Submitting author: !--author-handle-->@mathieuboudreau@pbellec@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00025 Repository archive: 10.5281/zenodo.10844540 Data archive: 10.5281/zenodo.10844542 Book archive: 10.5281/zenodo.10844538 Docker archive: 10.5281/zenodo.10844544

Status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a"><img src="https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a/status.svg)](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a)

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 @pbellec know.

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

Checklists

@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:

@roboneuro generate pdf

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1002/mrm.29528 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.neuroimage.2016.10.009 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/nrneurol.2015.80 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41582-019-0270-5 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0730-725X(01)00300-9 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/jmri.20245 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1118/1.595995 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.10137 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.neuroimage.2017.10.041 is INVALID because of 'https://doi.org/' prefix

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (261.5 files/s, 52371.4 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Jupyter Notebook                  1              0           1013            601
TeX                               1             13              5            237
Markdown                          2             43              0            117
YAML                              4             13             17             62
CSS                               1              6              0             46
Bourne Again Shell                1              7              0             18
JSON                              1              0              0              5
--------------------------------------------------------------------------------
SUM:                             11             82           1035           1086
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

Wordcount for paper.md is 736

@roboneuro build book

🔴 Binder build has failed 🥀

Status: Failed b5ac4850 Last updated: 2024-02-15 02:42:19 PST

: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/repo2dockergv7psj34'...
HEAD is now at 3116b16 Update data to release in this repo instead of depricated repo
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> ae378de4f5b9
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 08a78cfb4049
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> fbceb2a67733
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 3cf70612d1fc
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 54727b822f5d
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> dc588c857c02
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 5e06214b4b44
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> 42ff2be77138
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> bd417f3d3dd4
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> b60430c82d10
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 5e458aff2510
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> a438632f3dc3
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 0942e47ae895
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> bad1e96f449e
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> 73090ab9c46f
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 3a4d18f1d969
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 0475c612f284
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 4a2d8b0fcc6c
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> d1a029699546
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> b14a9e7011ae
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 7bb964d87d10
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 56b69ac27d81
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 55a865e1b0ca
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> d82b4d87d277
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
 ---> Using cache
 ---> d3f1fef730ce
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 9ba1874bc4c7
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 9152c383d252
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 51d7e1747282
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 22ddec68b188
Step 31/53 : USER root
 ---> Using cache
 ---> d5972cb0f670
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 33c7bdbe312e
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 479614e3035e
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 4f3657da5f62
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 9f85fe4764c0
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 932d4b31c401
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 981d892d58f3
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 75c1ad851985
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> cd686d3d3ad1
Step 40/53 : USER ${NB_USER}
 ---> Running in 9e54512930fa
Removing intermediate container 9e54512930fa
 ---> 3d844cef328b
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in 6f905bf80fc9
Collecting jupyter-book==0.13.0
  Downloading jupyter_book-0.13.0-py3-none-any.whl (43 kB)
Collecting plotly
  Downloading plotly-5.18.0-py3-none-any.whl (15.6 MB)
Collecting seaborn
  Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
Collecting markdown
  Downloading Markdown-3.5.2-py3-none-any.whl (103 kB)
Collecting datalad
  Downloading datalad-0.19.6-py3-none-any.whl (1.3 MB)
Collecting matplotlib
  Downloading matplotlib-3.7.4-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (9.2 MB)
Collecting nibabel
  Downloading nibabel-5.2.0-py3-none-any.whl (3.3 MB)
Requirement already satisfied: notebook in /srv/conda/envs/notebook/lib/python3.8/site-packages (from -r binder/requirements.txt (line 8)) (6.3.0)
Collecting numpy
  Downloading numpy-1.24.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
Collecting pandas
  Downloading pandas-2.0.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB)
Collecting scipy
  Downloading scipy-1.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB)
Collecting statsmodels
  Downloading statsmodels-0.14.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (10.9 MB)
Collecting repo2data
  Downloading repo2data-2.9.1-py3-none-any.whl (7.6 kB)
Collecting myst-nb~=0.13.1
  Downloading myst_nb-0.13.2-py3-none-any.whl (41 kB)
Requirement already satisfied: jsonschema<4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.2.0)
Collecting sphinx-comments
  Downloading sphinx_comments-0.0.3-py3-none-any.whl (4.6 kB)
Collecting sphinx-copybutton
  Downloading sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB)
Collecting sphinx-external-toc~=0.2.3
  Downloading sphinx_external_toc-0.2.4-py3-none-any.whl (25 kB)
Requirement already satisfied: Jinja2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.0.1)
Collecting docutils<0.18,>=0.15
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
Collecting sphinx<5,>=4
  Downloading Sphinx-4.5.0-py3-none-any.whl (3.1 MB)
Collecting sphinxcontrib-bibtex<=2.5.0,>=2.2.0
  Downloading sphinxcontrib_bibtex-2.5.0-py3-none-any.whl (39 kB)
Collecting sphinx-jupyterbook-latex~=0.4.6
  Downloading sphinx_jupyterbook_latex-0.4.7-py3-none-any.whl (13 kB)
Collecting sphinx-thebe~=0.1.1
  Downloading sphinx_thebe-0.1.2-py3-none-any.whl (8.3 kB)
Collecting linkify-it-py~=1.0.1
  Downloading linkify_it_py-1.0.3-py3-none-any.whl (19 kB)
Collecting click<9,>=7.1
  Downloading click-8.1.7-py3-none-any.whl (97 kB)
Collecting sphinx-design~=0.1.0
  Downloading sphinx_design-0.1.0-py3-none-any.whl (1.9 MB)
Collecting pyyaml
  Downloading PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (736 kB)
Collecting sphinx-multitoc-numbering~=0.1.3
  Downloading sphinx_multitoc_numbering-0.1.3-py3-none-any.whl (4.6 kB)
Collecting sphinx_book_theme~=0.3.2
  Downloading sphinx_book_theme-0.3.3-py3-none-any.whl (345 kB)
Collecting sphinx_togglebutton
  Downloading sphinx_togglebutton-0.3.2-py3-none-any.whl (8.2 kB)
Collecting tenacity>=6.2.0
  Downloading tenacity-8.2.3-py3-none-any.whl (24 kB)
Requirement already satisfied: packaging in /srv/conda/envs/notebook/lib/python3.8/site-packages (from plotly->-r binder/requirements.txt (line 2)) (21.0)
Requirement already satisfied: importlib-metadata>=4.4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from markdown->-r binder/requirements.txt (line 4)) (4.6.3)
Collecting typing-extensions>=4.0.0
  Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB)
Collecting annexremote
  Downloading annexremote-1.6.4-py3-none-any.whl (25 kB)
Collecting keyring!=23.9.0,>=20.0
  Downloading keyring-24.3.0-py3-none-any.whl (38 kB)
Collecting distro
  Downloading distro-1.9.0-py3-none-any.whl (20 kB)
Collecting tqdm>=4.32.0
  Downloading tqdm-4.66.2-py3-none-any.whl (78 kB)
Collecting looseversion
  Downloading looseversion-1.3.0-py2.py3-none-any.whl (8.2 kB)
Collecting python-gitlab
  Downloading python_gitlab-4.4.0-py3-none-any.whl (138 kB)
Collecting importlib-resources>=3.0
  Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB)
Collecting iso8601
  Downloading iso8601-2.1.0-py3-none-any.whl (7.5 kB)
Requirement already satisfied: chardet>=3.0.4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from datalad->-r binder/requirements.txt (line 5)) (4.0.0)
Collecting fasteners>=0.14
  Downloading fasteners-0.19-py3-none-any.whl (18 kB)
Collecting platformdirs
  Downloading platformdirs-4.2.0-py3-none-any.whl (17 kB)
Collecting patool>=1.7
  Downloading patool-1.12-py2.py3-none-any.whl (77 kB)
Collecting msgpack
  Downloading msgpack-1.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (534 kB)
Collecting humanize
  Downloading humanize-4.9.0-py3-none-any.whl (126 kB)
Collecting keyrings.alt
  Downloading keyrings.alt-5.0.0-py3-none-any.whl (18 kB)
Requirement already satisfied: requests>=1.2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from datalad->-r binder/requirements.txt (line 5)) (2.26.0)
Collecting boto
  Downloading boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting contourpy>=1.0.1
  Downloading contourpy-1.1.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (301 kB)
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: pyparsing>=2.3.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from matplotlib->-r binder/requirements.txt (line 6)) (2.4.7)
Collecting cycler>=0.10
  Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Collecting pillow>=6.2.0
  Downloading pillow-10.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
Collecting fonttools>=4.22.0
  Downloading fonttools-4.48.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)
Requirement already satisfied: python-dateutil>=2.7 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from matplotlib->-r binder/requirements.txt (line 6)) (2.8.2)
Requirement already satisfied: nbconvert in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.0.7)
Requirement already satisfied: ipykernel in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.0.3)
Requirement already satisfied: nbformat in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (5.1.3)
Requirement already satisfied: argon2-cffi in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (20.1.0)
Requirement already satisfied: terminado>=0.8.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (0.10.1)
Requirement already satisfied: jupyter-core>=4.6.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (4.7.1)
Requirement already satisfied: Send2Trash>=1.5.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (1.7.1)
Requirement already satisfied: pyzmq>=17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (22.1.0)
Requirement already satisfied: ipython-genutils in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (0.2.0)
Requirement already satisfied: jupyter-client>=5.3.4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.1.12)
Requirement already satisfied: traitlets>=4.2.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (5.0.5)
Requirement already satisfied: tornado>=6.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.1)
Requirement already satisfied: prometheus-client in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (0.11.0)
Requirement already satisfied: pytz>=2020.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from pandas->-r binder/requirements.txt (line 10)) (2021.1)
Collecting tzdata>=2022.1
  Downloading tzdata-2024.1-py2.py3-none-any.whl (345 kB)
Collecting patsy>=0.5.4
  Downloading patsy-0.5.6-py2.py3-none-any.whl (233 kB)
Collecting packaging
  Downloading packaging-23.2-py3-none-any.whl (53 kB)
Collecting gdown
  Downloading gdown-5.1.0-py3-none-any.whl (17 kB)
Collecting awscli
  Downloading awscli-1.32.42-py3-none-any.whl (4.4 MB)
Collecting zenodo-get
  Downloading zenodo_get-1.5.1-py2.py3-none-any.whl (17 kB)
Collecting osfclient
  Downloading osfclient-0.0.5-py2.py3-none-any.whl (39 kB)
Requirement already satisfied: zipp>=0.5 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from importlib-metadata>=4.4->markdown->-r binder/requirements.txt (line 4)) (3.5.0)
Requirement already satisfied: six>=1.11.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.16.0)
Requirement already satisfied: setuptools in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (49.6.0.post20210108)
Requirement already satisfied: attrs>=17.4.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (21.2.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.17.3)
Collecting jeepney>=0.4.2
  Downloading jeepney-0.8.0-py3-none-any.whl (48 kB)
Collecting importlib-metadata>=4.4
  Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Collecting jaraco.classes
  Downloading jaraco.classes-3.3.1-py3-none-any.whl (6.8 kB)
Collecting SecretStorage>=3.2
  Downloading SecretStorage-3.3.3-py3-none-any.whl (15 kB)
Collecting uc-micro-py
  Downloading uc_micro_py-1.0.3-py3-none-any.whl (6.2 kB)
Collecting jupyter-cache~=0.4.1
  Downloading jupyter_cache-0.4.3-py3-none-any.whl (31 kB)
Requirement already satisfied: ipython in /srv/conda/envs/notebook/lib/python3.8/site-packages (from myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (7.26.0)
Requirement already satisfied: ipywidgets<8,>=7.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (7.6.3)
Collecting jupyter-sphinx~=0.3.2
  Downloading jupyter_sphinx-0.3.2-py3-none-any.whl (20 kB)
Collecting myst-parser~=0.15.2
  Downloading myst_parser-0.15.2-py3-none-any.whl (46 kB)
Requirement already satisfied: widgetsnbextension~=3.5.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipywidgets<8,>=7.0.0->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.5.1)
Requirement already satisfied: jupyterlab-widgets>=1.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipywidgets<8,>=7.0.0->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.0.0)
Requirement already satisfied: debugpy<2.0,>=1.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipykernel->notebook->-r binder/requirements.txt (line 8)) (1.4.1)
Requirement already satisfied: matplotlib-inline<0.2.0,>=0.1.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipykernel->notebook->-r binder/requirements.txt (line 8)) (0.1.2)
Requirement already satisfied: pexpect>4.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (4.8.0)
Requirement already satisfied: jedi>=0.16 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.18.0)
Requirement already satisfied: pygments in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (2.9.0)
Requirement already satisfied: decorator in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (5.0.9)
Requirement already satisfied: backcall in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.2.0)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.0.19)
Requirement already satisfied: pickleshare in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.7.5)
Requirement already satisfied: parso<0.9.0,>=0.8.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jedi>=0.16->ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.8.2)
Requirement already satisfied: sqlalchemy<1.5,>=1.3.12 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.4.22)
Requirement already satisfied: nbclient<0.6,>=0.2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.5.3)
Collecting nbdime
  Downloading nbdime-4.0.1-py3-none-any.whl (5.9 MB)
Collecting markdown-it-py<2.0.0,>=1.0.0
  Downloading markdown_it_py-1.1.0-py3-none-any.whl (83 kB)
Collecting mdit-py-plugins~=0.2.8
  Downloading mdit_py_plugins-0.2.8-py3-none-any.whl (41 kB)
Requirement already satisfied: async-generator in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbclient<0.6,>=0.2->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.10)
Requirement already satisfied: nest-asyncio in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbclient<0.6,>=0.2->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.5.1)
Requirement already satisfied: defusedxml in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.7.1)
Requirement already satisfied: entrypoints>=0.2.2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.3)
Requirement already satisfied: testpath in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.5.0)
Requirement already satisfied: pandocfilters>=1.4.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (1.4.2)
Requirement already satisfied: jupyterlab-pygments in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.1.2)
Requirement already satisfied: bleach in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (3.3.1)
Requirement already satisfied: mistune<2,>=0.8.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.8.4)
Requirement already satisfied: MarkupSafe>=2.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from Jinja2->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (2.0.1)
Requirement already satisfied: ptyprocess>=0.5 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from pexpect>4.3->ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.7.0)
Requirement already satisfied: wcwidth in /srv/conda/envs/notebook/lib/python3.8/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.2.5)
Requirement already satisfied: charset-normalizer~=2.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (2.0.0)
Requirement already satisfied: certifi>=2017.4.17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (2021.5.30)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (1.26.6)
Requirement already satisfied: idna<4,>=2.5 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (3.1)
Requirement already satisfied: cryptography>=2.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (3.4.7)
Requirement already satisfied: cffi>=1.12 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from cryptography>=2.0->SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (1.14.6)
Requirement already satisfied: pycparser in /srv/conda/envs/notebook/lib/python3.8/site-packages (from cffi>=1.12->cryptography>=2.0->SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (2.20)
Collecting alabaster<0.8,>=0.7
  Downloading alabaster-0.7.13-py3-none-any.whl (13 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
Collecting imagesize
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting sphinxcontrib-qthelp
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Requirement already satisfied: babel>=1.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sphinx<5,>=4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (2.9.1)
Collecting sphinxcontrib-serializinghtml>=1.1.5
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Collecting sphinxcontrib-applehelp
  Downloading sphinxcontrib_applehelp-1.0.4-py3-none-any.whl (120 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0
  Downloading sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl (99 kB)
Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting pydata-sphinx-theme~=0.8.0
  Downloading pydata_sphinx_theme-0.8.1-py3-none-any.whl (3.3 MB)
Collecting beautifulsoup4
  Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB)
Requirement already satisfied: wheel in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sphinx_togglebutton->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.36.2)
Collecting pybtex-docutils>=1.0.0
  Downloading pybtex_docutils-1.0.3-py3-none-any.whl (6.4 kB)
Collecting pybtex>=0.24
  Downloading pybtex-0.24.0-py2.py3-none-any.whl (561 kB)
Collecting latexcodec>=1.0.4
  Downloading latexcodec-2.0.1-py2.py3-none-any.whl (18 kB)
Requirement already satisfied: greenlet!=0.4.17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sqlalchemy<1.5,>=1.3.12->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.1.0)
Collecting s3transfer<0.11.0,>=0.10.0
  Downloading s3transfer-0.10.0-py3-none-any.whl (82 kB)
Collecting colorama<0.4.5,>=0.2.5
  Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
Collecting botocore==1.34.42
  Downloading botocore-1.34.42-py3-none-any.whl (12.0 MB)
Collecting docutils<0.18,>=0.15
  Downloading docutils-0.16-py2.py3-none-any.whl (548 kB)
Collecting rsa<4.8,>=3.1.2
  Downloading rsa-4.7.2-py3-none-any.whl (34 kB)
Collecting jmespath<2.0.0,>=0.7.1
  Downloading jmespath-1.0.1-py3-none-any.whl (20 kB)
Collecting pyasn1>=0.1.3
  Downloading pyasn1-0.5.1-py2.py3-none-any.whl (84 kB)
Collecting soupsieve>1.2
  Downloading soupsieve-2.5-py3-none-any.whl (36 kB)
Requirement already satisfied: webencodings in /srv/conda/envs/notebook/lib/python3.8/site-packages (from bleach->nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.5.1)
Collecting filelock
  Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Collecting more-itertools
  Downloading more_itertools-10.2.0-py3-none-any.whl (57 kB)
Collecting jupyter-server-mathjax>=0.2.2
  Downloading jupyter_server_mathjax-0.2.6-py3-none-any.whl (3.1 MB)
Collecting gitpython!=2.1.4,!=2.1.5,!=2.1.6
  Downloading GitPython-3.1.41-py3-none-any.whl (196 kB)
Requirement already satisfied: jupyter-server in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.10.1)
Collecting gitdb<5,>=4.0.1
  Downloading gitdb-4.0.11-py3-none-any.whl (62 kB)
Collecting smmap<6,>=3.0.1
  Downloading smmap-5.0.1-py3-none-any.whl (24 kB)
Requirement already satisfied: websocket-client in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.57.0)
Requirement already satisfied: anyio<4,>=3.1.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.3.0)
Requirement already satisfied: requests-unixsocket in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.2.0)
Requirement already satisfied: sniffio>=1.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from anyio<4,>=3.1.0->jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.2.0)
Collecting requests-toolbelt>=0.10.1
  Downloading requests_toolbelt-1.0.0-py2.py3-none-any.whl (54 kB)
Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (1.7.1)
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=bebd666d278899563178ddceffae86e1b5bf29fd9fc810c42a51ffc016018c16
  Stored in directory: /tmp/pip-ephem-wheel-cache-bdho_ldd/wheels/bd/a8/c3/3cf2c14a1837a4e04bd98631724e81f33f462d86a1d895fae0
Successfully built wget
Installing collected packages: packaging, smmap, gitdb, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, more-itertools, markdown-it-py, latexcodec, jupyter-server-mathjax, jmespath, jeepney, importlib-metadata, imagesize, gitpython, docutils, colorama, alabaster, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, numpy, nbdime, mdit-py-plugins, jaraco.classes, importlib-resources, botocore, beautifulsoup4, wget, uc-micro-py, tzdata, typing-extensions, tqdm, sphinx-togglebutton, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, pillow, patool, myst-parser, msgpack, looseversion, kiwisolver, keyrings.alt, keyring, jupyter-sphinx, jupyter-cache, iso8601, humanize, fonttools, filelock, fasteners, distro, cycler, contourpy, click, boto, annexremote, zenodo-get, tenacity, sphinxcontrib-bibtex, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, scipy, patsy, pandas, osfclient, myst-nb, matplotlib, linkify-it-py, gdown, datalad, awscli, statsmodels, seaborn, repo2data, plotly, nibabel, markdown, jupyter-book
  Attempting uninstall: packaging
    Found existing installation: packaging 21.0
    Uninstalling packaging-21.0:
      Successfully uninstalled packaging-21.0
  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 alabaster-0.7.13 annexremote-1.6.4 awscli-1.32.42 beautifulsoup4-4.12.3 boto-2.49.0 botocore-1.34.42 click-8.1.7 colorama-0.4.4 contourpy-1.1.1 cycler-0.12.1 datalad-0.19.6 distro-1.9.0 docutils-0.16 fasteners-0.19 filelock-3.13.1 fonttools-4.48.1 gdown-5.1.0 gitdb-4.0.11 gitpython-3.1.41 humanize-4.9.0 imagesize-1.4.1 importlib-metadata-7.0.1 importlib-resources-6.1.1 iso8601-2.1.0 jaraco.classes-3.3.1 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.13.0 jupyter-cache-0.4.3 jupyter-server-mathjax-0.2.6 jupyter-sphinx-0.3.2 keyring-24.3.0 keyrings.alt-5.0.0 kiwisolver-1.4.5 latexcodec-2.0.1 linkify-it-py-1.0.3 looseversion-1.3.0 markdown-3.5.2 markdown-it-py-1.1.0 matplotlib-3.7.4 mdit-py-plugins-0.2.8 more-itertools-10.2.0 msgpack-1.0.7 myst-nb-0.13.2 myst-parser-0.15.2 nbdime-4.0.1 nibabel-5.2.0 numpy-1.24.4 osfclient-0.0.5 packaging-23.2 pandas-2.0.3 patool-1.12 patsy-0.5.6 pillow-10.2.0 platformdirs-4.2.0 plotly-5.18.0 pyasn1-0.5.1 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.8.1 python-gitlab-4.4.0 pyyaml-6.0.1 repo2data-2.9.1 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.10.0 scipy-1.10.1 seaborn-0.13.2 smmap-5.0.1 snowballstemmer-2.2.0 soupsieve-2.5 sphinx-4.5.0 sphinx-book-theme-0.3.3 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.1.0 sphinx-external-toc-0.2.4 sphinx-jupyterbook-latex-0.4.7 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.1.2 sphinx-togglebutton-0.3.2 sphinxcontrib-applehelp-1.0.4 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 statsmodels-0.14.1 tenacity-8.2.3 tqdm-4.66.2 typing-extensions-4.9.0 tzdata-2024.1 uc-micro-py-1.0.3 wget-3.2 zenodo-get-1.5.1
Removing intermediate container 6f905bf80fc9
 ---> 48f0784fcf61
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> fd4fd6dbe67b
Step 43/53 : LABEL repo2docker.ref="3116b16edcc00fcb465831d8d8a51f98805d6374"
 ---> Running in 2d9ff712f48f
Removing intermediate container 2d9ff712f48f
 ---> d4b6931a1e3c
Step 44/53 : LABEL repo2docker.repo="https://github.com/shimming-toolbox/rf-shimming-7t"
 ---> Running in f59fc4511ca0
Removing intermediate container f59fc4511ca0
 ---> 30d80299ea5e
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 71d6756eccbc
Removing intermediate container 71d6756eccbc
 ---> e6a165621857
Step 46/53 : USER ${NB_USER}
 ---> Running in 719c78712a9a
Removing intermediate container 719c78712a9a
 ---> 84fd1c625d00
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in 5a70d4006e71
Removing intermediate container 5a70d4006e71
 ---> 35d6c33e0f6e
Step 48/53 : RUN ./binder/postBuild
 ---> Running in 4d785d5b87a6
---- repo2data starting ----
/srv/conda/envs/notebook/lib/python3.8/site-packages/repo2data
Config from file :
../binder/data_requirement.json
Destination:
../data/rf-shimming-7t

File downloaded to: ../data/rf-shimming-7t/ds004906.zip
patool: Extracting ../data/rf-shimming-7t/ds004906.zip ...
patool: ... ../data/rf-shimming-7t/ds004906.zip extracted to `../data/rf-shimming-7t'.
Info : ds004906.zip Decompressed
[91mCloning into '/home/jovyan/content/sct'...
[0m
[0;32m
*******************************
* Welcome to SCT installation *
*******************************
[0m

[0;32mChecking OS type and version...[0m

Linux 4d785d5b87a6 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

[0;32mChecking requirements...[0m

[0;32mOK![0m

SCT version ......... 6.2.dev0
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /home/jovyan/.bashrc

[0;32mSCT will be installed here: [/home/jovyan/content/sct][0m

[0;92m
Do you agree? [y]es/[n]o: [0m
[0;32mSkipping copy of source files (source and destination folders are the same)[0m

[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: [0m
[0;32mDownloading Miniconda...[0m

[0;34mwget -nv -O /tmp/tmp.Fd9nSqpTBQ/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh[0m

2024-02-15 10:25:56 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [141613749/141613749] -> "/tmp/tmp.Fd9nSqpTBQ/miniconda.sh" [1]

[0;32mInstalling Miniconda...[0m

[0;34mbash /tmp/tmp.Fd9nSqpTBQ/miniconda.sh -p /home/jovyan/content/sct/python -b -f[0m

PREFIX=/home/jovyan/content/sct/python
Unpacking payload ...

