Commit e8274f63 authored by Luigi Sbailo's avatar Luigi Sbailo
Browse files

Use cp instead of symb links for tutorials, data

This avoids that running tests modify tutorials permissions
parent 2cd216c3
......@@ -241,18 +241,18 @@ ARG TUTORIALS_HOME=$HOME/tutorials
RUN fix-permissions /opt/tutorials \
&& fix-permissions $CONDA_DIR
# Linking all the notebooks of the tutorials
# Copy all the notebooks of the tutorials
WORKDIR $TUTORIALS_HOME
RUN ln -s /opt/tutorials/*/*.ipynb . \
RUN cp /opt/tutorials/*/*.ipynb . \
&& jupyter-trust -y *.ipynb
# Linking images or other assets may required by the tutorials
# Copy images or other assets may required by the tutorials
WORKDIR $TUTORIALS_HOME/assets
RUN ln -s /opt/tutorials/*/assets/* .
RUN cp -r /opt/tutorials/*/assets/* .
# Linking data may be required by the tutorials
# Copy data may be required by the tutorials
WORKDIR $TUTORIALS_HOME/data
RUN mkdir data && ln -s /opt/tutorials/*/data/* .
RUN cp -r /opt/tutorials/*/data/* .
WORKDIR $HOME
......@@ -261,27 +261,27 @@ RUN cp -r tutorials test_tutorials
WORKDIR $HOME/test_tutorials
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "ARISE.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "atomic_features.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "clustering_tutorial.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "cmlkit.ipynb"
# # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "CO2_SGD.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "compressed_sensing.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "convolutional_nn.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "decision_tree.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "descriptor_role.ipynb"
# # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "error_estimates.ipynb"
# # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "exploratory_analysis.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "gap_si_surface.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "grain_boundaries.ipynb"
# # RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "kaggle_competition.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "krr4mat.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "nn_regression.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "perovskites_tolerance_factor.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=5000 --to notebook --execute "query_nomad_archive.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_alloys_oxygen_reduction_evolution.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "soap_atomic_charges.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tcmi.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tetradymite_PRM2020.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "atomic_features.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "clustering_tutorial.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "cmlkit.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "CO2_SGD.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "compressed_sensing.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "convolutional_nn.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "decision_tree.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "descriptor_role.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "error_estimates.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "exploratory_analysis.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "gap_si_surface.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "grain_boundaries.ipynb"
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "kaggle_competition.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "krr4mat.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "nn_regression.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "perovskites_tolerance_factor.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=5000 --to notebook --execute "query_nomad_archive.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "sgd_alloys_oxygen_reduction_evolution.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "soap_atomic_charges.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tcmi.ipynb"
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "tetradymite_PRM2020.ipynb"
# Remove following tutorial because test is too long
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=20000 --to notebook --execute "domain_of_applicability.ipynb"
......
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