ---> 0ef56e9173a5\\n", "Step 16/73 : RUN apt-get -qq update &&     apt-get -qq install --yes        libapparmor1        lsb-release        psmisc        sudo        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*", "\\n", " ---> Using cache\\n", " ---> 770576e59ff3\\n", "Step 17/73 : EXPOSE 8888", "\\n", " ---> Using cache\\n", " ---> 130d098cba78\\n", "Step 18/73 : ENV APP_BASE /srv", "\\n", " ---> Using cache\\n", " ---> f037dc2337bb\\n", "Step 19/73 : ENV NPM_DIR ${APP_BASE}/npm", "\\n", " ---> Using cache\\n", " ---> 89c6e559ebe3\\n", "Step 20/73 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc", "\\n", " ---> Using cache\\n", " ---> ecc75a2ccca6\\n", "Step 21/73 : ENV CONDA_DIR ${APP_BASE}/conda", "\\n", " ---> Using cache\\n", " ---> 25135aefdc65\\n", "Step 22/73 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook", "\\n", " ---> Using cache\\n", " ---> ca64ca4ac5b9\\n", "Step 23/73 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock", "\\n", " ---> Using cache\\n", " ---> e5a2e1a1df8c\\n", "Step 24/73 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}", "\\n", " ---> Using cache\\n", " ---> c2a77158ce94\\n", "Step 25/73 : ENV R_LIBS_USER ${APP_BASE}/rlibs", "\\n", " ---> Using cache\\n", " ---> 48e7259d58b4\\n", "Step 26/73 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:/usr/lib/rstudio-server/bin/:${PATH}", "\\n", " ---> Using cache\\n", " ---> 2576e21d417b\\n", "Step 27/73 : 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", "\\n", " ---> Using cache\\n", " ---> 570823594fd9\\n", "Step 28/73 : 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", "\\n", " ---> Using cache\\n", " ---> e398454596b6\\n", "Step 29/73 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash", "\\n", " ---> Using cache\\n", " ---> a557db671811\\n", "Step 30/73 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}", "\\n", " ---> Using cache\\n", " ---> ff5fd376f060\\n", "Step 31/73 : USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> 3202a46189e5\\n", "Step 32/73 : RUN npm config --global set prefix ${NPM_DIR}", "\\n", " ---> Using cache\\n", " ---> 4311133b29a6\\n", "Step 33/73 : USER root", "\\n", " ---> Using cache\\n", " ---> dc4553c7f047\\n", "Step 34/73 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env", "\\n", " ---> Using cache\\n", " ---> 534ae36be864\\n", "Step 35/73 : RUN echo \\\"deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/\\\" > /etc/apt/sources.list.d/r-ubuntu.list", "\\n", " ---> Using cache\\n", " ---> d1170283741f\\n", "Step 36/73 : RUN wget --quiet -O - 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xe298a3a825c0d65dfd57cbb651716619e084dab9' | apt-key add -", "\\n", " ---> Using cache\\n", " ---> f1ea9ba717c2\\n", "Step 37/73 : RUN apt-get update && apt-get install --yes r-base=3.6.1-3bionic      r-base-dev=3.6.1-3bionic      r-recommended=3.6.1-3bionic      libclang-dev && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*", "\\n", " ---> Using cache\\n", " ---> 6bda36dc9369\\n", "Step 38/73 : RUN mkdir -p ${R_LIBS_USER} && chown -R ${NB_USER}:${NB_USER} ${R_LIBS_USER}", "\\n", " ---> Using cache\\n", " ---> 5afa310c67ab\\n", "Step 39/73 : RUN curl --silent --location --fail https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5001-amd64.deb > /tmp/rstudio.deb && echo 'd33881b9ab786c09556c410e7dc477de /tmp/rstudio.deb' | md5sum -c - && apt-get update && apt install -y /tmp/rstudio.deb && rm /tmp/rstudio.deb && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*", "\\n", " ---> Using cache\\n", " ---> b08fa5d2e138\\n", "Step 40/73 : RUN curl --silent --location --fail https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb > /tmp/shiny.deb && echo '9aeef6613e7f58f21c97a4600921340e /tmp/shiny.deb' | md5sum -c - && dpkg -i /tmp/shiny.deb && rm /tmp/shiny.deb", "\\n", " ---> Using cache\\n", " ---> ff887d5f7ff1\\n", "Step 41/73 : USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> b28da5d2d593\\n", "Step 42/73 : RUN pip install --no-cache-dir jupyter-server-proxy==1.4.0 && pip install --no-cache-dir https://github.com/jupyterhub/jupyter-rsession-proxy/archive/d5efed5455870556fc414f30871d0feca675a4b4.zip && pip install --no-cache-dir https://github.com/ryanlovett/jupyter-shiny-proxy/archive/47557dc47e2aeeab490eb5f3eeae414cdde4a6a9.zip && jupyter serverextension enable jupyter_server_proxy --sys-prefix && jupyter nbextension install --py jupyter_server_proxy --sys-prefix && jupyter nbextension enable --py jupyter_server_proxy --sys-prefix", "\\n", " ---> Using cache\\n", " ---> 12991f56f20d\\n", "Step 43/73 : USER root", "\\n", " ---> Using cache\\n", " ---> 03900c3c3b07\\n", "Step 44/73 : RUN install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid", "\\n", " ---> Using cache\\n", " ---> aa337ce344b4\\n", "Step 45/73 : RUN sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && echo \\\"R_LIBS_USER=${R_LIBS_USER}\\\" >> /etc/R/Renviron", "\\n", " ---> Using cache\\n", " ---> fb92a07e90f0\\n", "Step 46/73 : USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> ec5f75efb42e\\n", "Step 47/73 : RUN R --quiet -e \\\"install.packages('devtools', repos='https://mran.microsoft.com/snapshot/2018-02-01', method='libcurl')\\\" && R --quiet -e \\\"devtools::install_github('IRkernel/IRkernel', ref='1.1')\\\" && R --quiet -e \\\"IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')\\\"", "\\n", " ---> Using