Add fix permissions $CONDA_DIR after tests

Dockerfile

@@ -217,9 +217,6 @@ RUN pip install numpy==1.17
 
 USER root
 
-RUN fix-permissions /opt/tutorials \
- && fix-permissions $CONDA_DIR
-
 # Trick to stop caching
 ARG CACHE_DATE=2021-1-26
 
@@ -229,9 +226,21 @@ COPY files files
 RUN pip install Pillow
 RUN python generate_headers.py
 
+# Customize jupyter 
+WORKDIR $HOME
+COPY files/custom.css custom.css
+COPY files/logo.png logo.png
+COPY files/Titillium Titillium
+RUN mkdir .jupyter/custom 
+RUN mv custom.css .jupyter/custom \
+ && mv logo.png .jupyter/custom \
+ && mv Titillium .jupyter/custom
 ARG TUTORIALS_HOME=$HOME/tutorials
 
 
+RUN fix-permissions /opt/tutorials \
+ && fix-permissions $CONDA_DIR
+
 # Linking all the notebooks of the tutorials
 WORKDIR $TUTORIALS_HOME
 RUN ln -s /opt/tutorials/*/*.ipynb . \
@@ -241,55 +250,47 @@ RUN ln -s /opt/tutorials/*/*.ipynb . \
 WORKDIR $TUTORIALS_HOME/assets
 RUN ln -s /opt/tutorials/*/assets/*  .
 
-# Linking data may required by the tutorials
+# Linking data may be required by the tutorials
 WORKDIR $TUTORIALS_HOME/data
 RUN mkdir data && ln -s /opt/tutorials/*/data/* .
 
-# Customize jupyter 
-WORKDIR $HOME
-COPY files/custom.css custom.css
-COPY files/logo.png logo.png
-COPY files/Titillium Titillium
-RUN mkdir .jupyter/custom 
-RUN mv custom.css .jupyter/custom \
- && mv logo.png .jupyter/custom \
- && mv Titillium .jupyter/custom
-
 # Testing tutorials 
-#RUN  cp -r tutorials test_tutorials
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/ARISE.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/atomic_features.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/clustering_tutorial.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/cmlkit.ipynb" 
-## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/CO2_SGD.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/compressed_sensing.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/convolutional_nn.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/decision_tree.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/descriptor_role.ipynb" 
-## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/error_estimates.ipynb" 
-## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/exploratory_analysis.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/gap_si_surface.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/grain_boundaries.ipynb" 
-## RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/kaggle_competition.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/krr4mat.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/nn_regression.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/perovskites_tolerance_factor.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=5000 --to notebook --execute "test_tutorials/query_nomad_archive.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/sgd_alloys_oxygen_reduction_evolution.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/soap_atomic_charges.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/tcmi.ipynb" 
-#RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/tetradymite_PRM2020.ipynb" 
-## Remove following tutorial because test is too long
-## RUN jupyter nbconvert --ExecutePreprocessor.timeout=20000 --to notebook --execute "test_tutorials/domain_of_applicability.ipynb" 
-
-#RUN rm -r test_tutorials    
+RUN  cp -r tutorials test_tutorials
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/ARISE.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/atomic_features.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/clustering_tutorial.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/cmlkit.ipynb" 
+# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/CO2_SGD.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/compressed_sensing.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/convolutional_nn.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/decision_tree.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/descriptor_role.ipynb" 
+# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/error_estimates.ipynb" 
+# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/exploratory_analysis.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/gap_si_surface.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/grain_boundaries.ipynb" 
+# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/kaggle_competition.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/krr4mat.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/nn_regression.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/perovskites_tolerance_factor.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=5000 --to notebook --execute "test_tutorials/query_nomad_archive.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/sgd_alloys_oxygen_reduction_evolution.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/soap_atomic_charges.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/tcmi.ipynb" 
+RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/tetradymite_PRM2020.ipynb" 
+# Remove following tutorial because test is too long
+# RUN jupyter nbconvert --ExecutePreprocessor.timeout=20000 --to notebook --execute "test_tutorials/domain_of_applicability.ipynb" 
+
+RUN rm -r test_tutorials    
 
 # ================================================================================
 # Switch back to jovyan to avoid accidental container runs as root
 # ================================================================================
 
 WORKDIR $HOME
+
 RUN fix-permissions $TUTORIALS_HOME \
- && fix-permissions $HOME/.local/share/jupyter
- 
+ && fix-permissions $HOME/.local/share/jupyter \
+ && fix-permissions $CONDA_DIR
+
 USER $NB_UID