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Update ambertools and remove packmol in Dockerfile #55

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Merged
jimboid merged 5 commits into from
Sep 18, 2026
Merged

Update ambertools and remove packmol in Dockerfile #55

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789482c
Update ambertools version in Dockerfile
jimboid Sep 18, 2026
8010f90
Update Dockerfile
jimboid Sep 18, 2026
f2550af
Remove commented-out COPY instruction in Dockerfile
jimboid Sep 18, 2026
ea3fd30
Modify package installation to use minimum versions
jimboid Sep 18, 2026
4fd9153
Update badge URL in README.md
jimboid Sep 18, 2026
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# CCPBioSim OpenForcefield Workshop

[![ci](https://github.com/ccpbiosim/openff-workshop/actions/workflows/build.yaml/badge.svg?branch=main)](https://github.com/ccpbiosim/openff-workshop/actions/workflows/build.yaml)
[![latest](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fccpbiosim.github.io%2Fworkshop.json&query=%24.containers.openff-workshop.latest&labelColor=grey&logo=github&logoColor=white&label=latest&color=purple)](https://github.com/ccpbiosim/openff-workshop/pkgs/container/openff-workshop)
[![latest](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fccpbiosim.github.io%2Fassets.json&query=%24.containers.openff-workshop.latest&labelColor=grey&logo=github&logoColor=white&label=latest&color=purple)](https://github.com/ccpbiosim/openff-workshop/pkgs/container/openff-workshop)
[![issues](https://img.shields.io/github/issues/ccpbiosim/openff-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/openff-workshop/issues)
[![pr](https://img.shields.io/github/issues-pr/ccpbiosim/openff-workshop?logo=github&labelColor=grey)](https://github.com/CCPBioSim/openff-workshop/pulls)

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10 changes: 4 additions & 6 deletions docker/Dockerfile
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Expand Up @@ -9,11 +9,10 @@ USER $NB_USER
WORKDIR $HOME

# Install workshop deps
RUN conda install -y -c conda-forge \
conda-forge::openff-toolkit-examples=0.19.0 \
conda-forge::openff-interchange=0.5.4 \
conda-forge::packmol=21.2.1 \
conda-forge::ambertools=26.0 \
RUN mamba install -y -c conda-forge \
conda-forge::openff-toolkit-examples>=0.19.0 \
conda-forge::openff-interchange>=0.5.4 \
conda-forge::ambertools>=26.3 \
conda-forge::MDAnalysis=2.10.0 \
conda-forge::prolif=2.2.1 \
conda-forge::py3dmol=2.5.4 \
Expand All @@ -29,6 +28,5 @@ RUN rm -rf .gitignore .pre-commit-config.yaml environment.yaml LICENSE Makefile
# Copy updated lab workspace
#COPY --chown=1000:100 docker/default-37a8.jupyterlab-workspace /home/jovyan/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace


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