From 9b21d8df7f424dd352472a1734fbfdf4a2bbe307 Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Mon, 7 Nov 2022 13:22:00 +0100
Subject: [PATCH 01/14] ENH: Container recipe for jupyterlab docker
 stack-derived SurfaceTopography image

---
 .../jupyterlab-SurfaceTopography/Dockerfile   |  56 +++
 .../jupyterlab-SurfaceTopography/README.md    | 141 ++++++
 .../conda-requirements.in                     |   2 +
 .../etc/fonts.conf                            |   6 +
 .../requirements.in                           |  32 ++
 .../requirements.txt                          | 442 ++++++++++++++++++
 .../start-wrapper.sh                          |  18 +
 7 files changed, 697 insertions(+)
 create mode 100644 docker/jupyterlab/jupyterlab-SurfaceTopography/Dockerfile
 create mode 100644 docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
 create mode 100644 docker/jupyterlab/jupyterlab-SurfaceTopography/conda-requirements.in
 create mode 100644 docker/jupyterlab/jupyterlab-SurfaceTopography/etc/fonts.conf
 create mode 100644 docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
 create mode 100644 docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
 create mode 100755 docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/Dockerfile b/docker/jupyterlab/jupyterlab-SurfaceTopography/Dockerfile
new file mode 100644
index 0000000..c60152f
--- /dev/null
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/Dockerfile
@@ -0,0 +1,56 @@
+# Build from within repository root 
+#
+# Modify conda enviornment running jupyter notebooks
+FROM jupyter/scipy-notebook:latest
+
+COPY --chown=${NB_UID}:${NB_GID} jupyterlab-SurfaceTopography/conda-requirements.in "/home/${NB_USER}/"
+RUN pip install pip-tools
+RUN pip-compile "/home/${NB_USER}/conda-requirements.in" > "/home/${NB_USER}/conda-requirements.txt"
+RUN pip install --quiet --no-cache-dir --requirement "/home/${NB_USER}/conda-requirements.txt" && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+# FROM imkteksim/dtool-jupyter:latest
+# Install from requirements.txt file
+USER root
+RUN apt-get --yes update && \
+    apt-get --yes install \
+        clang cmake curl g++ gdb git m4 wget \
+        libboost-test-dev \ 
+        libcurl4-openssl-dev \
+        libeigen3-dev \
+        libfftw3-dev \
+        libgmp-dev \
+        libnetcdf-dev \
+        libopenblas-base \
+        libopenblas-dev \
+        python3-pip \
+        python3-dev \
+        python3-netcdf4 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+USER ${NB_UID}
+
+# Workaround for building packages and introducing an ipykernel outside of the jupyterlab conda environment
+RUN PATH=$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g') && ( \
+        pip install --no-binary numpy SurfaceTopography && \
+        pip install ipykernel && \
+        python3 -m ipykernel install --user --name SurfaceTopography --display-name "Python (SurfaceTopography)" && \
+        echo "c.MultiKernelManager.default_kernel_name = 'SurfaceTopography'" >> ${HOME}/.jupyter/jupyter_notebook_config.py) && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+# Workaround for modifying system python outside of the jupyterlab conda environment
+COPY --chown=${NB_UID}:${NB_GID} jupyterlab-SurfaceTopography/requirements.txt "/home/${NB_USER}/"
+RUN PATH="/home/${NB_USER}/.local/bin:$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g')" && ( \
+        pip install --quiet --no-cache-dir --requirement "/home/${NB_USER}/requirements.txt" )
+
+WORKDIR /home/jovyan/work
+
+# Custom fonts config
+COPY jupyterlab-SurfaceTopography/start-wrapper.sh /usr/local/bin/
+RUN mkdir -p /home/${NB_USER}/.config/fontconfig
+COPY jupyterlab-SurfaceTopography/etc/fonts.conf /home/${NB_USER}/.config/fontconfig/fonts.conf
+RUN mkdir -p /home/${NB_USER}/.fonts
+RUN rm -rf /home/${NB_USER}/.cache/matplotlib
+CMD ["start-wrapper.sh", "start-notebook.sh"]
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
new file mode 100644
index 0000000..c991d84
--- /dev/null
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
@@ -0,0 +1,141 @@
+# Sample setup jupyterlab-SurfaceTopography
+
+## Python requirements
+
+To (re-)generate a `requirements.txt` with fixed package versions, use
+
+```console
+python3 -m venv venv
+source venv/bin/activate
+
+pip install --upgrade pip
+pip install wheel
+pip install pip-tools
+
+pip-compile requirements.in > requirements.txt
+```
+
+## Build container
+
+Build container from parent directory (`docker/jupyterlab`) with
+
+    docker build -t imteksim/jupyterlab-SurfaceTopography -f jupyterlab-SurfaceTopography/Dockerfile .
+
+or write directly to tar for transfer with
+
+    docker build --output type=tar,dest=imteksim-jupyterlab-SurfaceTopography.tar -t imteksim/jupyterlab-SurfaceTopography -f jupyterlab-SurfaceTopography/Dockerfile .
+
+and load at target destination with
+
+    docker load --input imteksim-jupyterlab-SurfaceTopography.tar
+
+## Certificates with acme.sh
+
+Identify the public hostname used for issuing SSL certificates, i.e.
+
+    export HOSTNAME="SOME-UUID.fr.bw-cloud-instance.org"
+
+for a public bw-cloud instance and a seecure directory to hold certificates, i.e.
+
+    export CERTDIR=${HOME}/acme.sh
+
+and use
+
+    mkdir -p acme.sh
+
+    # zerossl
+    docker run -v "${CERTDIR}:/acme.sh" --rm neilpang/acme.sh:latest \
+      acme.sh --register-account -m ${MY_EMAIL_ADDRESS}
+    docker run -v "${CERTDIR}:/acme.sh" -p 80:80 --rm neilpang/acme.sh:latest \
+      acme.sh --issue -d "${HOSTNAME}" --standalone --force
+
+    # or, letsencrypt
+    docker run -v "${CERTDIR}:/acme.sh" --rm neilpang/acme.sh:latest \
+      acme.sh --server letsencrypt --register-account -m ${MY_EMAIL_ADDRESS}
+    docker run -v "${CERTDIR}:/acme.sh" -p 80:80 --rm neilpang/acme.sh:latest \
+      acme.sh --server letsencrypt --issue -d "${HOSTNAME}" --standalone --force
+
+    sudo chown -R $USER:$USER $HOME/acme.sh
+
+to (re-)issue certiicates.
+
+## Fonts
+
+Microsoft fonts can be installed with
+
+    sudo apt-get install -y fontconfig
+    sudo apt-get install -y ttf-mscorefonts-installer
+    sudo fc-cache -f
+
+Check with
+
+    $ fc-match Arial
+    LiberationSans-Regular.ttf: "Liberation Sans" "Regular"
+
+Find location of installed fonts with
+
+    $ dpkg-query -L ttf-mscorefonts-installer
+    /.
+    /usr