cache\\n", " ---> db63c10f0160\\n", "Step 48/73 : RUN R --quiet -e \\\"install.packages('shiny', repos='https://mran.microsoft.com/snapshot/2019-04-12', method='libcurl')\\\"", "\\n", " ---> Using cache\\n", " ---> 31f5802b43f2\\n", "Step 49/73 : USER root", "\\n", " ---> Using cache\\n", " ---> 3428c0d0cb59\\n", "Step 50/73 : RUN echo \\\"options(repos = c(CRAN='https://mran.microsoft.com/snapshot/2019-04-12'), download.file.method = 'libcurl')\\\" > /etc/R/Rprofile.site", "\\n", " ---> Using cache\\n", " ---> a3e758c53f70\\n", "Step 51/73 : ARG REPO_DIR=${HOME}", "\\n", " ---> Using cache\\n", " ---> 22598bf923ce\\n", "Step 52/73 : ENV REPO_DIR ${REPO_DIR}", "\\n", " ---> Using cache\\n", " ---> 1c94d91fcbb7\\n", "Step 53/73 : WORKDIR ${REPO_DIR}", "\\n", " ---> Using cache\\n", " ---> 43be1350b5df\\n", "Step 54/73 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}", "\\n", " ---> Using cache\\n", " ---> 6e22474eacae\\n", "Step 55/73 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}", "\\n", " ---> Using cache\\n", " ---> e26c63f6abc7\\n", "Step 56/73 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}", "\\n", " ---> Using cache\\n", " ---> cfe399241740\\n", "Step 57/73 : COPY --chown=1000:1000 src/binder/install.R ${REPO_DIR}/binder/install.R", "\\n", " ---> Using cache\\n", " ---> 7d7f4d80a2c1\\n", "Step 58/73 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt", "\\n", " ---> Using cache\\n", " ---> 0871048b014e\\n", "Step 59/73 : USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> 30b3a1db585c\\n", "Step 60/73 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r \\\"binder/requirements.txt\\\"", "\\n", " ---> Using cache\\n", " ---> a6830ed02c9b\\n", "Step 61/73 : RUN Rscript binder/install.R && touch /tmp/.preassembled || true", "\\n", " ---> Using cache\\n", " ---> 7ff7e3420890\\n", "Step 62/73 : COPY --chown=1000:1000 src/ ${REPO_DIR}", "\\n", " ---> fcd6c39fc00c\\n", "Step 63/73 : USER ${NB_USER}", "\\n", " ---> Running in 42e3ac6799c9\\n", "Removing intermediate container 42e3ac6799c9\\n", " ---> 144f74fe85a9\\n", "Step 64/73 : RUN if [ ! -f /tmp/.preassembled ]; then Rscript binder/install.R; fi", "\\n", " ---> Running in bf5b6fbaec4e\\n", "Removing intermediate container bf5b6fbaec4e\\n", " ---> 75c73819cc3a\\n", "Step 65/73 : LABEL repo2docker.ref=\\\"518c8a57b3612b5c8fe03efab8b76ea6e95b2b47\\\"", "\\n", " ---> Running in aa453d17f4b6\\n", "Removing intermediate container aa453d17f4b6\\n", " ---> c535c4795651\\n", "Step 66/73 : LABEL repo2docker.repo=\\\"https://github.com/Notebook-Factory/myelin-meta-analysis\\\"", "\\n", " ---> Running in 71444cd53627\\n", "Removing intermediate container 71444cd53627\\n", " ---> b35e19c1da78\\n", "Step 67/73 : LABEL repo2docker.version=\\\"2021.08.0\\\"", "\\n", " ---> Running in 29869f935892\\n", "Removing intermediate container 29869f935892\\n", " ---> 8be6f99f39b9\\n", "Step 68/73 : USER ${NB_USER}", "\\n", " ---> Running in 59d63fc25a55\\n", "Removing intermediate container 59d63fc25a55\\n", " ---> 04f8ae619eec\\n", "Step 69/73 : ENV PYTHONUNBUFFERED=1", "\\n", " ---> Running in e21b8a622c75\\n", "Removing intermediate container e21b8a622c75\\n", " ---> 78a43ce8565e\\n", "Step 70/73 : COPY /python3-login /usr/local/bin/python3-login", "\\n", " ---> 9179823f33e8\\n", "Step 71/73 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint", "\\n", " ---> 8fbf65ca249b\\n", "Step 72/73 : ENTRYPOINT [\\\"/usr/local/bin/repo2docker-entrypoint\\\"]", "\\n", " ---> Running in 95b833309d30\\n", "Removing intermediate container 95b833309d30\\n", " ---> 6231b0010ae0\\n", "Step 73/73 : CMD [\\\"jupyter\\\", \\\"notebook\\\", \\\"--ip\\\", \\\"0.0.0.0\\\"]", "\\n", " ---> Running in df40f1823145\\n", "Removing intermediate container df40f1823145\\n", " ---> adbc95f17f9a\\n", "{\\\"aux\\\": {\\\"ID\\\": \\\"sha256:adbc95f17f9ace993d1f35b27d8714daa01028a65b69e38935ae12fe90e41288\\\"}}", "Successfully built adbc95f17f9a\\n", "Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-notebook-2dfactory-2dmyelin-2dmeta-2danalysis-a6e591:518c8a57b3612b5c8fe03efab8b76ea6e95b2b47\\n", "Pushing image\\n\", \"progress\": {\"bcc0f8244d41\": \"Pushed\", \"72e1c9b84ca8\": \"Pushed\", \"b9918c2901c4\": {\"current\": 16112640, \"total\": 64860866}, \"4454bdebeb9c\": \"Layer already exists\", \"446fa2fd60e5\": \"Layer already exists\", \"f89b75246b21\": \"Layer already exists\", \"2baf656695f6\": \"Layer already exists\", \"99cd365777a9\": \"Layer already exists\", \"832cfc31ef5a\": \"Layer already exists\", \"2ebdbffa93fb\": \"Layer already exists\", \"02094ca65671\": \"Layer already exists\", \"a1daca3fba6c\": \"Layer already exists\", \"bc94d28383d7\": \"Layer already exists\", \"b0c8b573027a\": \"Layer already exists\", \"7ce056fa1215\": \"Layer already exists\", \"7d5f01871cf0\": \"Layer already exists\", \"0533efc0b1ce\": \"Layer already exists\", \"0e7d48c24f72\": \"Layer already exists\", \"3d9bb5e7f5bf\": \"Layer already exists\", \"5d60a281ed14\": \"Layer already exists\", \"de1499cf71d8\": \"Layer already exists\", \"2b2226787540\": \"Layer already exists\", \"d1364abfbc46\": \"Layer already exists\", \"57865b2561dc\": \"Layer already exists\", 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agahkarakuzu commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