  0%|          | 0/73 [00:00 conda-forge::ca-certificates-2024.2.2-hbcca054_0 
  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5 
  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5 
  libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5 
  openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0 

The following packages will be SUPERSEDED by a higher-priority channel:

  _libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu 

Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)
Collecting pip!=21.2.*
  Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)
Downloading pip-24.0-py3-none-any.whl (2.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 10.7 MB/s eta 0:00:00
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 23.3.1
    Uninstalling pip-23.3.1:
      Successfully uninstalled pip-23.3.1
Successfully installed pip-24.0

[0;32mInstalling Python dependencies...[0m

[0;32mUsing requirements.txt (git installation)[0m

Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Collecting dipy!=1.6.*,!=1.7.*,!=1.8.* (from -r requirements.txt (line 7))
  Downloading dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.9/7.9 MB 4.2 MB/s eta 0:00:00
Collecting ivadomed (from -r requirements.txt (line 11))
  Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB)
Collecting matplotlib (from -r requirements.txt (line 12))
  Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-5.2.0-py3-none-any.whl.metadata (8.8 kB)
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB)
Collecting nnunetv2 (from -r requirements.txt (line 23))
  Downloading nnunetv2-2.2.1.tar.gz (178 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 178.6/178.6 kB 1.4 MB/s eta 0:00:00
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting numpy<1.24 (from -r requirements.txt (line 27))
  Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 23.4 MB/s eta 0:00:00
Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31))
  Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.2 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting portalocker (from -r requirements.txt (line 33))
  Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)
Collecting psutil (from -r requirements.txt (line 34))
  Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39))
  Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (62.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.4/62.4 MB 9.0 MB/s eta 0:00:00
Collecting pytest (from -r requirements.txt (line 40))
  Downloading pytest-8.0.0-py3-none-any.whl.metadata (7.8 kB)
Collecting pytest-cov (from -r requirements.txt (line 41))
  Downloading pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB)
Collecting requests (from -r requirements.txt (line 42))
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting requirements-parser (from -r requirements.txt (line 43))
  Downloading requirements_parser-0.5.0-py3-none-any.whl (18 kB)
Collecting scipy (from -r requirements.txt (line 44))
  Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 709.4 kB/s eta 0:00:00
Collecting scikit-image (from -r requirements.txt (line 45))
  Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting scikit-learn (from -r requirements.txt (line 46))
  Downloading scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting xlwt (from -r requirements.txt (line 47))
  Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 732.2 kB/s eta 0:00:00
Collecting tqdm (from -r requirements.txt (line 48))
  Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 600.0 kB/s eta 0:00:00
Collecting transforms3d (from -r requirements.txt (line 49))
  Downloading transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB)
Collecting urllib3 (from -r requirements.txt (line 50))
  Downloading urllib3-2.2.0-py3-none-any.whl.metadata (6.4 kB)
Collecting pytest_console_scripts (from -r requirements.txt (line 51))
  Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB)
Collecting pyyaml (from -r requirements.txt (line 52))
  Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting voxelmorph (from -r requirements.txt (line 53))
  Downloading voxelmorph-0.2-py3-none-any.whl (54 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.2/54.2 kB 311.5 kB/s eta 0:00:00
Collecting wquantiles (from -r requirements.txt (line 54))
  Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)
Collecting xlsxwriter (from -r requirements.txt (line 57))
  Downloading XlsxWriter-3.1.9-py3-none-any.whl.metadata (2.6 kB)
Collecting monai[nibabel] (from -r requirements.txt (line 13))
  Downloading monai-1.3.0-202310121228-py3-none-any.whl.metadata (10 kB)
Collecting PyQt5_sip<13,>=4.19.14 (from pyqt5==5.12.3->-r requirements.txt (line 39))
  Downloading PyQt5_sip-12.13.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (504 bytes)
Collecting h5py>=2.8.0 (from dipy!=1.6.*,!=1.7.*,!=1.8.*->-r requirements.txt (line 7))
  Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting pyparsing<3,>=2.0.2 (from ivadomed->-r requirements.txt (line 11))
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.8/67.8 kB 728.0 kB/s eta 0:00:00
Collecting csv-diff>=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading csv_diff-1.1-py3-none-any.whl (12 kB)
Collecting loguru~=0.5 (from ivadomed->-r requirements.txt (line 11))
  Downloading loguru-0.7.2-py3-none-any.whl.metadata (23 kB)
Collecting imageio>=2.31.4 (from ivadomed->-r requirements.txt (line 11))
  Downloading imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB)
Collecting joblib~=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-3.2.2-py3-none-any.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 5.6 MB/s eta 0:00:00
Collecting onnx (from ivadomed->-r requirements.txt (line 11))
  Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (15 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-1.4.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 51.8 MB/s eta 0:00:00
Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading pybids-0.15.5-py3-none-any.whl (14.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.9/14.9 MB 7.3 MB/s eta 0:00:00
Collecting seaborn~=0.11 (from ivadomed->-r requirements.txt (line 11))
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard-2.16.1-py3-none-any.whl.metadata (1.6 kB)
Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 11))
  Downloading torchio-0.19.5-py2.py3-none-any.whl.metadata (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.2/48.2 kB 136.7 kB/s eta 0:00:00
Collecting torch>=1.8.1 (from ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/cpu/torch-2.2.0%2Bcpu-cp39-cp39-linux_x86_64.whl (186.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 186.8/186.8 MB 4.1 MB/s eta 0:00:00
Collecting torchvision>=0.9.1 (from ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.17.0%2Bcpu-cp39-cp39-linux_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 9.7 MB/s eta 0:00:00
Collecting wandb>=0.12.11 (from ivadomed->-r requirements.txt (line 11))
  Downloading wandb-0.16.3-py3-none-any.whl.metadata (9.9 kB)
Collecting contourpy>=1.0.1 (from matplotlib->-r requirements.txt (line 12))
  Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib->-r requirements.txt (line 12))
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading fonttools-4.48.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (158 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 158.9/158.9 kB 315.0 kB/s eta 0:00:00
Collecting kiwisolver>=1.3.1 (from matplotlib->-r requirements.txt (line 12))
  Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.4 kB)
Collecting packaging>=20.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pillow>=8 (from matplotlib->-r requirements.txt (line 12))
  Downloading https://download.pytorch.org/whl/pillow-10.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 16.1 MB/s eta 0:00:00
Collecting python-dateutil>=2.7 (from matplotlib->-r requirements.txt (line 12))
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 2.7 MB/s eta 0:00:00
Collecting importlib-resources>=3.2.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading importlib_resources-6.1.1-py3-none-any.whl.metadata (4.1 kB)
Collecting setuptools (from nibabel->-r requirements.txt (line 21))
  Using cached setuptools-69.1.0-py3-none-any.whl.metadata (6.1 kB)
Collecting lxml (from nilearn->-r requirements.txt (line 22))
  Downloading lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.5 kB)
INFO: pip is looking at multiple versions of nilearn to determine which version is compatible with other requirements. This could take a while.
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.2-py3-none-any.whl.metadata (7.8 kB)
Collecting acvl-utils>=0.2 (from nnunetv2->-r requirements.txt (line 23))
  Downloading acvl_utils-0.2.tar.gz (18 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dynamic-network-architectures>=0.2 (from nnunetv2->-r requirements.txt (line 23))
  Downloading dynamic_network_architectures-0.2.tar.gz (20 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dicom2nifti (from nnunetv2->-r requirements.txt (line 23))
  Downloading dicom2nifti-2.4.10-py3-none-any.whl.metadata (1.3 kB)
Collecting batchgenerators>=0.25 (from nnunetv2->-r requirements.txt (line 23))
  Downloading batchgenerators-0.25.tar.gz (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.7/61.7 kB 59.8 kB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting SimpleITK>=2.2.1 (from nnunetv2->-r requirements.txt (line 23))
  Downloading SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.9 kB)
Collecting graphviz (from nnunetv2->-r requirements.txt (line 23))
  Downloading graphviz-0.20.1-py3-none-any.whl (47 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 kB 893.5 kB/s eta 0:00:00
Collecting tifffile (from nnunetv2->-r requirements.txt (line 23))
  Downloading tifffile-2024.2.12-py3-none-any.whl.metadata (31 kB)
Collecting imagecodecs (from nnunetv2->-r requirements.txt (line 23))
  Downloading imagecodecs-2024.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting yacs (from nnunetv2->-r requirements.txt (line 23))
  Downloading yacs-0.1.8-py3-none-any.whl (14 kB)
Collecting coloredlogs (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.0/46.0 kB 116.4 kB/s eta 0:00:00
Collecting flatbuffers (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading flatbuffers-23.5.26-py2.py3-none-any.whl.metadata (850 bytes)
Collecting protobuf (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading protobuf-4.25.2-cp37-abi3-manylinux2014_x86_64.whl.metadata (541 bytes)
Collecting sympy (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/sympy-1.12-py3-none-any.whl (5.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.7/5.7 MB 24.3 MB/s eta 0:00:00
Collecting pytz>=2020.1 (from pandas->-r requirements.txt (line 32))
  Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting iniconfig (from pytest->-r requirements.txt (line 40))
  Downloading iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Collecting pluggy<2.0,>=1.3.0 (from pytest->-r requirements.txt (line 40))
  Downloading pluggy-1.4.0-py3-none-any.whl.metadata (4.3 kB)
Collecting exceptiongroup>=1.0.0rc8 (from pytest->-r requirements.txt (line 40))
  Downloading exceptiongroup-1.2.0-py3-none-any.whl.metadata (6.6 kB)
Collecting tomli>=1.0.0 (from pytest->-r requirements.txt (line 40))
  Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting coverage>=5.2.1 (from coverage[toml]>=5.2.1->pytest-cov->-r requirements.txt (line 41))
  Downloading coverage-7.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.2 kB)
Collecting charset-normalizer<4,>=2 (from requests->-r requirements.txt (line 42))
  Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests->-r requirements.txt (line 42))
  Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting types-setuptools>=57.0.0 (from requirements-parser->-r requirements.txt (line 43))
  Downloading types_setuptools-69.1.0.20240215-py3-none-any.whl.metadata (1.6 kB)
Collecting networkx>=2.8 (from scikit-image->-r requirements.txt (line 45))
  Downloading https://download.pytorch.org/whl/networkx-3.2.1-py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 5.1 MB/s eta 0:00:00
Collecting lazy_loader>=0.3 (from scikit-image->-r requirements.txt (line 45))
  Downloading lazy_loader-0.3-py3-none-any.whl.metadata (4.3 kB)
Collecting threadpoolctl>=2.0.0 (from scikit-learn->-r requirements.txt (line 46))
  Downloading threadpoolctl-3.3.0-py3-none-any.whl.metadata (13 kB)
Collecting importlib-metadata>=3.6 (from pytest_console_scripts->-r requirements.txt (line 51))
  Downloading importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting neurite>=0.2 (from voxelmorph->-r requirements.txt (line 53))
  Downloading neurite-0.2-py3-none-any.whl (108 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 kB 783.4 kB/s eta 0:00:00
Collecting connected-components-3d (from acvl-utils>=0.2->nnunetv2->-r requirements.txt (line 23))
  Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (29 kB)
Collecting future (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading future-0.18.3.tar.gz (840 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 840.9/840.9 kB 8.9 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting unittest2 (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.4/96.4 kB 305.3 kB/s eta 0:00:00
Collecting click (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting dictdiffer (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB)
Collecting zipp>=0.5 (from importlib-metadata>=3.6->pytest_console_scripts->-r requirements.txt (line 51))
  Downloading zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB)
Collecting six (from neurite>=0.2->voxelmorph->-r requirements.txt (line 53))
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pystrum>=0.2 (from neurite>=0.2->voxelmorph->-r requirements.txt (line 53))
  Downloading pystrum-0.4.tar.gz (17 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting formulaic<0.4,>=0.2.4 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading formulaic-0.3.4-py3-none-any.whl (68 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.2/68.2 kB 147.5 kB/s eta 0:00:00
Collecting sqlalchemy<1.4.0.dev0 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading SQLAlchemy-1.3.24-cp39-cp39-manylinux2010_x86_64.whl (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 6.2 MB/s eta 0:00:00
Collecting bids-validator (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading bids_validator-1.14.0-py3-none-any.whl.metadata (38 kB)
Collecting num2words (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading num2words-0.5.13-py3-none-any.whl.metadata (12 kB)
Collecting absl-py>=0.4 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting grpcio>=1.48.2 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
Collecting markdown>=2.6.8 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading Markdown-3.5.2-py3-none-any.whl.metadata (7.0 kB)
Collecting tensorboard-data-server<0.8.0,>=0.7.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard_data_server-0.7.2-py3-none-any.whl.metadata (1.1 kB)
Collecting tf-keras>=2.15.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tf_keras-2.15.0-py3-none-any.whl.metadata (1.6 kB)
Collecting werkzeug>=1.0.1 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading werkzeug-3.0.1-py3-none-any.whl.metadata (4.1 kB)
Collecting filelock (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB)
Collecting typing-extensions>=4.8.0 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)
Collecting jinja2 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Collecting fsspec (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading fsspec-2024.2.0-py3-none-any.whl.metadata (6.8 kB)
Collecting Deprecated (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)
Collecting humanize (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading humanize-4.9.0-py3-none-any.whl.metadata (7.9 kB)
Collecting typer[all] (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading typer-0.9.0-py3-none-any.whl.metadata (14 kB)
Collecting GitPython!=3.1.29,>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading GitPython-3.1.41-py3-none-any.whl.metadata (14 kB)
Collecting sentry-sdk>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl.metadata (9.7 kB)
Collecting docker-pycreds>=0.4.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Collecting setproctitle (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.9 kB)
Collecting appdirs>=1.4.3 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting humanfriendly>=9.1 (from coloredlogs->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 kB 211.2 kB/s eta 0:00:00
Collecting pydicom>=2.2.0 (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading pydicom-2.4.4-py3-none-any.whl.metadata (7.8 kB)
Collecting python-gdcm (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
Collecting mpmath>=0.19 (from sympy->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 553.5 kB/s eta 0:00:00
Collecting astor>=0.8 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting interface-meta<2.0.0,>=1.2.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading interface_meta-1.3.0-py3-none-any.whl (14 kB)
Collecting wrapt>=1.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting gitdb<5,>=4.0.1 (from GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Collecting MarkupSafe>=2.1.1 (from werkzeug>=1.0.1->tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting docopt>=0.6.2 (from num2words->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting colorama<0.5.0,>=0.4.3 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting shellingham<2.0.0,>=1.3.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting rich<14.0.0,>=10.11.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading rich-13.7.0-py3-none-any.whl.metadata (18 kB)
Collecting argparse (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Collecting traceback2 (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB)
Collecting markdown-it-py>=2.2.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting pygments<3.0.0,>=2.13.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
Collecting linecache2 (from traceback2->unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB)
Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Downloading certifi-2024.2.2-py3-none-any.whl (163 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.8/163.8 kB 944.6 kB/s eta 0:00:00
Downloading ivadomed-2.9.9-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.4/240.4 kB 674.5 kB/s eta 0:00:00
Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 13.3 MB/s eta 0:00:00
Downloading nilearn-0.10.2-py3-none-any.whl (10.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.4/10.4 MB 8.9 MB/s eta 0:00:00
Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.8/6.8 MB 14.1 MB/s eta 0:00:00
Downloading portalocker-2.8.2-py3-none-any.whl (17 kB)
Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 1.2 MB/s eta 0:00:00
Downloading pytest-8.0.0-py3-none-any.whl (334 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 334.0/334.0 kB 904.9 kB/s eta 0:00:00
Downloading pytest_cov-4.1.0-py3-none-any.whl (21 kB)
Downloading requests-2.31.0-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 213.6 kB/s eta 0:00:00
Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.5/38.5 MB 16.7 MB/s eta 0:00:00
Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.7/14.7 MB 22.6 MB/s eta 0:00:00
Downloading scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.1/12.1 MB 27.3 MB/s eta 0:00:00
Downloading tqdm-4.66.2-py3-none-any.whl (78 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.3/78.3 kB 840.7 kB/s eta 0:00:00
Downloading transforms3d-0.4.1-py3-none-any.whl (1.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 11.3 MB/s eta 0:00:00
Downloading urllib3-2.2.0-py3-none-any.whl (120 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.9/120.9 kB 1.9 MB/s eta 0:00:00
Downloading pytest_console_scripts-1.4.1-py3-none-any.whl (10 kB)
Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 738.9/738.9 kB 6.2 MB/s eta 0:00:00
Downloading XlsxWriter-3.1.9-py3-none-any.whl (154 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.8/154.8 kB 1.1 MB/s eta 0:00:00
Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.3/142.3 kB 443.9 kB/s eta 0:00:00
Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (310 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 311.0/311.0 kB 4.6 MB/s eta 0:00:00
Downloading coverage-7.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (233 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.6/233.6 kB 916.2 kB/s eta 0:00:00
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading exceptiongroup-1.2.0-py3-none-any.whl (16 kB)
Downloading fonttools-4.48.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 14.1 MB/s eta 0:00:00
Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 19.8 MB/s eta 0:00:00
Downloading idna-3.6-py3-none-any.whl (61 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 442.3 kB/s eta 0:00:00
Downloading imageio-2.34.0-py3-none-any.whl (313 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 313.4/313.4 kB 3.8 MB/s eta 0:00:00
Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB)
Downloading joblib-1.3.2-py3-none-any.whl (302 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 302.2/302.2 kB 5.6 MB/s eta 0:00:00
Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 12.1 MB/s eta 0:00:00
Downloading lazy_loader-0.3-py3-none-any.whl (9.1 kB)
Downloading loguru-0.7.2-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.5/62.5 kB 2.5 MB/s eta 0:00:00
Downloading packaging-23.2-py3-none-any.whl (53 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.0/53.0 kB 2.3 MB/s eta 0:00:00
Downloading pluggy-1.4.0-py3-none-any.whl (20 kB)
Downloading PyQt5_sip-12.13.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (335 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 335.7/335.7 kB 2.2 MB/s eta 0:00:00
Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 505.5/505.5 kB 2.6 MB/s eta 0:00:00
Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.9/294.9 kB 1.2 MB/s eta 0:00:00
Downloading SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (52.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.7/52.7 MB 12.8 MB/s eta 0:00:00
Downloading tensorboard-2.16.1-py3-none-any.whl (5.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.5/5.5 MB 37.7 MB/s eta 0:00:00
Downloading protobuf-4.25.2-cp37-abi3-manylinux2014_x86_64.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.6/294.6 kB 800.6 kB/s eta 0:00:00
Using cached setuptools-69.1.0-py3-none-any.whl (819 kB)
Downloading threadpoolctl-3.3.0-py3-none-any.whl (17 kB)
Downloading tifffile-2024.2.12-py3-none-any.whl (224 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 224.5/224.5 kB 1.0 MB/s eta 0:00:00
Downloading torchio-0.19.5-py2.py3-none-any.whl (173 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 173.1/173.1 kB 3.7 MB/s eta 0:00:00
Downloading types_setuptools-69.1.0.20240215-py3-none-any.whl (51 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.8/51.8 kB 297.9 kB/s eta 0:00:00
Downloading wandb-0.16.3-py3-none-any.whl (2.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 14.0 MB/s eta 0:00:00
Downloading dicom2nifti-2.4.10-py3-none-any.whl (43 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.6/43.6 kB 572.5 kB/s eta 0:00:00
Downloading flatbuffers-23.5.26-py2.py3-none-any.whl (26 kB)
Downloading imagecodecs-2024.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.7/39.7 MB 17.2 MB/s eta 0:00:00
Downloading lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.0/8.0 MB 26.1 MB/s eta 0:00:00
Downloading monai-1.3.0-202310121228-py3-none-any.whl (1.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 7.0 MB/s eta 0:00:00
Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 36.0 MB/s eta 0:00:00
Downloading absl_py-2.1.0-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.7/133.7 kB 1.0 MB/s eta 0:00:00
Downloading click-8.1.7-py3-none-any.whl (97 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 1.0 MB/s eta 0:00:00
Downloading GitPython-3.1.41-py3-none-any.whl (196 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 196.4/196.4 kB 5.3 MB/s eta 0:00:00
Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 31.1 MB/s eta 0:00:00
Downloading Markdown-3.5.2-py3-none-any.whl (103 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.9/103.9 kB 897.4 kB/s eta 0:00:00
Downloading pydicom-2.4.4-py3-none-any.whl (1.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 32.8 MB/s eta 0:00:00
Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl (257 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 257.9/257.9 kB 505.4 kB/s eta 0:00:00
Downloading tensorboard_data_server-0.7.2-py3-none-any.whl (2.4 kB)
Downloading tf_keras-2.15.0-py3-none-any.whl (1.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 7.1 MB/s eta 0:00:00
Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB)
Downloading werkzeug-3.0.1-py3-none-any.whl (226 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 226.7/226.7 kB 11.5 MB/s eta 0:00:00
Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB)
Downloading bids_validator-1.14.0-py3-none-any.whl (21 kB)
Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 10.3 MB/s eta 0:00:00
Downloading Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB)
Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Downloading fsspec-2024.2.0-py3-none-any.whl (170 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.9/170.9 kB 1.7 MB/s eta 0:00:00
Downloading humanize-4.9.0-py3-none-any.whl (126 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.8/126.8 kB 629.5 kB/s eta 0:00:00
Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 332.8 kB/s eta 0:00:00
Downloading num2words-0.5.13-py3-none-any.whl (143 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.3/143.3 kB 710.5 kB/s eta 0:00:00
Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.0/13.0 MB 12.3 MB/s eta 0:00:00
Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (30 kB)
Downloading gitdb-4.0.11-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.7/62.7 kB 873.2 kB/s eta 0:00:00
Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Downloading rich-13.7.0-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.6/240.6 kB 705.1 kB/s eta 0:00:00
Downloading shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)
Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.1/80.1 kB 728.8 kB/s eta 0:00:00
Downloading typer-0.9.0-py3-none-any.whl (45 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.9/45.9 kB 555.9 kB/s eta 0:00:00
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 141.6 kB/s eta 0:00:00
Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 5.5 MB/s eta 0:00:00
Downloading smmap-5.0.1-py3-none-any.whl (24 kB)
Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, future, docopt
  Building wheel for nnunetv2 (pyproject.toml): started
  Building wheel for nnunetv2 (pyproject.toml): finished with status 'done'
  Created wheel for nnunetv2: filename=nnunetv2-2.2.1-py3-none-any.whl size=237457 sha256=1b947385ff4fcebafeee0317a9bbfe7bb15dc331116d9875f4c5f464c4043ce5
  Stored in directory: /home/jovyan/.cache/pip/wheels/a9/7a/70/acdee60dabd3de1dcce9e5b13c6abb0215a20e034e7e8118c7
  Building wheel for acvl-utils (setup.py): started
  Building wheel for acvl-utils (setup.py): finished with status 'done'
  Created wheel for acvl-utils: filename=acvl_utils-0.2-py3-none-any.whl size=22438 sha256=cfe25fb7aed728cfbe30eb12d12b185fa856da4b877d9dc1dedd6ccbfe53499f
  Stored in directory: /home/jovyan/.cache/pip/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7
  Building wheel for batchgenerators (setup.py): started
  Building wheel for batchgenerators (setup.py): finished with status 'done'
  Created wheel for batchgenerators: filename=batchgenerators-0.25-py3-none-any.whl size=89008 sha256=8ae81eb6486465b079687e82be13a5c3730be2d1791da7c8641868aaca2497d8
  Stored in directory: /home/jovyan/.cache/pip/wheels/41/e7/c9/91b1589e2a08ad83bdd96b0beb3a496effda855580ef698568
  Building wheel for dynamic-network-architectures (setup.py): started
  Building wheel for dynamic-network-architectures (setup.py): finished with status 'done'
  Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.2-py3-none-any.whl size=27245 sha256=2e4819b9ed1fcca3857d858e54c4c1b7f67b690157c531571cf09c3eed8d8537
  Stored in directory: /home/jovyan/.cache/pip/wheels/4e/c0/70/740949411012a24276008fa6e920f42701ae6fa18ce6122eb5
  Building wheel for pystrum (setup.py): started
  Building wheel for pystrum (setup.py): finished with status 'done'
  Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19533 sha256=b959af28bc15e0ef1ce76ef68d4f570e647f1926b5229d072469b3a7e79fd0df
  Stored in directory: /home/jovyan/.cache/pip/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492024 sha256=f0ce2e69fddafa745552c517ae34a70aaad10a7e470a4d2dae07336fe9e6d373
  Stored in directory: /home/jovyan/.cache/pip/wheels/bf/5d/6a/2e53874f7ec4e2bede522385439531fafec8fafe005b5c3d1b
  Building wheel for docopt (setup.py): started
  Building wheel for docopt (setup.py): finished with status 'done'
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=4657c8ea432b2bfa2bd128d8f8a113fc329b44d09d8dbba53e86253483a6bc37
  Stored in directory: /home/jovyan/.cache/pip/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b
Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum future docopt
Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tf-keras, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, PyQt5_sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed
Successfully installed Deprecated-1.2.14 GitPython-3.1.41 MarkupSafe-2.1.5 PyQt5_sip-12.13.0 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.1 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.2 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.48.1 formulaic-0.3.4 fsspec-2024.2.0 future-0.18.3 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.60.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.1 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.2.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.0 packaging-23.2 pandas-1.4.4 pillow-10.2.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.2 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-2.4.7 pyqt5-5.12.3 pystrum-0.4 pytest-8.0.0 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.0 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.4 setproctitle-1.3.3 setuptools-68.2.2 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.1 tensorboard-data-server-0.7.2 tf-keras-2.15.0 threadpoolctl-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.0+cpu torchio-0.19.5 torchvision-0.17.0+cpu tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240215 typing-extensions-4.9.0 unittest2-1.1.0 urllib3-2.2.0 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.1.9 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0

[0;32mInstalling spinalcordtoolbox...[0m

Obtaining file:///home/jovyan/content/sct
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-6.2.dev0

[0;32mCreating launchers for Python scripts...[0m

[0;32mInstalling binaries...[0m

[0;34msct_download_data -d binaries_linux -k[0m

--
Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)

sct_download_data -d binaries_linux -k
--

Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz
Downloading: spinalcordtoolbox-binaries_linux.tar.gz

Status:   0%|          | 0.00/83.7M [00:00 034b7c549c0f
Step 49/53 : ENV PYTHONUNBUFFERED=1
 ---> Running in a44ea4f558f4
Removing intermediate container a44ea4f558f4
 ---> 1fbce215a846
Step 50/53 : COPY /python3-login /usr/local/bin/python3-login
 ---> de81665bdba8
Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> 3c0b2c1dacf0
Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in b2a8ac757f00
Removing intermediate container b2a8ac757f00
 ---> 5ad1c1370c7c
Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in f15fa369c30c
Removing intermediate container f15fa369c30c
 ---> 7cd85151c78a
{"aux": {"ID": "sha256:7cd85151c78ac2a6c5d4a1820828c41b6cecb491c2bfc4e6452c73e17697d581"}}Successfully built 7cd85151c78a
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-shimming-2dtoolbox-2drf-2dshimming-2d7t-406654:3116b16edcc00fcb465831d8d8a51f98805d6374
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
received unexpected HTTP status: 500 Internal Server Error

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

I could not find any book log for shimming-toolbox/rf-shimming-7t at 3116b16edcc00fcb465831d8d8a51f98805d6374

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

For guidelines, please see the relevant documentation.

