# Info of jupyter/minimal-notebook:python-3.8.8

# Copyright (c) Jupyter Development Team.

# Distributed under the terms of the Modified BSD License.

# Info of the current HDDM docker image:

## The buid from the base of minimal-notebook, based on python 3.8.8

## Modified by Dr. Hu Chuan-Peng, Nanjing Normal University, Nanjing, China.

## Please contact [email protected] if you have any question with the curretn HDDM image

## In this version, jupyter lab and jupyter are updated to higher version:

# jupyterlab - 3.0.14

# jupyter_client - 6.1.12

# jupyter_core - 4.7.1

## Which means that some extension for plotting in jupyter should be upgraded too:

# ipympl >= 0.8

# matplotlib >= 3.3.1

# ipywidgets >= 0.76

# jupyter_widget *

#

## p_tqdm is installed for parallel processing, not working very well with jupyter lab.

# ARG BASE_CONTAINER=jupyter/minimal-notebook:python-3.8.8

FROM jupyter/minimal-notebook:python-3.8.8

LABEL maintainer="Hu Chuan-Peng <[email protected]>"

USER root

# ffmpeg for matplotlib anim & dvipng for latex labels

RUN apt-get update && \

# apt-get install -y --no-install-recommends apt-utils && \

apt-get install -y --no-install-recommends ffmpeg dvipng && \

rm -rf /var/lib/apt/lists/*

USER $NB_UID

# Install Python 3 packages

RUN conda install --quiet --yes \

'arviz=0.11.4' \

'beautifulsoup4=4.9.*' \

'conda-forge::blas=*=openblas' \

'bokeh=2.4.*' \

'bottleneck=1.3.*' \

'cloudpickle=1.4.*' \

'cython=0.29.*' \

'dask=2.15.*' \

'dill=0.3.*' \

'h5py=2.10.*' \

'hdf5=1.10.*' \

'ipywidgets=7.6.*' \

'ipympl=0.8.*' \

'jupyter_bokeh' \

'jupyterlab_widgets' \

'matplotlib-base=3.3.*' \

# numba update to 0.49 fails resolving deps.

'numba=0.48.*' \

'numexpr=2.7.*' \

'pandas=1.0.*' \

'patsy=0.5.*' \

'protobuf=3.11.*' \

'pytables=3.6.*' \

'scikit-image=0.16.*' \

'scikit-learn=0.22.*' \

'scipy=1.4.*' \

'seaborn=0.11.*' \

'sqlalchemy=1.3.*' \

'statsmodels=0.11.*' \

'sympy=1.5.*' \

'vincent=0.4.*' \

'widgetsnbextension=3.5.*'\

'xlrd=1.2.*' \

'pymc=2.3.8' \

'git' \

'mkl-service' \

&& \

conda clean --all -f -y && \

fix-permissions "/home/${NB_USER}"

# USER root

# RUN jupyter notebook --generate-config -y

USER $NB_UID

RUN pip install --upgrade pip && \

# install plotly and its chart studio extension

pip install --no-cache-dir 'chart_studio==1.1.0' && \

pip install --no-cache-dir 'plotly==4.14.3' && \

pip install --no-cache-dir 'cufflinks==0.17.3' && \

# install ptitprince for raincloud plot in python

pip install --no-cache-dir 'ptitprince==0.2.*' && \

pip install --no-cache-dir 'feather-format' && \

pip install --no-cache-dir 'p_tqdm' && \

fix-permissions "/home/${NB_USER}"

# install kabuki and hddm from Github

RUN pip install --no-cache-dir git git://github.com/hddm-devs/kabuki.git && \

pip install --no-cache-dir git https://github.com/hddm-devs/hddm && \

fix-permissions "/home/${NB_USER}"

# Install PyTorch, CPU-only

RUN conda install -c pytorch --quiet --yes \

'pytorch==1.7.0' \

'torchvision==0.8.0' \

'torchaudio==0.7.0' \

'cpuonly' \

&& \

conda clean --all -f -y && \

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}"

## Activate ipywidgets extension

# Activate ipywidgets extension in the environment that runs the notebook server

# Below we install jupyterlab extensions, please check compatibility for each of them:

# https://npm.io/package/@jupyter-widgets/jupyterlab-manager

# # compatibility with bokeh, installed via conda

# # compatibility with matplotlib: https://www.npmjs.com/package/jupyter-matplotlib

USER $NB_UID

RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build && \

jupyter labextension install jupyter-matplotlib --no-build && \

jupyter lab build && \

jupyter lab clean && \

jlpm cache clean && \

npm cache clean --force && \

rm -rf "/home/${NB_USER}/.cache/yarn" && \

rm -rf "/home/${NB_USER}/.node-gyp" && \

fix-permissions "/home/${NB_USER}"

USER $NB_UID

WORKDIR $HOME

# Create a folder for example

RUN mkdir /home/$NB_USER/examples && \

rm -r /home/$NB_USER/work && \

fix-permissions /home/$NB_USER

# Copy example data and scripts to the example folder

COPY /hddm/examples/hddm_demo_docker.ipynb /home/${NB_USER}/examples

COPY /hddm/examples/Test_HDDMnn.ipynb /home/${NB_USER}/examples