Dockerfile

FROM jupyter/datascience-notebook

RUN mamba install --quiet --yes \
    jupyterlab_code_formatter \
    black \
    yapf \
    isort \
    autopep8 \
    jupytext \
    nbgitpuller \
    jupyter-book \
    jupyterlab-myst \
    jupyterlab-spellchecker \
    git-lfs \
    lmfit \
    plotly \
    pymatgen \
    openpyxl \
    scikit-optimize \
    jax \
    pre-commit && \
    mamba clean --all -f -y && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"
    
RUN jupyter labextension install jupyterlab-jupytext

# OCP repo requirements
RUN echo '' > /opt/conda/conda-meta/pinned
RUN mamba uninstall nomkl --quiet --yes
RUN mamba install --quiet --yes \
    -c pyg -c pytorch -c conda-forge -c nvidia \
    numba \
    lmdb \
    ase \
    pip \
    pyyaml \
    tqdm \
    tensorboard \
    pandoc \
    nbsphinx \
    sphinx \
    black \
    wandb \
    lmdb \
    submitit \
    pytest \
    python-lmdb \
    pyg \
    'pytorch=1.11' \
    torchvision \
    torchaudio \
    'python=3.9' && \
    mamba clean --all -f -y && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

ENV OMP_NUM_THREADS=1 

# Install OCP
USER root
RUN git clone https://github.com/Open-Catalyst-Project/ocp /opt/ocp && fix-permissions /opt/ocp
USER $NB_UID
RUN cd /opt/ocp && python setup.py develop


# Install matminer
RUN pip install --no-deps matminer

# Add texlive-science for mhchem package.
# Also update the default latex format in nbconvert to add the mhchem package and disable all require statements
USER root
RUN apt-get update --yes && \
    apt-get install --yes --no-install-recommends \
    texlive-science && \
    apt-get clean && rm -rf /var/lib/apt/lists/*USER $NB_UID
USER $NB_UID
RUN sed -i '/{titling}/i \\\usepackage{mhchem}\n\\newcommand{\\require}[1]{}' /opt/conda/share/jupyter/nbconvert/templates/latex/base.tex.j2