@mathieuboudreau this error is due to built image size, nothing on your end. I am working on it.

Update: OK, now the registry is behind nginx with a generous upload limit, let's see!

@roboneuro build book

🔴 Binder build has failed 🥀

Status: Failed 4e356305 Last updated: 2024-02-15 04:49:26 PST

: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/repo2dockerzqkm_ub7'...
HEAD is now at 3116b16 Update data to release in this repo instead of depricated repo
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 4b304d0760ef
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 7f1b7259e459
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 7bb3d08f1de8
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 809b33e2cf15
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 4d00855d4ac4
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> e0eb756531cb
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> e08d1a12464e
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> a62ae68913e8
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 93b9c163c81a
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 97d1693ed76c
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 8daf0d2d790c
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 4eda22e52ebf
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 4a0588a11031
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3916bc471288
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> f3bda1e3877d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 86a774284ed1
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> d5211a98f273
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e2f328dd7a4e
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> e3a9180d2511
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 3954f09301c7
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5ea52513ec0f
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 995ff224d88d
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 9b184daf53f4
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b270ac4976f5
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
 ---> Using cache
 ---> c686d3b638a4
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 78d0bdd256b4
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> e38b8fcb0fbd
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 35dbdf6176db
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 77ef363567fb
Step 31/53 : USER root
 ---> Using cache
 ---> 9848a0cccf77
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 4e3241167052
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> fee82a54343b
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 4fb91435c67e
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> be3e63cb11d8
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 4f20431eee2a
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 40e55985010d
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 5971166c5297
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> 17d6eea84084
Step 40/53 : USER ${NB_USER}
 ---> Running in 3469264d3b66
Removing intermediate container 3469264d3b66
 ---> f7275c32720b
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Running in bf16a21c1a5d
Collecting jupyter-book==0.13.0
  Downloading jupyter_book-0.13.0-py3-none-any.whl (43 kB)
Collecting plotly
  Downloading plotly-5.18.0-py3-none-any.whl (15.6 MB)
Collecting seaborn
  Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
Collecting markdown
  Downloading Markdown-3.5.2-py3-none-any.whl (103 kB)
Collecting datalad
  Downloading datalad-0.19.6-py3-none-any.whl (1.3 MB)
Collecting matplotlib
  Downloading matplotlib-3.7.4-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (9.2 MB)
Collecting nibabel
  Downloading nibabel-5.2.0-py3-none-any.whl (3.3 MB)
Requirement already satisfied: notebook in /srv/conda/envs/notebook/lib/python3.8/site-packages (from -r binder/requirements.txt (line 8)) (6.3.0)
Collecting numpy
  Downloading numpy-1.24.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
Collecting pandas
  Downloading pandas-2.0.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB)
Collecting scipy
  Downloading scipy-1.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB)
Collecting statsmodels
  Downloading statsmodels-0.14.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (10.9 MB)
Collecting repo2data
  Downloading repo2data-2.9.1-py3-none-any.whl (7.6 kB)
Collecting sphinx-copybutton
  Downloading sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB)
Collecting sphinx_togglebutton
  Downloading sphinx_togglebutton-0.3.2-py3-none-any.whl (8.2 kB)
Collecting sphinx_book_theme~=0.3.2
  Downloading sphinx_book_theme-0.3.3-py3-none-any.whl (345 kB)
Collecting sphinx-jupyterbook-latex~=0.4.6
  Downloading sphinx_jupyterbook_latex-0.4.7-py3-none-any.whl (13 kB)
Collecting sphinxcontrib-bibtex<=2.5.0,>=2.2.0
  Downloading sphinxcontrib_bibtex-2.5.0-py3-none-any.whl (39 kB)
Collecting pyyaml
  Downloading PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (736 kB)
Collecting sphinx-design~=0.1.0
  Downloading sphinx_design-0.1.0-py3-none-any.whl (1.9 MB)
Collecting sphinx-comments
  Downloading sphinx_comments-0.0.3-py3-none-any.whl (4.6 kB)
Collecting sphinx-multitoc-numbering~=0.1.3
  Downloading sphinx_multitoc_numbering-0.1.3-py3-none-any.whl (4.6 kB)
Collecting linkify-it-py~=1.0.1
  Downloading linkify_it_py-1.0.3-py3-none-any.whl (19 kB)
Collecting myst-nb~=0.13.1
  Downloading myst_nb-0.13.2-py3-none-any.whl (41 kB)
Collecting docutils<0.18,>=0.15
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
Collecting sphinx<5,>=4
  Downloading Sphinx-4.5.0-py3-none-any.whl (3.1 MB)
Collecting sphinx-thebe~=0.1.1
  Downloading sphinx_thebe-0.1.2-py3-none-any.whl (8.3 kB)
Requirement already satisfied: jsonschema<4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.2.0)
Collecting click<9,>=7.1
  Downloading click-8.1.7-py3-none-any.whl (97 kB)
Requirement already satisfied: Jinja2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.0.1)
Collecting sphinx-external-toc~=0.2.3
  Downloading sphinx_external_toc-0.2.4-py3-none-any.whl (25 kB)
Requirement already satisfied: packaging in /srv/conda/envs/notebook/lib/python3.8/site-packages (from plotly->-r binder/requirements.txt (line 2)) (21.0)
Collecting tenacity>=6.2.0
  Downloading tenacity-8.2.3-py3-none-any.whl (24 kB)
Requirement already satisfied: importlib-metadata>=4.4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from markdown->-r binder/requirements.txt (line 4)) (4.6.3)
Collecting msgpack
  Downloading msgpack-1.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (534 kB)
Collecting annexremote
  Downloading annexremote-1.6.4-py3-none-any.whl (25 kB)
Collecting patool>=1.7
  Downloading patool-1.12-py2.py3-none-any.whl (77 kB)
Collecting looseversion
  Downloading looseversion-1.3.0-py2.py3-none-any.whl (8.2 kB)
Collecting fasteners>=0.14
  Downloading fasteners-0.19-py3-none-any.whl (18 kB)
Collecting humanize
  Downloading humanize-4.9.0-py3-none-any.whl (126 kB)
Collecting importlib-resources>=3.0
  Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB)
Collecting boto
  Downloading boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting keyring!=23.9.0,>=20.0
  Downloading keyring-24.3.0-py3-none-any.whl (38 kB)
Collecting python-gitlab
  Downloading python_gitlab-4.4.0-py3-none-any.whl (138 kB)
Collecting platformdirs
  Downloading platformdirs-4.2.0-py3-none-any.whl (17 kB)
Requirement already satisfied: chardet>=3.0.4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from datalad->-r binder/requirements.txt (line 5)) (4.0.0)
Collecting keyrings.alt
  Downloading keyrings.alt-5.0.0-py3-none-any.whl (18 kB)
Collecting distro
  Downloading distro-1.9.0-py3-none-any.whl (20 kB)
Requirement already satisfied: requests>=1.2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from datalad->-r binder/requirements.txt (line 5)) (2.26.0)
Collecting tqdm>=4.32.0
  Downloading tqdm-4.66.2-py3-none-any.whl (78 kB)
Collecting iso8601
  Downloading iso8601-2.1.0-py3-none-any.whl (7.5 kB)
Collecting typing-extensions>=4.0.0
  Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB)
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: python-dateutil>=2.7 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from matplotlib->-r binder/requirements.txt (line 6)) (2.8.2)
Requirement already satisfied: pyparsing>=2.3.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from matplotlib->-r binder/requirements.txt (line 6)) (2.4.7)
Collecting cycler>=0.10
  Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Collecting contourpy>=1.0.1
  Downloading contourpy-1.1.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (301 kB)
Collecting pillow>=6.2.0
  Downloading pillow-10.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
Collecting fonttools>=4.22.0
  Downloading fonttools-4.48.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)
Requirement already satisfied: argon2-cffi in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (20.1.0)
Requirement already satisfied: jupyter-core>=4.6.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (4.7.1)
Requirement already satisfied: pyzmq>=17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (22.1.0)
Requirement already satisfied: prometheus-client in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (0.11.0)
Requirement already satisfied: nbformat in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (5.1.3)
Requirement already satisfied: nbconvert in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.0.7)
Requirement already satisfied: ipython-genutils in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (0.2.0)
Requirement already satisfied: jupyter-client>=5.3.4 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.1.12)
Requirement already satisfied: ipykernel in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.0.3)
Requirement already satisfied: Send2Trash>=1.5.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (1.7.1)
Requirement already satisfied: terminado>=0.8.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (0.10.1)
Requirement already satisfied: tornado>=6.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (6.1)
Requirement already satisfied: traitlets>=4.2.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from notebook->-r binder/requirements.txt (line 8)) (5.0.5)
Requirement already satisfied: pytz>=2020.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from pandas->-r binder/requirements.txt (line 10)) (2021.1)
Collecting tzdata>=2022.1
  Downloading tzdata-2024.1-py2.py3-none-any.whl (345 kB)
Collecting patsy>=0.5.4
  Downloading patsy-0.5.6-py2.py3-none-any.whl (233 kB)
Collecting packaging
  Downloading packaging-23.2-py3-none-any.whl (53 kB)
Collecting osfclient
  Downloading osfclient-0.0.5-py2.py3-none-any.whl (39 kB)
Collecting gdown
  Downloading gdown-5.1.0-py3-none-any.whl (17 kB)
Collecting awscli
  Downloading awscli-1.32.42-py3-none-any.whl (4.4 MB)
Collecting zenodo-get
  Downloading zenodo_get-1.5.1-py2.py3-none-any.whl (17 kB)
Requirement already satisfied: zipp>=0.5 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from importlib-metadata>=4.4->markdown->-r binder/requirements.txt (line 4)) (3.5.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.17.3)
Requirement already satisfied: attrs>=17.4.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (21.2.0)
Requirement already satisfied: setuptools in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (49.6.0.post20210108)
Requirement already satisfied: six>=1.11.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jsonschema<4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.16.0)
Collecting jeepney>=0.4.2
  Downloading jeepney-0.8.0-py3-none-any.whl (48 kB)
Collecting SecretStorage>=3.2
  Downloading SecretStorage-3.3.3-py3-none-any.whl (15 kB)
Collecting importlib-metadata>=4.4
  Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Collecting jaraco.classes
  Downloading jaraco.classes-3.3.1-py3-none-any.whl (6.8 kB)
Collecting uc-micro-py
  Downloading uc_micro_py-1.0.3-py3-none-any.whl (6.2 kB)
Requirement already satisfied: ipywidgets<8,>=7.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (7.6.3)
Collecting myst-parser~=0.15.2
  Downloading myst_parser-0.15.2-py3-none-any.whl (46 kB)
Requirement already satisfied: ipython in /srv/conda/envs/notebook/lib/python3.8/site-packages (from myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (7.26.0)
Collecting jupyter-cache~=0.4.1
  Downloading jupyter_cache-0.4.3-py3-none-any.whl (31 kB)
Collecting jupyter-sphinx~=0.3.2
  Downloading jupyter_sphinx-0.3.2-py3-none-any.whl (20 kB)
Requirement already satisfied: widgetsnbextension~=3.5.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipywidgets<8,>=7.0.0->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.5.1)
Requirement already satisfied: jupyterlab-widgets>=1.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipywidgets<8,>=7.0.0->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.0.0)
Requirement already satisfied: debugpy<2.0,>=1.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipykernel->notebook->-r binder/requirements.txt (line 8)) (1.4.1)
Requirement already satisfied: matplotlib-inline<0.2.0,>=0.1.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipykernel->notebook->-r binder/requirements.txt (line 8)) (0.1.2)
Requirement already satisfied: backcall in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.2.0)
Requirement already satisfied: decorator in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (5.0.9)
Requirement already satisfied: pickleshare in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.7.5)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.0.19)
Requirement already satisfied: pygments in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (2.9.0)
Requirement already satisfied: pexpect>4.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (4.8.0)
Requirement already satisfied: jedi>=0.16 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.18.0)
Requirement already satisfied: parso<0.9.0,>=0.8.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jedi>=0.16->ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.8.2)
Requirement already satisfied: sqlalchemy<1.5,>=1.3.12 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.4.22)
Requirement already satisfied: nbclient<0.6,>=0.2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.5.3)
Collecting nbdime
  Downloading nbdime-4.0.1-py3-none-any.whl (5.9 MB)
Collecting mdit-py-plugins~=0.2.8
  Downloading mdit_py_plugins-0.2.8-py3-none-any.whl (41 kB)
Collecting markdown-it-py<2.0.0,>=1.0.0
  Downloading markdown_it_py-1.1.0-py3-none-any.whl (83 kB)
Requirement already satisfied: nest-asyncio in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbclient<0.6,>=0.2->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.5.1)
Requirement already satisfied: async-generator in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbclient<0.6,>=0.2->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.10)
Requirement already satisfied: defusedxml in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.7.1)
Requirement already satisfied: testpath in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.5.0)
Requirement already satisfied: mistune<2,>=0.8.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.8.4)
Requirement already satisfied: bleach in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (3.3.1)
Requirement already satisfied: pandocfilters>=1.4.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (1.4.2)
Requirement already satisfied: entrypoints>=0.2.2 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.3)
Requirement already satisfied: jupyterlab-pygments in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.1.2)
Requirement already satisfied: MarkupSafe>=2.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from Jinja2->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (2.0.1)
Requirement already satisfied: ptyprocess>=0.5 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from pexpect>4.3->ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.7.0)
Requirement already satisfied: wcwidth in /srv/conda/envs/notebook/lib/python3.8/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.2.5)
Requirement already satisfied: certifi>=2017.4.17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (2021.5.30)
Requirement already satisfied: charset-normalizer~=2.0.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (2.0.0)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (1.26.6)
Requirement already satisfied: idna<4,>=2.5 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (3.1)
Requirement already satisfied: cryptography>=2.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (3.4.7)
Requirement already satisfied: cffi>=1.12 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from cryptography>=2.0->SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (1.14.6)
Requirement already satisfied: pycparser in /srv/conda/envs/notebook/lib/python3.8/site-packages (from cffi>=1.12->cryptography>=2.0->SecretStorage>=3.2->keyring!=23.9.0,>=20.0->datalad->-r binder/requirements.txt (line 5)) (2.20)
Collecting sphinxcontrib-qthelp
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.5
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
Collecting imagesize
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting alabaster<0.8,>=0.7
  Downloading alabaster-0.7.13-py3-none-any.whl (13 kB)
Requirement already satisfied: babel>=1.3 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sphinx<5,>=4->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (2.9.1)
Collecting sphinxcontrib-applehelp
  Downloading sphinxcontrib_applehelp-1.0.4-py3-none-any.whl (120 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0
  Downloading sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl (99 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
Collecting pydata-sphinx-theme~=0.8.0
  Downloading pydata_sphinx_theme-0.8.1-py3-none-any.whl (3.3 MB)
Collecting beautifulsoup4
  Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB)
Requirement already satisfied: wheel in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sphinx_togglebutton->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.36.2)
Collecting pybtex>=0.24
  Downloading pybtex-0.24.0-py2.py3-none-any.whl (561 kB)
Collecting pybtex-docutils>=1.0.0
  Downloading pybtex_docutils-1.0.3-py3-none-any.whl (6.4 kB)
Collecting latexcodec>=1.0.4
  Downloading latexcodec-2.0.1-py2.py3-none-any.whl (18 kB)
Requirement already satisfied: greenlet!=0.4.17 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from sqlalchemy<1.5,>=1.3.12->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.1.0)
Collecting docutils<0.18,>=0.15
  Downloading docutils-0.16-py2.py3-none-any.whl (548 kB)
Collecting s3transfer<0.11.0,>=0.10.0
  Downloading s3transfer-0.10.0-py3-none-any.whl (82 kB)
Collecting colorama<0.4.5,>=0.2.5
  Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
Collecting rsa<4.8,>=3.1.2
  Downloading rsa-4.7.2-py3-none-any.whl (34 kB)
Collecting botocore==1.34.42
  Downloading botocore-1.34.42-py3-none-any.whl (12.0 MB)
Collecting jmespath<2.0.0,>=0.7.1
  Downloading jmespath-1.0.1-py3-none-any.whl (20 kB)
Collecting pyasn1>=0.1.3
  Downloading pyasn1-0.5.1-py2.py3-none-any.whl (84 kB)
Collecting soupsieve>1.2
  Downloading soupsieve-2.5-py3-none-any.whl (36 kB)
Requirement already satisfied: webencodings in /srv/conda/envs/notebook/lib/python3.8/site-packages (from bleach->nbconvert->notebook->-r binder/requirements.txt (line 8)) (0.5.1)
Collecting filelock
  Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Collecting more-itertools
  Downloading more_itertools-10.2.0-py3-none-any.whl (57 kB)
Requirement already satisfied: jupyter-server in /srv/conda/envs/notebook/lib/python3.8/site-packages (from nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.10.1)
Collecting jupyter-server-mathjax>=0.2.2
  Downloading jupyter_server_mathjax-0.2.6-py3-none-any.whl (3.1 MB)
Collecting gitpython!=2.1.4,!=2.1.5,!=2.1.6
  Downloading GitPython-3.1.41-py3-none-any.whl (196 kB)
Collecting gitdb<5,>=4.0.1
  Downloading gitdb-4.0.11-py3-none-any.whl (62 kB)
Collecting smmap<6,>=3.0.1
  Downloading smmap-5.0.1-py3-none-any.whl (24 kB)
Requirement already satisfied: requests-unixsocket in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.2.0)
Requirement already satisfied: anyio<4,>=3.1.0 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (3.3.0)
Requirement already satisfied: websocket-client in /srv/conda/envs/notebook/lib/python3.8/site-packages (from jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (0.57.0)
Requirement already satisfied: sniffio>=1.1 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from anyio<4,>=3.1.0->jupyter-server->nbdime->jupyter-cache~=0.4.1->myst-nb~=0.13.1->jupyter-book==0.13.0->-r binder/requirements.txt (line 1)) (1.2.0)
Collecting requests-toolbelt>=0.10.1
  Downloading requests_toolbelt-1.0.0-py2.py3-none-any.whl (54 kB)
Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /srv/conda/envs/notebook/lib/python3.8/site-packages (from requests>=1.2->datalad->-r binder/requirements.txt (line 5)) (1.7.1)
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=748d64a9ab54fef0bbd3173eace4639a8e8d0ace37a00765219edf5cfe00d4c3
  Stored in directory: /tmp/pip-ephem-wheel-cache-m0r69j9m/wheels/bd/a8/c3/3cf2c14a1837a4e04bd98631724e81f33f462d86a1d895fae0
Successfully built wget
Installing collected packages: packaging, smmap, gitdb, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, snowballstemmer, pyyaml, more-itertools, markdown-it-py, latexcodec, jupyter-server-mathjax, jmespath, jeepney, importlib-metadata, imagesize, gitpython, docutils, colorama, alabaster, sphinx, SecretStorage, requests-toolbelt, pybtex, pyasn1, numpy, nbdime, mdit-py-plugins, jaraco.classes, importlib-resources, botocore, beautifulsoup4, wget, uc-micro-py, tzdata, typing-extensions, tqdm, sphinx-togglebutton, s3transfer, rsa, python-gitlab, pydata-sphinx-theme, pybtex-docutils, platformdirs, pillow, patool, myst-parser, msgpack, looseversion, kiwisolver, keyrings.alt, keyring, jupyter-sphinx, jupyter-cache, iso8601, humanize, fonttools, filelock, fasteners, distro, cycler, contourpy, click, boto, annexremote, zenodo-get, tenacity, sphinxcontrib-bibtex, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, sphinx-book-theme, scipy, patsy, pandas, osfclient, myst-nb, matplotlib, linkify-it-py, gdown, datalad, awscli, statsmodels, seaborn, repo2data, plotly, nibabel, markdown, jupyter-book
  Attempting uninstall: packaging
    Found existing installation: packaging 21.0
    Uninstalling packaging-21.0:
      Successfully uninstalled packaging-21.0
  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 alabaster-0.7.13 annexremote-1.6.4 awscli-1.32.42 beautifulsoup4-4.12.3 boto-2.49.0 botocore-1.34.42 click-8.1.7 colorama-0.4.4 contourpy-1.1.1 cycler-0.12.1 datalad-0.19.6 distro-1.9.0 docutils-0.16 fasteners-0.19 filelock-3.13.1 fonttools-4.48.1 gdown-5.1.0 gitdb-4.0.11 gitpython-3.1.41 humanize-4.9.0 imagesize-1.4.1 importlib-metadata-7.0.1 importlib-resources-6.1.1 iso8601-2.1.0 jaraco.classes-3.3.1 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.13.0 jupyter-cache-0.4.3 jupyter-server-mathjax-0.2.6 jupyter-sphinx-0.3.2 keyring-24.3.0 keyrings.alt-5.0.0 kiwisolver-1.4.5 latexcodec-2.0.1 linkify-it-py-1.0.3 looseversion-1.3.0 markdown-3.5.2 markdown-it-py-1.1.0 matplotlib-3.7.4 mdit-py-plugins-0.2.8 more-itertools-10.2.0 msgpack-1.0.7 myst-nb-0.13.2 myst-parser-0.15.2 nbdime-4.0.1 nibabel-5.2.0 numpy-1.24.4 osfclient-0.0.5 packaging-23.2 pandas-2.0.3 patool-1.12 patsy-0.5.6 pillow-10.2.0 platformdirs-4.2.0 plotly-5.18.0 pyasn1-0.5.1 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.8.1 python-gitlab-4.4.0 pyyaml-6.0.1 repo2data-2.9.1 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.10.0 scipy-1.10.1 seaborn-0.13.2 smmap-5.0.1 snowballstemmer-2.2.0 soupsieve-2.5 sphinx-4.5.0 sphinx-book-theme-0.3.3 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.1.0 sphinx-external-toc-0.2.4 sphinx-jupyterbook-latex-0.4.7 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.1.2 sphinx-togglebutton-0.3.2 sphinxcontrib-applehelp-1.0.4 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 statsmodels-0.14.1 tenacity-8.2.3 tqdm-4.66.2 typing-extensions-4.9.0 tzdata-2024.1 uc-micro-py-1.0.3 wget-3.2 zenodo-get-1.5.1
Removing intermediate container bf16a21c1a5d
 ---> d1ac2e317c84
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 6d844373e9f7
Step 43/53 : LABEL repo2docker.ref="3116b16edcc00fcb465831d8d8a51f98805d6374"
 ---> Running in 0b567743cad5
Removing intermediate container 0b567743cad5
 ---> e2be33fd595b
Step 44/53 : LABEL repo2docker.repo="https://github.com/shimming-toolbox/rf-shimming-7t"
 ---> Running in e5f2fddecd39
Removing intermediate container e5f2fddecd39
 ---> b4b8e931c8d0
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 8aa62b89a846
Removing intermediate container 8aa62b89a846
 ---> dee41d5c058a
Step 46/53 : USER ${NB_USER}
 ---> Running in 0ec3ab6b5c29
Removing intermediate container 0ec3ab6b5c29
 ---> cfecd99cc710
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in 786adce18938
Removing intermediate container 786adce18938
 ---> 65529961e529
Step 48/53 : RUN ./binder/postBuild
 ---> Running in 4ed497b87397
---- repo2data starting ----
/srv/conda/envs/notebook/lib/python3.8/site-packages/repo2data
Config from file :
../binder/data_requirement.json
Destination:
../data/rf-shimming-7t

File downloaded to: ../data/rf-shimming-7t/ds004906.zip
patool: Extracting ../data/rf-shimming-7t/ds004906.zip ...
patool: ... ../data/rf-shimming-7t/ds004906.zip extracted to `../data/rf-shimming-7t'.
Info : ds004906.zip Decompressed
[91mCloning into '/home/jovyan/content/sct'...
[0m
[0;32m
*******************************
* Welcome to SCT installation *
*******************************
[0m

[0;32mChecking OS type and version...[0m

Linux 4ed497b87397 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

[0;32mChecking requirements...[0m

[0;32mOK![0m

SCT version ......... 6.2.dev0
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /home/jovyan/.bashrc

[0;32mSCT will be installed here: [/home/jovyan/content/sct][0m

[0;92m
Do you agree? [y]es/[n]o: [0m
[0;32mSkipping copy of source files (source and destination folders are the same)[0m

[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: [0m
[0;32mDownloading Miniconda...[0m

[0;34mwget -nv -O /tmp/tmp.Fdc2SXT4NL/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh[0m

2024-02-15 12:39:36 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [141613749/141613749] -> "/tmp/tmp.Fdc2SXT4NL/miniconda.sh" [1]

[0;32mInstalling Miniconda...[0m

[0;34mbash /tmp/tmp.Fdc2SXT4NL/miniconda.sh -p /home/jovyan/content/sct/python -b -f[0m

PREFIX=/home/jovyan/content/sct/python
Unpacking payload ...