+    /usr/lib
+    /usr/lib/msttcorefonts
+    /usr/lib/msttcorefonts/update-ms-fonts
+    /usr/share
+    /usr/share/doc
+    /usr/share/doc/ttf-mscorefonts-installer
+    /usr/share/doc/ttf-mscorefonts-installer/README.Debian
+    /usr/share/doc/ttf-mscorefonts-installer/changelog.gz
+    /usr/share/doc/ttf-mscorefonts-installer/copyright
+    /usr/share/fonts
+    /usr/share/fonts/truetype
+    /usr/share/lintian
+    /usr/share/lintian/overrides
+    /usr/share/lintian/overrides/ttf-mscorefonts-installer
+    /usr/share/package-data-downloads
+    /usr/share/package-data-downloads/ttf-mscorefonts-installer
+    /var
+    /var/lib
+    /var/lib/msttcorefonts
+
+## Run Jupyter Lab
+
+Identify a persistent workspace directory, i.e.
+    
+    export WORKDIR=${HOME}/work
+
+and, optionally, a directory of additional fonts to make available to matplotlib, i.e. as above
+
+    export FONTDIR=/usr/share/fonts/truetype/msttcorefonts
+
+Run public Jupyter Lab on default https port with fixed password
+
+    docker run -d --rm -p 443:443 \
+        -v ${WORKDIR}:/home/jovyan/work \
+        -v ${FONTDIR}:/home/jovyan/.fonts \
+        -v ${CERTDIR}/${HOSTNAME}:/etc/ssl/notebook \
+        imteksim/jupyterlab-SurfaceTopography \
+        start-notebook.sh \
+        --ServerApp.keyfile=/etc/ssl/notebook/${HOSTNAME}.key \
+        --ServerApp.certfile=/etc/ssl/notebook/${HOSTNAME}.cer \
+        --ServerApp.password='argon2:$argon2id$v=19$m=10240,t=10,p=8$Jg1gFoiE0ybmBCVG+1s6uA$Jxz4/1591Z7so7JK2M1lRA' \
+        --ServerApp.ip='*' \
+        --ServerApp.port=443
+
+Note that the hash of the password is passed.
+
+    argon2:$argon2id$v=19$m=10240,t=10,p=8$Jg1gFoiE0ybmBCVG+1s6uA$Jxz4/1591Z7so7JK2M1lRA
+
+corresponds to password `imtek-simulation` and has been generated with
+
+    from notebook.auth import passwd
+    passwd()
+
+Add
+
+    --user root -e GRANT_SUDO=yes -e NB_GID=100 -e NB_USER=jovyan
+
+to the docker command line arguments if you need passwordless `sudo` within the container.
+
+## Access Jupyter Lab web interface
+
+Make sure `https` port 443 is reachable, navigate browser to `https://${HOSTNAME}` and log in with password specified on Jupyter Lab launch.
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/conda-requirements.in b/docker/jupyterlab/jupyterlab-SurfaceTopography/conda-requirements.in
new file mode 100644
index 0000000..b8384fb
--- /dev/null
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/conda-requirements.in
@@ -0,0 +1,2 @@
+jupyterlab_autorun_cells
+jupytext
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/etc/fonts.conf b/docker/jupyterlab/jupyterlab-SurfaceTopography/etc/fonts.conf
new file mode 100644
index 0000000..f8b8752
--- /dev/null
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/etc/fonts.conf
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
+<!-- ~/.fonts.conf for per-user font configuration -->
+<fontconfig>
+<dir>~/.fonts</dir>
+</fontconfig>
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
new file mode 100644
index 0000000..9a1a1b9
--- /dev/null
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
@@ -0,0 +1,32 @@
+click
+pep517
+tomli
+ase
+asgiref
+cycler
+dtool
+dtool_lookup_api
+dtoolcore
+dtool-s3
+gromacs
+GromacsWrapper
+imteksimfw
+ipython
+ipywidgets
+Jinja2
+matplotlib
+MDAnalysis
+miniball
+nglview
+numpy
+openpyxl
+ovito<=3.6.0
+pandas
+panedr
+ParmEd
+pymongo
+PySide2
+PyYAML
+scipy
+scikit-learn
+seaborn
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
new file mode 100644
index 0000000..03c0fbb
--- /dev/null
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
@@ -0,0 +1,442 @@
+#
+# This file is autogenerated by pip-compile with python 3.8
+# To update, run:
+#
+#    pip-compile requirements.in
+#
+aiohttp==3.8.3
+    # via dtool-lookup-api
+aiosignal==1.2.0
+    # via aiohttp
+arrow==1.2.3
+    # via jinja2-time
+ase==3.22.1
+    # via -r requirements.in
+asgiref==3.5.2
+    # via
+    #   -r requirements.in
+    #   dtool-lookup-api
+asttokens==2.0.8
+    # via stack-data
+async-timeout==4.0.2
+    # via aiohttp
+attrs==22.1.0
+    # via aiohttp
+backcall==0.2.0
+    # via ipython
+bcrypt==4.0.1
+    # via paramiko
+biopython==1.79
+    # via mdanalysis
+boto3==1.25.2
+    # via dtool-s3
+botocore==1.28.2
+    # via
+    #   boto3
+    #   s3transfer
+certifi==2022.9.24
+    # via requests
+cffi==1.15.1
+    # via
+    #   cryptography
+    #   pynacl
+charset-normalizer==2.1.1
+    # via
+    #   aiohttp
+    #   requests
+click==8.1.3
+    # via
+    #   -r requirements.in
+    #   click-plugins
+    #   dtool-annotation
+    #   dtool-cli
+    #   dtool-config
+    #   dtool-create
+    #   dtool-info
+    #   dtool-overlay
+    #   dtool-s3
+    #   dtool-tag
+    #   flask
+click-plugins==1.1.1
+    # via dtool-cli
+contourpy==1.0.5
+    # via matplotlib
+cryptography==38.0.1
+    # via paramiko
+cycler==0.11.0
+    # via
+    #   -r requirements.in
+    #   matplotlib
+debugpy==1.6.3
+    # via ipykernel
+decorator==5.1.1
+    # via ipython
+dill==0.3.6
+    # via imteksimfw
+dnspython==2.2.1
+    # via pymongo
+dtool==3.26.2
+    # via -r requirements.in
+dtool-annotation==0.1.1
+    # via dtool
+dtool-cli==0.7.1
+    # via
+    #   dtool
+    #   dtool-annotation
+    #   dtool-create
+    #   dtool-info
+    #   dtool-overlay
+    #   dtool-s3
+    #   dtool-tag
+dtool-config==0.4.1
+    # via dtool
+dtool-create==0.23.4
+    # via
+    #   dtool
+    #   imteksimfw
+dtool-http==0.5.1
+    # via
+    #   dtool
+    #   dtool-create
+dtool-info==0.16.2
+    # via dtool
+dtool-lookup-api==0.5.1
+    # via
+    #   -r requirements.in
+    #   imteksimfw
+dtool-overlay==0.3.1
+    # via dtool
+dtool-s3==0.14.1
+    # via -r requirements.in
+dtool-symlink==0.3.1
+    # via
+    #   dtool
+    #   dtool-create
+dtool-tag==0.1.1
+    # via dtool
+dtoolcore==3.18.2
+    # via
+    #   -r requirements.in
+    #   dtool
+    #   dtool-annotation
+    #   dtool-cli
+    #   dtool-config
+    #   dtool-create
+    #   dtool-http
+    #   dtool-info
+    #   dtool-lookup-api
+    #   dtool-overlay
+    #   dtool-s3
+    #   dtool-symlink
+    #   dtool-tag
+entrypoints==0.4
+    # via jupyter-client
+et-xmlfile==1.1.0
+    # via openpyxl
+executing==1.1.1
+    # via stack-data
+fasteners==0.18
+    # via mdanalysis
+fireworks==2.0.3
