WIP: 2022-03-16 jupyter docker

docker/jupyter/.gitignore

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+venv

docker/jupyter/Dockerfile

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+# Start from a core stack version
+FROM jupyter/scipy-notebook:latest
+# Install from requirements.txt file
+COPY --chown=${NB_UID}:${NB_GID} requirements.txt /tmp/
+RUN pip install --quiet --no-cache-dir --requirement /tmp/requirements.txt && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+COPY start-wrapper.sh /usr/local/bin/
+
+# Custom fonts config
+RUN mkdir -p /home/${NB_USER}/.config/fontconfig
+COPY etc/fonts.conf /home/${NB_USER}/.config/fontconfig/fonts.conf
+COPY etc/fonts /home/${NB_USER}/.fonts
+RUN rm -rf /home/${NB_USER}/.cache/matplotlib
+RUN fc-cache --force
+RUN python3 -c 'import matplotlib.font_manager; matplotlib.font_manager._load_fontmanager(try_read_cache=False)'
+CMD ["start-wrapper.sh", "start-notebook.sh"]

docker/jupyter/README.md

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+# JupyterLab with jupytext and other custom extensions
+
+## Build & run
+
+
+    docker build -t imkteksim/dtool-jupyter .
+    docker run -it -p 8888:8888 -v ${HOME}/.config/dtool:/home/jovyan/.config/dtool -v ${HOME}:/home/jovyan/work imkteksim/dtool-jupyter
+
+## Creation protocol
+
+Describes how to extract imports from python scripts and dump as pip-processible `requirements.txt`.
+
+```console
+python3 -m venv venv
+source venv/bin/activate
+
+pip install --upgrade pip
+pip install wheel
+pip install pip-tools
+
+pip freeze > initial.txt
+cat initial.txt | sed 's/==.*//g' > initial.in
+
+# extract requirements from some scripts with pipreqs
+cat pipreqs_requirements.txt | sed 's/==.*//g' > pipreqs_requirements.in
+
+cp pipreqs_requirements.in edited_requirements.in  # and edit manually
+
+cat initial.in edited_requirements.in
+
+cat initial.in edited_requirements.in > requirements.in
+
+# remove pkg_resources from requirements.in,
+# manually add packages, i.e. jupytext, openpyxl, ...
+
+pip-compile requirements.in
+```

docker/jupyter/edited_requirements.in

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+ase
+asgiref
+cycler
+dtool
+dtool_lookup_api
+dtoolcore
+dtool-s3
+gromacs
+GromacsWrapper
+imteksimfw
+ipython
+ipywidgets
+Jinja2
+matplotlib
+MDAnalysis
+miniball
+nglview
+numpy
+ovito
+pandas
+panedr
+ParmEd
+pymongo
+PySide2
+PyYAML
+scipy

docker/jupyter/etc/.gitignore

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+fonts/*

docker/jupyter/etc/fonts.conf

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+<?xml version="1.0"?>
+<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
+<!-- ~/.fonts.conf for per-user font configuration -->
+<fontconfig>
+<dir>~/.fonts</dir>
+</fontconfig>

docker/jupyter/initial.in

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+click
+pep517
+pip-tools
+pkg_resources
+tomli

docker/jupyter/initial.txt

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+click==8.0.4
+pep517==0.12.0
+pip-tools==6.5.1
+pkg_resources==0.0.0
+tomli==2.0.1

docker/jupyter/pipreqs_requirements.in

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+ase
+asgiref
+cycler
+dtool_lookup_api
+dtoolcore
+fireworks
+FireWorks.egg
+gromacs
+GromacsWrapper
+imteksimfw
+imteksimfw.egg
+ipython
+ipywidgets
+Jinja2
+matplotlib
+MDAnalysis
+miniball
+nglview
+numpy
+ovito
+pandas
+panedr
+ParmEd
+pymongo
+PySide2
+PyYAML
+scikit_learn
+scipy
+SurfaceTopography

docker/jupyter/pipreqs_requirements.txt

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+ase==3.21.1
+asgiref==3.3.1
+cycler==0.10.0
+dtool_lookup_api==0.5.0
+dtoolcore==3.18.0
+fireworks==2.0.2
+FireWorks.egg==info
+gromacs==0.0.0
+GromacsWrapper==0.8.0
+imteksimfw==0.5.1
+imteksimfw.egg==info
+ipython==8.1.1
+ipywidgets==7.6.3
+Jinja2==2.11.2
+matplotlib==3.3.3
+MDAnalysis==2.1.0
+miniball==1.0.4
+nglview==2.7.7
+numpy==1.19.5
+ovito==3.6.0
+pandas==1.2.1
+panedr==0.5.2
+ParmEd==3.2.0
+pymongo==3.11.2
+PySide2==5.15.2.1
+PyYAML==6.0
+scikit_learn==1.0.2
+scipy==1.6.0
+SurfaceTopography==0.101.3

docker/jupyter/requirements.in

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+click
+pep517
+pip-tools
+tomli
+ase
+asgiref
+cycler
+dtool
+dtool_lookup_api
+dtoolcore
+dtool-s3
+gromacs
+GromacsWrapper
+igraph
+imteksimfw
+ipython
+ipywidgets
+Jinja2
+jupyterlab_autorun_cells
+jupytext
+matplotlib
+MDAnalysis
+miniball
+nglview
+numpy
+openpyxl
+ovito
+pandas
+panedr
+ParmEd
+pymongo
+PySide2
+PyYAML
+scipy