  0%|          | 0/73 [00:00 conda-forge::ca-certificates-2024.2.2-hbcca054_0 
  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5 
  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5 
  libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5 
  openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0 

The following packages will be SUPERSEDED by a higher-priority channel:

  _libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu 

Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)
Collecting pip!=21.2.*
  Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)
Downloading pip-24.0-py3-none-any.whl (2.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 3.8 MB/s eta 0:00:00
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 23.3.1
    Uninstalling pip-23.3.1:
      Successfully uninstalled pip-23.3.1
Successfully installed pip-24.0

[0;32mInstalling Python dependencies...[0m

[0;32mUsing requirements.txt (git installation)[0m

Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Collecting dipy!=1.6.*,!=1.7.*,!=1.8.* (from -r requirements.txt (line 7))
  Downloading dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.9/7.9 MB 16.4 MB/s eta 0:00:00
Collecting ivadomed (from -r requirements.txt (line 11))
  Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB)
Collecting matplotlib (from -r requirements.txt (line 12))
  Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-5.2.0-py3-none-any.whl.metadata (8.8 kB)
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB)
Collecting nnunetv2 (from -r requirements.txt (line 23))
  Downloading nnunetv2-2.2.1.tar.gz (178 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 178.6/178.6 kB 1.7 MB/s eta 0:00:00
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting numpy<1.24 (from -r requirements.txt (line 27))
  Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 12.7 MB/s eta 0:00:00
Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31))
  Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.2 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting portalocker (from -r requirements.txt (line 33))
  Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)
Collecting psutil (from -r requirements.txt (line 34))
  Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39))
  Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (62.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.4/62.4 MB 7.6 MB/s eta 0:00:00
Collecting pytest (from -r requirements.txt (line 40))
  Downloading pytest-8.0.0-py3-none-any.whl.metadata (7.8 kB)
Collecting pytest-cov (from -r requirements.txt (line 41))
  Downloading pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB)
Collecting requests (from -r requirements.txt (line 42))
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting requirements-parser (from -r requirements.txt (line 43))
  Downloading requirements_parser-0.5.0-py3-none-any.whl (18 kB)
Collecting scipy (from -r requirements.txt (line 44))
  Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 57.3 kB/s eta 0:00:00
Collecting scikit-image (from -r requirements.txt (line 45))
  Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting scikit-learn (from -r requirements.txt (line 46))
  Downloading scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting xlwt (from -r requirements.txt (line 47))
  Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 209.5 kB/s eta 0:00:00
Collecting tqdm (from -r requirements.txt (line 48))
  Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 158.4 kB/s eta 0:00:00
Collecting transforms3d (from -r requirements.txt (line 49))
  Downloading transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB)
Collecting urllib3 (from -r requirements.txt (line 50))
  Downloading urllib3-2.2.0-py3-none-any.whl.metadata (6.4 kB)
Collecting pytest_console_scripts (from -r requirements.txt (line 51))
  Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB)
Collecting pyyaml (from -r requirements.txt (line 52))
  Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting voxelmorph (from -r requirements.txt (line 53))
  Downloading voxelmorph-0.2-py3-none-any.whl (54 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.2/54.2 kB 512.0 kB/s eta 0:00:00
Collecting wquantiles (from -r requirements.txt (line 54))
  Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)
Collecting xlsxwriter (from -r requirements.txt (line 57))
  Downloading XlsxWriter-3.1.9-py3-none-any.whl.metadata (2.6 kB)
Collecting monai[nibabel] (from -r requirements.txt (line 13))
  Downloading monai-1.3.0-202310121228-py3-none-any.whl.metadata (10 kB)
Collecting PyQt5_sip<13,>=4.19.14 (from pyqt5==5.12.3->-r requirements.txt (line 39))
  Downloading PyQt5_sip-12.13.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (504 bytes)
Collecting h5py>=2.8.0 (from dipy!=1.6.*,!=1.7.*,!=1.8.*->-r requirements.txt (line 7))
  Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting pyparsing<3,>=2.0.2 (from ivadomed->-r requirements.txt (line 11))
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.8/67.8 kB 297.1 kB/s eta 0:00:00
Collecting csv-diff>=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading csv_diff-1.1-py3-none-any.whl (12 kB)
Collecting loguru~=0.5 (from ivadomed->-r requirements.txt (line 11))
  Downloading loguru-0.7.2-py3-none-any.whl.metadata (23 kB)
Collecting imageio>=2.31.4 (from ivadomed->-r requirements.txt (line 11))
  Downloading imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB)
Collecting joblib~=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-3.2.2-py3-none-any.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 10.3 MB/s eta 0:00:00
Collecting onnx (from ivadomed->-r requirements.txt (line 11))
  Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (15 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-1.4.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 12.2 MB/s eta 0:00:00
Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading pybids-0.15.5-py3-none-any.whl (14.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.9/14.9 MB 11.9 MB/s eta 0:00:00
Collecting seaborn~=0.11 (from ivadomed->-r requirements.txt (line 11))
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard-2.16.1-py3-none-any.whl.metadata (1.6 kB)
Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 11))
  Downloading torchio-0.19.5-py2.py3-none-any.whl.metadata (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.2/48.2 kB 135.3 kB/s eta 0:00:00
Collecting torch>=1.8.1 (from ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/cpu/torch-2.2.0%2Bcpu-cp39-cp39-linux_x86_64.whl (186.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 186.8/186.8 MB 4.0 MB/s eta 0:00:00
Collecting torchvision>=0.9.1 (from ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.17.0%2Bcpu-cp39-cp39-linux_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 2.5 MB/s eta 0:00:00
Collecting wandb>=0.12.11 (from ivadomed->-r requirements.txt (line 11))
  Downloading wandb-0.16.3-py3-none-any.whl.metadata (9.9 kB)
Collecting contourpy>=1.0.1 (from matplotlib->-r requirements.txt (line 12))
  Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib->-r requirements.txt (line 12))
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading fonttools-4.48.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (158 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 158.9/158.9 kB 1.3 MB/s eta 0:00:00
Collecting kiwisolver>=1.3.1 (from matplotlib->-r requirements.txt (line 12))
  Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.4 kB)
Collecting packaging>=20.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pillow>=8 (from matplotlib->-r requirements.txt (line 12))
  Downloading https://download.pytorch.org/whl/pillow-10.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 28.9 MB/s eta 0:00:00
Collecting python-dateutil>=2.7 (from matplotlib->-r requirements.txt (line 12))
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 2.4 MB/s eta 0:00:00
Collecting importlib-resources>=3.2.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading importlib_resources-6.1.1-py3-none-any.whl.metadata (4.1 kB)
Collecting setuptools (from nibabel->-r requirements.txt (line 21))
  Using cached setuptools-69.1.0-py3-none-any.whl.metadata (6.1 kB)
Collecting lxml (from nilearn->-r requirements.txt (line 22))
  Downloading lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.5 kB)
INFO: pip is looking at multiple versions of nilearn to determine which version is compatible with other requirements. This could take a while.
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.2-py3-none-any.whl.metadata (7.8 kB)
Collecting acvl-utils>=0.2 (from nnunetv2->-r requirements.txt (line 23))
  Downloading acvl_utils-0.2.tar.gz (18 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dynamic-network-architectures>=0.2 (from nnunetv2->-r requirements.txt (line 23))
  Downloading dynamic_network_architectures-0.2.tar.gz (20 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dicom2nifti (from nnunetv2->-r requirements.txt (line 23))
  Downloading dicom2nifti-2.4.10-py3-none-any.whl.metadata (1.3 kB)
Collecting batchgenerators>=0.25 (from nnunetv2->-r requirements.txt (line 23))
  Downloading batchgenerators-0.25.tar.gz (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.7/61.7 kB 96.5 kB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting SimpleITK>=2.2.1 (from nnunetv2->-r requirements.txt (line 23))
  Downloading SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.9 kB)
Collecting graphviz (from nnunetv2->-r requirements.txt (line 23))
  Downloading graphviz-0.20.1-py3-none-any.whl (47 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 kB 401.8 kB/s eta 0:00:00
Collecting tifffile (from nnunetv2->-r requirements.txt (line 23))
  Downloading tifffile-2024.2.12-py3-none-any.whl.metadata (31 kB)
Collecting imagecodecs (from nnunetv2->-r requirements.txt (line 23))
  Downloading imagecodecs-2024.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting yacs (from nnunetv2->-r requirements.txt (line 23))
  Downloading yacs-0.1.8-py3-none-any.whl (14 kB)
Collecting coloredlogs (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.0/46.0 kB 512.0 kB/s eta 0:00:00
Collecting flatbuffers (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading flatbuffers-23.5.26-py2.py3-none-any.whl.metadata (850 bytes)
Collecting protobuf (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading protobuf-4.25.2-cp37-abi3-manylinux2014_x86_64.whl.metadata (541 bytes)
Collecting sympy (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/sympy-1.12-py3-none-any.whl (5.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.7/5.7 MB 10.9 MB/s eta 0:00:00
Collecting pytz>=2020.1 (from pandas->-r requirements.txt (line 32))
  Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting iniconfig (from pytest->-r requirements.txt (line 40))
  Downloading iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Collecting pluggy<2.0,>=1.3.0 (from pytest->-r requirements.txt (line 40))
  Downloading pluggy-1.4.0-py3-none-any.whl.metadata (4.3 kB)
Collecting exceptiongroup>=1.0.0rc8 (from pytest->-r requirements.txt (line 40))
  Downloading exceptiongroup-1.2.0-py3-none-any.whl.metadata (6.6 kB)
Collecting tomli>=1.0.0 (from pytest->-r requirements.txt (line 40))
  Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting coverage>=5.2.1 (from coverage[toml]>=5.2.1->pytest-cov->-r requirements.txt (line 41))
  Downloading coverage-7.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.2 kB)
Collecting charset-normalizer<4,>=2 (from requests->-r requirements.txt (line 42))
  Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests->-r requirements.txt (line 42))
  Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting types-setuptools>=57.0.0 (from requirements-parser->-r requirements.txt (line 43))
  Downloading types_setuptools-69.1.0.20240215-py3-none-any.whl.metadata (1.6 kB)
Collecting networkx>=2.8 (from scikit-image->-r requirements.txt (line 45))
  Downloading https://download.pytorch.org/whl/networkx-3.2.1-py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 7.3 MB/s eta 0:00:00
Collecting lazy_loader>=0.3 (from scikit-image->-r requirements.txt (line 45))
  Downloading lazy_loader-0.3-py3-none-any.whl.metadata (4.3 kB)
Collecting threadpoolctl>=2.0.0 (from scikit-learn->-r requirements.txt (line 46))
  Downloading threadpoolctl-3.3.0-py3-none-any.whl.metadata (13 kB)
Collecting importlib-metadata>=3.6 (from pytest_console_scripts->-r requirements.txt (line 51))
  Downloading importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting neurite>=0.2 (from voxelmorph->-r requirements.txt (line 53))
  Downloading neurite-0.2-py3-none-any.whl (108 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 kB 271.8 kB/s eta 0:00:00
Collecting connected-components-3d (from acvl-utils>=0.2->nnunetv2->-r requirements.txt (line 23))
  Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (29 kB)
Collecting future (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading future-0.18.3.tar.gz (840 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 840.9/840.9 kB 1.8 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting unittest2 (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.4/96.4 kB 180.7 kB/s eta 0:00:00
Collecting click (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting dictdiffer (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB)
Collecting zipp>=0.5 (from importlib-metadata>=3.6->pytest_console_scripts->-r requirements.txt (line 51))
  Downloading zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB)
Collecting six (from neurite>=0.2->voxelmorph->-r requirements.txt (line 53))
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pystrum>=0.2 (from neurite>=0.2->voxelmorph->-r requirements.txt (line 53))
  Downloading pystrum-0.4.tar.gz (17 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting formulaic<0.4,>=0.2.4 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading formulaic-0.3.4-py3-none-any.whl (68 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.2/68.2 kB 72.4 kB/s eta 0:00:00
Collecting sqlalchemy<1.4.0.dev0 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading SQLAlchemy-1.3.24-cp39-cp39-manylinux2010_x86_64.whl (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 3.7 MB/s eta 0:00:00
Collecting bids-validator (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading bids_validator-1.14.0-py3-none-any.whl.metadata (38 kB)
Collecting num2words (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading num2words-0.5.13-py3-none-any.whl.metadata (12 kB)
Collecting absl-py>=0.4 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting grpcio>=1.48.2 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
Collecting markdown>=2.6.8 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading Markdown-3.5.2-py3-none-any.whl.metadata (7.0 kB)
Collecting tensorboard-data-server<0.8.0,>=0.7.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard_data_server-0.7.2-py3-none-any.whl.metadata (1.1 kB)
Collecting tf-keras>=2.15.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tf_keras-2.15.0-py3-none-any.whl.metadata (1.6 kB)
Collecting werkzeug>=1.0.1 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading werkzeug-3.0.1-py3-none-any.whl.metadata (4.1 kB)
Collecting filelock (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB)
Collecting typing-extensions>=4.8.0 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)
Collecting jinja2 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Collecting fsspec (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading fsspec-2024.2.0-py3-none-any.whl.metadata (6.8 kB)
Collecting Deprecated (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)
Collecting humanize (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading humanize-4.9.0-py3-none-any.whl.metadata (7.9 kB)
Collecting typer[all] (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading typer-0.9.0-py3-none-any.whl.metadata (14 kB)
Collecting GitPython!=3.1.29,>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading GitPython-3.1.41-py3-none-any.whl.metadata (14 kB)
Collecting sentry-sdk>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl.metadata (9.7 kB)
Collecting docker-pycreds>=0.4.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Collecting setproctitle (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.9 kB)
Collecting appdirs>=1.4.3 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting humanfriendly>=9.1 (from coloredlogs->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 kB 241.4 kB/s eta 0:00:00
Collecting pydicom>=2.2.0 (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading pydicom-2.4.4-py3-none-any.whl.metadata (7.8 kB)
Collecting python-gdcm (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
Collecting mpmath>=0.19 (from sympy->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 403.3 kB/s eta 0:00:00
Collecting astor>=0.8 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting interface-meta<2.0.0,>=1.2.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading interface_meta-1.3.0-py3-none-any.whl (14 kB)
Collecting wrapt>=1.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting gitdb<5,>=4.0.1 (from GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Collecting MarkupSafe>=2.1.1 (from werkzeug>=1.0.1->tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting docopt>=0.6.2 (from num2words->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting colorama<0.5.0,>=0.4.3 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting shellingham<2.0.0,>=1.3.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting rich<14.0.0,>=10.11.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading rich-13.7.0-py3-none-any.whl.metadata (18 kB)
Collecting argparse (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Collecting traceback2 (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB)
Collecting markdown-it-py>=2.2.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting pygments<3.0.0,>=2.13.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
Collecting linecache2 (from traceback2->unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB)
Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Downloading certifi-2024.2.2-py3-none-any.whl (163 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.8/163.8 kB 353.3 kB/s eta 0:00:00
Downloading ivadomed-2.9.9-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.4/240.4 kB 431.2 kB/s eta 0:00:00
Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 12.6 MB/s eta 0:00:00
Downloading nilearn-0.10.2-py3-none-any.whl (10.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.4/10.4 MB 20.6 MB/s eta 0:00:00
Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.8/6.8 MB 16.0 MB/s eta 0:00:00
Downloading portalocker-2.8.2-py3-none-any.whl (17 kB)
Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 932.8 kB/s eta 0:00:00
Downloading pytest-8.0.0-py3-none-any.whl (334 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 334.0/334.0 kB 925.7 kB/s eta 0:00:00
Downloading pytest_cov-4.1.0-py3-none-any.whl (21 kB)
Downloading requests-2.31.0-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 2.2 MB/s eta 0:00:00
Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.5/38.5 MB 16.4 MB/s eta 0:00:00
Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.7/14.7 MB 7.4 MB/s eta 0:00:00
Downloading scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.1/12.1 MB 13.1 MB/s eta 0:00:00
Downloading tqdm-4.66.2-py3-none-any.whl (78 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.3/78.3 kB 197.4 kB/s eta 0:00:00
Downloading transforms3d-0.4.1-py3-none-any.whl (1.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 3.8 MB/s eta 0:00:00
Downloading urllib3-2.2.0-py3-none-any.whl (120 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.9/120.9 kB 1.2 MB/s eta 0:00:00
Downloading pytest_console_scripts-1.4.1-py3-none-any.whl (10 kB)
Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 738.9/738.9 kB 8.0 MB/s eta 0:00:00
Downloading XlsxWriter-3.1.9-py3-none-any.whl (154 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.8/154.8 kB 754.3 kB/s eta 0:00:00
Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.3/142.3 kB 3.8 MB/s eta 0:00:00
Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (310 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 311.0/311.0 kB 4.5 MB/s eta 0:00:00
Downloading coverage-7.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (233 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.6/233.6 kB 2.2 MB/s eta 0:00:00
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading exceptiongroup-1.2.0-py3-none-any.whl (16 kB)
Downloading fonttools-4.48.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 22.6 MB/s eta 0:00:00
Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 5.0 MB/s eta 0:00:00
Downloading idna-3.6-py3-none-any.whl (61 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 697.0 kB/s eta 0:00:00
Downloading imageio-2.34.0-py3-none-any.whl (313 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 313.4/313.4 kB 544.2 kB/s eta 0:00:00
Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB)
Downloading joblib-1.3.2-py3-none-any.whl (302 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 302.2/302.2 kB 668.7 kB/s eta 0:00:00
Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 2.1 MB/s eta 0:00:00
Downloading lazy_loader-0.3-py3-none-any.whl (9.1 kB)
Downloading loguru-0.7.2-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.5/62.5 kB 132.8 kB/s eta 0:00:00
Downloading packaging-23.2-py3-none-any.whl (53 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.0/53.0 kB 275.5 kB/s eta 0:00:00
Downloading pluggy-1.4.0-py3-none-any.whl (20 kB)
Downloading PyQt5_sip-12.13.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (335 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 335.7/335.7 kB 6.6 MB/s eta 0:00:00
Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 505.5/505.5 kB 6.7 MB/s eta 0:00:00
Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.9/294.9 kB 3.5 MB/s eta 0:00:00
Downloading SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (52.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.7/52.7 MB 10.8 MB/s eta 0:00:00
Downloading tensorboard-2.16.1-py3-none-any.whl (5.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.5/5.5 MB 7.0 MB/s eta 0:00:00
Downloading protobuf-4.25.2-cp37-abi3-manylinux2014_x86_64.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.6/294.6 kB 1.0 MB/s eta 0:00:00
Using cached setuptools-69.1.0-py3-none-any.whl (819 kB)
Downloading threadpoolctl-3.3.0-py3-none-any.whl (17 kB)
Downloading tifffile-2024.2.12-py3-none-any.whl (224 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 224.5/224.5 kB 484.6 kB/s eta 0:00:00
Downloading torchio-0.19.5-py2.py3-none-any.whl (173 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 173.1/173.1 kB 613.3 kB/s eta 0:00:00
Downloading types_setuptools-69.1.0.20240215-py3-none-any.whl (51 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.8/51.8 kB 218.8 kB/s eta 0:00:00
Downloading wandb-0.16.3-py3-none-any.whl (2.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 9.4 MB/s eta 0:00:00
Downloading dicom2nifti-2.4.10-py3-none-any.whl (43 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.6/43.6 kB 179.6 kB/s eta 0:00:00
Downloading flatbuffers-23.5.26-py2.py3-none-any.whl (26 kB)
Downloading imagecodecs-2024.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.7/39.7 MB 16.4 MB/s eta 0:00:00
Downloading lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.0/8.0 MB 20.8 MB/s eta 0:00:00
Downloading monai-1.3.0-202310121228-py3-none-any.whl (1.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 1.0 MB/s eta 0:00:00
Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 9.9 MB/s eta 0:00:00
Downloading absl_py-2.1.0-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.7/133.7 kB 529.2 kB/s eta 0:00:00
Downloading click-8.1.7-py3-none-any.whl (97 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 218.7 kB/s eta 0:00:00
Downloading GitPython-3.1.41-py3-none-any.whl (196 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 196.4/196.4 kB 933.5 kB/s eta 0:00:00
Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 7.3 MB/s eta 0:00:00
Downloading Markdown-3.5.2-py3-none-any.whl (103 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.9/103.9 kB 149.1 kB/s eta 0:00:00
Downloading pydicom-2.4.4-py3-none-any.whl (1.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 6.4 MB/s eta 0:00:00
Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl (257 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 257.9/257.9 kB 1.3 MB/s eta 0:00:00
Downloading tensorboard_data_server-0.7.2-py3-none-any.whl (2.4 kB)
Downloading tf_keras-2.15.0-py3-none-any.whl (1.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 9.8 MB/s eta 0:00:00
Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB)
Downloading werkzeug-3.0.1-py3-none-any.whl (226 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 226.7/226.7 kB 7.6 MB/s eta 0:00:00
Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB)
Downloading bids_validator-1.14.0-py3-none-any.whl (21 kB)
Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 8.2 MB/s eta 0:00:00
Downloading Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB)
Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Downloading fsspec-2024.2.0-py3-none-any.whl (170 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.9/170.9 kB 1.3 MB/s eta 0:00:00
Downloading humanize-4.9.0-py3-none-any.whl (126 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.8/126.8 kB 616.8 kB/s eta 0:00:00
Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 1.5 MB/s eta 0:00:00
Downloading num2words-0.5.13-py3-none-any.whl (143 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.3/143.3 kB 420.0 kB/s eta 0:00:00
Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.0/13.0 MB 19.7 MB/s eta 0:00:00
Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (30 kB)
Downloading gitdb-4.0.11-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.7/62.7 kB 553.0 kB/s eta 0:00:00
Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Downloading rich-13.7.0-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.6/240.6 kB 526.7 kB/s eta 0:00:00
Downloading shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)
Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.1/80.1 kB 873.0 kB/s eta 0:00:00
Downloading typer-0.9.0-py3-none-any.whl (45 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.9/45.9 kB 16.5 kB/s eta 0:00:00
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 253.1 kB/s eta 0:00:00
Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 7.2 MB/s eta 0:00:00
Downloading smmap-5.0.1-py3-none-any.whl (24 kB)
Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, future, docopt
  Building wheel for nnunetv2 (pyproject.toml): started
  Building wheel for nnunetv2 (pyproject.toml): finished with status 'done'
  Created wheel for nnunetv2: filename=nnunetv2-2.2.1-py3-none-any.whl size=237457 sha256=45f3095e90859f59f0e8dee0f96e9c3b2c6ad628ee7255074d5e13d2e2dd4e2b
  Stored in directory: /home/jovyan/.cache/pip/wheels/a9/7a/70/acdee60dabd3de1dcce9e5b13c6abb0215a20e034e7e8118c7
  Building wheel for acvl-utils (setup.py): started
  Building wheel for acvl-utils (setup.py): finished with status 'done'
  Created wheel for acvl-utils: filename=acvl_utils-0.2-py3-none-any.whl size=22438 sha256=670ad56c209d1f74ff71b1f2b59d6c15de3594ecfaf8fa29e068fa054846da81
  Stored in directory: /home/jovyan/.cache/pip/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7
  Building wheel for batchgenerators (setup.py): started
  Building wheel for batchgenerators (setup.py): finished with status 'done'
  Created wheel for batchgenerators: filename=batchgenerators-0.25-py3-none-any.whl size=89008 sha256=a82e54edbc0f638d96c109556f653217ce6910605a658bc99c89c8b88c756adb
  Stored in directory: /home/jovyan/.cache/pip/wheels/41/e7/c9/91b1589e2a08ad83bdd96b0beb3a496effda855580ef698568
  Building wheel for dynamic-network-architectures (setup.py): started
  Building wheel for dynamic-network-architectures (setup.py): finished with status 'done'
  Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.2-py3-none-any.whl size=27245 sha256=68fed9709bcd7f814cbf728a9f5ef96893a9c31eab36386a8f3d05f448fa2f77
  Stored in directory: /home/jovyan/.cache/pip/wheels/4e/c0/70/740949411012a24276008fa6e920f42701ae6fa18ce6122eb5
  Building wheel for pystrum (setup.py): started
  Building wheel for pystrum (setup.py): finished with status 'done'
  Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19533 sha256=eb1f91e68ddd7956d8e86c30e57223900f5b49353660a82eca5bc90160aa1014
  Stored in directory: /home/jovyan/.cache/pip/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492024 sha256=05b00794d24c1384a5d761804ebf4fd405d77fb747361b1319eb9712dbc53bfd
  Stored in directory: /home/jovyan/.cache/pip/wheels/bf/5d/6a/2e53874f7ec4e2bede522385439531fafec8fafe005b5c3d1b
  Building wheel for docopt (setup.py): started
  Building wheel for docopt (setup.py): finished with status 'done'
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=f1a91ce41f7a92a458420045c0653a448a69fa05634bea1efc7ab0d9f1dc1c52
  Stored in directory: /home/jovyan/.cache/pip/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b
Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum future docopt
Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tf-keras, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, PyQt5_sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed
Successfully installed Deprecated-1.2.14 GitPython-3.1.41 MarkupSafe-2.1.5 PyQt5_sip-12.13.0 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.1 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.2 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.48.1 formulaic-0.3.4 fsspec-2024.2.0 future-0.18.3 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.60.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.1 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.2.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.0 packaging-23.2 pandas-1.4.4 pillow-10.2.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.2 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-2.4.7 pyqt5-5.12.3 pystrum-0.4 pytest-8.0.0 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.0 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.4 setproctitle-1.3.3 setuptools-68.2.2 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.1 tensorboard-data-server-0.7.2 tf-keras-2.15.0 threadpoolctl-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.0+cpu torchio-0.19.5 torchvision-0.17.0+cpu tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240215 typing-extensions-4.9.0 unittest2-1.1.0 urllib3-2.2.0 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.1.9 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0

[0;32mInstalling spinalcordtoolbox...[0m

Obtaining file:///home/jovyan/content/sct
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-6.2.dev0

[0;32mCreating launchers for Python scripts...[0m

[0;32mInstalling binaries...[0m

[0;34msct_download_data -d binaries_linux -k[0m

--
Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)

sct_download_data -d binaries_linux -k
--

Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz
Downloading: spinalcordtoolbox-binaries_linux.tar.gz