+    # via imteksimfw
+flask==2.2.2
+    # via
+    #   fireworks
+    #   flask-paginate
+flask-paginate==2022.1.8
+    # via fireworks
+fonttools==4.38.0
+    # via matplotlib
+frozenlist==1.3.1
+    # via
+    #   aiohttp
+    #   aiosignal
+griddataformats==1.0.1
+    # via mdanalysis
+gromacs==0.0.0
+    # via -r requirements.in
+gromacswrapper==0.8.2
+    # via -r requirements.in
+gsd==2.6.0
+    # via mdanalysis
+gunicorn==20.1.0
+    # via fireworks
+idna==3.4
+    # via
+    #   requests
+    #   yarl
+importlib-metadata==5.0.0
+    # via flask
+imteksimfw==0.5.1
+    # via -r requirements.in
+ipykernel==6.16.2
+    # via ipywidgets
+ipython==8.5.0
+    # via
+    #   -r requirements.in
+    #   ipykernel
+    #   ipywidgets
+ipywidgets==8.0.2
+    # via
+    #   -r requirements.in
+    #   nglview
+itsdangerous==2.1.2
+    # via flask
+jedi==0.18.1
+    # via ipython
+jinja2==3.1.2
+    # via
+    #   -r requirements.in
+    #   dtool-info
+    #   fireworks
+    #   flask
+    #   imteksimfw
+    #   jinja2-time
+jinja2-time==0.2.0
+    # via imteksimfw
+jmespath==1.0.1
+    # via
+    #   boto3
+    #   botocore
+joblib==1.2.0
+    # via
+    #   mdanalysis
+    #   scikit-learn
+jupyter-client==7.4.4
+    # via ipykernel
+jupyter-core==4.11.2
+    # via jupyter-client
+jupyterlab-widgets==3.0.3
+    # via
+    #   ipywidgets
+    #   nglview
+kiwisolver==1.4.4
+    # via matplotlib
+markupsafe==2.1.1
+    # via
+    #   jinja2
+    #   werkzeug
+matplotlib==3.6.0
+    # via
+    #   -r requirements.in
+    #   ase
+    #   gromacswrapper
+    #   mdanalysis
+    #   seaborn
+matplotlib-inline==0.1.6
+    # via
+    #   ipykernel
+    #   ipython
+mdanalysis==2.3.0
+    # via -r requirements.in
+miniball==1.1.0
+    # via -r requirements.in
+mmtf-python==1.1.3
+    # via mdanalysis
+monty==2022.9.9
+    # via
+    #   fireworks
+    #   imteksimfw
+mrcfile==1.4.3
+    # via griddataformats
+msgpack==1.0.4
+    # via mmtf-python
+multidict==6.0.2
+    # via
+    #   aiohttp
+    #   yarl
+nest-asyncio==1.5.6
+    # via
+    #   ipykernel
+    #   jupyter-client
+networkx==2.8.7
+    # via mdanalysis
+nglview==3.0.3
+    # via -r requirements.in
+numkit==1.2.2
+    # via gromacswrapper
+numpy==1.23.4
+    # via
+    #   -r requirements.in
+    #   ase
+    #   biopython
+    #   contourpy
+    #   griddataformats
+    #   gromacswrapper
+    #   gsd
+    #   matplotlib
+    #   mdanalysis
+    #   miniball
+    #   mrcfile
+    #   nglview
+    #   numkit
+    #   ovito
+    #   pandas
+    #   pyedr
+    #   scikit-learn
+    #   scipy
+    #   seaborn
+openpyxl==3.0.10
+    # via -r requirements.in
+ovito==3.6.0
+    # via -r requirements.in
+packaging==21.3
+    # via
+    #   dtool-s3
+    #   ipykernel
+    #   matplotlib
+    #   mdanalysis
+pandas==1.5.1
+    # via
+    #   -r requirements.in
+    #   panedr
+    #   seaborn
+panedr==0.7.0
+    # via -r requirements.in
+paramiko==2.11.0
+    # via imteksimfw
+parmed==3.4.3
+    # via -r requirements.in
+parse==1.19.0
+    # via dtool-overlay
+parso==0.8.3
+    # via jedi
+pbr==5.11.0
+    # via
+    #   panedr
+    #   pyedr
+pep517==0.13.0
+    # via -r requirements.in
+pexpect==4.8.0
+    # via ipython
+pickleshare==0.7.5
+    # via ipython
+pillow==9.2.0
+    # via matplotlib
+prompt-toolkit==3.0.31
+    # via ipython
+psutil==5.9.3
+    # via ipykernel
+ptyprocess==0.7.0
+    # via pexpect
+pure-eval==0.2.2
+    # via stack-data
+pycparser==2.21
+    # via cffi
+pyedr==0.7.0
+    # via panedr
+pygments==2.13.0
+    # via
+    #   dtool-info
+    #   ipython
+pymongo==4.3.2
+    # via
+    #   -r requirements.in
+    #   fireworks
+pynacl==1.5.0
+    # via paramiko
+pyparsing==3.0.9
+    # via
+    #   matplotlib
+    #   packaging
+pyside2==5.15.2.1
+    # via
+    #   -r requirements.in
+    #   ovito
+python-dateutil==2.8.2
+    # via
+    #   arrow
+    #   botocore
+    #   fireworks
+    #   jupyter-client
+    #   matplotlib
+    #   pandas
+pytz==2022.5
+    # via pandas
+pyyaml==6.0
+    # via
+    #   -r requirements.in
+    #   dtool-lookup-api
+pyzmq==24.0.1
+    # via
+    #   ipykernel
+    #   jupyter-client
+requests==2.28.1
+    # via dtool-http
+ruamel-yaml==0.17.21
+    # via
+    #   dtool-create
+    #   fireworks
+    #   imteksimfw
+ruamel-yaml-clib==0.2.7
+    # via ruamel-yaml
+s3transfer==0.6.0
+    # via boto3
+scikit-learn==1.1.3
+    # via -r requirements.in
+scipy==1.9.3
+    # via
+    #   -r requirements.in
+    #   ase
+    #   griddataformats
+    #   mdanalysis
+    #   numkit
+    #   scikit-learn
+seaborn==0.12.1
+    # via -r requirements.in
+shiboken2==5.15.2.1
+    # via pyside2
+six==1.16.0
+    # via
+    #   asttokens
+    #   fireworks
+    #   gromacswrapper
+    #   imteksimfw
+    #   numkit
+    #   paramiko
+    #   python-dateutil
+stack-data==0.5.1
+    # via ipython
+tabulate==0.9.0
+    # via fireworks
+threadpoolctl==3.1.0
+    # via
+    #   mdanalysis
+    #   scikit-learn
+tomli==2.0.1
+    # via
+    #   -r requirements.in
+    #   pep517
+tornado==6.2
+    # via
+    #   ipykernel
+    #   jupyter-client
+tqdm==4.64.1
+    # via
+    #   fireworks
+    #   mdanalysis
+traitlets==5.5.0
+    # via
+    #   ipykernel
+    #   ipython
+    #   ipywidgets
+    #   jupyter-client
+    #   jupyter-core
+    #   matplotlib-inline
+urllib3==1.26.12
+    # via
+    #   botocore
+    #   requests
+wcwidth==0.2.5
+    # via prompt-toolkit
+werkzeug==2.2.2
+    # via flask
+widgetsnbextension==4.0.3
+    # via ipywidgets
+yarl==1.8.1
+    # via aiohttp
+zipp==3.10.0
+    # via importlib-metadata
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh b/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh
new file mode 100755
index 0000000..bfd6eef
--- /dev/null
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+
+# delete and rebuild matplotlib font cache
+rm -rf /home/${NB_USER}/.cache/matplotlib
+fc-cache --force
+python3 -c 'import matplotlib.font_manager; matplotlib.font_manager._load_fontmanager(try_read_cache=False)'
+
+echo
+echo "matplotlib cache dir:"
+echo
+python3 -c "import matplotlib; print(matplotlib.get_cachedir())"
+echo
+echo "matplotlib fonts:"
+echo
+python3 -c "import matplotlib.font_manager ; [print(f) for f in matplotlib.font_manager.findSystemFonts(fontpaths=None)]"
+echo
+exec "$@"

