Merge pull request #68 from CCPBioSim/nglview-fix

fix the nglview mismatch error in a graceful way

Author: jimboid

docker/Dockerfile

@@ -9,8 +9,17 @@ USER $NB_USER
 WORKDIR $HOME
 
 # Install workshop deps
-RUN mamba install matplotlib numpy pandas nglview ipywidgets -y
-RUN pip install mdtraj
+RUN conda install -y -c conda-forge \
+    matplotlib=3.11.1 \
+    numpy=2.5.3 \
+    pandas=3.0.5 \
+    nglview=4.0.1 \
+    ipywidgets=8.1.9
+RUN pip install --no-cache-dir \ 
+    mdtraj==1.11.1
+
+COPY docker/fix-nglview.sh /tmp/fix-nglview.sh
+RUN bash /tmp/fix-nglview.sh
 
 # Get workshop files and move them to jovyan directory.
 COPY --chown=1000:100 . .

docker/fix-nglview.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Locate nglview's Python frontend file
+NGLVIEW_DIR=$(python -c "import nglview, os; print(os.path.dirname(nglview.__file__))")
+FRONTEND_FILE="$NGLVIEW_DIR/_frontend.py"
+
+if [[ ! -f "$FRONTEND_FILE" ]]; then
+    echo "nglview _frontend.py not found, skipping patch" >&2
+    exit 0
+fi
+
+# Locate the installed labextension's package.json by searching
+# every labextensions directory Jupyter knows about (handles conda's
+# $CONDA_PREFIX/share/jupyter/labextensions layout automatically)
+LABEXT_PKG=$(python -c "
+from jupyter_core.paths import jupyter_path
+import os, sys
+for d in jupyter_path('labextensions'):
+    candidate = os.path.join(d, 'nglview-js-widgets', 'package.json')
+    if os.path.isfile(candidate):
+        print(candidate)
+        sys.exit(0)
+sys.exit(1)
+") || { echo "nglview-js-widgets labextension not found, skipping patch" >&2; exit 0; }
+
+PY_VERSION=$(python -c "import re; print(re.search(r\"__frontend_version__ = '([^']+)'\", open('$FRONTEND_FILE').read()).group(1))")
+JS_VERSION=$(python -c "import json; print(json.load(open('$LABEXT_PKG'))['version'])")
+
+# If there is a version mismatch then make them the same python side.
+if [[ "$PY_VERSION" != "$JS_VERSION" ]]; then
+    echo "nglview mismatch: python=$PY_VERSION js=$JS_VERSION (found at $LABEXT_PKG) -- patching"
+    sed -i "s/__frontend_version__ = '$PY_VERSION'/__frontend_version__ = '$JS_VERSION'/" "$FRONTEND_FILE"
+else
+    echo "nglview versions already match ($PY_VERSION), skipping patch"
+fi