Status:   0%|          | 0.00/83.7M [00:00 4935503ea914
Step 49/53 : ENV PYTHONUNBUFFERED=1
 ---> Running in 012cd8520712
Removing intermediate container 012cd8520712
 ---> 4afebb5c046c
Step 50/53 : COPY /python3-login /usr/local/bin/python3-login
 ---> ccf339ce6efd
Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> 914417716b38
Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in a5be14cf683f
Removing intermediate container a5be14cf683f
 ---> e68e088d1d1d
Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in 821f4ba7c674
Removing intermediate container 821f4ba7c674
 ---> 467cd9499fd7
{"aux": {"ID": "sha256:467cd9499fd76a91ee9b82e893165a8af037a2660c731a99d7d73bc078d8fa53"}}Successfully built 467cd9499fd7
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-shimming-2dtoolbox-2drf-2dshimming-2d7t-406654:3116b16edcc00fcb465831d8d8a51f98805d6374
unknown blob

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

I could not find any book log for shimming-toolbox/rf-shimming-7t at 3116b16edcc00fcb465831d8d8a51f98805d6374

🐞 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 7578ec35 Last updated: 2024-02-15 06:32:33 PST

: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...
Collecting importlib-metadata>=3.6 (from pytest_console_scripts->-r requirements.txt (line 51))
  Downloading importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting neurite>=0.2 (from voxelmorph->-r requirements.txt (line 53))
  Downloading neurite-0.2-py3-none-any.whl (108 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 kB 859.1 kB/s eta 0:00:00
Collecting connected-components-3d (from acvl-utils>=0.2->nnunetv2->-r requirements.txt (line 23))
  Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (29 kB)
Collecting future (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading future-0.18.3.tar.gz (840 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 840.9/840.9 kB 1.3 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting unittest2 (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.4/96.4 kB 139.9 kB/s eta 0:00:00
Collecting click (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting dictdiffer (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB)
Collecting zipp>=0.5 (from importlib-metadata>=3.6->pytest_console_scripts->-r requirements.txt (line 51))
  Downloading zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB)
Collecting six (from neurite>=0.2->voxelmorph->-r requirements.txt (line 53))
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pystrum>=0.2 (from neurite>=0.2->voxelmorph->-r requirements.txt (line 53))
  Downloading pystrum-0.4.tar.gz (17 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting formulaic<0.4,>=0.2.4 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading formulaic-0.3.4-py3-none-any.whl (68 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.2/68.2 kB 118.2 kB/s eta 0:00:00
Collecting sqlalchemy<1.4.0.dev0 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading SQLAlchemy-1.3.24-cp39-cp39-manylinux2010_x86_64.whl (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 2.7 MB/s eta 0:00:00
Collecting bids-validator (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading bids_validator-1.14.0-py3-none-any.whl.metadata (38 kB)
Collecting num2words (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading num2words-0.5.13-py3-none-any.whl.metadata (12 kB)
Collecting absl-py>=0.4 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting grpcio>=1.48.2 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
Collecting markdown>=2.6.8 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading Markdown-3.5.2-py3-none-any.whl.metadata (7.0 kB)
Collecting tensorboard-data-server<0.8.0,>=0.7.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard_data_server-0.7.2-py3-none-any.whl.metadata (1.1 kB)
Collecting tf-keras>=2.15.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tf_keras-2.15.0-py3-none-any.whl.metadata (1.6 kB)
Collecting werkzeug>=1.0.1 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading werkzeug-3.0.1-py3-none-any.whl.metadata (4.1 kB)
Collecting filelock (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB)
Collecting typing-extensions>=4.8.0 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)
Collecting jinja2 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Collecting fsspec (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading fsspec-2024.2.0-py3-none-any.whl.metadata (6.8 kB)
Collecting Deprecated (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)
Collecting humanize (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading humanize-4.9.0-py3-none-any.whl.metadata (7.9 kB)
Collecting typer[all] (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading typer-0.9.0-py3-none-any.whl.metadata (14 kB)
Collecting GitPython!=3.1.29,>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading GitPython-3.1.41-py3-none-any.whl.metadata (14 kB)
Collecting sentry-sdk>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl.metadata (9.7 kB)
Collecting docker-pycreds>=0.4.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Collecting setproctitle (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.9 kB)
Collecting appdirs>=1.4.3 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting humanfriendly>=9.1 (from coloredlogs->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 kB 902.7 kB/s eta 0:00:00
Collecting pydicom>=2.2.0 (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading pydicom-2.4.4-py3-none-any.whl.metadata (7.8 kB)
Collecting python-gdcm (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
Collecting mpmath>=0.19 (from sympy->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 1.1 MB/s eta 0:00:00
Collecting astor>=0.8 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting interface-meta<2.0.0,>=1.2.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading interface_meta-1.3.0-py3-none-any.whl (14 kB)
Collecting wrapt>=1.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting gitdb<5,>=4.0.1 (from GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Collecting MarkupSafe>=2.1.1 (from werkzeug>=1.0.1->tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting docopt>=0.6.2 (from num2words->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting colorama<0.5.0,>=0.4.3 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting shellingham<2.0.0,>=1.3.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting rich<14.0.0,>=10.11.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading rich-13.7.0-py3-none-any.whl.metadata (18 kB)
Collecting argparse (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Collecting traceback2 (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB)
Collecting markdown-it-py>=2.2.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting pygments<3.0.0,>=2.13.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
Collecting linecache2 (from traceback2->unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB)
Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Downloading certifi-2024.2.2-py3-none-any.whl (163 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.8/163.8 kB 207.5 kB/s eta 0:00:00
Downloading ivadomed-2.9.9-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.4/240.4 kB 758.8 kB/s eta 0:00:00
Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 20.2 MB/s eta 0:00:00
Downloading nilearn-0.10.2-py3-none-any.whl (10.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.4/10.4 MB 21.8 MB/s eta 0:00:00
Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.8/6.8 MB 11.1 MB/s eta 0:00:00
Downloading portalocker-2.8.2-py3-none-any.whl (17 kB)
Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 271.2 kB/s eta 0:00:00
Downloading pytest-8.0.0-py3-none-any.whl (334 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 334.0/334.0 kB 473.9 kB/s eta 0:00:00
Downloading pytest_cov-4.1.0-py3-none-any.whl (21 kB)
Downloading requests-2.31.0-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 2.4 MB/s eta 0:00:00
Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.5/38.5 MB 9.9 MB/s eta 0:00:00
Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.7/14.7 MB 30.3 MB/s eta 0:00:00
Downloading scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.1/12.1 MB 14.3 MB/s eta 0:00:00
Downloading tqdm-4.66.2-py3-none-any.whl (78 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.3/78.3 kB 178.5 kB/s eta 0:00:00
Downloading transforms3d-0.4.1-py3-none-any.whl (1.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 7.3 MB/s eta 0:00:00
Downloading urllib3-2.2.0-py3-none-any.whl (120 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.9/120.9 kB 447.8 kB/s eta 0:00:00
Downloading pytest_console_scripts-1.4.1-py3-none-any.whl (10 kB)
Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 738.9/738.9 kB 2.6 MB/s eta 0:00:00
Downloading XlsxWriter-3.1.9-py3-none-any.whl (154 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.8/154.8 kB 949.9 kB/s eta 0:00:00
Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.3/142.3 kB 2.6 MB/s eta 0:00:00
Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (310 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 311.0/311.0 kB 3.3 MB/s eta 0:00:00
Downloading coverage-7.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (233 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.6/233.6 kB 199.8 kB/s eta 0:00:00
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading exceptiongroup-1.2.0-py3-none-any.whl (16 kB)
Downloading fonttools-4.48.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 11.2 MB/s eta 0:00:00
Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 35.8 MB/s eta 0:00:00
Downloading idna-3.6-py3-none-any.whl (61 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 1.2 MB/s eta 0:00:00
Downloading imageio-2.34.0-py3-none-any.whl (313 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 313.4/313.4 kB 885.3 kB/s eta 0:00:00
Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB)
Downloading joblib-1.3.2-py3-none-any.whl (302 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 302.2/302.2 kB 3.0 MB/s eta 0:00:00
Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 6.1 MB/s eta 0:00:00
Downloading lazy_loader-0.3-py3-none-any.whl (9.1 kB)
Downloading loguru-0.7.2-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.5/62.5 kB 141.8 kB/s eta 0:00:00
Downloading packaging-23.2-py3-none-any.whl (53 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.0/53.0 kB 122.0 kB/s eta 0:00:00
Downloading pluggy-1.4.0-py3-none-any.whl (20 kB)
Downloading PyQt5_sip-12.13.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (335 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 335.7/335.7 kB 1.6 MB/s eta 0:00:00
Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 505.5/505.5 kB 1.4 MB/s eta 0:00:00
Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.9/294.9 kB 909.1 kB/s eta 0:00:00
Downloading SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (52.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.7/52.7 MB 12.4 MB/s eta 0:00:00
Downloading tensorboard-2.16.1-py3-none-any.whl (5.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.5/5.5 MB 10.2 MB/s eta 0:00:00
Downloading protobuf-4.25.2-cp37-abi3-manylinux2014_x86_64.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.6/294.6 kB 694.6 kB/s eta 0:00:00
Using cached setuptools-69.1.0-py3-none-any.whl (819 kB)
Downloading threadpoolctl-3.3.0-py3-none-any.whl (17 kB)
Downloading tifffile-2024.2.12-py3-none-any.whl (224 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 224.5/224.5 kB 196.0 kB/s eta 0:00:00
Downloading torchio-0.19.5-py2.py3-none-any.whl (173 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 173.1/173.1 kB 123.7 kB/s eta 0:00:00
Downloading types_setuptools-69.1.0.20240215-py3-none-any.whl (51 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.8/51.8 kB 77.7 kB/s eta 0:00:00
Downloading wandb-0.16.3-py3-none-any.whl (2.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 3.6 MB/s eta 0:00:00
Downloading dicom2nifti-2.4.10-py3-none-any.whl (43 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.6/43.6 kB 37.9 kB/s eta 0:00:00
Downloading flatbuffers-23.5.26-py2.py3-none-any.whl (26 kB)
Downloading imagecodecs-2024.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.7/39.7 MB 13.3 MB/s eta 0:00:00
Downloading lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.0/8.0 MB 16.3 MB/s eta 0:00:00
Downloading monai-1.3.0-202310121228-py3-none-any.whl (1.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 8.0 MB/s eta 0:00:00
Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 11.8 MB/s eta 0:00:00
Downloading absl_py-2.1.0-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.7/133.7 kB 213.0 kB/s eta 0:00:00
Downloading click-8.1.7-py3-none-any.whl (97 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 1.2 MB/s eta 0:00:00
Downloading GitPython-3.1.41-py3-none-any.whl (196 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 196.4/196.4 kB 872.1 kB/s eta 0:00:00
Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 23.3 MB/s eta 0:00:00
Downloading Markdown-3.5.2-py3-none-any.whl (103 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.9/103.9 kB 252.0 kB/s eta 0:00:00
Downloading pydicom-2.4.4-py3-none-any.whl (1.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 3.9 MB/s eta 0:00:00
Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl (257 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 257.9/257.9 kB 371.3 kB/s eta 0:00:00
Downloading tensorboard_data_server-0.7.2-py3-none-any.whl (2.4 kB)
Downloading tf_keras-2.15.0-py3-none-any.whl (1.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 10.0 MB/s eta 0:00:00
Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB)
Downloading werkzeug-3.0.1-py3-none-any.whl (226 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 226.7/226.7 kB 168.4 kB/s eta 0:00:00
Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB)
Downloading bids_validator-1.14.0-py3-none-any.whl (21 kB)
Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 6.4 MB/s eta 0:00:00
Downloading Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB)
Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Downloading fsspec-2024.2.0-py3-none-any.whl (170 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.9/170.9 kB 970.9 kB/s eta 0:00:00
Downloading humanize-4.9.0-py3-none-any.whl (126 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.8/126.8 kB 133.8 kB/s eta 0:00:00
Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 408.7 kB/s eta 0:00:00
Downloading num2words-0.5.13-py3-none-any.whl (143 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.3/143.3 kB 1.1 MB/s eta 0:00:00
Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.0/13.0 MB 27.8 MB/s eta 0:00:00
Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (30 kB)
Downloading gitdb-4.0.11-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.7/62.7 kB 419.4 kB/s eta 0:00:00
Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Downloading rich-13.7.0-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.6/240.6 kB 2.6 MB/s eta 0:00:00
Downloading shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)
Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.1/80.1 kB 482.1 kB/s eta 0:00:00
Downloading typer-0.9.0-py3-none-any.whl (45 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.9/45.9 kB 95.5 kB/s eta 0:00:00
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 2.0 MB/s eta 0:00:00
Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 2.1 MB/s eta 0:00:00
Downloading smmap-5.0.1-py3-none-any.whl (24 kB)
Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, future, docopt
  Building wheel for nnunetv2 (pyproject.toml): started
  Building wheel for nnunetv2 (pyproject.toml): finished with status 'done'
  Created wheel for nnunetv2: filename=nnunetv2-2.2.1-py3-none-any.whl size=237457 sha256=5a19350c1bce1bd59a2a83e3060ded185ed5197df551c332c10613226edefa15
  Stored in directory: /home/jovyan/.cache/pip/wheels/a9/7a/70/acdee60dabd3de1dcce9e5b13c6abb0215a20e034e7e8118c7
  Building wheel for acvl-utils (setup.py): started
  Building wheel for acvl-utils (setup.py): finished with status 'done'
  Created wheel for acvl-utils: filename=acvl_utils-0.2-py3-none-any.whl size=22438 sha256=9ddf72ef785639631b8d98d78c2eb33374b4cc1c6cadad133ad0158c2e1646d3
  Stored in directory: /home/jovyan/.cache/pip/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7
  Building wheel for batchgenerators (setup.py): started
  Building wheel for batchgenerators (setup.py): finished with status 'done'
  Created wheel for batchgenerators: filename=batchgenerators-0.25-py3-none-any.whl size=89008 sha256=5764d94cd8be74c6cfd5852e26efa3642274a44bd964fbe916b6fc708a9c8467
  Stored in directory: /home/jovyan/.cache/pip/wheels/41/e7/c9/91b1589e2a08ad83bdd96b0beb3a496effda855580ef698568
  Building wheel for dynamic-network-architectures (setup.py): started
  Building wheel for dynamic-network-architectures (setup.py): finished with status 'done'
  Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.2-py3-none-any.whl size=27245 sha256=9d0380d13d405c83254250b6e5854568c06c9e64536f8fd58a6cacca0d01494d
  Stored in directory: /home/jovyan/.cache/pip/wheels/4e/c0/70/740949411012a24276008fa6e920f42701ae6fa18ce6122eb5
  Building wheel for pystrum (setup.py): started
  Building wheel for pystrum (setup.py): finished with status 'done'
  Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19533 sha256=8c23cd65d050211f78efdec2881e6327510a81f53b54584636af75f2ef8641ab
  Stored in directory: /home/jovyan/.cache/pip/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492024 sha256=5fdd8564bfae2e6c0078d185be2e1d909b9805cbeec338b28452eb2497c04461
  Stored in directory: /home/jovyan/.cache/pip/wheels/bf/5d/6a/2e53874f7ec4e2bede522385439531fafec8fafe005b5c3d1b
  Building wheel for docopt (setup.py): started
  Building wheel for docopt (setup.py): finished with status 'done'
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=d209651a42057b06d7575eecccea3a0ebec48a1af1ada9dcbfc3e60ac0206292
  Stored in directory: /home/jovyan/.cache/pip/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b
Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum future docopt
Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tf-keras, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, PyQt5_sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed
Successfully installed Deprecated-1.2.14 GitPython-3.1.41 MarkupSafe-2.1.5 PyQt5_sip-12.13.0 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.1 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.2 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.48.1 formulaic-0.3.4 fsspec-2024.2.0 future-0.18.3 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.60.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.1 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.2.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.0 packaging-23.2 pandas-1.4.4 pillow-10.2.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.2 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-2.4.7 pyqt5-5.12.3 pystrum-0.4 pytest-8.0.0 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.0 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.4 setproctitle-1.3.3 setuptools-68.2.2 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.1 tensorboard-data-server-0.7.2 tf-keras-2.15.0 threadpoolctl-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.0+cpu torchio-0.19.5 torchvision-0.17.0+cpu tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240215 typing-extensions-4.9.0 unittest2-1.1.0 urllib3-2.2.0 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.1.9 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0

[0;32mInstalling spinalcordtoolbox...[0m

Obtaining file:///home/jovyan/content/sct
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-6.2.dev0

[0;32mCreating launchers for Python scripts...[0m

[0;32mInstalling binaries...[0m

[0;34msct_download_data -d binaries_linux -k[0m

--
Spinal Cord Toolbox (git-master-f8d6d1fbb0a3ec0ffe4124a5bf4e01fdfc4357d9)

sct_download_data -d binaries_linux -k
--

Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz
Downloading: spinalcordtoolbox-binaries_linux.tar.gz

Status:   0%|          | 0.00/83.7M [00:00 295ab521f30b
Step 49/53 : ENV PYTHONUNBUFFERED=1
 ---> Running in bde6afaee674
Removing intermediate container bde6afaee674
 ---> ba175ccd1c3c
Step 50/53 : COPY /python3-login /usr/local/bin/python3-login
 ---> 6f7b32adac39
Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> a183e7b3ca73
Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in 1f167b924790
Removing intermediate container 1f167b924790
 ---> b5fc6e143d60
Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in f88e44addbfe
Removing intermediate container f88e44addbfe
 ---> 1e6e06b9d60a
{"aux": {"ID": "sha256:1e6e06b9d60ab617371c38f6d0fe5afb409be67e9de0de5f3980f5574c00de1c"}}Successfully built 1e6e06b9d60a
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-shimming-2dtoolbox-2drf-2dshimming-2d7t-406654:3116b16edcc00fcb465831d8d8a51f98805d6374
unknown blob

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

I could not find any book log for shimming-toolbox/rf-shimming-7t at 3116b16edcc00fcb465831d8d8a51f98805d6374

🐞 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 52a7d825 Last updated: 2024-02-15 06:45:35 PST

: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/repo2dockervoqc6kqv'...
HEAD is now at 3116b16 Update data to release in this repo instead of depricated repo
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 4b304d0760ef
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 7f1b7259e459
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 7bb3d08f1de8
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 809b33e2cf15
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 4d00855d4ac4
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> e0eb756531cb
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> e08d1a12464e
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> a62ae68913e8
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 93b9c163c81a
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 97d1693ed76c
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 8daf0d2d790c
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 4eda22e52ebf
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 4a0588a11031
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3916bc471288
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> f3bda1e3877d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 86a774284ed1
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> d5211a98f273
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e2f328dd7a4e
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> e3a9180d2511
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 3954f09301c7
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5ea52513ec0f
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 995ff224d88d
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 9b184daf53f4
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b270ac4976f5
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
 ---> Using cache
 ---> c686d3b638a4
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 78d0bdd256b4
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> e38b8fcb0fbd
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 35dbdf6176db
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 77ef363567fb
Step 31/53 : USER root
 ---> Using cache
 ---> 9848a0cccf77
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 4e3241167052
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> fee82a54343b
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 4fb91435c67e
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> be3e63cb11d8
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 4f20431eee2a
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 40e55985010d
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 5971166c5297
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 17d6eea84084
Step 40/53 : USER ${NB_USER}
 ---> Using cache
 ---> f7275c32720b
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> d1ac2e317c84
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> 5503202ada55
Step 43/53 : LABEL repo2docker.ref="3116b16edcc00fcb465831d8d8a51f98805d6374"
 ---> Running in aca4a2631536
Removing intermediate container aca4a2631536
 ---> f52e1187b517
Step 44/53 : LABEL repo2docker.repo="https://github.com/shimming-toolbox/rf-shimming-7t"
 ---> Running in 0206851ad9c0
Removing intermediate container 0206851ad9c0
 ---> 1846414b0a3b
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 51ea4a3376e4
Removing intermediate container 51ea4a3376e4
 ---> 5004dcf29919
Step 46/53 : USER ${NB_USER}
 ---> Running in 0355fceed8a2
Removing intermediate container 0355fceed8a2
 ---> 5a3bd7ca88fe
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in ef05d4bf4531
Removing intermediate container ef05d4bf4531
 ---> 1be0fd512824
Step 48/53 : RUN ./binder/postBuild
 ---> Running in 858b9b6ec130
---- repo2data starting ----
/srv/conda/envs/notebook/lib/python3.8/site-packages/repo2data
Config from file :
../binder/data_requirement.json
Destination:
../data/rf-shimming-7t

File downloaded to: ../data/rf-shimming-7t/ds004906.zip
patool: Extracting ../data/rf-shimming-7t/ds004906.zip ...
patool: ... ../data/rf-shimming-7t/ds004906.zip extracted to `../data/rf-shimming-7t'.
Info : ds004906.zip Decompressed
[91mCloning into '/home/jovyan/content/sct'...
[0m
[0;32m
*******************************
* Welcome to SCT installation *
*******************************
[0m

[0;32mChecking OS type and version...[0m

Linux 858b9b6ec130 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

[0;32mChecking requirements...[0m

[0;32mOK![0m

SCT version ......... 6.2.dev0
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /home/jovyan/.bashrc

[0;32mSCT will be installed here: [/home/jovyan/content/sct][0m

[0;92m
Do you agree? [y]es/[n]o: [0m
[0;32mSkipping copy of source files (source and destination folders are the same)[0m

[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: [0m
[0;32mDownloading Miniconda...[0m

[0;34mwget -nv -O /tmp/tmp.R5RFeZvt3B/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh[0m

2024-02-15 14:41:40 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [141613749/141613749] -> "/tmp/tmp.R5RFeZvt3B/miniconda.sh" [1]

[0;32mInstalling Miniconda...[0m

[0;34mbash /tmp/tmp.R5RFeZvt3B/miniconda.sh -p /home/jovyan/content/sct/python -b -f[0m

PREFIX=/home/jovyan/content/sct/python
Unpacking payload ...

  0%|          | 0/73 [00:00 conda-forge::ca-certificates-2024.2.2-hbcca054_0 
  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5 
  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5 
  libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5 
  openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0 

The following packages will be SUPERSEDED by a higher-priority channel:

  _libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu 

Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)
Collecting pip!=21.2.*
  Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)
Downloading pip-24.0-py3-none-any.whl (2.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 22.2 MB/s eta 0:00:00
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 23.3.1
    Uninstalling pip-23.3.1:
      Successfully uninstalled pip-23.3.1
Successfully installed pip-24.0

[0;32mInstalling Python dependencies...[0m

[0;32mUsing requirements.txt (git installation)[0m

Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Collecting dipy!=1.6.*,!=1.7.*,!=1.8.* (from -r requirements.txt (line 7))
  Downloading dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.9/7.9 MB 19.3 MB/s eta 0:00:00
Collecting ivadomed (from -r requirements.txt (line 11))
  Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB)
Collecting matplotlib (from -r requirements.txt (line 12))
  Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-5.2.0-py3-none-any.whl.metadata (8.8 kB)
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB)
Collecting nnunetv2 (from -r requirements.txt (line 23))
  Downloading nnunetv2-2.2.1.tar.gz (178 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 178.6/178.6 kB 742.4 kB/s eta 0:00:00
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting numpy<1.24 (from -r requirements.txt (line 27))
  Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 15.5 MB/s eta 0:00:00
Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31))
  Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.2 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting portalocker (from -r requirements.txt (line 33))
  Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)
Collecting psutil (from -r requirements.txt (line 34))
  Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39))
  Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (62.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.4/62.4 MB 11.8 MB/s eta 0:00:00
Collecting pytest (from -r requirements.txt (line 40))
  Downloading pytest-8.0.0-py3-none-any.whl.metadata (7.8 kB)
Collecting pytest-cov (from -r requirements.txt (line 41))
  Downloading pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB)
Collecting requests (from -r requirements.txt (line 42))
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting requirements-parser (from -r requirements.txt (line 43))
  Downloading requirements_parser-0.5.0-py3-none-any.whl (18 kB)
Collecting scipy (from -r requirements.txt (line 44))
  Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 722.7 kB/s eta 0:00:00
Collecting scikit-image (from -r requirements.txt (line 45))
  Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting scikit-learn (from -r requirements.txt (line 46))
  Downloading scikit_learn-1.4.0-1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting xlwt (from -r requirements.txt (line 47))
  Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 722.7 kB/s eta 0:00:00
Collecting tqdm (from -r requirements.txt (line 48))
  Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 334.6 kB/s eta 0:00:00
Collecting transforms3d (from -r requirements.txt (line 49))
  Downloading transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB)
Collecting urllib3 (from -r requirements.txt (line 50))
  Downloading urllib3-2.2.0-py3-none-any.whl.metadata (6.4 kB)
Collecting pytest_console_scripts (from -r requirements.txt (line 51))
  Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB)
Collecting pyyaml (from -r requirements.txt (line 52))
  Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting voxelmorph (from -r requirements.txt (line 53))
  Downloading voxelmorph-0.2-py3-none-any.whl (54 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.2/54.2 kB 3.1 MB/s eta 0:00:00
Collecting wquantiles (from -r requirements.txt (line 54))
  Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)
Collecting xlsxwriter (from -r requirements.txt (line 57))
  Downloading XlsxWriter-3.1.9-py3-none-any.whl.metadata (2.6 kB)
Collecting monai[nibabel] (from -r requirements.txt (line 13))
  Downloading monai-1.3.0-202310121228-py3-none-any.whl.metadata (10 kB)
Collecting PyQt5_sip<13,>=4.19.14 (from pyqt5==5.12.3->-r requirements.txt (line 39))
  Downloading PyQt5_sip-12.13.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (504 bytes)
Collecting h5py>=2.8.0 (from dipy!=1.6.*,!=1.7.*,!=1.8.*->-r requirements.txt (line 7))
  Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting pyparsing<3,>=2.0.2 (from ivadomed->-r requirements.txt (line 11))
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.8/67.8 kB 207.4 kB/s eta 0:00:00
Collecting csv-diff>=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading csv_diff-1.1-py3-none-any.whl (12 kB)
Collecting loguru~=0.5 (from ivadomed->-r requirements.txt (line 11))
  Downloading loguru-0.7.2-py3-none-any.whl.metadata (23 kB)
Collecting imageio>=2.31.4 (from ivadomed->-r requirements.txt (line 11))
  Downloading imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB)
Collecting joblib~=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-3.2.2-py3-none-any.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 11.7 MB/s eta 0:00:00
Collecting onnx (from ivadomed->-r requirements.txt (line 11))
  Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (15 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-1.4.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 9.4 MB/s eta 0:00:00
Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading pybids-0.15.5-py3-none-any.whl (14.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.9/14.9 MB 14.0 MB/s eta 0:00:00
Collecting seaborn~=0.11 (from ivadomed->-r requirements.txt (line 11))
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard-2.16.1-py3-none-any.whl.metadata (1.6 kB)
Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 11))
  Downloading torchio-0.19.5-py2.py3-none-any.whl.metadata (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.2/48.2 kB 306.3 kB/s eta 0:00:00
Collecting torch>=1.8.1 (from ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/cpu/torch-2.2.0%2Bcpu-cp39-cp39-linux_x86_64.whl (186.8 MB)
     ━━━╸                                    18.0/186.8 MB 12.4 MB/s eta 0:00:14
ERROR: Exception:
Traceback (most recent call last):
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 438, in _error_catcher
    yield
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 561, in read
    data = self._fp_read(amt) if not fp_closed else b""
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 527, in _fp_read
    return self._fp.read(amt) if amt is not None else self._fp.read()
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 98, in read
    data: bytes = self.__fp.read(amt)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/http/client.py", line 463, in read
    n = self.readinto(b)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/http/client.py", line 507, in readinto
    n = self.fp.readinto(b)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/socket.py", line 704, in readinto
    return self._sock.recv_into(b)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/ssl.py", line 1275, in recv_into
    return self.read(nbytes, buffer)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/ssl.py", line 1133, in read
    return self._sslobj.read(len, buffer)
socket.timeout: The read operation timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
    status = run_func(*args)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper
    return func(self, options, args)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 377, in run
    requirement_set = resolver.resolve(
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 95, in resolve
    result = self._result = resolver.resolve(
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve
    state = resolution.resolve(requirements, max_rounds=max_rounds)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 427, in resolve
    failure_causes = self._attempt_to_pin_criterion(name)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 239, in _attempt_to_pin_criterion
    criteria = self._get_updated_criteria(candidate)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 230, in _get_updated_criteria
    self._add_to_criteria(criteria, requirement, parent=candidate)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria
    if not criterion.candidates:
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/resolvelib/structs.py", line 156, in __bool__
    return bool(self._sequence)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__
    return any(self)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in 
    return (c for c in iterator if id(c) not in self._incompatible_ids)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built
    candidate = func()
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 182, in _make_candidate_from_link
    base: Optional[BaseCandidate] = self._make_base_candidate_from_link(
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link
    self._link_candidate_cache[link] = LinkCandidate(
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__
    super().__init__(
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__
    self.dist = self._prepare()
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare
    dist = self._prepare_distribution()
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution
    return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement
    return self._prepare_linked_requirement(req, parallel_builds)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 596, in _prepare_linked_requirement
    local_file = unpack_url(
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 168, in unpack_url
    file = get_http_url(
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 109, in get_http_url
    from_path, content_type = download(link, temp_dir.path)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/network/download.py", line 147, in __call__
    for chunk in chunks:
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/cli/progress_bars.py", line 53, in _rich_progress_bar
    for chunk in iterable:
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_internal/network/utils.py", line 63, in response_chunks
    for chunk in response.raw.stream(
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 622, in stream
    data = self.read(amt=amt, decode_content=decode_content)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 587, in read
    raise IncompleteRead(self._fp_bytes_read, self.length_remaining)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/home/jovyan/content/sct/python/envs/venv_sct/lib/python3.9/site-packages/pip/_vendor/urllib3/response.py", line 443, in _error_catcher
    raise ReadTimeoutError(self._pool, None, "Read timed out.")
pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='download.pytorch.org', port=443): Read timed out.

