full enviroment

notebook/Dockerfile

@@ -120,8 +120,8 @@ RUN . $CONDA_DIR/etc/profile.d/conda.sh \
     'plotly' \
     'lxml' \
  && conda activate python2 \
- && pip install keras-tqdm pyquaternion spsim \
- && conda remove --quiet --yes --force qt pyqt \
+ && pip install keras-tqdm pyquaternion \
+ && conda remove --quiet --yes --force qt pyqt libtiff \
  && conda clean -tipsy \
  && fix-permissions $CONDA_DIR \
  && fix-permissions /home/$NB_USER
@@ -139,36 +139,36 @@ USER $NB_USER
 # RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" \
 #  && fix-permissions /home/$NB_USER
 
-#a# ================================================================================
-##  QUIP + GAP + quippy
-## ================================================================================
-#
-## All the QUIPs go here; added to path in the end.
-#WORKDIR /opt/quip
-#
-## QUIP for general use is the OpenMP version.
-#ENV QUIP_ARCH linux_x86_64_gfortran_openmp
-#
-#ENV QUIP_INSTALLDIR /opt/quip/bin
-#ENV PATH $QUIP_INSTALLDIR:$PATH
-#
-#COPY 3rdparty/QUIP .
-#COPY 3rdparty/GAP src/GAP
-#COPY 3rdparty/Makefile.inc build/$QUIP_ARCH/
-#COPY 3rdparty/GIT_VERSION .
-#COPY 3rdparty/GAP_VERSION src/GAP/
-#
-#USER root
-#RUN chown -R $NB_USER:$NB_GID $PWD
-#USER $NB_USER
-#
-## Installs with no suffix, e.g. quip
-#RUN make > /dev/null 2>&1 \
-# && make install \
-# # Installs quippy using python2 environment
-# && . $CONDA_DIR/etc/profile.d/conda.sh \
-# && conda activate python2 \
-# && make install-quippy > /dev/null 2>&1
+# ================================================================================
+#  QUIP + GAP + quippy
+# ================================================================================
+
+# All the QUIPs go here; added to path in the end.
+WORKDIR /opt/quip
+
+# QUIP for general use is the OpenMP version.
+ENV QUIP_ARCH linux_x86_64_gfortran_openmp
+
+ENV QUIP_INSTALLDIR /opt/quip/bin
+ENV PATH $QUIP_INSTALLDIR:$PATH
+
+COPY 3rdparty/QUIP .
+COPY 3rdparty/GAP src/GAP
+COPY 3rdparty/Makefile.inc build/$QUIP_ARCH/
+COPY 3rdparty/GIT_VERSION .
+COPY 3rdparty/GAP_VERSION src/GAP/
+
+USER root
+RUN chown -R $NB_USER:$NB_GID $PWD
+USER $NB_USER
+
+# Installs with no suffix, e.g. quip
+RUN make > /dev/null 2>&1 \
+ && make install \
+ # Installs quippy using python2 environment
+ && . $CONDA_DIR/etc/profile.d/conda.sh \
+ && conda activate python2 \
+ && make install-quippy > /dev/null 2>&1
 
 # ================================================================================
 # nomad_sim + nomad_sim_visualization + nomadcore
@@ -253,97 +253,97 @@ RUN . $CONDA_DIR/etc/profile.d/conda.sh \
  && conda activate python2 \
  && python setup.py install
 