From dd340696e24d351b4a1de744dfb0dca1b4ecabdc Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Mon, 7 Nov 2022 13:24:37 +0100
Subject: [PATCH 02/14] DOC: README

---
 docker/jupyterlab/README.md                              | 4 ++++
 docker/jupyterlab/jupyterlab-SurfaceTopography/README.md | 6 +++---
 2 files changed, 7 insertions(+), 3 deletions(-)
 create mode 100644 docker/jupyterlab/README.md

diff --git a/docker/jupyterlab/README.md b/docker/jupyterlab/README.md
new file mode 100644
index 0000000..b31e878
--- /dev/null
+++ b/docker/jupyterlab/README.md
@@ -0,0 +1,4 @@
+# Content
+
+Container recipes derived from the Jupyter Docker Stacks at https://jupyter-docker-stacks.readthedocs.io
+
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
index c991d84..451cd42 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
@@ -19,11 +19,11 @@ pip-compile requirements.in > requirements.txt
 
 Build container from parent directory (`docker/jupyterlab`) with
 
-    docker build -t imteksim/jupyterlab-SurfaceTopography -f jupyterlab-SurfaceTopography/Dockerfile .
+    docker build -t imteksim/jupyterlab-surfacetopography -f jupyterlab-SurfaceTopography/Dockerfile .
 
 or write directly to tar for transfer with
 
-    docker build --output type=tar,dest=imteksim-jupyterlab-SurfaceTopography.tar -t imteksim/jupyterlab-SurfaceTopography -f jupyterlab-SurfaceTopography/Dockerfile .
+    docker build --output type=tar,dest=imteksim-jupyterlab-SurfaceTopography.tar -t imteksim/jupyterlab-surfacetopography -f jupyterlab-SurfaceTopography/Dockerfile .
 
 and load at target destination with
 
@@ -113,7 +113,7 @@ Run public Jupyter Lab on default https port with fixed password
         -v ${WORKDIR}:/home/jovyan/work \
         -v ${FONTDIR}:/home/jovyan/.fonts \
         -v ${CERTDIR}/${HOSTNAME}:/etc/ssl/notebook \
-        imteksim/jupyterlab-SurfaceTopography \
+        imteksim/jupyterlab-surfacetopography \
         start-notebook.sh \
         --ServerApp.keyfile=/etc/ssl/notebook/${HOSTNAME}.key \
         --ServerApp.certfile=/etc/ssl/notebook/${HOSTNAME}.cer \

