Install Python dependencies via APT

Docker/github_ci_dockerfile

@@ -1,68 +1,57 @@
 FROM ubuntu:22.04 AS base
 
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+      ca-certificates \
       cmake \
+      curl \
+      cython3 \
       g++-12 \
       gfortran-12 \
       git \
       hdf5-tools \
-      liblapack-dev \
       libboost-dev \
       libfftw3-dev \
-      libnfft3-dev \
       libgfortran5 \
       libgmp-dev \
       libhdf5-dev \
+      liblapack-dev \
+      libnfft3-dev \
+      libomp-dev \
       libopenmpi-dev \
-      cython3 \
+      libpython3-dev \
       openmpi-bin \
       openmpi-common \
       openmpi-doc \
+      openssl \
+      pandoc \
       python-is-python3 \
+      python3-ase \
+      python3-decorator \
       python3-dev \
+      python3-jinja2 \
       python3-mako \
-      python3-numpy \
-      python3-scipy \
       python3-matplotlib \
+      python3-monty \
       python3-mpi4py \
-      python3-pip \
-      python3-sphinx \
+      python3-myst-parser \
       python3-nbsphinx \
-      python3-skimage \
       python3-notebook \
-      libpython3-dev \
-      curl \
-      ca-certificates \
-      openssl \
-      wget \
+      python3-numpy \
+      python3-pip \
+      python3-pytest \
+      python3-scipy \
+      python3-shapely \
+      python3-skimage \
+      python3-sphinx \
+      python3-sphinx-rtd-theme \
       rsync \
-      libomp-dev \
       sudo \
-      nodejs \
-      npm \
+      wget \
       && \
       apt-get autoremove --purge -y && \
       apt-get autoclean -y && \
       rm -rf /var/cache/apt/* /var/lib/apt/lists/*
 
-RUN pip3 install --no-cache-dir \
-    cython \
-    decorator \
-    pytest \
-    shapely \
-    monty \
-    mpi4py \
-    Jinja2 \
-    Mako \
-    ase \
-    tornado \
-    zmq \
-    tk  \
-    myst_parser \
-    sphinx_rtd_theme  \
-    linkify-it-py \
-    Pandoc
-
 # the above is cached by the github action workflow
 FROM base AS pkgs
 

Docker/jupyter_start.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
-# start script for jupyterlab
-jupyter-lab --no-browser --port 8378 --ip=0.0.0.0 
+# start script for jupyter notebook
+jupyter notebook --no-browser --port 8378 --ip=0.0.0.0 

Docker/mpich_dockerfile

@@ -36,21 +36,34 @@ RUN apt-get update && \
     libc++-${LLVM}-dev \
     libc++abi-${LLVM}-dev \
     libboost-dev \
+    jupyter-notebook \
+    pandoc \
     python-is-python3 \
+    python3-ase \
+    python3-decorator \
+    python3-dev \
+    python3-jinja2 \
+    python3-mako \
+    python3-matplotlib \
+    python3-monty \
+    python3-mpi4py \
+    python3-myst-parser \
+    python3-nbsphinx \
+    python3-notebook \
+    python3-numpy \
+    python3-pandas \
     python3-pip \
+    python3-pytest \
+    python3-scipy \
     python3-setuptools \
-    python3-dev \
+    python3-shapely \
+    python3-skimage \
+    python3-sphinx \
+    python3-sphinx-rtd-theme \
     libfftw3-dev \
     libnfft3-dev \
     less \
     vim \
-# Jupyter lab packages
-    texlive \
-    dvipng \
-    texlive-latex-extra \
-    texlive-fonts-recommended \
-    nodejs \
-    npm \
     && \
     apt-get autoremove --purge -y && \
     apt-get autoclean -y && \
@@ -63,44 +76,6 @@ RUN apt-get update && \
 
 RUN ldconfig -v
 
-##################################################
-# Python modules                                 #
-##################################################
-
-# Install python packages
-RUN pip3 install --no-cache-dir \
-    cython \
-    numpy \
-    scipy \
-    matplotlib \
-    decorator \
-    jupyter \
-    ipywidgets \
-    pytest \
-    pylint \
-    pandas \
-    shapely \
-    monty \
-    mpi4py \
-    pymatgen \
-    Jinja2 \
-    Mako \
-    tornado \
-    zmq \
-    notebook \
-    tk \
-    scikit-image \
-    # Jupyter lab packages
-    jupyterlab \
-    descartes \
-    ipympl \
-    RISE
-
-# jupyter lab extension
-# TODO: fix, right now it crashes with "nodejs required"
-#RUN jupyter-labextension install @jupyter-widgets/jupyterlab-manager jupyter-matplotlib @jupyterlab/toc
-#RUN jupyter-lab build
-
 ##################################################
 # TRIQS and its packages                         #
 ##################################################

