From e0f97c228ab8a56504280459b377eaec6ffa8abf Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 1 May 2026 17:50:18 +0100 Subject: [PATCH 1/8] Update AMBERTOOLS version to 26 --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 558ed43..9e3ae8a 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -6,7 +6,7 @@ LABEL maintainer="James Gebbie-Rayet " ARG TARGETPLATFORM ARG AMBERTOOLS_DL=null -ARG AMBERTOOLS_VER=25 +ARG AMBERTOOLS_VER=26 # Switch to jovyan user. USER $NB_USER From 2d8926e667c1a1572b23af9ff109917a29feed46 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 1 May 2026 17:57:13 +0100 Subject: [PATCH 2/8] Add additional dependencies to Dockerfile --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 9e3ae8a..ab22a08 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -13,7 +13,7 @@ USER $NB_USER WORKDIR $HOME # Install workshop deps -RUN mamba install nglview pandas numpy matplotlib scipy -y +RUN mamba install nglview pandas numpy matplotlib scipy numba gemmi Bio rich freesasa sklearn -y WORKDIR /tmp RUN wget --no-verbose $AMBERTOOLS_DL/ambertools$AMBERTOOLS_VER.tar.bz2 && \ From 8e97a76f41bdd2e3c24f5eb28fa7fa104ac3c510 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 1 May 2026 18:05:34 +0100 Subject: [PATCH 3/8] Update package installation in Dockerfile --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index ab22a08..1473b7a 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -13,7 +13,7 @@ USER $NB_USER WORKDIR $HOME # Install workshop deps -RUN mamba install nglview pandas numpy matplotlib scipy numba gemmi Bio rich freesasa sklearn -y +RUN mamba install nglview pandas numpy matplotlib scipy numba gemmi bioconda::bio rich freesasa scikit-learn -y WORKDIR /tmp RUN wget --no-verbose $AMBERTOOLS_DL/ambertools$AMBERTOOLS_VER.tar.bz2 && \ From 1f5603c5c5d8a4437727ee8cb709591a652a030f Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 1 May 2026 18:15:44 +0100 Subject: [PATCH 4/8] Add sympy and networkx to workshop dependencies --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 1473b7a..e96f3c9 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -13,7 +13,7 @@ USER $NB_USER WORKDIR $HOME # Install workshop deps -RUN mamba install nglview pandas numpy matplotlib scipy numba gemmi bioconda::bio rich freesasa scikit-learn -y +RUN mamba install nglview pandas numpy matplotlib scipy numba gemmi bioconda::bio rich freesasa scikit-learn sympy networkx -y WORKDIR /tmp RUN wget --no-verbose $AMBERTOOLS_DL/ambertools$AMBERTOOLS_VER.tar.bz2 && \ From 926c78f6ec7f275fdbeb42261db81a465594ca73 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Fri, 1 May 2026 20:26:56 +0100 Subject: [PATCH 5/8] Update Dockerfile --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index e96f3c9..4d3eacc 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -27,7 +27,7 @@ RUN mkdir /tmp/build WORKDIR /tmp/build RUN cmake /tmp/ambertools_src -DCMAKE_INSTALL_PREFIX=/opt/conda -DPYTHON_EXECUTABLE=/opt/conda/bin/python -DUSE_CONDA_LIBS=TRUE -DBUILD_PYTHON=TRUE -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE -DDOWNLOAD_MINICONDA=FALSE -DCOMPILER=MANUAL -DBUILD_GUI=FALSE -DCOMPILER=GNU -DOPENMP=TRUE -DCUDA=FALSE -DMPI=FALSE -DUSE_FFT=True -DBUILD_DEPRECATED=False -DBUILD_INDEV=False -DBUILD_PERL=True -DOPTIMIZE=True -RUN make -j8 +RUN make RUN make install # Cleanup. From f95cc15a1787b55ec49114e386895986b95be748 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Tue, 2 Jun 2026 07:51:07 +0100 Subject: [PATCH 6/8] Update Dockerfile to build PyTraj with Cython Added steps to build PyTraj with Cython in the Dockerfile. --- docker/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docker/Dockerfile b/docker/Dockerfile index 4d3eacc..9fd4f24 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -23,6 +23,8 @@ RUN wget --no-verbose $AMBERTOOLS_DL/ambertools$AMBERTOOLS_VER.tar.bz2 && \ WORKDIR /tmp/ambertools_src RUN ./update_amber --update +WORKDIR /tmp/ambertools_src/AmberTools/src/pytraj +RUN python setup.py --cythonize RUN mkdir /tmp/build WORKDIR /tmp/build From 2fe1b8f206ddf72ffab2e3279e621539b4560a9a Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Tue, 2 Jun 2026 08:09:49 +0100 Subject: [PATCH 7/8] Set environment variables for Amber and WHAM paths Added environment variables for AMBERHOME and WHAM_HOME. --- docker/Dockerfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 9fd4f24..c35d4ec 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -12,6 +12,10 @@ ARG AMBERTOOLS_VER=26 USER $NB_USER WORKDIR $HOME +# Add key locations to the env. +ENV AMBERHOME=/opt/conda +ENV WHAM_HOME=/opt/wham + # Install workshop deps RUN mamba install nglview pandas numpy matplotlib scipy numba gemmi bioconda::bio rich freesasa scikit-learn sympy networkx -y WORKDIR /tmp @@ -51,10 +55,6 @@ RUN cd /opt && \ USER $NB_USER WORKDIR $HOME -# Add the exec to the path. -ENV AMBERHOME=/opt/conda -ENV WHAM_HOME=/opt/wham - # Add all of the workshop files to the home directory COPY --chown=1000:100 . . RUN rm -rf AUTHORS LICENSE _config.yml README.md docker .git .github From 0d38e96b5052e342eead198f97d21d21363a8fe1 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Tue, 2 Jun 2026 08:32:27 +0100 Subject: [PATCH 8/8] Disable pytraj build in Dockerfile Comment out pytraj build steps in Dockerfile. --- docker/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index c35d4ec..773985f 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -27,8 +27,8 @@ RUN wget --no-verbose $AMBERTOOLS_DL/ambertools$AMBERTOOLS_VER.tar.bz2 && \ WORKDIR /tmp/ambertools_src RUN ./update_amber --update -WORKDIR /tmp/ambertools_src/AmberTools/src/pytraj -RUN python setup.py --cythonize +#WORKDIR /tmp/ambertools_src/AmberTools/src/pytraj +#RUN python setup.py --cythonize RUN mkdir /tmp/build WORKDIR /tmp/build