From b5e7ab434b868e6a388dd1f449e70f05b0925ef9 Mon Sep 17 00:00:00 2001
From: Antoine Sanner <40853209+sannant@users.noreply.github.com>
Date: Wed, 9 Nov 2022 09:10:25 +0100
Subject: [PATCH 03/14] Add requirements

---
 .../jupyterlab/jupyterlab-SurfaceTopography/requirements.in   | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
index 9a1a1b9..59c5e4c 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
@@ -30,3 +30,7 @@ PyYAML
 scipy
 scikit-learn
 seaborn
+git+https://github.com/IMTEK-Simulation/code-snippets.git
+pytest
+ruamel.yaml
+jupytext

From bf82cb734ed596a16293e32212f1e8fae7c28acb Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 9 Nov 2022 09:30:12 +0100
Subject: [PATCH 04/14] DOC: Notes on modifying the container

---
 .../jupyterlab-SurfaceTopography/README.md           | 12 ++++++++++++
 .../jupyterlab-SurfaceTopography/requirements.in     |  2 --
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
index 451cd42..25dcd45 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
@@ -1,5 +1,17 @@
 # Sample setup jupyterlab-SurfaceTopography
 
+## Changes to the container
+
+This docker image bases on the [Jupyter Docker Stacks](https://jupyter-docker-stacks.readthedocs.io/en/latest/).
+These base images use condato run a JupyterLab instance. Extensions to the Jupyter ecosystem (i.e. `jupytext`) 
+must hence go into the `conda-requirements.in` file. 
+
+`SurfaceTopography` does not work well within a conda environment. Instead, this image introduces a separate 
+ipython kernel `SurfaceTopography? that just uses the container-internal system Python and a few system libraries,
+i.e. `numpy`. Anything needed for production in connection with `SurfaceTopography` goes in `requirements.in` or
+into `requirements.txt` directly. When modifying `requirements.in`, regenerate `requirments.txt`with pinned versions
+as described below.
+
 ## Python requirements
 
 To (re-)generate a `requirements.txt` with fixed package versions, use
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
index 59c5e4c..8cbb163 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
@@ -32,5 +32,3 @@ scikit-learn
 seaborn
 git+https://github.com/IMTEK-Simulation/code-snippets.git
 pytest
-ruamel.yaml
-jupytext

From bdd5607cc6b5231a419681ae8a4896a9d7e25d90 Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 9 Nov 2022 09:33:03 +0100
Subject: [PATCH 05/14] MAINT: sorted requirments.in

---
 docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
index 8cbb163..ebdcb25 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
@@ -25,10 +25,10 @@ pandas
 panedr
 ParmEd
 pymongo
+pytest
 PySide2
 PyYAML
 scipy
 scikit-learn
 seaborn
 git+https://github.com/IMTEK-Simulation/code-snippets.git
-pytest

From c126786c87a83432b5c889c95bd28c573c5ad3b6 Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 9 Nov 2022 09:33:24 +0100
Subject: [PATCH 06/14] MAINT: regenerated requirements.txt

---
 .../requirements.txt                          | 57 ++++++++++++-------
 1 file changed, 37 insertions(+), 20 deletions(-)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
index 03c0fbb..a152c12 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
@@ -6,7 +6,7 @@
 #
 aiohttp==3.8.3
     # via dtool-lookup-api
-aiosignal==1.2.0
+aiosignal==1.3.1
     # via aiohttp
 arrow==1.2.3
     # via jinja2-time
@@ -16,21 +16,23 @@ asgiref==3.5.2
     # via
     #   -r requirements.in
     #   dtool-lookup-api
-asttokens==2.0.8
+asttokens==2.1.0
     # via stack-data
 async-timeout==4.0.2
     # via aiohttp
 attrs==22.1.0
-    # via aiohttp
+    # via
+    #   aiohttp
+    #   pytest
 backcall==0.2.0
     # via ipython
 bcrypt==4.0.1
     # via paramiko
 biopython==1.79
     # via mdanalysis
-boto3==1.25.2
+boto3==1.26.5
     # via dtool-s3
-botocore==1.28.2
+botocore==1.29.5
     # via
     #   boto3
     #   s3transfer
@@ -59,9 +61,9 @@ click==8.1.3
     #   flask
 click-plugins==1.1.1
     # via dtool-cli
-contourpy==1.0.5
+contourpy==1.0.6
     # via matplotlib
-cryptography==38.0.1
+cryptography==38.0.3
     # via paramiko
 cycler==0.11.0
     # via
@@ -133,7 +135,9 @@ entrypoints==0.4
     # via jupyter-client
 et-xmlfile==1.1.0
     # via openpyxl
-executing==1.1.1
+exceptiongroup==1.0.1
+    # via pytest
+executing==1.2.0
     # via stack-data
 fasteners==0.18
     # via mdanalysis
@@ -147,7 +151,7 @@ flask-paginate==2022.1.8
     # via fireworks
 fonttools==4.38.0
     # via matplotlib
-frozenlist==1.3.1
+frozenlist==1.3.3
     # via
     #   aiohttp
     #   aiosignal
@@ -157,7 +161,7 @@ gromacs==0.0.0
     # via -r requirements.in
 gromacswrapper==0.8.2
     # via -r requirements.in
-gsd==2.6.0
+gsd==2.6.1
     # via mdanalysis
 gunicorn==20.1.0
     # via fireworks
@@ -167,11 +171,15 @@ idna==3.4
     #   yarl
 importlib-metadata==5.0.0
     # via flask
+imteksimcs @ git+https://github.com/IMTEK-Simulation/code-snippets.git
+    # via -r requirements.in
 imteksimfw==0.5.1
     # via -r requirements.in
-ipykernel==6.16.2
+iniconfig==1.1.1
+    # via pytest
+ipykernel==6.17.0
     # via ipywidgets
-ipython==8.5.0
+ipython==8.6.0
     # via
     #   -r requirements.in
     #   ipykernel
@@ -216,7 +224,7 @@ markupsafe==2.1.1
     # via
     #   jinja2
     #   werkzeug
-matplotlib==3.6.0
+matplotlib==3.6.2
     # via
     #   -r requirements.in
     #   ase
@@ -249,7 +257,7 @@ nest-asyncio==1.5.6
     # via
     #   ipykernel
     #   jupyter-client
-networkx==2.8.7
+networkx==2.8.8
     # via mdanalysis
 nglview==3.0.3
     # via -r requirements.in
@@ -264,6 +272,7 @@ numpy==1.23.4
     #   griddataformats
     #   gromacswrapper
     #   gsd
+    #   imteksimcs
     #   matplotlib
     #   mdanalysis
     #   miniball
@@ -286,14 +295,16 @@ packaging==21.3
     #   ipykernel
     #   matplotlib
     #   mdanalysis
+    #   pytest
 pandas==1.5.1
     # via
     #   -r requirements.in
+    #   imteksimcs
     #   panedr
     #   seaborn
 panedr==0.7.0
     # via -r requirements.in
-paramiko==2.11.0
+paramiko==2.12.0
     # via imteksimfw
 parmed==3.4.3
     # via -r requirements.in
@@ -311,11 +322,13 @@ pexpect==4.8.0
     # via ipython
 pickleshare==0.7.5
     # via ipython
-pillow==9.2.0
+pillow==9.3.0
     # via matplotlib
-prompt-toolkit==3.0.31
+pluggy==1.0.0
+    # via pytest
+prompt-toolkit==3.0.32
     # via ipython
-psutil==5.9.3
+psutil==5.9.4
     # via ipykernel
 ptyprocess==0.7.0
     # via pexpect
@@ -343,6 +356,8 @@ pyside2==5.15.2.1
     # via
     #   -r requirements.in
     #   ovito
+pytest==7.2.0
+    # via -r requirements.in
 python-dateutil==2.8.2
     # via
     #   arrow
@@ -351,7 +366,7 @@ python-dateutil==2.8.2
     #   jupyter-client
     #   matplotlib
     #   pandas
-pytz==2022.5
+pytz==2022.6
     # via pandas
 pyyaml==6.0
     # via
@@ -379,6 +394,7 @@ scipy==1.9.3
     #   -r requirements.in
     #   ase
     #   griddataformats
+    #   imteksimcs
     #   mdanalysis
     #   numkit
     #   scikit-learn
@@ -395,7 +411,7 @@ six==1.16.0
     #   numkit
     #   paramiko
     #   python-dateutil
-stack-data==0.5.1
+stack-data==0.6.0
     # via ipython
 tabulate==0.9.0
     # via fireworks
@@ -407,6 +423,7 @@ tomli==2.0.1
     # via
     #   -r requirements.in
     #   pep517
+    #   pytest
 tornado==6.2
     # via
     #   ipykernel