roboneuro commented 2 years ago

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

agahkarakuzu commented 2 years ago

Thanks @emdupre, now it works! Quite fast 🏎

agahkarakuzu commented 2 years ago

@roboneuro generate nl-notebook

roboneuro commented 2 years ago

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

roboneuro commented 2 years ago

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

ltetrel commented 2 years ago

@emdupre @agahkarakuzu To make sure I re-run all the notebooks for this latest commit. Everything seems to work as expected! It is ready to be pushed on the website.

pbellec commented 2 years ago

are we ready to publish? I think you've been working on pushing the artefacts on zenodo and adding a DOI that way. Is that ready to go or should we wait for that feature to be complete?

ltetrel commented 2 years ago

We should talk about that on another thread. I don't think the DOI is ready, neither the zenodo push, Agah do you have feedback maybe ? An example lookup table is at /DATA/submission_lookup_table on prod

agahkarakuzu commented 2 years ago

@pbellec

... artefacts on zenodo and adding a DOI that way

Those DOIs are intended for non-PDF components, but for PDF DOI minting (crossref), not sure where we are bureaucratically .

@ltetrel if it is not possible to have BinderHub serve a repository from the server (i.e. a repo cloned on the server), I'll draft a pipeline with forking. I'll take a look at the lookup table and let you know, thanks!

emdupre commented 2 years ago

@ltetrel if it is not possible to have BinderHub serve a repository from the server (i.e. a repo cloned on the server),

I don't think we want to fork. We wanted to pull the built artifacts from the test server, no ? Or is that what you meant ?

agahkarakuzu commented 2 years ago

@emdupre even if we pull the artifacts, we'll need the linked repository to serve BindeHub sessions. In that case whenever a session is requested we'll either need a fork on GitHub or a local clone.

emdupre commented 2 years ago

I was under the impression we were going to have a local clone already. I remember I previously confirmed that repo2docker can serve from a local path.

Am I missing other information, here ?

agahkarakuzu commented 2 years ago

I discussed this with Loic previously, that's why I wanted to check in with him to see if he was able to give that a try.

emdupre commented 2 years ago

OK, would be great to have the rationale documented. Per @ltetrel 's suggestion, I've opened https://github.com/neurolibre/roboneuro/issues/19 to continue this discussion and free up this issue for the submission's review !