-#a# ================================================================================
-## Python 3.x environment
-## ================================================================================
-#
-## Add any additional packages you want available for use in a Python 3 notebook
-## to the first line here (e.g., pandas, matplotlib, etc.)
-## Remove pyqt and qt pulled in for matplotlib since we're only ever going to
-## use notebook-friendly backends in these images
-#RUN conda install --quiet --yes \
-#    'conda-forge::blas=*=openblas' \
-#    'numpy' \
-#    'pandas' \
-#    'scipy' \
-#    'scikit-learn' \
-#    'pytorch::pytorch-cpu' \
-#    'pytorch::torchvision-cpu' \
-#    'bokeh' \
-#    'matplotlib' \
-#    'ipywidgets' \
-#    'nglview' \
-#    'cython' \
-#    'numba' \
-#    'ase' \
-#    'tqdm' \
-#    'tensorflow' \
-#    'keras'  \
-#    'colorcet'  \
-# && pip install --quiet git+https://github.com/raghakot/keras-vis.git \
-# && conda remove --quiet --yes --force qt pyqt \
-# && conda clean -tipsy \
-# # Activate ipywidgets extension in the environment that runs the notebook server
-# && jupyter nbextension enable --py widgetsnbextension --sys-prefix \
-# && npm cache clean --force \
-# && rm -rf $CONDA_DIR/share/jupyter/lab/staging \
-# && rm -rf /home/$NB_USER/.cache/yarn \
-# && rm -rf /home/$NB_USER/.node-gyp \
-# && fix-permissions $CONDA_DIR \
-# && fix-permissions /home/$NB_USER
-#
-## Import matplotlib the first time to build the font cache.
-#ENV XDG_CACHE_HOME=/home/$NB_USER/.cache/
-#RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" \
-# && fix-permissions /home/$NB_USER
-#
-## ================================================================================
-## Python 3.6 environment
-## ================================================================================
-#
-#RUN . $CONDA_DIR/etc/profile.d/conda.sh \
-# && conda  create --name python36  -c conda-forge --quiet  --yes \
-#    'python=3.6' \
-#    'conda-forge::blas=*=openblas' \
-#    'ipython' \
-#    'ipykernel' \
-#    'ipywidgets' \
-#    'kernda' \
-#    'numpy' \
-#    'scipy' \
-#    'scikit-learn' \
-#    'matplotlib' \
-#    'cython' \
-#    'numba' \
-#    'ase' \
-#    'asap3' \
-#    'nglview' \
-# && conda activate python36 \
-# && jupyter nbextension enable --py --sys-prefix widgetsnbextension \
-# && jupyter-nbextension enable --py --sys-prefix nglview \
-# && conda remove --quiet --yes --force qt pyqt \
-# && conda clean -tipsy \
-# && fix-permissions $CONDA_DIR \
-# && fix-permissions /home/$NB_USER
-#
-## Create a global kernelspec in the image and modify it so that it properly activates
-## the python36 conda environment.
-#USER root
-#RUN . $CONDA_DIR/etc/profile.d/conda.sh \
-# && conda activate python36 \
-# && ipython kernel install --name python36 --display-name 'Python 3.6'
-#USER $NB_USER
-#
-## https://github.com/ipython-contrib/jupyter_contrib_nbextensions
-#RUN conda install --quiet --yes \
-#    'jupyter_contrib_nbextensions' \
-#    'jupyter_nbextensions_configurator' \
-# && conda clean -tipsy \
-# && jupyter nbextensions_configurator enable --user \
-# && jupyter nbextension install nglview --py --sys-prefix \
-# && jupyter nbextension enable nglview --py --sys-prefix \
-# && jupyter nbextension enable execute_time/ExecuteTime \
-# && jupyter nbextension enable init_cell/main
+# ================================================================================
+# Python 3.x environment
+# ================================================================================
+
+# Add any additional packages you want available for use in a Python 3 notebook
+# to the first line here (e.g., pandas, matplotlib, etc.)
+# Remove pyqt and qt pulled in for matplotlib since we're only ever going to
+# use notebook-friendly backends in these images
+RUN conda install --quiet --yes \
+    'conda-forge::blas=*=openblas' \
+    'numpy' \
+    'pandas' \
+    'scipy' \
+    'scikit-learn' \
+    'pytorch::pytorch-cpu' \
+    'pytorch::torchvision-cpu' \
+    'bokeh' \
+    'matplotlib' \
+    'ipywidgets' \
+    'nglview' \
+    'cython' \
+    'numba' \
+    'ase' \
+    'tqdm' \
+    'tensorflow' \
+    'keras'  \
+    'colorcet'  \
+ && pip install --quiet git+https://github.com/raghakot/keras-vis.git \
+ && conda remove --quiet --yes --force qt pyqt \
+ && conda clean -tipsy \
+ # Activate ipywidgets extension in the environment that runs the notebook server
+ && jupyter nbextension enable --py widgetsnbextension --sys-prefix \
+ && npm cache clean --force \
+ && rm -rf $CONDA_DIR/share/jupyter/lab/staging \
+ && rm -rf /home/$NB_USER/.cache/yarn \
+ && rm -rf /home/$NB_USER/.node-gyp \
+ && fix-permissions $CONDA_DIR \
+ && fix-permissions /home/$NB_USER
+
+# Import matplotlib the first time to build the font cache.
+ENV XDG_CACHE_HOME=/home/$NB_USER/.cache/
+RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" \
+ && fix-permissions /home/$NB_USER
+
+# ================================================================================
+# Python 3.6 environment
+# ================================================================================
+
+RUN . $CONDA_DIR/etc/profile.d/conda.sh \
+ && conda  create --name python36  -c conda-forge --quiet  --yes \
+    'python=3.6' \
+    'conda-forge::blas=*=openblas' \
+    'ipython' \
+    'ipykernel' \
+    'ipywidgets' \
+    'kernda' \
+    'numpy' \
+    'scipy' \
+    'scikit-learn' \
+    'matplotlib' \
+    'cython' \
+    'numba' \
+    'ase' \
+    'asap3' \
+    'nglview' \
+ && conda activate python36 \
+ && jupyter nbextension enable --py --sys-prefix widgetsnbextension \
+ && jupyter-nbextension enable --py --sys-prefix nglview \
+ && conda remove --quiet --yes --force qt pyqt \
+ && conda clean -tipsy \
+ && fix-permissions $CONDA_DIR \
+ && fix-permissions /home/$NB_USER
+
+# Create a global kernelspec in the image and modify it so that it properly activates
+# the python36 conda environment.
+USER root
+RUN . $CONDA_DIR/etc/profile.d/conda.sh \
+ && conda activate python36 \
+ && ipython kernel install --name python36 --display-name 'Python 3.6'
+USER $NB_USER
+
+# https://github.com/ipython-contrib/jupyter_contrib_nbextensions
+RUN conda install --quiet --yes \
+    'jupyter_contrib_nbextensions' \
+    'jupyter_nbextensions_configurator' \
+ && conda clean -tipsy \
+ && jupyter nbextensions_configurator enable --user \
+ && jupyter nbextension install nglview --py --sys-prefix \
+ && jupyter nbextension enable nglview --py --sys-prefix \
+ && jupyter nbextension enable execute_time/ExecuteTime \
+ && jupyter nbextension enable init_cell/main
 
 
 # ================================================================================