Commit f1601458 authored by Xiangyue Liu's avatar Xiangyue Liu
Browse files

full enviroment

parent 2713e8bb
......@@ -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
# ================================================================================
......
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