[0;31mFailed running pip install: 2[0m

[0;31mInstallation failed!

Please find the file "/home/jovyan/content/sct/install_sct_log.txt",
then upload it as a .txt attachment in a new topic on SCT's forum:
--> http://forum.spinalcordmri.org/c/sct[0m

Removing intermediate container 858b9b6ec130
The command '/bin/sh -c ./binder/postBuild' returned a non-zero code: 1Built image, launching...

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

I could not find any book log for shimming-toolbox/rf-shimming-7t at 3116b16edcc00fcb465831d8d8a51f98805d6374

🐞 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 b1e599a4 Last updated: 2024-02-16 02:49:14 PST

: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/repo2dockerb8tq14y2'...
HEAD is now at 47f08c4 Comment out repo2data in postBuild
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 4b304d0760ef
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 7f1b7259e459
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 7bb3d08f1de8
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 809b33e2cf15
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 4d00855d4ac4
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> e0eb756531cb
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> e08d1a12464e
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> a62ae68913e8
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 93b9c163c81a
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 97d1693ed76c
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 8daf0d2d790c
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 4eda22e52ebf
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 4a0588a11031
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3916bc471288
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> f3bda1e3877d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 86a774284ed1
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> d5211a98f273
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> e2f328dd7a4e
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> e3a9180d2511
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 3954f09301c7
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5ea52513ec0f
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 995ff224d88d
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 9b184daf53f4
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b270ac4976f5
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
 ---> Using cache
 ---> c686d3b638a4
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 78d0bdd256b4
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> e38b8fcb0fbd
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 35dbdf6176db
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 77ef363567fb
Step 31/53 : USER root
 ---> Using cache
 ---> 9848a0cccf77
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 4e3241167052
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> fee82a54343b
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 4fb91435c67e
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> be3e63cb11d8
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 4f20431eee2a
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 40e55985010d
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 5971166c5297
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> 17d6eea84084
Step 40/53 : USER ${NB_USER}
 ---> Using cache
 ---> f7275c32720b
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> d1ac2e317c84
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> a793bb39bb75
Step 43/53 : LABEL repo2docker.ref="47f08c4a054636c29aacb31a1bd1d33972874b82"
 ---> Running in ef161d654a16
Removing intermediate container ef161d654a16
 ---> 056f9ee24c61
Step 44/53 : LABEL repo2docker.repo="https://github.com/shimming-toolbox/rf-shimming-7t"
 ---> Running in 5b1f4ccceaa9
Removing intermediate container 5b1f4ccceaa9
 ---> a088cf3db8b0
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in 8f81015e3e8e
Removing intermediate container 8f81015e3e8e
 ---> 0eb3f830cd1b
Step 46/53 : USER ${NB_USER}
 ---> Running in efcfdbd420fd
Removing intermediate container efcfdbd420fd
 ---> 797cf904a455
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in 6f5c90a5784b
Removing intermediate container 6f5c90a5784b
 ---> 2bf71939ad8e
Step 48/53 : RUN ./binder/postBuild
 ---> Running in 54c3a4382265
[91mCloning into '/home/jovyan/content/sct'...
[0m
[0;32m
*******************************
* Welcome to SCT installation *
*******************************
[0m

[0;32mChecking OS type and version...[0m

Linux 54c3a4382265 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

[0;32mChecking requirements...[0m

[0;32mOK![0m

SCT version ......... 6.3.dev0
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /home/jovyan/.bashrc

[0;32mSCT will be installed here: [/home/jovyan/content/sct][0m

[0;92m
Do you agree? [y]es/[n]o: [0m
[0;32mSkipping copy of source files (source and destination folders are the same)[0m

[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: [0m
[0;32mDownloading Miniconda...[0m

[0;34mwget -nv -O /tmp/tmp.s8hYF9AA16/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh[0m

2024-02-16 10:34:54 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [141613749/141613749] -> "/tmp/tmp.s8hYF9AA16/miniconda.sh" [1]

[0;32mInstalling Miniconda...[0m

[0;34mbash /tmp/tmp.s8hYF9AA16/miniconda.sh -p /home/jovyan/content/sct/python -b -f[0m

PREFIX=/home/jovyan/content/sct/python
Unpacking payload ...

  0%|          | 0/73 [00:00 conda-forge::ca-certificates-2024.2.2-hbcca054_0 
  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5 
  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5 
  libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5 
  openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0 

The following packages will be SUPERSEDED by a higher-priority channel:

  _libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu 

Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)
Collecting pip!=21.2.*
  Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)
Downloading pip-24.0-py3-none-any.whl (2.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 7.1 MB/s eta 0:00:00
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 23.3.1
    Uninstalling pip-23.3.1:
      Successfully uninstalled pip-23.3.1
Successfully installed pip-24.0

[0;32mInstalling Python dependencies...[0m

[0;32mUsing requirements.txt (git installation)[0m

Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Collecting dipy!=1.6.*,!=1.7.*,!=1.8.* (from -r requirements.txt (line 7))
  Downloading dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.9/7.9 MB 10.2 MB/s eta 0:00:00
Collecting ivadomed (from -r requirements.txt (line 11))
  Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB)
Collecting matplotlib (from -r requirements.txt (line 12))
  Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-5.2.0-py3-none-any.whl.metadata (8.8 kB)
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB)
Collecting nnunetv2 (from -r requirements.txt (line 23))
  Downloading nnunetv2-2.2.1.tar.gz (178 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 178.6/178.6 kB 332.5 kB/s eta 0:00:00
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting numpy<1.24 (from -r requirements.txt (line 27))
  Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 24.1 MB/s eta 0:00:00
Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31))
  Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.2 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting portalocker (from -r requirements.txt (line 33))
  Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)
Collecting psutil (from -r requirements.txt (line 34))
  Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39))
  Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (62.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.4/62.4 MB 10.9 MB/s eta 0:00:00
Collecting pyqt5-sip<12.13.0 (from -r requirements.txt (line 41))
  Downloading PyQt5_sip-12.12.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (504 bytes)
Collecting pytest (from -r requirements.txt (line 42))
  Downloading pytest-8.0.0-py3-none-any.whl.metadata (7.8 kB)
Collecting pytest-cov (from -r requirements.txt (line 43))
  Downloading pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB)
Collecting requests (from -r requirements.txt (line 44))
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting requirements-parser (from -r requirements.txt (line 45))
  Downloading requirements_parser-0.5.0-py3-none-any.whl (18 kB)
Collecting scipy (from -r requirements.txt (line 46))
  Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 1.6 MB/s eta 0:00:00
Collecting scikit-image (from -r requirements.txt (line 47))
  Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting scikit-learn (from -r requirements.txt (line 48))
  Downloading scikit_learn-1.4.1.post1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting xlwt (from -r requirements.txt (line 49))
  Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 580.6 kB/s eta 0:00:00
Collecting tqdm (from -r requirements.txt (line 50))
  Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 186.3 kB/s eta 0:00:00
Collecting transforms3d (from -r requirements.txt (line 51))
  Downloading transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB)
Collecting urllib3 (from -r requirements.txt (line 52))
  Downloading urllib3-2.2.0-py3-none-any.whl.metadata (6.4 kB)
Collecting pytest_console_scripts (from -r requirements.txt (line 53))
  Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB)
Collecting pyyaml (from -r requirements.txt (line 54))
  Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting voxelmorph (from -r requirements.txt (line 55))
  Downloading voxelmorph-0.2-py3-none-any.whl (54 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.2/54.2 kB 167.0 kB/s eta 0:00:00
Collecting wquantiles (from -r requirements.txt (line 56))
  Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)
Collecting xlsxwriter (from -r requirements.txt (line 59))
  Downloading XlsxWriter-3.1.9-py3-none-any.whl.metadata (2.6 kB)
Collecting monai[nibabel] (from -r requirements.txt (line 13))
  Downloading monai-1.3.0-202310121228-py3-none-any.whl.metadata (10 kB)
Collecting h5py>=2.8.0 (from dipy!=1.6.*,!=1.7.*,!=1.8.*->-r requirements.txt (line 7))
  Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting pyparsing<3,>=2.0.2 (from ivadomed->-r requirements.txt (line 11))
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.8/67.8 kB 265.4 kB/s eta 0:00:00
Collecting csv-diff>=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading csv_diff-1.1-py3-none-any.whl (12 kB)
Collecting loguru~=0.5 (from ivadomed->-r requirements.txt (line 11))
  Downloading loguru-0.7.2-py3-none-any.whl.metadata (23 kB)
Collecting imageio>=2.31.4 (from ivadomed->-r requirements.txt (line 11))
  Downloading imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB)
Collecting joblib~=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-3.2.2-py3-none-any.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 10.2 MB/s eta 0:00:00
Collecting onnx (from ivadomed->-r requirements.txt (line 11))
  Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (15 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-1.4.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 22.0 MB/s eta 0:00:00
Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading pybids-0.15.5-py3-none-any.whl (14.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.9/14.9 MB 11.4 MB/s eta 0:00:00
Collecting seaborn~=0.11 (from ivadomed->-r requirements.txt (line 11))
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard-2.16.1-py3-none-any.whl.metadata (1.6 kB)
Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 11))
  Downloading torchio-0.19.5-py2.py3-none-any.whl.metadata (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.2/48.2 kB 251.7 kB/s eta 0:00:00
Collecting torch>=1.8.1 (from ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/cpu/torch-2.2.0%2Bcpu-cp39-cp39-linux_x86_64.whl (186.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 186.8/186.8 MB 3.5 MB/s eta 0:00:00
Collecting torchvision>=0.9.1 (from ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.17.0%2Bcpu-cp39-cp39-linux_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 3.8 MB/s eta 0:00:00
Collecting wandb>=0.12.11 (from ivadomed->-r requirements.txt (line 11))
  Downloading wandb-0.16.3-py3-none-any.whl.metadata (9.9 kB)
Collecting contourpy>=1.0.1 (from matplotlib->-r requirements.txt (line 12))
  Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib->-r requirements.txt (line 12))
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading fonttools-4.49.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (159 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 159.1/159.1 kB 1.1 MB/s eta 0:00:00
Collecting kiwisolver>=1.3.1 (from matplotlib->-r requirements.txt (line 12))
  Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.4 kB)
Collecting packaging>=20.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pillow>=8 (from matplotlib->-r requirements.txt (line 12))
  Downloading https://download.pytorch.org/whl/pillow-10.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 12.5 MB/s eta 0:00:00
Collecting python-dateutil>=2.7 (from matplotlib->-r requirements.txt (line 12))
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 1.0 MB/s eta 0:00:00
Collecting importlib-resources>=3.2.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading importlib_resources-6.1.1-py3-none-any.whl.metadata (4.1 kB)
Collecting setuptools (from nibabel->-r requirements.txt (line 21))
  Using cached setuptools-69.1.0-py3-none-any.whl.metadata (6.1 kB)
Collecting lxml (from nilearn->-r requirements.txt (line 22))
  Downloading lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.5 kB)
INFO: pip is looking at multiple versions of nilearn to determine which version is compatible with other requirements. This could take a while.
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.2-py3-none-any.whl.metadata (7.8 kB)
Collecting acvl-utils>=0.2 (from nnunetv2->-r requirements.txt (line 23))
  Downloading acvl_utils-0.2.tar.gz (18 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dynamic-network-architectures>=0.2 (from nnunetv2->-r requirements.txt (line 23))
  Downloading dynamic_network_architectures-0.2.tar.gz (20 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dicom2nifti (from nnunetv2->-r requirements.txt (line 23))
  Downloading dicom2nifti-2.4.10-py3-none-any.whl.metadata (1.3 kB)
Collecting batchgenerators>=0.25 (from nnunetv2->-r requirements.txt (line 23))
  Downloading batchgenerators-0.25.tar.gz (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.7/61.7 kB 607.1 kB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting SimpleITK>=2.2.1 (from nnunetv2->-r requirements.txt (line 23))
  Downloading SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.9 kB)
Collecting graphviz (from nnunetv2->-r requirements.txt (line 23))
  Downloading graphviz-0.20.1-py3-none-any.whl (47 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 kB 76.6 kB/s eta 0:00:00
Collecting tifffile (from nnunetv2->-r requirements.txt (line 23))
  Downloading tifffile-2024.2.12-py3-none-any.whl.metadata (31 kB)
Collecting imagecodecs (from nnunetv2->-r requirements.txt (line 23))
  Downloading imagecodecs-2024.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting yacs (from nnunetv2->-r requirements.txt (line 23))
  Downloading yacs-0.1.8-py3-none-any.whl (14 kB)
Collecting coloredlogs (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.0/46.0 kB 95.6 kB/s eta 0:00:00
Collecting flatbuffers (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading flatbuffers-23.5.26-py2.py3-none-any.whl.metadata (850 bytes)
Collecting protobuf (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading protobuf-4.25.3-cp37-abi3-manylinux2014_x86_64.whl.metadata (541 bytes)
Collecting sympy (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/sympy-1.12-py3-none-any.whl (5.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.7/5.7 MB 7.3 MB/s eta 0:00:00
Collecting pytz>=2020.1 (from pandas->-r requirements.txt (line 32))
  Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting iniconfig (from pytest->-r requirements.txt (line 42))
  Downloading iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Collecting pluggy<2.0,>=1.3.0 (from pytest->-r requirements.txt (line 42))
  Downloading pluggy-1.4.0-py3-none-any.whl.metadata (4.3 kB)
Collecting exceptiongroup>=1.0.0rc8 (from pytest->-r requirements.txt (line 42))
  Downloading exceptiongroup-1.2.0-py3-none-any.whl.metadata (6.6 kB)
Collecting tomli>=1.0.0 (from pytest->-r requirements.txt (line 42))
  Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting coverage>=5.2.1 (from coverage[toml]>=5.2.1->pytest-cov->-r requirements.txt (line 43))
  Downloading coverage-7.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.2 kB)
Collecting charset-normalizer<4,>=2 (from requests->-r requirements.txt (line 44))
  Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests->-r requirements.txt (line 44))
  Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting types-setuptools>=57.0.0 (from requirements-parser->-r requirements.txt (line 45))
  Downloading types_setuptools-69.1.0.20240215-py3-none-any.whl.metadata (1.6 kB)
Collecting networkx>=2.8 (from scikit-image->-r requirements.txt (line 47))
  Downloading https://download.pytorch.org/whl/networkx-3.2.1-py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 26.9 MB/s eta 0:00:00
Collecting lazy_loader>=0.3 (from scikit-image->-r requirements.txt (line 47))
  Downloading lazy_loader-0.3-py3-none-any.whl.metadata (4.3 kB)
Collecting threadpoolctl>=2.0.0 (from scikit-learn->-r requirements.txt (line 48))
  Downloading threadpoolctl-3.3.0-py3-none-any.whl.metadata (13 kB)
Collecting importlib-metadata>=3.6 (from pytest_console_scripts->-r requirements.txt (line 53))
  Downloading importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting neurite>=0.2 (from voxelmorph->-r requirements.txt (line 55))
  Downloading neurite-0.2-py3-none-any.whl (108 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 kB 300.5 kB/s eta 0:00:00
Collecting connected-components-3d (from acvl-utils>=0.2->nnunetv2->-r requirements.txt (line 23))
  Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (29 kB)
Collecting future (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading future-0.18.3.tar.gz (840 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 840.9/840.9 kB 3.8 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting unittest2 (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.4/96.4 kB 731.2 kB/s eta 0:00:00
Collecting click (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting dictdiffer (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB)
Collecting zipp>=0.5 (from importlib-metadata>=3.6->pytest_console_scripts->-r requirements.txt (line 53))
  Downloading zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB)
Collecting six (from neurite>=0.2->voxelmorph->-r requirements.txt (line 55))
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pystrum>=0.2 (from neurite>=0.2->voxelmorph->-r requirements.txt (line 55))
  Downloading pystrum-0.4.tar.gz (17 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting formulaic<0.4,>=0.2.4 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading formulaic-0.3.4-py3-none-any.whl (68 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.2/68.2 kB 661.7 kB/s eta 0:00:00
Collecting sqlalchemy<1.4.0.dev0 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading SQLAlchemy-1.3.24-cp39-cp39-manylinux2010_x86_64.whl (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 1.2 MB/s eta 0:00:00
Collecting bids-validator (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading bids_validator-1.14.0-py3-none-any.whl.metadata (38 kB)
Collecting num2words (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading num2words-0.5.13-py3-none-any.whl.metadata (12 kB)
Collecting absl-py>=0.4 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting grpcio>=1.48.2 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
Collecting markdown>=2.6.8 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading Markdown-3.5.2-py3-none-any.whl.metadata (7.0 kB)
Collecting tensorboard-data-server<0.8.0,>=0.7.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard_data_server-0.7.2-py3-none-any.whl.metadata (1.1 kB)
Collecting tf-keras>=2.15.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tf_keras-2.15.0-py3-none-any.whl.metadata (1.6 kB)
Collecting werkzeug>=1.0.1 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading werkzeug-3.0.1-py3-none-any.whl.metadata (4.1 kB)
Collecting filelock (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB)
Collecting typing-extensions>=4.8.0 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)
Collecting jinja2 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Collecting fsspec (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading fsspec-2024.2.0-py3-none-any.whl.metadata (6.8 kB)
Collecting Deprecated (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)
Collecting humanize (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading humanize-4.9.0-py3-none-any.whl.metadata (7.9 kB)
Collecting typer[all] (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading typer-0.9.0-py3-none-any.whl.metadata (14 kB)
Collecting GitPython!=3.1.29,>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading GitPython-3.1.42-py3-none-any.whl.metadata (12 kB)
Collecting sentry-sdk>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl.metadata (9.7 kB)
Collecting docker-pycreds>=0.4.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Collecting setproctitle (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.9 kB)
Collecting appdirs>=1.4.3 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting humanfriendly>=9.1 (from coloredlogs->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 kB 102.5 kB/s eta 0:00:00
Collecting pydicom>=2.2.0 (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading pydicom-2.4.4-py3-none-any.whl.metadata (7.8 kB)
Collecting python-gdcm (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
Collecting mpmath>=0.19 (from sympy->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 5.5 MB/s eta 0:00:00
Collecting astor>=0.8 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting interface-meta<2.0.0,>=1.2.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading interface_meta-1.3.0-py3-none-any.whl (14 kB)
Collecting wrapt>=1.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting gitdb<5,>=4.0.1 (from GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Collecting MarkupSafe>=2.1.1 (from werkzeug>=1.0.1->tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting docopt>=0.6.2 (from num2words->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting colorama<0.5.0,>=0.4.3 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting shellingham<2.0.0,>=1.3.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting rich<14.0.0,>=10.11.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading rich-13.7.0-py3-none-any.whl.metadata (18 kB)
Collecting argparse (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Collecting traceback2 (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB)
Collecting markdown-it-py>=2.2.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting pygments<3.0.0,>=2.13.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
Collecting linecache2 (from traceback2->unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB)
Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Downloading certifi-2024.2.2-py3-none-any.whl (163 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.8/163.8 kB 1.1 MB/s eta 0:00:00
Downloading ivadomed-2.9.9-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.4/240.4 kB 2.0 MB/s eta 0:00:00
Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 14.7 MB/s eta 0:00:00
Downloading nilearn-0.10.2-py3-none-any.whl (10.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.4/10.4 MB 17.8 MB/s eta 0:00:00
Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.8/6.8 MB 41.1 MB/s eta 0:00:00
Downloading portalocker-2.8.2-py3-none-any.whl (17 kB)
Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 849.0 kB/s eta 0:00:00
Downloading PyQt5_sip-12.12.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (335 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 335.3/335.3 kB 1.2 MB/s eta 0:00:00
Downloading pytest-8.0.0-py3-none-any.whl (334 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 334.0/334.0 kB 522.7 kB/s eta 0:00:00
Downloading pytest_cov-4.1.0-py3-none-any.whl (21 kB)
Downloading requests-2.31.0-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 151.3 kB/s eta 0:00:00
Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.5/38.5 MB 18.0 MB/s eta 0:00:00
Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.7/14.7 MB 16.1 MB/s eta 0:00:00
Downloading scikit_learn-1.4.1.post1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.2/12.2 MB 16.4 MB/s eta 0:00:00
Downloading tqdm-4.66.2-py3-none-any.whl (78 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.3/78.3 kB 87.2 kB/s eta 0:00:00
Downloading transforms3d-0.4.1-py3-none-any.whl (1.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 11.0 MB/s eta 0:00:00
Downloading urllib3-2.2.0-py3-none-any.whl (120 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.9/120.9 kB 119.9 kB/s eta 0:00:00
Downloading pytest_console_scripts-1.4.1-py3-none-any.whl (10 kB)
Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 738.9/738.9 kB 2.2 MB/s eta 0:00:00
Downloading XlsxWriter-3.1.9-py3-none-any.whl (154 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.8/154.8 kB 545.2 kB/s eta 0:00:00
Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.3/142.3 kB 555.4 kB/s eta 0:00:00
Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (310 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 311.0/311.0 kB 1.3 MB/s eta 0:00:00
Downloading coverage-7.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (233 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.6/233.6 kB 2.3 MB/s eta 0:00:00
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading exceptiongroup-1.2.0-py3-none-any.whl (16 kB)
Downloading fonttools-4.49.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 13.1 MB/s eta 0:00:00
Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 6.1 MB/s eta 0:00:00
Downloading idna-3.6-py3-none-any.whl (61 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 3.6 MB/s eta 0:00:00
Downloading imageio-2.34.0-py3-none-any.whl (313 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 313.4/313.4 kB 343.2 kB/s eta 0:00:00
Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB)
Downloading joblib-1.3.2-py3-none-any.whl (302 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 302.2/302.2 kB 1.3 MB/s eta 0:00:00
Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 5.2 MB/s eta 0:00:00
Downloading lazy_loader-0.3-py3-none-any.whl (9.1 kB)
Downloading loguru-0.7.2-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.5/62.5 kB 441.9 kB/s eta 0:00:00
Downloading packaging-23.2-py3-none-any.whl (53 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.0/53.0 kB 48.2 kB/s eta 0:00:00
Downloading pluggy-1.4.0-py3-none-any.whl (20 kB)
Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 505.5/505.5 kB 1.1 MB/s eta 0:00:00
Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.9/294.9 kB 772.1 kB/s eta 0:00:00
Downloading SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (52.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.7/52.7 MB 7.1 MB/s eta 0:00:00
Downloading tensorboard-2.16.1-py3-none-any.whl (5.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.5/5.5 MB 7.8 MB/s eta 0:00:00
Downloading protobuf-4.25.3-cp37-abi3-manylinux2014_x86_64.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.6/294.6 kB 590.0 kB/s eta 0:00:00
Using cached setuptools-69.1.0-py3-none-any.whl (819 kB)
Downloading threadpoolctl-3.3.0-py3-none-any.whl (17 kB)
Downloading tifffile-2024.2.12-py3-none-any.whl (224 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 224.5/224.5 kB 2.5 MB/s eta 0:00:00
Downloading torchio-0.19.5-py2.py3-none-any.whl (173 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 173.1/173.1 kB 542.0 kB/s eta 0:00:00
Downloading types_setuptools-69.1.0.20240215-py3-none-any.whl (51 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.8/51.8 kB 116.2 kB/s eta 0:00:00
Downloading wandb-0.16.3-py3-none-any.whl (2.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 7.2 MB/s eta 0:00:00
Downloading dicom2nifti-2.4.10-py3-none-any.whl (43 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.6/43.6 kB 333.3 kB/s eta 0:00:00
Downloading flatbuffers-23.5.26-py2.py3-none-any.whl (26 kB)
Downloading imagecodecs-2024.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.7/39.7 MB 7.9 MB/s eta 0:00:00
Downloading lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.0/8.0 MB 16.7 MB/s eta 0:00:00
Downloading monai-1.3.0-202310121228-py3-none-any.whl (1.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 10.2 MB/s eta 0:00:00
Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 19.6 MB/s eta 0:00:00
Downloading absl_py-2.1.0-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.7/133.7 kB 2.2 MB/s eta 0:00:00
Downloading click-8.1.7-py3-none-any.whl (97 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 433.3 kB/s eta 0:00:00
Downloading GitPython-3.1.42-py3-none-any.whl (195 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 195.4/195.4 kB 461.4 kB/s eta 0:00:00
Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 13.9 MB/s eta 0:00:00
Downloading Markdown-3.5.2-py3-none-any.whl (103 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.9/103.9 kB 204.3 kB/s eta 0:00:00
Downloading pydicom-2.4.4-py3-none-any.whl (1.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 11.1 MB/s eta 0:00:00
Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl (257 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 257.9/257.9 kB 4.3 MB/s eta 0:00:00
Downloading tensorboard_data_server-0.7.2-py3-none-any.whl (2.4 kB)
Downloading tf_keras-2.15.0-py3-none-any.whl (1.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 2.6 MB/s eta 0:00:00
Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB)
Downloading werkzeug-3.0.1-py3-none-any.whl (226 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 226.7/226.7 kB 1.8 MB/s eta 0:00:00
Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB)
Downloading bids_validator-1.14.0-py3-none-any.whl (21 kB)
Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 30.3 MB/s eta 0:00:00
Downloading Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB)
Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Downloading fsspec-2024.2.0-py3-none-any.whl (170 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.9/170.9 kB 1.4 MB/s eta 0:00:00
Downloading humanize-4.9.0-py3-none-any.whl (126 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.8/126.8 kB 1.1 MB/s eta 0:00:00
Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 896.3 kB/s eta 0:00:00
Downloading num2words-0.5.13-py3-none-any.whl (143 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.3/143.3 kB 1.7 MB/s eta 0:00:00
Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.0/13.0 MB 16.3 MB/s eta 0:00:00
Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (30 kB)
Downloading gitdb-4.0.11-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.7/62.7 kB 476.4 kB/s eta 0:00:00
Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Downloading rich-13.7.0-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.6/240.6 kB 1.1 MB/s eta 0:00:00
Downloading shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)
Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.1/80.1 kB 207.1 kB/s eta 0:00:00
Downloading typer-0.9.0-py3-none-any.whl (45 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.9/45.9 kB 37.6 kB/s eta 0:00:00
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 682.5 kB/s eta 0:00:00
Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 4.4 MB/s eta 0:00:00
Downloading smmap-5.0.1-py3-none-any.whl (24 kB)
Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, future, docopt
  Building wheel for nnunetv2 (pyproject.toml): started
  Building wheel for nnunetv2 (pyproject.toml): finished with status 'done'
  Created wheel for nnunetv2: filename=nnunetv2-2.2.1-py3-none-any.whl size=237457 sha256=d1f163dbb30f38550e2ad03312711a93eb4c547898c18f6b7ea0034d2eecb423
  Stored in directory: /home/jovyan/.cache/pip/wheels/a9/7a/70/acdee60dabd3de1dcce9e5b13c6abb0215a20e034e7e8118c7
  Building wheel for acvl-utils (setup.py): started
  Building wheel for acvl-utils (setup.py): finished with status 'done'
  Created wheel for acvl-utils: filename=acvl_utils-0.2-py3-none-any.whl size=22438 sha256=946c8de311b1a7d293cffdbd75b96b28e500115ececbf7e9955c124becf0463b
  Stored in directory: /home/jovyan/.cache/pip/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7
  Building wheel for batchgenerators (setup.py): started
  Building wheel for batchgenerators (setup.py): finished with status 'done'
  Created wheel for batchgenerators: filename=batchgenerators-0.25-py3-none-any.whl size=89008 sha256=cf97138ab5e4ffe8324353f8dd47d8ae7aa4d8f05c94bc41b093846af6ca59a7
  Stored in directory: /home/jovyan/.cache/pip/wheels/41/e7/c9/91b1589e2a08ad83bdd96b0beb3a496effda855580ef698568
  Building wheel for dynamic-network-architectures (setup.py): started
  Building wheel for dynamic-network-architectures (setup.py): finished with status 'done'
  Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.2-py3-none-any.whl size=27245 sha256=2c0f07517695fdd192ad06b9b6aaf6ffb1e3a8fe4fba419f8aa03f483065cc12
  Stored in directory: /home/jovyan/.cache/pip/wheels/4e/c0/70/740949411012a24276008fa6e920f42701ae6fa18ce6122eb5
  Building wheel for pystrum (setup.py): started
  Building wheel for pystrum (setup.py): finished with status 'done'
  Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19533 sha256=cc2aa73bc876f544b97515ec0daf71c95d5b2c150d137d2f995c5f9bff752a92
  Stored in directory: /home/jovyan/.cache/pip/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492024 sha256=bd984687474811870e347bd06ee25445a6fe6f69d7f833da3fd1414b245a9a36
  Stored in directory: /home/jovyan/.cache/pip/wheels/bf/5d/6a/2e53874f7ec4e2bede522385439531fafec8fafe005b5c3d1b
  Building wheel for docopt (setup.py): started
  Building wheel for docopt (setup.py): finished with status 'done'
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=0558a834ddf304d308827da2933dba8f40deb3665898103703025e2bb4b73584
  Stored in directory: /home/jovyan/.cache/pip/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b
Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum future docopt
Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tf-keras, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, pyqt5-sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed
Successfully installed Deprecated-1.2.14 GitPython-3.1.42 MarkupSafe-2.1.5 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.1 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.2 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.49.0 formulaic-0.3.4 fsspec-2024.2.0 future-0.18.3 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.60.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.1 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.2.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.0 packaging-23.2 pandas-1.4.4 pillow-10.2.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.3 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-2.4.7 pyqt5-5.12.3 pyqt5-sip-12.12.2 pystrum-0.4 pytest-8.0.0 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.1.post1 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.4 setproctitle-1.3.3 setuptools-68.2.2 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.1 tensorboard-data-server-0.7.2 tf-keras-2.15.0 threadpoolctl-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.0+cpu torchio-0.19.5 torchvision-0.17.0+cpu tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240215 typing-extensions-4.9.0 unittest2-1.1.0 urllib3-2.2.0 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.1.9 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0

