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Fix binder configuration #3139

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Merged
dweindl merged 8 commits into from
Feb 28, 2026
Merged

Fix binder configuration #3139

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7fae6ca
Fix binder image default user
dweindl Feb 26, 2026
5d3c518
venv
dweindl Feb 26, 2026
2927ffe
LegacyKeyValueFormat: "ENV key=value" should be used instead of legac…
dweindl Feb 26, 2026
9198dcc
home
dweindl Feb 26, 2026
ba99da3
build
dweindl Feb 26, 2026
00052fb
pysb mess
dweindl Feb 26, 2026
d135e9c
jax extra
dweindl Feb 27, 2026
2532872
sciml extras
dweindl Feb 27, 2026
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38 changes: 24 additions & 14 deletions binder/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ FROM ubuntu:24.04
RUN apt-get update && apt-get install -y \
g++ \
git \
libatlas-base-dev \
libboost-serialization-dev \
libboost-chrono-dev \
libhdf5-serial-dev \
Expand All @@ -19,17 +18,26 @@ RUN apt-get update && apt-get install -y \
# BEGIN BINDER
ARG NB_USER=jovyan
ARG NB_UID=1000
ENV USER ${NB_USER}
ENV NB_UID ${NB_UID}
ENV HOME /home/${NB_USER}
ENV PATH="${PATH}:$HOME/.local/bin"
RUN adduser --disabled-password \
--gecos "Default user" \
--uid ${NB_UID} \
${NB_USER}
ENV USER=${NB_USER}
ENV NB_UID=${NB_UID}
ENV HOME=/home/${NB_USER}
ENV VENV_PATH=${HOME}/venv
ENV PATH="${VENV_PATH}/bin:${PATH}"
# If there is no default 1000 user:
#RUN adduser --disabled-password \
# --gecos "Default user" \
# --uid ${NB_UID} \
# ${NB_USER}
# On ubuntu>=24.04 images there is ubuntu(1000)
# see https://bugs.launchpad.net/cloud-images/+bug/2005129
RUN usermod -l ${NB_USER} ubuntu && \
mv /home/ubuntu ${HOME} && \
usermod -d ${HOME} ${NB_USER} && \
chown -R ${NB_UID}:${NB_UID} ${HOME}
USER ${NB_USER}
RUN python3 -m pip install --upgrade build wheel setuptools pip && \
python3 -m pip install --no-cache-dir notebook jupyterlab jupyterhub jax[cpu] antimony
RUN python3 -m venv ${VENV_PATH} && \
${VENV_PATH}/bin/pip install --upgrade build wheel setuptools pip && \
${VENV_PATH}/bin/pip install --no-cache-dir notebook jupyterlab jupyterhub jax[cpu] antimony
# END BINDER

# BEGIN BINDER
Expand All @@ -41,9 +49,11 @@ USER ${NB_USER}
# END BINDER

WORKDIR ${HOME}
RUN . ./.profile && python3 -m build --sdist python/sdist && \
python3 -m pip install -v $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,pysb,vis] && \
python3 -m pip install "git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python&egg=benchmark_models_petab" && \
RUN . ./.profile && ${VENV_PATH}/bin/python3 -m build --sdist python/sdist && \
${VENV_PATH}/bin/pip install git+https://github.com/pysb/pysb@master && \
${VENV_PATH}/bin/pip install -U sympy && \
${VENV_PATH}/bin/pip install -v $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,vis,jax,sciml] && \
${VENV_PATH}/bin/pip install "git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python&egg=benchmark_models_petab" && \
scripts/buildBNGL.sh

ENV BNGPATH="${HOME}/ThirdParty/BioNetGen-2.7.0"
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