From 789482c7b2ed3b3d97adddab893a814a3ad20423 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 18 Sep 2026 11:53:22 +0100 Subject: [PATCH 1/5] Update ambertools version in Dockerfile Updated ambertools version from 26.0 to 26.3 in Dockerfile. --- docker/Dockerfile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 7e2bb6e..4c3e384 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -12,8 +12,7 @@ WORKDIR $HOME 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 \ + conda-forge::ambertools=26.3 \ conda-forge::MDAnalysis=2.10.0 \ conda-forge::prolif=2.2.1 \ conda-forge::py3dmol=2.5.4 \ From 8010f90553837ffaca56d59813ac5baaf9074720 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 18 Sep 2026 12:10:06 +0100 Subject: [PATCH 2/5] Update Dockerfile --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 4c3e384..2ef5b7d 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -9,7 +9,7 @@ USER $NB_USER WORKDIR $HOME # Install workshop deps -RUN conda install -y -c conda-forge \ +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 \ From f2550af0dca5d27e62fe2ad4dce54a821ce2dc23 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 18 Sep 2026 12:10:17 +0100 Subject: [PATCH 3/5] Remove commented-out COPY instruction in Dockerfile Removed commented-out line for copying JupyterLab workspace. --- docker/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 2ef5b7d..516c8f1 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -28,6 +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 From ea3fd3035476183b658c7dcaf22b523147d3b806 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 18 Sep 2026 12:15:49 +0100 Subject: [PATCH 4/5] Modify package installation to use minimum versions Updated package versions to allow for newer releases. --- docker/Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 516c8f1..8b06ffd 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -10,9 +10,9 @@ WORKDIR $HOME # Install workshop deps 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::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 \ From 4fd9153970069ee26c85e0bd46b49a2fbf22ed39 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 18 Sep 2026 12:26:14 +0100 Subject: [PATCH 5/5] Update badge URL in README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 37b2952..bf76973 100644 --- a/README.md +++ b/README.md @@ -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)