From ca07d9504400e374c8d79b13d2f1f697a4b377f5 Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 9 Nov 2022 09:41:03 +0100
Subject: [PATCH 07/14] DOC: Note on installing packages in running container

---
 .../jupyterlab/jupyterlab-SurfaceTopography/README.md  | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
index 25dcd45..6e41b90 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
@@ -7,11 +7,19 @@ These base images use condato run a JupyterLab instance. Extensions to the Jupyt
 must hence go into the `conda-requirements.in` file. 
 
 `SurfaceTopography` does not work well within a conda environment. Instead, this image introduces a separate 
-ipython kernel `SurfaceTopography? that just uses the container-internal system Python and a few system libraries,
+ipython kernel `SurfaceTopography` that just uses the container-internal system Python and a few system libraries,
 i.e. `numpy`. Anything needed for production in connection with `SurfaceTopography` goes in `requirements.in` or
 into `requirements.txt` directly. When modifying `requirements.in`, regenerate `requirments.txt`with pinned versions
 as described below.
 
+If in need to quickly modify the `SurfaceTopography` kernel environment at runtime, pay attention to
+breaking out of the default conda enviornment in the shell
+
+* `conda deactivate`, and
+* removing any conda-related artifacts from the `$PATH`, i.e. with `export PATH=$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g')`
+
+The latter is necessary to avoid conda compiler interfering with custom build steps when compiling against system libraries.
+
 ## Python requirements
 
 To (re-)generate a `requirements.txt` with fixed package versions, use

From 56f47eda049c466db41d27d2ffbd03ad5bd15e16 Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 9 Nov 2022 09:58:48 +0100
Subject: [PATCH 08/14] MAINT: added contactmechanics

---
 docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
index ebdcb25..fcf66d2 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
@@ -3,6 +3,7 @@ pep517
 tomli
 ase
 asgiref
+contactmechanics
 cycler
 dtool
 dtool_lookup_api

From 1c98cc70f5c52c5e19b8d2e7d3be189b09f8c85c Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 9 Nov 2022 10:00:33 +0100
Subject: [PATCH 09/14] WIP: see whether contactmechanics and its dependencies
 work by just adding to requirements.txt