[0;32mInstalling spinalcordtoolbox...[0m

Obtaining file:///home/jovyan/content/sct
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-6.3.dev0

[0;32mCreating launchers for Python scripts...[0m

[0;32mInstalling binaries...[0m

[0;34msct_download_data -d binaries_linux -k[0m

--
Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)

sct_download_data -d binaries_linux -k
--

Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz
Downloading: spinalcordtoolbox-binaries_linux.tar.gz

Status:   0%|          | 0.00/83.7M [00:00 63a0cc0007f3
Step 49/53 : ENV PYTHONUNBUFFERED=1
 ---> Running in 033bc7cb7cf6
Removing intermediate container 033bc7cb7cf6
 ---> 8870f7401a0a
Step 50/53 : COPY /python3-login /usr/local/bin/python3-login
 ---> 5c04ab56e187
Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> eefcf7517471
Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in f344ae8fa9bb
Removing intermediate container f344ae8fa9bb
 ---> d1110a253aef
Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in 0de95c662fa1
Removing intermediate container 0de95c662fa1
 ---> 112b28e19ac8
{"aux": {"ID": "sha256:112b28e19ac8b32a5eab3d53c936fb3d2fc22bb0f0b4a0aa06c32cc1210dcc1d"}}Successfully built 112b28e19ac8
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-shimming-2dtoolbox-2drf-2dshimming-2d7t-406654:47f08c4a054636c29aacb31a1bd1d33972874b82
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
received unexpected HTTP status: 500 Internal Server Error

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

I could not find any book log for shimming-toolbox/rf-shimming-7t at 47f08c4a054636c29aacb31a1bd1d33972874b82

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

For guidelines, please see the relevant documentation.

The issue is caused by large image size, the docker image with data included is ~9GB and w/o about 7.23GB.

I'll remove the size limit altogether and see if it works.

Yeah those are about the sizes I saw locally too; I thought it would be ok because it's under the 10GB limit posted on the NeuroLibre docs: https://docs.neurolibre.org/en/latest/FAQ.html#what-are-the-hardware-limits-on-neurolibre

That 10GB is listed there per DockerHub's documentation, but the real issue is that one layer ends up being ~5GB (postbuild layer) and that fails to push after 1.34GB.

I am deploying another registry to see if issue pertains to a specific site.

That 10GB is listed there per DockerHub's documentation, but the real issue is that one layer ends up being ~5GB (postbuild layer) and that fails to push after 1.34GB.

Gocha! For future reference, I think this indicates that we've hit the max capacity of the requirements.txt/postBuild way of building an image, and for a case like this maybe writing a Dockerfile with the SCT install in just one of the RUN steps would have made possibly made the layer sizes more manigeable

@roboneuro build book

🔴 Binder build has failed 🥀

Status: Failed e9ad2aba Last updated: 2024-02-17 06:32:40 PST

:information_source: See details

The next comment will forward the logs

@mathieuboudreau good news, the image is pushed and binderhub can actually spawn the pod!

Data has been downloaded, the first book build was attempted. This is the error:

# Function for Benjamini-Hochberg FDR correction
def benjamini_hochberg(p_values):
    n = len(p_values)
    sorted_p_values = np.sort(p_values)
    sorted_index = np.argsort(p_values)
    adjusted_p_values = np.zeros(n)

    for i, p in enumerate(sorted_p_values):
        adjusted_p_values[sorted_index[i]] = min(p * n / (i + 1), 1)

    return adjusted_p_values

# Applying Benjamini-Hochberg FDR correction
adjusted_p_values = benjamini_hochberg(p_values)

# Creating a summary DataFrame
comparison_results = pd.DataFrame({'Pair': pairs, 'P-Value': p_values, 'Adjusted P-Value': adjusted_p_values})

# Save to CSV
comparison_results.to_csv(os.path.join(path_results, 'stats_t2starw_paired_ttest.csv'), index=False)

print(f"Paired t-tests:\n{comparison_results}")
------------------

---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
/tmp/ipykernel_132/897641024.py in <module>
      3 # Convert to DataFrame and save to CSV
      4 df_stats = pd.DataFrame(data_stats, columns=['Subject', 'Shim_Mode', 'Average', 'Standard_Deviation'])
----> 5 df_stats.to_csv(os.path.join(path_results, 'stats_t2starw.csv'), index=False)
      6 
      7 # Compute statistics across subjects

/srv/conda/envs/notebook/lib/python3.8/site-packages/pandas/core/generic.py in to_csv(self, path_or_buf, sep, na_rep, float_format, columns, header, index, index_label, mode, encoding, compression, quoting, quotechar, lineterminator, chunksize, date_format, doublequote, escapechar, decimal, errors, storage_options)
   3770         )
   3771 
-> 3772         return DataFrameRenderer(formatter).to_csv(
   3773             path_or_buf,
   3774             lineterminator=lineterminator,

/srv/conda/envs/notebook/lib/python3.8/site-packages/pandas/io/formats/format.py in to_csv(self, path_or_buf, encoding, sep, columns, index_label, mode, compression, quoting, quotechar, lineterminator, chunksize, date_format, doublequote, escapechar, errors, storage_options)
   1184             formatter=self.fmt,
   1185         )
-> 1186         csv_formatter.save()
   1187 
   1188         if created_buffer:

/srv/conda/envs/notebook/lib/python3.8/site-packages/pandas/io/formats/csvs.py in save(self)
    238         """
    239         # apply compression and byte/text conversion
--> 240         with get_handle(
    241             self.filepath_or_buffer,
    242             self.mode,

/srv/conda/envs/notebook/lib/python3.8/site-packages/pandas/io/common.py in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)
    857         if ioargs.encoding and "b" not in ioargs.mode:
    858             # Encoding
--> 859             handle = open(
    860                 handle,
    861                 ioargs.mode,

OSError: [Errno 30] Read-only file system: '/home/jovyan/data/rf-shimming-7t/ds004906/derivatives/results/stats_t2starw.csv'
OSError: [Errno 30] Read-only file system: '/home/jovyan/data/rf-shimming-7t/ds004906/derivatives/results/stats_t2starw.csv'

The data directory mounted to the root of the project is read-only.

I think the following is trying to write outputs at that location:

comparison_results.to_csv(os.path.join(path_results, 'stats_t2starw_paired_ttest.csv'), index=False)

Instead, for outputs, you can create a folder results and save them there. That directory will be ephemeral and will be destroyed after the session is closed, but people can still observe outputs and download them before leaving the binderhub if they want to.

@roboneuro build book

🟢 Successfully built

Status: Success bd4fc27e Last updated: 2024-02-18 04:21:50 PST

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

:robot::speech_balloon::confetti_ball::rocket: Congratulations on successfully building the neurolibre reproducible preprint for your paper on RF shimming in the cervical spinal cord at 7T! Your innovative work showcases the power of collaboration and technology in advancing MRI 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.

@roboneuro generate pdf

@roboneuro build book

🔴 Binder build has failed 🥀

Status: Failed c8d156a7 Last updated: 2024-02-18 11:18:59 PST

:information_source: See details

The next comment will forward the logs

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

🥀 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/repo2docker32sckf_c'...
HEAD is now at 3e65cec Update paper.md for pdf
Building conda environment for python=3.8Using PythonBuildPack builder
Building conda environment for python=3.8Building conda environment for python=3.8Step 1/53 : FROM buildpack-deps:bionic
 ---> bf89ebf6b3e4
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> ae378de4f5b9
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 08a78cfb4049
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> fbceb2a67733
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> 3cf70612d1fc
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 54727b822f5d
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> dc588c857c02
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 5e06214b4b44
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> 42ff2be77138
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> bd417f3d3dd4
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> b60430c82d10
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 5e458aff2510
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> a438632f3dc3
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 0942e47ae895
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> bad1e96f449e
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> 73090ab9c46f
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 3a4d18f1d969
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 0475c612f284
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 4a2d8b0fcc6c
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> d1a029699546
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> b14a9e7011ae
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 7bb964d87d10
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 56b69ac27d81
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> 55a865e1b0ca
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> d82b4d87d277
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e8-2elock-61be8f /tmp/env/environment.lock
 ---> Using cache
 ---> d3f1fef730ce
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> 9ba1874bc4c7
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 9152c383d252
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 51d7e1747282
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 22ddec68b188
Step 31/53 : USER root
 ---> Using cache
 ---> d5972cb0f670
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 33c7bdbe312e
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 479614e3035e
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 4f3657da5f62
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 9f85fe4764c0
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> 932d4b31c401
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> 981d892d58f3
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 75c1ad851985
Step 39/53 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
 ---> Using cache
 ---> af6e8a93567d
Step 40/53 : USER ${NB_USER}
 ---> Using cache
 ---> 2cb0f5027b3e
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
 ---> Using cache
 ---> 6d3cea3fd2d2
Step 42/53 : COPY --chown=1000:1000 src/ ${REPO_DIR}
 ---> e8b350769db8
Step 43/53 : LABEL repo2docker.ref="3e65cec20c065ebc0e077866bd10976b3e0a13f3"
 ---> Running in 2146aba9127e
Removing intermediate container 2146aba9127e
 ---> 55273cd878ec
Step 44/53 : LABEL repo2docker.repo="https://github.com/shimming-toolbox/rf-shimming-7t"
 ---> Running in 4c4e7915f00d
Removing intermediate container 4c4e7915f00d
 ---> cc7eadcd8224
Step 45/53 : LABEL repo2docker.version="2021.08.0"
 ---> Running in f3358f7bbe68
Removing intermediate container f3358f7bbe68
 ---> 7d22c8ece08c
Step 46/53 : USER ${NB_USER}
 ---> Running in 64f01df68e03
Removing intermediate container 64f01df68e03
 ---> da926cf7c705
Step 47/53 : RUN chmod +x binder/postBuild
 ---> Running in 382df17795a0
Removing intermediate container 382df17795a0
 ---> 5697ded1abfa
Step 48/53 : RUN ./binder/postBuild
 ---> Running in ee8309e777ca
[91mCloning into '/home/jovyan/content/sct'...
[0m
[0;32m
*******************************
* Welcome to SCT installation *
*******************************
[0m

[0;32mChecking OS type and version...[0m

Linux ee8309e777ca 5.4.0-139-generic #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

[0;32mChecking requirements...[0m

[0;32mOK![0m

SCT version ......... 6.3.dev0
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /home/jovyan/.bashrc

[0;32mSCT will be installed here: [/home/jovyan/content/sct][0m

[0;92m
Do you agree? [y]es/[n]o: [0m
[0;32mSkipping copy of source files (source and destination folders are the same)[0m

[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: [0m
[0;32mDownloading Miniconda...[0m

[0;34mwget -nv -O /tmp/tmp.tfXc8xP1m9/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh[0m

2024-02-18 19:04:17 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [141613749/141613749] -> "/tmp/tmp.tfXc8xP1m9/miniconda.sh" [1]

[0;32mInstalling Miniconda...[0m

[0;34mbash /tmp/tmp.tfXc8xP1m9/miniconda.sh -p /home/jovyan/content/sct/python -b -f[0m

PREFIX=/home/jovyan/content/sct/python
Unpacking payload ...

  0%|          | 0/73 [00:00 conda-forge::ca-certificates-2024.2.2-hbcca054_0 
  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5 
  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5 
  libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5 
  openssl              pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0 

The following packages will be SUPERSEDED by a higher-priority channel:

  _libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu 

Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1)
Collecting pip!=21.2.*
  Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)
Downloading pip-24.0-py3-none-any.whl (2.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 8.3 MB/s eta 0:00:00
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 23.3.1
    Uninstalling pip-23.3.1:
      Successfully uninstalled pip-23.3.1
Successfully installed pip-24.0

