Adds pydot and graphviz for plotting model layer graphs

Duke-GCB · Nov 27, 2024 · 01a1593 · 01a1593
1 parent 70603d0
commit 01a1593
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diff --git a/Dockerfile-pyonly b/Dockerfile-pyonly
@@ -62,7 +62,14 @@ RUN [[ -n ${CUDA} ]] && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Additional packages we may need
+# Install graphviz for pydot, which is needed by keras.util.plot_model
+RUN mamba install --yes \
+    'graphviz' && \
+    mamba clean --all -f -y && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+    # Additional packages we may need
 COPY common-requirements.txt requirements.tf-${TENSORFLOW_VERSION}.txt /tmp/
 RUN pip install --no-cache-dir \
     tensorflow==${TENSORFLOW_VERSION} \

diff --git a/common-requirements.txt b/common-requirements.txt
@@ -20,3 +20,5 @@ oaklib
 matplotlib<3.9.0
 seaborn
 coolbox
+# pydot will need graphviz as dependency
+pydot
-Original file line number
+Diff line change
@@ Expand Up / @@ -20,3 +20,5 @@ oaklib @@
     matplotlib<3.9.0
     seaborn
     coolbox
+    # pydot will need graphviz as dependency
+    pydot