---
 .../requirements.txt                          | 39 ++++++++++++++++++-
 1 file changed, 37 insertions(+), 2 deletions(-)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
index a152c12..f2cbc5c 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
@@ -61,6 +61,8 @@ click==8.1.3
     #   flask
 click-plugins==1.1.1
     # via dtool-cli
+contactmechanics==1.0.0
+    # via -r requirements.in
 contourpy==1.0.6
     # via matplotlib
 cryptography==38.0.3
@@ -73,6 +75,8 @@ debugpy==1.6.3
     # via ipykernel
 decorator==5.1.1
     # via ipython
+defusedxml==0.7.1
+    # via surfacetopography
 dill==0.3.6
     # via imteksimfw
 dnspython==2.2.1
@@ -165,10 +169,14 @@ gsd==2.6.1
     # via mdanalysis
 gunicorn==20.1.0
     # via fireworks
+h5py==3.7.0
+    # via surfacetopography
 idna==3.4
     # via
     #   requests
     #   yarl
+igor==0.3
+    # via surfacetopography
 importlib-metadata==5.0.0
     # via flask
 imteksimcs @ git+https://github.com/IMTEK-Simulation/code-snippets.git
@@ -231,6 +239,7 @@ matplotlib==3.6.2
     #   gromacswrapper
     #   mdanalysis
     #   seaborn
+    #   surfacetopography
 matplotlib-inline==0.1.6
     # via
     #   ipykernel
@@ -245,10 +254,16 @@ monty==2022.9.9
     # via
     #   fireworks
     #   imteksimfw
+mpi4py==3.1.4
+    # via mufft
 mrcfile==1.4.3
     # via griddataformats
 msgpack==1.0.4
     # via mmtf-python
+mufft==0.23.1
+    # via
+    #   contactmechanics
+    #   surfacetopography
 multidict==6.0.2
     # via
     #   aiohttp
@@ -263,28 +278,40 @@ nglview==3.0.3
     # via -r requirements.in
 numkit==1.2.2
     # via gromacswrapper
+numpi==0.3.1
+    # via
+    #   contactmechanics
+    #   surfacetopography
 numpy==1.23.4
     # via
     #   -r requirements.in
     #   ase
     #   biopython
+    #   contactmechanics
     #   contourpy
     #   griddataformats
     #   gromacswrapper
     #   gsd
+    #   h5py
     #   imteksimcs
     #   matplotlib
     #   mdanalysis
     #   miniball
     #   mrcfile
+    #   mufft
     #   nglview
     #   numkit
+    #   numpi
+    #   numpyencoder
     #   ovito
     #   pandas
     #   pyedr
     #   scikit-learn
     #   scipy
     #   seaborn
+    #   surfacetopography
+numpyencoder==0.3.0
+    # via surfacetopography
 openpyxl==3.0.10
     # via -r requirements.in
 ovito==3.6.0
@@ -323,7 +350,9 @@ pexpect==4.8.0
 pickleshare==0.7.5
     # via ipython
 pillow==9.3.0
-    # via matplotlib
+    # via
+    #   matplotlib
+    #   surfacetopography
 pluggy==1.0.0
     # via pytest
 prompt-toolkit==3.0.32
@@ -366,18 +395,22 @@ python-dateutil==2.8.2
     #   jupyter-client
     #   matplotlib
     #   pandas
+    #   surfacetopography
 pytz==2022.6
     # via pandas
 pyyaml==6.0
     # via
     #   -r requirements.in
     #   dtool-lookup-api
+    #   surfacetopography
 pyzmq==24.0.1
     # via
     #   ipykernel
     #   jupyter-client
 requests==2.28.1
-    # via dtool-http
+    # via
+    #   dtool-http
+    #   surfacetopography
 ruamel-yaml==0.17.21
     # via
     #   dtool-create
@@ -413,6 +446,8 @@ six==1.16.0
     #   python-dateutil
 stack-data==0.6.0
     # via ipython
+surfacetopography==1.1
+    # via contactmechanics
 tabulate==0.9.0
     # via fireworks
 threadpoolctl==3.1.0

From fecdf66528097322de66b712d471277dd0c31322 Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 9 Nov 2022 10:56:05 +0100
Subject: [PATCH 10/14] MAINT: manually removed mpi4py dep again

---
 docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt | 2 --
 1 file changed, 2 deletions(-)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
index f2cbc5c..9fdcf41 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
@@ -254,8 +254,6 @@ monty==2022.9.9
     # via
     #   fireworks
     #   imteksimfw
-mpi4py==3.1.4
-    # via mufft
 mrcfile==1.4.3
     # via griddataformats
 msgpack==1.0.4

From 4a9eaa6c3bbe4a0b9d13263452c70a4759c8913a Mon Sep 17 00:00:00 2001
From: sannant <antoine.sanner@imtek.uni-freiburg.de>
Date: Wed, 9 Nov 2022 11:24:14 +0100
Subject: [PATCH 11/14] add adhesion

---
 docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
index fcf66d2..33cc704 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.in
@@ -1,6 +1,7 @@
 click
 pep517
 tomli
+adhesion
 ase
 asgiref
 contactmechanics

From 55a223420e641bdf7ea6a17bf39cbc6c5a5cb773 Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 9 Nov 2022 14:15:15 +0100
Subject: [PATCH 12/14] ENH: adhesion in requirements.txt

---
 .../requirements.txt                            | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
index 9fdcf41..d87e00b 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/requirements.txt
@@ -4,6 +4,8 @@
 #
 #    pip-compile requirements.in
 #
+adhesion==0.90.0
+    # via -r requirements.in
 aiohttp==3.8.3
     # via dtool-lookup-api
 aiosignal==1.3.1
@@ -62,7 +64,9 @@ click==8.1.3
 click-plugins==1.1.1
     # via dtool-cli
 contactmechanics==1.0.0
-    # via -r requirements.in
+    # via
+    #   -r requirements.in
+    #   adhesion
 contourpy==1.0.6
     # via matplotlib
 cryptography==38.0.3
@@ -220,7 +224,7 @@ joblib==1.2.0
     #   scikit-learn
 jupyter-client==7.4.4
     # via ipykernel
-jupyter-core==4.11.2
+jupyter-core==5.0.0
     # via jupyter-client
 jupyterlab-widgets==3.0.3
     # via
@@ -260,6 +264,7 @@ msgpack==1.0.4
     # via mmtf-python
 mufft==0.23.1
     # via
+    #   adhesion
     #   contactmechanics
     #   surfacetopography
 multidict==6.0.2
@@ -278,11 +283,13 @@ numkit==1.2.2
     # via gromacswrapper
 numpi==0.3.1
     # via
+    #   adhesion
     #   contactmechanics
     #   surfacetopography
 numpy==1.23.4
     # via
     #   -r requirements.in
+    #   adhesion
     #   ase
     #   biopython
     #   contactmechanics
@@ -351,6 +358,8 @@ pillow==9.3.0
     # via
     #   matplotlib
     #   surfacetopography
+platformdirs==2.5.3
+    # via jupyter-core
 pluggy==1.0.0
     # via pytest
 prompt-toolkit==3.0.32
@@ -445,7 +454,9 @@ six==1.16.0
 stack-data==0.6.0
     # via ipython
 surfacetopography==1.1
-    # via contactmechanics
+    # via
+    #   adhesion
+    #   contactmechanics
 tabulate==0.9.0
     # via fireworks
 threadpoolctl==3.1.0

From 076076996f3f1a6cf81b3912820b04dd0b3d62a9 Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Thu, 10 Nov 2022 17:04:30 +0100
Subject: [PATCH 13/14] WIP: An attempt to make this image independent on user
 'jovyan'

---
 .../jupyterlab-SurfaceTopography/Dockerfile   | 31 ++++++++++++-------
 .../jupyterlab-SurfaceTopography/README.md    |  2 +-
 .../etc/fonts.conf                            |  2 +-
 .../start-wrapper.sh                          |  6 ++--
 4 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/Dockerfile b/docker/jupyterlab/jupyterlab-SurfaceTopography/Dockerfile
index c60152f..50ecdfd 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/Dockerfile
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/Dockerfile
@@ -1,7 +1,9 @@
 # Build from within repository root 
 #
 # Modify conda enviornment running jupyter notebooks
-FROM jupyter/scipy-notebook:latest
+FROM jupyter/minimal-notebook:latest
+
+USER root
 
