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update conda install syntax and add renovate config to manage deps- #60 #63

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86f515f
Update Renovate schedule and add custom managers
jimboid Sep 16, 2026
a4ac4e9
Refactor Dockerfile for dependency installation
jimboid Sep 16, 2026
b6acd84
Remove curl and unzip installation from Dockerfile
jimboid Sep 16, 2026
ffba05c
Update conda install command for aiida-gromacs
jimboid Sep 16, 2026
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31 changes: 30 additions & 1 deletion .github/renovate.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
"helpers:pinGitHubActionDigestsToSemver"
],
"timezone": "Europe/London",
"schedule": ["after 9am and before 5pm every weekday"],
"schedule": ["after 5am and before 5pm every weekday"],
"dependencyDashboard": true,
"assignees": ["jimboid"],
"minimumReleaseAge": "3 days",
Expand All @@ -15,5 +15,34 @@
"groupName": "GitHub Actions",
"addLabels": ["ci", "dependencies"]
}
],
"customManagers": [
{
"customType": "regex",
"managerFilePatterns": [
"/(^|/)Dockerfile[^/]*$/"
],
"matchStringsStrategy": "recursive",
"matchStrings": [
"pip3? install[\\s\\S]*?(?<packages>(?:[\\w.-]+==[\\w.-]+[\\s\\\\]*)+)",
"(?<depName>[\\w.-]+)==(?<currentValue>[\\w.-]+)"
],
"datasourceTemplate": "pypi",
"versioningTemplate": "pep440"
},
{
"customType": "regex",
"managerFilePatterns": [
"/(^|/)Dockerfile[^/]*$/"
],
"matchStringsStrategy": "recursive",
"matchStrings": [
"(?:mamba|conda) install[\\s\\S]*?(?<packages>(?:(?:[\\w-]+::)?[\\w.-]+=[\\w.-]+[\\s\\\\]*)+)",
"(?:(?<channel>[\\w-]+)::)?(?<depName>[\\w.-]+)=(?<currentValue>[\\w.-]+)"
],
"datasourceTemplate": "conda",
"registryUrlTemplate": "https://api.anaconda.org/package/{{#if channel}}{{channel}}{{else}}conda-forge{{/if}}/",
"versioningTemplate": "pep440"
}
]
}
33 changes: 7 additions & 26 deletions docker/Dockerfile
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Expand Up @@ -5,34 +5,17 @@ FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE
LABEL maintainer="James Gebbie-Rayet <james.gebbie@stfc.ac.uk>"
ARG TARGETPLATFORM

USER root
WORKDIR /opt/

# Install RabbitMQ for Mac
RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \
curl \
ca-certificates \
erlang \
unzip && \
apt-get clean && rm -rf /var/lib/apt/lists/* && \
wget -c --no-check-certificate https://github.com/rabbitmq/rabbitmq-server/releases/download/v3.10.14/rabbitmq-server-generic-unix-3.10.14.tar.xz && \
tar -xf rabbitmq-server-generic-unix-3.10.14.tar.xz && \
rm rabbitmq-server-generic-unix-3.10.14.tar.xz && \
ln -sf /opt/rabbitmq_server-3.10.14/sbin/* /usr/local/bin/ && \
chown -R 1000:100 /opt/rabbitmq_server-3.10.14

USER $NB_USER
WORKDIR $HOME

# Python Dependencies for the md_workshop
RUN mamba install -c conda-forge -y aiida-core
RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then \
mamba install conda-forge/linux-64::gromacs=2024.5=nompi_h5f56185_100 -y; \
elif [ "$TARGETPLATFORM" = "linux/arm64" ]; then \
mamba install conda-forge/linux-aarch64::gromacs=2024.5=nompi_h9afd374_100 -y; \
fi
RUN pip3 install aiida-gromacs mdtraj vermouth
RUN conda install -y -c conda-forge -c ccpbiosim \
conda-forge::aiida-core=2.9.2 \
ccpbiosim::aiida-gromacs=2.2.2 \
conda-forge::gromacs=2026.3=nompi_*
RUN pip install --no-cache-dir \
mdtraj==1.11.1.post2 \
vermouth==0.15.0

RUN git clone https://github.com/PSDI-UK/aiida-gromacs.git && \
mv aiida-gromacs/examples/PTH2R_coarse-grained_files . && \
Expand All @@ -41,8 +24,6 @@ RUN git clone https://github.com/PSDI-UK/aiida-gromacs.git && \

RUN echo "./aiida-start" >> ~/.bashrc
COPY --chown=1000:100 docker/default-37a8.jupyterlab-workspace /home/jovyan/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace
COPY --chown=1000:100 aiida-start /home/jovyan/
COPY --chown=1000:100 aiida-stop /home/jovyan/

# Always finish with non-root user as a precaution.
USER $NB_USER
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