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| 0.1.5 | ||
| 0.2.0 |
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| # Copyright (c) Jupyter Development Team. | ||
| # Distributed under the terms of the Modified BSD License. | ||
| # uses ubuntu:22.04 as the root container. | ||
| ARG BASE_CONTAINER=jupyter/minimal-notebook | ||
| FROM $BASE_CONTAINER | ||
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| LABEL maintainer="@lrlunin" | ||
| LABEL description="Docker image for the MBI div B JupyterHub" | ||
| # Fix: https://github.com/hadolint/hadolint/wiki/DL4006 | ||
| # Fix: https://github.com/koalaman/shellcheck/wiki/SC3014 | ||
| COPY data/Fira_Sans.zip /tmp/Fira_Sans.zip | ||
| COPY scripts /tmp/scripts | ||
| SHELL ["/bin/bash", "-o", "pipefail", "-c"] | ||
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| USER root | ||
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| RUN apt-get update --yes && \ | ||
| apt-get install --yes --no-install-recommends \ | ||
| # for cython: https://cython.readthedocs.io/en/latest/src/quickstart/install.html | ||
| build-essential \ | ||
| # for latex labels | ||
| cm-super \ | ||
| dvipng \ | ||
| fontconfig \ | ||
| # for slsdetectorlib | ||
| cmake \ | ||
| libzmq5-dev \ | ||
| libtiff5-dev \ | ||
| # user requests | ||
| imagemagick \ | ||
| # for matplotlib anim | ||
| ffmpeg && \ | ||
| apt-get clean && rm -rf /var/lib/apt/lists/* | ||
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| RUN chmod +x /tmp/scripts/install-mbistyles-fonts.sh && /tmp/scripts/install-mbistyles-fonts.sh | ||
| RUN chmod +x /tmp/scripts/install-slsdetector-package.sh && /tmp/scripts/install-slsdetector-package.sh | ||
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| # RUN chmod -R 777 /home/${NB_USER}/.jupyter/ | ||
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| USER ${NB_UID} | ||
| #Install Python 3 packages | ||
| RUN mamba install --yes \ | ||
| 'altair' \ | ||
| 'beautifulsoup4' \ | ||
| 'bokeh' \ | ||
| 'bottleneck' \ | ||
| 'cloudpickle' \ | ||
| 'conda-forge::blas=*=openblas' \ | ||
| 'cython' \ | ||
| 'dask' \ | ||
| 'dill' \ | ||
| 'h5py' \ | ||
| 'ipympl=0.9.3' \ | ||
| 'ipywidgets=8.0.6' \ | ||
| 'jupyterlab-git' \ | ||
| 'matplotlib-base=3.7.1' \ | ||
| 'numba' \ | ||
| 'numexpr' \ | ||
| 'openpyxl' \ | ||
| 'pandas' \ | ||
| 'patsy' \ | ||
| 'protobuf' \ | ||
| 'pytables' \ | ||
| 'scikit-image' \ | ||
| 'scikit-learn' \ | ||
| 'scipy' \ | ||
| 'seaborn' \ | ||
| 'sqlalchemy' \ | ||
| 'statsmodels' \ | ||
| 'sympy' \ | ||
| 'widgetsnbextension' \ | ||
| 'xlrd' \ | ||
| 'conda-forge::pyfai' \ | ||
| 'jupyterlab-h5web' \ | ||
| 'xarray' \ | ||
| 'netCDF4' \ | ||
| 'conda-forge::dask-labextension' && \ | ||
| mamba clean --all -f -y && \ | ||
| fix-permissions "${CONDA_DIR}" && \ | ||
| fix-permissions "/home/${NB_USER}" | ||
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| # Install packages missing in mamba with pip | ||
| # ultrafastfitfunctions need to be installed from git and commit after accepting the pull request | ||
| # https://github.com/EmCeBeh/ultrafastFitFunctions/pull/2 | ||
| RUN pip install --no-cache-dir udkm1Dsim \ | ||
| pyEvalData \ | ||
| git+https://github.com/lrlunin/ultrafastFitFunctions@5bd30901b405dab1b161f59c7c1d5238c2f12991 \ | ||
| git+https://github.com/MBI-Div-B/mbistyles.git \ | ||
| nbdime \ | ||
| jupyterlab-fasta \ | ||
| jupyterlab-geojson \ | ||
| jupyterlab-katex \ | ||
| jupyterlab-mathjax2 \ | ||
| jupyterlab-vega3 \ | ||
| jupyterlab-code-formatter \ | ||
| black && \ | ||
| fix-permissions "${CONDA_DIR}" && \ | ||
| fix-permissions "/home/${NB_USER}" | ||
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| # copying "new default" settings like black code formatter | ||
| COPY --chown=${NB_UID}:${NB_UID} data/user-settings /home/${NB_USER}/.jupyter/lab/user-settings | ||
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| # jupyterlab-code-formatter needs to be configured | ||
| # https://jupyterlab-code-formatter.readthedocs.io/configuration.html | ||
| # see more for jupyterhub https://jupyterlab-code-formatter.readthedocs.io/jupyterhub.html | ||
| # potentially: | ||
| # RUN jupyter serverextension enable --py jupyterlab_code_formatter --sys-prefix | ||
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| # Install facets which does not have a pip or conda package at the moment | ||
| WORKDIR /tmp | ||
| RUN git clone https://github.com/PAIR-code/facets.git && \ | ||
| jupyter nbextension install facets/facets-dist/ --sys-prefix && \ | ||
| rm -rf /tmp/facets && \ | ||
| fix-permissions "${CONDA_DIR}" && \ | ||
| fix-permissions "/home/${NB_USER}" | ||
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| # Import matplotlib the first time to build the font cache. | ||
| ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/" | ||
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| RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \ | ||
| fix-permissions "/home/${NB_USER}" | ||
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| USER ${NB_UID} | ||
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| WORKDIR "${HOME}" |
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| # Documentation | ||
| README.md | ||
| VERSION |
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