 COPY --chown=${NB_UID}:${NB_GID} jupyterlab-SurfaceTopography/conda-requirements.in "/home/${NB_USER}/"
 RUN pip install pip-tools
@@ -12,7 +14,6 @@ RUN pip install --quiet --no-cache-dir --requirement "/home/${NB_USER}/conda-req
 
 # FROM imkteksim/dtool-jupyter:latest
 # Install from requirements.txt file
-USER root
 RUN apt-get --yes update && \
     apt-get --yes install \
         clang cmake curl g++ gdb git m4 wget \
@@ -29,28 +30,34 @@ RUN apt-get --yes update && \
         python3-netcdf4 && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-USER ${NB_UID}
 
 # Workaround for building packages and introducing an ipykernel outside of the jupyterlab conda environment
 RUN PATH=$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g') && ( \
         pip install --no-binary numpy SurfaceTopography && \
         pip install ipykernel && \
-        python3 -m ipykernel install --user --name SurfaceTopography --display-name "Python (SurfaceTopography)" && \
-        echo "c.MultiKernelManager.default_kernel_name = 'SurfaceTopography'" >> ${HOME}/.jupyter/jupyter_notebook_config.py) && \
+        python3 -m ipykernel install --name SurfaceTopography --display-name "Python (SurfaceTopography)") && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
 # Workaround for modifying system python outside of the jupyterlab conda environment
 COPY --chown=${NB_UID}:${NB_GID} jupyterlab-SurfaceTopography/requirements.txt "/home/${NB_USER}/"
-RUN PATH="/home/${NB_USER}/.local/bin:$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g')" && ( \
+RUN PATH="$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g')" && ( \
         pip install --quiet --no-cache-dir --requirement "/home/${NB_USER}/requirements.txt" )
 
-WORKDIR /home/jovyan/work
+COPY jupyterlab-SurfaceTopography/start-wrapper.sh /usr/local/bin/
 
 # Custom fonts config
-COPY jupyterlab-SurfaceTopography/start-wrapper.sh /usr/local/bin/
-RUN mkdir -p /home/${NB_USER}/.config/fontconfig
-COPY jupyterlab-SurfaceTopography/etc/fonts.conf /home/${NB_USER}/.config/fontconfig/fonts.conf
-RUN mkdir -p /home/${NB_USER}/.fonts
-RUN rm -rf /home/${NB_USER}/.cache/matplotlib
+COPY jupyterlab-SurfaceTopography/etc/fonts.conf /etc/fonts/conf.avail/99-injected.conf
+RUN ln -s /etc/fonts/conf.avail/99-injected.conf /etc/fonts/conf.d/99-injected.conf
+RUN mkdir -p /fonts
+
+# Install from requirements.txt file
+RUN apt-get --yes update && \
+    apt-get --yes install fontconfig && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+WORKDIR /home/${NB_USER}/work
+USER ${NB_UID}
+
 CMD ["start-wrapper.sh", "start-notebook.sh"]
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
index 6e41b90..7af3aff 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/README.md
@@ -131,7 +131,7 @@ Run public Jupyter Lab on default https port with fixed password
 
     docker run -d --rm -p 443:443 \
         -v ${WORKDIR}:/home/jovyan/work \
-        -v ${FONTDIR}:/home/jovyan/.fonts \
+        -v ${FONTDIR}:/fonts \
         -v ${CERTDIR}/${HOSTNAME}:/etc/ssl/notebook \
         imteksim/jupyterlab-surfacetopography \
         start-notebook.sh \
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/etc/fonts.conf b/docker/jupyterlab/jupyterlab-SurfaceTopography/etc/fonts.conf
index f8b8752..0a2f35e 100644
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/etc/fonts.conf
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/etc/fonts.conf
@@ -2,5 +2,5 @@
 <!DOCTYPE fontconfig SYSTEM "fonts.dtd">
 <!-- ~/.fonts.conf for per-user font configuration -->
 <fontconfig>
-<dir>~/.fonts</dir>
+<dir>/fonts</dir>
 </fontconfig>
diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh b/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh
index bfd6eef..3294f28 100755
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh
@@ -4,15 +4,15 @@ set -e
 # delete and rebuild matplotlib font cache
 rm -rf /home/${NB_USER}/.cache/matplotlib
 fc-cache --force
-python3 -c 'import matplotlib.font_manager; matplotlib.font_manager._load_fontmanager(try_read_cache=False)'
+PATH=$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g') python3 -c 'import matplotlib.font_manager; matplotlib.font_manager._load_fontmanager(try_read_cache=False)'
 
 echo
 echo "matplotlib cache dir:"
 echo
-python3 -c "import matplotlib; print(matplotlib.get_cachedir())"
+PATH=$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g') python3 -c "import matplotlib; print(matplotlib.get_cachedir())"
 echo
 echo "matplotlib fonts:"
 echo
-python3 -c "import matplotlib.font_manager ; [print(f) for f in matplotlib.font_manager.findSystemFonts(fontpaths=None)]"
+PATH=$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g') python3 -c "import matplotlib.font_manager ; [print(f) for f in matplotlib.font_manager.findSystemFonts(fontpaths=None)]"
 echo
 exec "$@"

From 1cc10caa4c7255c074931fc87e943bc314adcc56 Mon Sep 17 00:00:00 2001
From: Johannes Laurin Hoermann <johannes.hoermann@imtek.uni-freiburg.de>
Date: Thu, 10 Nov 2022 21:43:54 +0100
Subject: [PATCH 14/14] MAINT: don't delete font cache

---
 docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh b/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh
index 3294f28..67c2320 100755
--- a/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh
+++ b/docker/jupyterlab/jupyterlab-SurfaceTopography/start-wrapper.sh
@@ -2,7 +2,7 @@
 set -e
 
 # delete and rebuild matplotlib font cache
-rm -rf /home/${NB_USER}/.cache/matplotlib
+# rm -rf /home/${NB_USER}/.cache/matplotlib
 fc-cache --force
 PATH=$(echo "$PATH" | sed -e 's|/opt/conda[^:]*:||g') python3 -c 'import matplotlib.font_manager; matplotlib.font_manager._load_fontmanager(try_read_cache=False)'