[0;32mInstalling Python dependencies...[0m

[0;32mUsing requirements.txt (git installation)[0m

Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Collecting dipy!=1.6.*,!=1.7.*,!=1.8.* (from -r requirements.txt (line 7))
  Downloading dipy-1.5.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.9/7.9 MB 19.0 MB/s eta 0:00:00
Collecting ivadomed (from -r requirements.txt (line 11))
  Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB)
Collecting matplotlib (from -r requirements.txt (line 12))
  Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-5.2.0-py3-none-any.whl.metadata (8.8 kB)
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB)
Collecting nnunetv2 (from -r requirements.txt (line 23))
  Downloading nnunetv2-2.2.1.tar.gz (178 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 178.6/178.6 kB 619.0 kB/s eta 0:00:00
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting numpy<1.24 (from -r requirements.txt (line 27))
  Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 18.4 MB/s eta 0:00:00
Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31))
  Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (4.2 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting portalocker (from -r requirements.txt (line 33))
  Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)
Collecting psutil (from -r requirements.txt (line 34))
  Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39))
  Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-manylinux1_x86_64.whl (62.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.4/62.4 MB 10.9 MB/s eta 0:00:00
Collecting pyqt5-sip<12.13.0 (from -r requirements.txt (line 41))
  Downloading PyQt5_sip-12.12.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (504 bytes)
Collecting pytest (from -r requirements.txt (line 42))
  Downloading pytest-8.0.1-py3-none-any.whl.metadata (7.7 kB)
Collecting pytest-cov (from -r requirements.txt (line 43))
  Downloading pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB)
Collecting requests (from -r requirements.txt (line 44))
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting requirements-parser (from -r requirements.txt (line 45))
  Downloading requirements_parser-0.5.0-py3-none-any.whl (18 kB)
Collecting scipy (from -r requirements.txt (line 46))
  Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 143.7 kB/s eta 0:00:00
Collecting scikit-image (from -r requirements.txt (line 47))
  Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting scikit-learn (from -r requirements.txt (line 48))
  Downloading scikit_learn-1.4.1.post1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting xlwt (from -r requirements.txt (line 49))
  Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 1.2 MB/s eta 0:00:00
Collecting tqdm (from -r requirements.txt (line 50))
  Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 136.7 kB/s eta 0:00:00
Collecting transforms3d (from -r requirements.txt (line 51))
  Downloading transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB)
Collecting urllib3 (from -r requirements.txt (line 52))
  Downloading urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB)
Collecting pytest_console_scripts (from -r requirements.txt (line 53))
  Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB)
Collecting pyyaml (from -r requirements.txt (line 54))
  Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting voxelmorph (from -r requirements.txt (line 55))
  Downloading voxelmorph-0.2-py3-none-any.whl (54 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.2/54.2 kB 619.8 kB/s eta 0:00:00
Collecting wquantiles (from -r requirements.txt (line 56))
  Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)
Collecting xlsxwriter (from -r requirements.txt (line 59))
  Downloading XlsxWriter-3.1.9-py3-none-any.whl.metadata (2.6 kB)
Collecting monai[nibabel] (from -r requirements.txt (line 13))
  Downloading monai-1.3.0-202310121228-py3-none-any.whl.metadata (10 kB)
Collecting h5py>=2.8.0 (from dipy!=1.6.*,!=1.7.*,!=1.8.*->-r requirements.txt (line 7))
  Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting pyparsing<3,>=2.0.2 (from ivadomed->-r requirements.txt (line 11))
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.8/67.8 kB 149.8 kB/s eta 0:00:00
Collecting csv-diff>=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading csv_diff-1.1-py3-none-any.whl (12 kB)
Collecting loguru~=0.5 (from ivadomed->-r requirements.txt (line 11))
  Downloading loguru-0.7.2-py3-none-any.whl.metadata (23 kB)
Collecting imageio>=2.31.4 (from ivadomed->-r requirements.txt (line 11))
  Downloading imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB)
Collecting joblib~=1.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting nibabel (from -r requirements.txt (line 21))
  Downloading nibabel-3.2.2-py3-none-any.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 22.0 MB/s eta 0:00:00
Collecting onnx (from ivadomed->-r requirements.txt (line 11))
  Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (15 kB)
Collecting pandas (from -r requirements.txt (line 32))
  Downloading pandas-1.4.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 46.4 MB/s eta 0:00:00
Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading pybids-0.15.5-py3-none-any.whl (14.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.9/14.9 MB 13.3 MB/s eta 0:00:00
Collecting seaborn~=0.11 (from ivadomed->-r requirements.txt (line 11))
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard-2.16.2-py3-none-any.whl.metadata (1.6 kB)
Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 11))
  Downloading torchio-0.19.5-py2.py3-none-any.whl.metadata (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.2/48.2 kB 169.3 kB/s eta 0:00:00
Collecting torch>=1.8.1 (from ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/cpu/torch-2.2.0%2Bcpu-cp39-cp39-linux_x86_64.whl (186.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 186.8/186.8 MB 4.1 MB/s eta 0:00:00
Collecting torchvision>=0.9.1 (from ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.17.0%2Bcpu-cp39-cp39-linux_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 2.3 MB/s eta 0:00:00
Collecting wandb>=0.12.11 (from ivadomed->-r requirements.txt (line 11))
  Downloading wandb-0.16.3-py3-none-any.whl.metadata (9.9 kB)
Collecting contourpy>=1.0.1 (from matplotlib->-r requirements.txt (line 12))
  Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib->-r requirements.txt (line 12))
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading fonttools-4.49.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (159 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 159.1/159.1 kB 198.2 kB/s eta 0:00:00
Collecting kiwisolver>=1.3.1 (from matplotlib->-r requirements.txt (line 12))
  Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.4 kB)
Collecting packaging>=20.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pillow>=8 (from matplotlib->-r requirements.txt (line 12))
  Downloading https://download.pytorch.org/whl/pillow-10.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 23.2 MB/s eta 0:00:00
Collecting python-dateutil>=2.7 (from matplotlib->-r requirements.txt (line 12))
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 2.8 MB/s eta 0:00:00
Collecting importlib-resources>=3.2.0 (from matplotlib->-r requirements.txt (line 12))
  Downloading importlib_resources-6.1.1-py3-none-any.whl.metadata (4.1 kB)
Collecting setuptools (from nibabel->-r requirements.txt (line 21))
  Using cached setuptools-69.1.0-py3-none-any.whl.metadata (6.1 kB)
Collecting lxml (from nilearn->-r requirements.txt (line 22))
  Downloading lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.5 kB)
INFO: pip is looking at multiple versions of nilearn to determine which version is compatible with other requirements. This could take a while.
Collecting nilearn (from -r requirements.txt (line 22))
  Downloading nilearn-0.10.2-py3-none-any.whl.metadata (7.8 kB)
Collecting acvl-utils>=0.2 (from nnunetv2->-r requirements.txt (line 23))
  Downloading acvl_utils-0.2.tar.gz (18 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dynamic-network-architectures>=0.2 (from nnunetv2->-r requirements.txt (line 23))
  Downloading dynamic_network_architectures-0.2.tar.gz (20 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dicom2nifti (from nnunetv2->-r requirements.txt (line 23))
  Downloading dicom2nifti-2.4.10-py3-none-any.whl.metadata (1.3 kB)
Collecting batchgenerators>=0.25 (from nnunetv2->-r requirements.txt (line 23))
  Downloading batchgenerators-0.25.tar.gz (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.7/61.7 kB 234.9 kB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting SimpleITK>=2.2.1 (from nnunetv2->-r requirements.txt (line 23))
  Downloading SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.9 kB)
Collecting graphviz (from nnunetv2->-r requirements.txt (line 23))
  Downloading graphviz-0.20.1-py3-none-any.whl (47 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 kB 118.8 kB/s eta 0:00:00
Collecting tifffile (from nnunetv2->-r requirements.txt (line 23))
  Downloading tifffile-2024.2.12-py3-none-any.whl.metadata (31 kB)
Collecting imagecodecs (from nnunetv2->-r requirements.txt (line 23))
  Downloading imagecodecs-2024.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting yacs (from nnunetv2->-r requirements.txt (line 23))
  Downloading yacs-0.1.8-py3-none-any.whl (14 kB)
Collecting coloredlogs (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.0/46.0 kB 124.2 kB/s eta 0:00:00
Collecting flatbuffers (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading flatbuffers-23.5.26-py2.py3-none-any.whl.metadata (850 bytes)
Collecting protobuf (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading protobuf-4.25.3-cp37-abi3-manylinux2014_x86_64.whl.metadata (541 bytes)
Collecting sympy (from onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/sympy-1.12-py3-none-any.whl (5.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.7/5.7 MB 17.2 MB/s eta 0:00:00
Collecting pytz>=2020.1 (from pandas->-r requirements.txt (line 32))
  Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting iniconfig (from pytest->-r requirements.txt (line 42))
  Downloading iniconfig-2.0.0-py3-none-any.whl.metadata (2.6 kB)
Collecting pluggy<2.0,>=1.3.0 (from pytest->-r requirements.txt (line 42))
  Downloading pluggy-1.4.0-py3-none-any.whl.metadata (4.3 kB)
Collecting exceptiongroup>=1.0.0rc8 (from pytest->-r requirements.txt (line 42))
  Downloading exceptiongroup-1.2.0-py3-none-any.whl.metadata (6.6 kB)
Collecting tomli>=1.0.0 (from pytest->-r requirements.txt (line 42))
  Downloading tomli-2.0.1-py3-none-any.whl (12 kB)
Collecting coverage>=5.2.1 (from coverage[toml]>=5.2.1->pytest-cov->-r requirements.txt (line 43))
  Downloading coverage-7.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.2 kB)
Collecting charset-normalizer<4,>=2 (from requests->-r requirements.txt (line 44))
  Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests->-r requirements.txt (line 44))
  Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting types-setuptools>=57.0.0 (from requirements-parser->-r requirements.txt (line 45))
  Downloading types_setuptools-69.1.0.20240217-py3-none-any.whl.metadata (1.6 kB)
Collecting networkx>=2.8 (from scikit-image->-r requirements.txt (line 47))
  Downloading https://download.pytorch.org/whl/networkx-3.2.1-py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 5.9 MB/s eta 0:00:00
Collecting lazy_loader>=0.3 (from scikit-image->-r requirements.txt (line 47))
  Downloading lazy_loader-0.3-py3-none-any.whl.metadata (4.3 kB)
Collecting threadpoolctl>=2.0.0 (from scikit-learn->-r requirements.txt (line 48))
  Downloading threadpoolctl-3.3.0-py3-none-any.whl.metadata (13 kB)
Collecting importlib-metadata>=3.6 (from pytest_console_scripts->-r requirements.txt (line 53))
  Downloading importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting neurite>=0.2 (from voxelmorph->-r requirements.txt (line 55))
  Downloading neurite-0.2-py3-none-any.whl (108 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 kB 530.4 kB/s eta 0:00:00
Collecting connected-components-3d (from acvl-utils>=0.2->nnunetv2->-r requirements.txt (line 23))
  Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (29 kB)
Collecting future (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading future-0.18.3.tar.gz (840 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 840.9/840.9 kB 2.5 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting unittest2 (from batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.4/96.4 kB 315.6 kB/s eta 0:00:00
Collecting click (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting dictdiffer (from csv-diff>=1.0->ivadomed->-r requirements.txt (line 11))
  Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB)
Collecting zipp>=0.5 (from importlib-metadata>=3.6->pytest_console_scripts->-r requirements.txt (line 53))
  Downloading zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB)
Collecting six (from neurite>=0.2->voxelmorph->-r requirements.txt (line 55))
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pystrum>=0.2 (from neurite>=0.2->voxelmorph->-r requirements.txt (line 55))
  Downloading pystrum-0.4.tar.gz (17 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting formulaic<0.4,>=0.2.4 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading formulaic-0.3.4-py3-none-any.whl (68 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.2/68.2 kB 294.2 kB/s eta 0:00:00
Collecting sqlalchemy<1.4.0.dev0 (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading SQLAlchemy-1.3.24-cp39-cp39-manylinux2010_x86_64.whl (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 5.5 MB/s eta 0:00:00
Collecting bids-validator (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading bids_validator-1.14.0-py3-none-any.whl.metadata (38 kB)
Collecting num2words (from pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading num2words-0.5.13-py3-none-any.whl.metadata (12 kB)
Collecting absl-py>=0.4 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting grpcio>=1.48.2 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
Collecting markdown>=2.6.8 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading Markdown-3.5.2-py3-none-any.whl.metadata (7.0 kB)
Collecting tensorboard-data-server<0.8.0,>=0.7.0 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading tensorboard_data_server-0.7.2-py3-none-any.whl.metadata (1.1 kB)
Collecting werkzeug>=1.0.1 (from tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading werkzeug-3.0.1-py3-none-any.whl.metadata (4.1 kB)
Collecting filelock (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB)
Collecting typing-extensions>=4.8.0 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)
Collecting jinja2 (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Collecting fsspec (from torch>=1.8.1->ivadomed->-r requirements.txt (line 11))
  Downloading fsspec-2024.2.0-py3-none-any.whl.metadata (6.8 kB)
Collecting Deprecated (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)
Collecting humanize (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading humanize-4.9.0-py3-none-any.whl.metadata (7.9 kB)
Collecting typer[all] (from torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading typer-0.9.0-py3-none-any.whl.metadata (14 kB)
Collecting GitPython!=3.1.29,>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading GitPython-3.1.42-py3-none-any.whl.metadata (12 kB)
Collecting sentry-sdk>=1.0.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl.metadata (9.7 kB)
Collecting docker-pycreds>=0.4.0 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Collecting setproctitle (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.9 kB)
Collecting appdirs>=1.4.3 (from wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting humanfriendly>=9.1 (from coloredlogs->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 kB 176.1 kB/s eta 0:00:00
Collecting pydicom>=2.2.0 (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading pydicom-2.4.4-py3-none-any.whl.metadata (7.8 kB)
Collecting python-gdcm (from dicom2nifti->nnunetv2->-r requirements.txt (line 23))
  Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
Collecting mpmath>=0.19 (from sympy->onnxruntime!=1.16.0,>=1.7.0->-r requirements.txt (line 31))
  Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 3.4 MB/s eta 0:00:00
Collecting astor>=0.8 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting interface-meta<2.0.0,>=1.2.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading interface_meta-1.3.0-py3-none-any.whl (14 kB)
Collecting wrapt>=1.0 (from formulaic<0.4,>=0.2.4->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting gitdb<5,>=4.0.1 (from GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Collecting MarkupSafe>=2.1.1 (from werkzeug>=1.0.1->tensorboard>=1.15.0->ivadomed->-r requirements.txt (line 11))
  Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting docopt>=0.6.2 (from num2words->pybids<0.15.6,>=0.14.0->ivadomed->-r requirements.txt (line 11))
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting colorama<0.5.0,>=0.4.3 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading https://download.pytorch.org/whl/colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting shellingham<2.0.0,>=1.3.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting rich<14.0.0,>=10.11.0 (from typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading rich-13.7.0-py3-none-any.whl.metadata (18 kB)
Collecting argparse (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Collecting traceback2 (from unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->GitPython!=3.1.29,>=1.0.0->wandb>=0.12.11->ivadomed->-r requirements.txt (line 11))
  Downloading smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB)
Collecting markdown-it-py>=2.2.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting pygments<3.0.0,>=2.13.0 (from rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
Collecting linecache2 (from traceback2->unittest2->batchgenerators>=0.25->nnunetv2->-r requirements.txt (line 23))
  Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB)
Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich<14.0.0,>=10.11.0->typer[all]->torchio>=0.18.68->ivadomed->-r requirements.txt (line 11))
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Downloading certifi-2024.2.2-py3-none-any.whl (163 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.8/163.8 kB 672.0 kB/s eta 0:00:00
Downloading ivadomed-2.9.9-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.4/240.4 kB 517.4 kB/s eta 0:00:00
Downloading matplotlib-3.8.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 14.2 MB/s eta 0:00:00
Downloading nilearn-0.10.2-py3-none-any.whl (10.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.4/10.4 MB 22.9 MB/s eta 0:00:00
Downloading onnxruntime-1.17.0-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.8/6.8 MB 33.9 MB/s eta 0:00:00
Downloading portalocker-2.8.2-py3-none-any.whl (17 kB)
Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (288 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 389.8 kB/s eta 0:00:00
Downloading PyQt5_sip-12.12.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (335 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 335.3/335.3 kB 1.9 MB/s eta 0:00:00
Downloading pytest-8.0.1-py3-none-any.whl (333 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 334.0/334.0 kB 1.2 MB/s eta 0:00:00
Downloading pytest_cov-4.1.0-py3-none-any.whl (21 kB)
Downloading requests-2.31.0-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 1.1 MB/s eta 0:00:00
Downloading scipy-1.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.5/38.5 MB 11.6 MB/s eta 0:00:00
Downloading scikit_image-0.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.7/14.7 MB 20.7 MB/s eta 0:00:00
Downloading scikit_learn-1.4.1.post1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.2/12.2 MB 37.5 MB/s eta 0:00:00
Downloading tqdm-4.66.2-py3-none-any.whl (78 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.3/78.3 kB 359.5 kB/s eta 0:00:00
Downloading transforms3d-0.4.1-py3-none-any.whl (1.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 12.3 MB/s eta 0:00:00
Downloading urllib3-2.2.1-py3-none-any.whl (121 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.1/121.1 kB 535.9 kB/s eta 0:00:00
Downloading pytest_console_scripts-1.4.1-py3-none-any.whl (10 kB)
Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 738.9/738.9 kB 9.2 MB/s eta 0:00:00
Downloading XlsxWriter-3.1.9-py3-none-any.whl (154 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.8/154.8 kB 389.7 kB/s eta 0:00:00
Downloading charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.3/142.3 kB 926.0 kB/s eta 0:00:00
Downloading contourpy-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (310 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 311.0/311.0 kB 3.7 MB/s eta 0:00:00
Downloading coverage-7.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (233 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.6/233.6 kB 2.8 MB/s eta 0:00:00
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading exceptiongroup-1.2.0-py3-none-any.whl (16 kB)
Downloading fonttools-4.49.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 8.7 MB/s eta 0:00:00
Downloading h5py-3.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 17.9 MB/s eta 0:00:00
Downloading idna-3.6-py3-none-any.whl (61 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 44.0 kB/s eta 0:00:00
Downloading imageio-2.34.0-py3-none-any.whl (313 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 313.4/313.4 kB 3.5 MB/s eta 0:00:00
Downloading importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Downloading importlib_resources-6.1.1-py3-none-any.whl (33 kB)
Downloading joblib-1.3.2-py3-none-any.whl (302 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 302.2/302.2 kB 4.6 MB/s eta 0:00:00
Downloading kiwisolver-1.4.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 9.1 MB/s eta 0:00:00
Downloading lazy_loader-0.3-py3-none-any.whl (9.1 kB)
Downloading loguru-0.7.2-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.5/62.5 kB 367.6 kB/s eta 0:00:00
Downloading packaging-23.2-py3-none-any.whl (53 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.0/53.0 kB 247.6 kB/s eta 0:00:00
Downloading pluggy-1.4.0-py3-none-any.whl (20 kB)
Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 505.5/505.5 kB 5.3 MB/s eta 0:00:00
Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.9/294.9 kB 429.0 kB/s eta 0:00:00
Downloading SimpleITK-2.3.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (52.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 52.7/52.7 MB 9.3 MB/s eta 0:00:00
Downloading tensorboard-2.16.2-py3-none-any.whl (5.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.5/5.5 MB 11.2 MB/s eta 0:00:00
Downloading protobuf-4.25.3-cp37-abi3-manylinux2014_x86_64.whl (294 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 294.6/294.6 kB 1.5 MB/s eta 0:00:00
Using cached setuptools-69.1.0-py3-none-any.whl (819 kB)
Downloading threadpoolctl-3.3.0-py3-none-any.whl (17 kB)
Downloading tifffile-2024.2.12-py3-none-any.whl (224 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 224.5/224.5 kB 605.5 kB/s eta 0:00:00
Downloading torchio-0.19.5-py2.py3-none-any.whl (173 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 173.1/173.1 kB 1.5 MB/s eta 0:00:00
Downloading types_setuptools-69.1.0.20240217-py3-none-any.whl (51 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.8/51.8 kB 260.6 kB/s eta 0:00:00
Downloading wandb-0.16.3-py3-none-any.whl (2.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 10.5 MB/s eta 0:00:00
Downloading dicom2nifti-2.4.10-py3-none-any.whl (43 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.6/43.6 kB 90.1 kB/s eta 0:00:00
Downloading flatbuffers-23.5.26-py2.py3-none-any.whl (26 kB)
Downloading imagecodecs-2024.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.7/39.7 MB 13.6 MB/s eta 0:00:00
Downloading iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Downloading lxml-5.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.0/8.0 MB 19.1 MB/s eta 0:00:00
Downloading monai-1.3.0-202310121228-py3-none-any.whl (1.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 5.8 MB/s eta 0:00:00
Downloading onnx-1.15.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 32.8 MB/s eta 0:00:00
Downloading absl_py-2.1.0-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.7/133.7 kB 1.0 MB/s eta 0:00:00
Downloading click-8.1.7-py3-none-any.whl (97 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 1.2 MB/s eta 0:00:00
Downloading GitPython-3.1.42-py3-none-any.whl (195 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 195.4/195.4 kB 2.7 MB/s eta 0:00:00
Downloading grpcio-1.60.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 11.5 MB/s eta 0:00:00
Downloading Markdown-3.5.2-py3-none-any.whl (103 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.9/103.9 kB 280.3 kB/s eta 0:00:00
Downloading pydicom-2.4.4-py3-none-any.whl (1.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 12.1 MB/s eta 0:00:00
Downloading sentry_sdk-1.40.4-py2.py3-none-any.whl (257 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 257.9/257.9 kB 4.1 MB/s eta 0:00:00
Downloading tensorboard_data_server-0.7.2-py3-none-any.whl (2.4 kB)
Downloading typing_extensions-4.9.0-py3-none-any.whl (32 kB)
Downloading werkzeug-3.0.1-py3-none-any.whl (226 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 226.7/226.7 kB 1.2 MB/s eta 0:00:00
Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB)
Downloading bids_validator-1.14.0-py3-none-any.whl (21 kB)
Downloading connected_components_3d-3.12.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 16.4 MB/s eta 0:00:00
Downloading Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB)
Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Downloading fsspec-2024.2.0-py3-none-any.whl (170 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.9/170.9 kB 2.8 MB/s eta 0:00:00
Downloading humanize-4.9.0-py3-none-any.whl (126 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.8/126.8 kB 1.9 MB/s eta 0:00:00
Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 2.4 MB/s eta 0:00:00
Downloading num2words-0.5.13-py3-none-any.whl (143 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.3/143.3 kB 566.3 kB/s eta 0:00:00
Downloading python_gdcm-3.0.23-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.0/13.0 MB 25.3 MB/s eta 0:00:00
Downloading setproctitle-1.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (30 kB)
Downloading gitdb-4.0.11-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.7/62.7 kB 648.3 kB/s eta 0:00:00
Downloading MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Downloading rich-13.7.0-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.6/240.6 kB 13.7 MB/s eta 0:00:00
Downloading shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)
Downloading wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.1/80.1 kB 537.2 kB/s eta 0:00:00
Downloading typer-0.9.0-py3-none-any.whl (45 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.9/45.9 kB 248.4 kB/s eta 0:00:00
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 608.7 kB/s eta 0:00:00
Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 4.2 MB/s eta 0:00:00
Downloading smmap-5.0.1-py3-none-any.whl (24 kB)
Building wheels for collected packages: nnunetv2, acvl-utils, batchgenerators, dynamic-network-architectures, pystrum, future, docopt
  Building wheel for nnunetv2 (pyproject.toml): started
  Building wheel for nnunetv2 (pyproject.toml): finished with status 'done'
  Created wheel for nnunetv2: filename=nnunetv2-2.2.1-py3-none-any.whl size=237457 sha256=1d5f41b3aa801a07df0c87b31367a8725fa6f0b1c843902810bb3933c2003206
  Stored in directory: /home/jovyan/.cache/pip/wheels/a9/7a/70/acdee60dabd3de1dcce9e5b13c6abb0215a20e034e7e8118c7
  Building wheel for acvl-utils (setup.py): started
  Building wheel for acvl-utils (setup.py): finished with status 'done'
  Created wheel for acvl-utils: filename=acvl_utils-0.2-py3-none-any.whl size=22438 sha256=40134eb5c4e77a2ddb6dff1aaf05849568a1da6c2cd21292aa41a16786b3b3bb
  Stored in directory: /home/jovyan/.cache/pip/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7
  Building wheel for batchgenerators (setup.py): started
  Building wheel for batchgenerators (setup.py): finished with status 'done'
  Created wheel for batchgenerators: filename=batchgenerators-0.25-py3-none-any.whl size=89008 sha256=4cc6a7d9474510f86263dbe077c07c706dd6b4df6c8fbb6677bd3a85dec18170
  Stored in directory: /home/jovyan/.cache/pip/wheels/41/e7/c9/91b1589e2a08ad83bdd96b0beb3a496effda855580ef698568
  Building wheel for dynamic-network-architectures (setup.py): started
  Building wheel for dynamic-network-architectures (setup.py): finished with status 'done'
  Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.2-py3-none-any.whl size=27245 sha256=51a9de35593bdf04e69790ee80ba2868b479c48ec34052268ac600f894ab8d2d
  Stored in directory: /home/jovyan/.cache/pip/wheels/4e/c0/70/740949411012a24276008fa6e920f42701ae6fa18ce6122eb5
  Building wheel for pystrum (setup.py): started
  Building wheel for pystrum (setup.py): finished with status 'done'
  Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19533 sha256=8d3d385f1dfcf8903b477d2318fde2af79ffb71bac6befab4022a7ae926a5a54
  Stored in directory: /home/jovyan/.cache/pip/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492024 sha256=745dfa68d388914db3c4c965d4ca24e3ad0c72ef6193ea258dd0030d68ada23f
  Stored in directory: /home/jovyan/.cache/pip/wheels/bf/5d/6a/2e53874f7ec4e2bede522385439531fafec8fafe005b5c3d1b
  Building wheel for docopt (setup.py): started
  Building wheel for docopt (setup.py): finished with status 'done'
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=1ce9d83e74fe7a65e05cfa281198c051068f181cba62e6fea3ee61de48619abf
  Stored in directory: /home/jovyan/.cache/pip/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b
Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum future docopt
Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, pyqt5-sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed
Successfully installed Deprecated-1.2.14 GitPython-3.1.42 MarkupSafe-2.1.5 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.1 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.2 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.49.0 formulaic-0.3.4 fsspec-2024.2.0 future-0.18.3 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.60.1 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.1 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.2.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.0 packaging-23.2 pandas-1.4.4 pillow-10.2.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.3 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-2.4.7 pyqt5-5.12.3 pyqt5-sip-12.12.2 pystrum-0.4 pytest-8.0.1 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.1.post1 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.4 setproctitle-1.3.3 setuptools-68.2.2 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.2 tensorboard-data-server-0.7.2 threadpoolctl-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.0+cpu torchio-0.19.5 torchvision-0.17.0+cpu tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240217 typing-extensions-4.9.0 unittest2-1.1.0 urllib3-2.2.1 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.1.9 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0

[0;32mInstalling spinalcordtoolbox...[0m

Obtaining file:///home/jovyan/content/sct
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-6.3.dev0

[0;32mCreating launchers for Python scripts...[0m

[0;32mInstalling binaries...[0m

[0;34msct_download_data -d binaries_linux -k[0m

--
Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407)

sct_download_data -d binaries_linux -k
--

Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz
Downloading: spinalcordtoolbox-binaries_linux.tar.gz

Status:   0%|          | 0.00/83.7M [00:00 4f8ad8a6cab0
Step 49/53 : ENV PYTHONUNBUFFERED=1
 ---> Running in 4a00d14e1593
Removing intermediate container 4a00d14e1593
 ---> 89cdae9c4635
Step 50/53 : COPY /python3-login /usr/local/bin/python3-login
 ---> f58ce9578a8f
Step 51/53 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
 ---> 18001216681e
Step 52/53 : ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
 ---> Running in b0bfda706aea
Removing intermediate container b0bfda706aea
 ---> a528a8b2aab6
Step 53/53 : CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
 ---> Running in 9e876167136b
Removing intermediate container 9e876167136b
 ---> 321c8ea13170
{"aux": {"ID": "sha256:321c8ea131709820fa3b957f0fa928a9a136255bdb9cd12e5b01a6033285eb02"}}Successfully built 321c8ea13170
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-shimming-2dtoolbox-2drf-2dshimming-2d7t-406654:3e65cec20c065ebc0e077866bd10976b3e0a13f3
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
Pushing image
received unexpected HTTP status: 500 Internal Server Error

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

I could not find any book log for shimming-toolbox/rf-shimming-7t at 3e65cec20c065ebc0e077866bd10976b3e0a13f3

🐞 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 96e41a5b Last updated: 2024-02-18 11:47:24 PST

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

:robot::speech_balloon::confetti_ball::rocket: Congratulations on successfully building the neurolibre reproducible preprint for your paper on RF shimming in the cervical spinal cord at 7T! Your work is electrifyingly impressive, sparking excitement in the MRI community.

: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 WDYT about the latest book and PDF builds? If they look good, can proceed with publishing.

@agahkarakuzu looks good at a quick glance, but I think @jcohenadad should take a look and confirm

Book build

🤖💬🎊🚀 Congratulations on successfully building the neurolibre reproducible preprint for your paper on RF shimming in the cervical spinal cord at 7T! Your work is electrifyingly impressive, sparking excitement in the MRI community.

🌺 Take a loot at the latest version of your NRP! 🌺

Important

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

NRP

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

@agahkarakuzu have you been able to test if the docker image builds and notebook runs on the servers NeuroLibre thought?

@agahkarakuzu looks good at a quick glance, but I think @jcohenadad should take a look and confirm

the PDF only shows fig 1, and there is no figure of the results-- is this expected?

@jcohenadad I think out of @stikov's preferences for prior submission, the results Figures are not shown in PDF/NeuroLibre landing page because this is not the preprint; the reproducible/interactive Jupyter Book is, an we want to encourage people to go read that page. Including all the content in the landing page/PDF might cause some people to just glance at this page and not the actual preprint. @agahkarakuzu can say more, I also know that the PDF is there for other purposes (DOI / search engine?)

@jcohenadad I think out of @stikov's preferences for prior submission, the results Figures are not shown in PDF/NeuroLibre landing page because this is not the preprint; the reproducible/interactive Jupyter Book is, an we want to encourage people to go read that page.

hum, i'm not sure i agree with that. My first reaction was: "hum, that preprint is really 'light', i'm surprised these researchers published something with so little information in there"

@jcohenadad I think out of @stikov's preferences for prior submission, the results Figures are not shown in PDF/NeuroLibre landing page because this is not the preprint; the reproducible/interactive Jupyter Book is, an we want to encourage people to go read that page.

hum, i'm not sure i agree with that. My first reaction was: "hum, that preprint is really 'light', i'm surprised these researchers published something with so little information in there"

No problem! We can definitely update the PDF so that it more-closely mirrors the interactive HTML page (eg same sections, static PNGs, etc). The one question I think I have if we do it that way is, do you want to include the code in the PDF or just keep the text and figures?

hum, i would not include the code in the PDF. thanks!

Ok, thanks for clarifying this point!

I will let Agah give you the full answer, I don't have as much insights into this html to pdf compilation as he does. But the pdf is primarily here so we have a full list of references. The html does not get published in a formal way, while the pdf is. We embed a lot of meta-data in that publication process, and that includes the citations. So from a practical perspective, we need to have the text in the pdf, but the figures are more of a bonus. We put a big disclaimer at the beginning of the pdf document explaining this limitation.

The other reason why we don't have the figures is that a lot of them are interactive (or . So we would need a mechanism to have some static version of each figure. This would require extra work for the authors (although I guess authors will have to do this work anyway for the regular journal publication), and it's not clear to me how easy it would be for neurolibre to support this dual figure generation (as usual, I'm sure Agah knows more about that than I do).

@roboneuro generate pdf

neurolibre / neurolibre-reviews

[REVIEW]: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T" #25

Status

Reviewer instructions & questions

Checklists

Book build

🌺 Take a loot at the latest version of your NRP! 🌺

NRP