Docker/openmpi_dockerfile

@@ -1,57 +1,62 @@
 FROM ubuntu:22.04 AS base
 ARG LLVM=15
-ARG NODE_MAJOR=20
-
-# install basics for modern nodejs required for sphinx
-RUN apt-get update &&  DEBIAN_FRONTEND=noninteractive apt-get install -y curl sudo wget git less rsync nano openssl ca-certificates make vim gnupg \
-    && mkdir -p /etc/apt/keyrings \
-    && curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | sudo gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg \
-    && echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | sudo tee /etc/apt/sources.list.d/nodesource.list
 
 # This platform includes dependencies for building docs
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+      clang-${LLVM} \
       cmake \
+      cython3 \
       g++ \
       gfortran \
-      llvm-${LLVM}-dev \
-      libclang-${LLVM}-dev \
-      clang-${LLVM} \
-      libc++-${LLVM}-dev \
-      libc++abi-${LLVM}-dev \
       hdf5-tools \
-      libmkl-dev \
-      libopenblas-dev \
+      jupyter-notebook \
       libboost-dev \
+      libc++-${LLVM}-dev \
+      libc++abi-${LLVM}-dev \
+      libclang-${LLVM}-dev \
+      libevent-dev \
+      libfabric-dev \
       libfftw3-dev \
-      libnfft3-dev \
       libgfortran5 \
       libgmp-dev \
       libhdf5-dev \
       libhwloc-dev \
-      libevent-dev \
-      libpmi2-0-dev \
-      cython3 \
-      # comment the next 4 lines if you want to build openmpi manually
+      libmkl-dev \
+      libnfft3-dev \
+      libomp-${LLVM}-dev \
+      libopenblas-dev \
       libopenmpi-dev \
+      libpmi2-0-dev \
+      libpython3-dev \
+      llvm-${LLVM}-dev \
       openmpi-bin \
       openmpi-common \
       openmpi-doc \
-      libfabric-dev \
-      libomp-${LLVM}-dev \
-      nodejs \
+      pandoc \
       python-is-python3 \
+      python3-ase \
+      python3-clang-${LLVM} \
+      python3-decorator \
       python3-dev \
+      python3-jinja2 \
       python3-mako \
-      python3-numpy \
-      python3-scipy \
       python3-matplotlib \
-      python3-pip \
-      python3-sphinx \
-      python3-clang-${LLVM} \
-      python3-skimage \
+      python3-monty \
+      python3-mpi4py \
+      python3-myst-parser \
       python3-nbsphinx \
       python3-notebook \
-      libpython3-dev \
+      python3-numpy \
+      python3-pandas \
+      python3-pip \
+      python3-pymatgen \
+      python3-pytest \
+      python3-scipy \
+      python3-shapely \
+      python3-skimage \
+      python3-sphinx \
+      python3-sphinx-rtd-theme \
+      wget \
       && \
       apt-get autoremove --purge -y && \
       apt-get autoclean -y && \
@@ -73,35 +78,6 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-ins
 #     && cd .. \
 #     && rm -rf openmpi-4.1.5.tar.gz openmpi-4.1.5
 
-RUN pip3 install --no-cache-dir \
-    mpi4py \
-    cython \
-    decorator \
-    jupyter \
-    ipywidgets \
-    pytest \
-    pandas \
-    shapely \
-    monty \
-    mpi4py \
-    pymatgen \
-    ase \
-    Jinja2 \
-    Mako \
-    tornado \
-    zmq \
-    notebook \
-    tk \
-    myst_parser \
-    sphinx_rtd_theme  \
-    linkify-it-py \
-    Pandoc \
-    # Jupyter lab packages
-    jupyterlab \
-    descartes \
-    ipympl \
-    RISE
-
 ENV PYTHON_VERSION=3.10 \
     CC=clang-${LLVM} CXX=clang++-${LLVM} CXXFLAGS="-stdlib=libc++"
 RUN update-alternatives --install /usr/bin/clang clang /usr/bin/clang-${LLVM} 60 --slave /usr/bin/clang++ clang++ /usr/bin/clang++-${LLVM} --slave /usr/bin/clang-cpp clang-cpp /usr/bin/clang-cpp-${LLVM}