automatic naming to make deploying hubs easier.

.env

@@ -6,43 +6,41 @@
 # values for environment variables in the configuration file IF the variables
 # are not set in the shell environment.
 
-EMAIL=consistentbayes@gmail.com
-DOMAIN_NAME=consistentbayes.com
-
 # To override these values, set the shell environment variables.
 JUPYTERHUB_VERSION=0.9.4
 
-# Name of Docker machine
+# Assign a port for the hub to be hosted on.
-DOCKER_MACHINE_NAME=jupyterhub
+# To check the ports that are in use, run `docker ps`. 
+# Generally, picking a random number between 8000-9999 won't be an issue.
+PORT_NUM=8001
+HUB_NAME=vcarey
 
 # Name of Docker network
-DOCKER_NETWORK_NAME=jupyterhub-network
+#DOCKER_NETWORK_NAME=stathub-network
 
 # Single-user Jupyter Notebook server container image
-DOCKER_NOTEBOOK_IMAGE=jupyter/datascience-notebook
+DOCKER_NOTEBOOK_IMAGE=jupyter/scipy-notebook
 
 # the local image we use, after pinning jupyterhub version
-LOCAL_NOTEBOOK_IMAGE=jupyterhub-user
+#LOCAL_NOTEBOOK_IMAGE=jupyterhub-user
 
 # Notebook directory in the container.
 # This will be /home/jovyan/work if the default
-# This directory is stored as a docker volume for each user
+# This directory is mapped to a docker volume for each user
 DOCKER_NOTEBOOK_DIR=/home/jovyan/work
 
 # Docker run command to use when spawning single-user containers
+# DO NOT CHANGE THIS. It is how the docker-stacks notebooks launch the single-user servers.
 DOCKER_SPAWN_CMD=start-singleuser.sh
 
 # Name of JupyterHub container data volume
-DATA_VOLUME_HOST=jupyterhub-data
+#DATA_VOLUME_HOST=stathub-data
 
 # Data volume container mount point
-DATA_VOLUME_CONTAINER=/data
+#DATA_VOLUME_CONTAINER=/data
 
 # Name of JupyterHub postgres database data volume
-DB_VOLUME_HOST=jupyterhub-db-data
+#DB_VOLUME_HOST=stathub-db-data
-
-# Postgres volume container mount point
-DB_VOLUME_CONTAINER=/var/lib/postgresql/data
 
 # The name of the postgres database containing JupyterHub state
-POSTGRES_DB=jupyterhub
+#POSTGRES_DB=stathub

Makefile

@@ -6,13 +6,11 @@ include .env
 .DEFAULT_GOAL=build
 
 network:
-	@docker network inspect $(DOCKER_NETWORK_NAME) >/dev/null 2>&1 || docker network create $(DOCKER_NETWORK_NAME)
+	@docker network inspect $(HUB_NAME)-network >/dev/null 2>&1 || docker network create $(HUB_NAME)-network
 
 volumes:
-	@docker volume inspect $(DATA_VOLUME_HOST) >/dev/null 2>&1 || docker volume create --name $(DATA_VOLUME_HOST)
+	@docker volume inspect $(HUB_NAME)-data >/dev/null 2>&1 || docker volume create --name $(HUB_NAME)-data
-	@docker volume inspect $(DB_VOLUME_HOST) >/dev/null 2>&1 || docker volume create --name $(DB_VOLUME_HOST)
+	@docker volume inspect $(HUB_NAME)-db-data >/dev/null 2>&1 || docker volume create --name $(HUB_NAME)-db-data
-	@docker volume inspect ro_shared_volume >/dev/null 2>&1 || docker volume create --name ro_shared_volume
-	@docker volume inspect rw_shared_volume >/dev/null 2>&1 || docker volume create --name rw_shared_volume
 
 secrets/postgres.env:
 	@echo "Generating postgres password in $@"
@@ -30,10 +28,6 @@ secrets/jupyterhub.key:
 	@echo "Need an SSL key in secrets/jupyterhub.key"
 	@exit 1
 
-secrets/acme.json:
-	@chmod 600 secrets/acme.json
-	@exit 1
-
 userlist:
 	@echo "Add usernames, one per line, to ./userlist, such as:"
 	@echo "    zoe admin"
@@ -48,13 +42,13 @@ userlist:
 #	cert_files=
 #endif
 
-check-files: userlist secrets/acme.json secrets/oauth.env secrets/postgres.env 
+check-files: userlist secrets/postgres.env 
 
 pull:
 	docker pull $(DOCKER_NOTEBOOK_IMAGE)
 
 notebook_image: pull singleuser/Dockerfile
-	docker build -t $(LOCAL_NOTEBOOK_IMAGE) \
+	docker build -t $(HUB_NAME)-user:latest \
 		--build-arg JUPYTERHUB_VERSION=$(JUPYTERHUB_VERSION) \
 		--build-arg DOCKER_NOTEBOOK_IMAGE=$(DOCKER_NOTEBOOK_IMAGE) \
 		singleuser

docker-compose.yml

@@ -7,15 +7,15 @@ version: "3"
 services:
   hub-db:
     image: postgres:9.5
-    container_name: jupyterhub-db
+    container_name: ${HUB_NAME}-db
     restart: always
     environment:
-      POSTGRES_DB: ${POSTGRES_DB}
+      POSTGRES_DB: ${HUB_NAME}
-      PGDATA: ${DB_VOLUME_CONTAINER}
+      PGDATA: "/var/lib/postgresql/data"
     env_file:
       - secrets/postgres.env
     volumes:
-      - "db:${DB_VOLUME_CONTAINER}"
+      - "db:/var/lib/postgresql/data"
 
   hub:
     depends_on:
@@ -26,31 +26,28 @@ services:
       args:
         JUPYTERHUB_VERSION: ${JUPYTERHUB_VERSION}
     restart: always
-    image: jupyterhub
+    image: ${HUB_NAME}
-    container_name: jupyterhub
+    container_name: ${HUB_NAME}
     volumes:
       # Bind Docker socket on the host so we can connect to the daemon from
       # within the container
       - "/var/run/docker.sock:/var/run/docker.sock:rw"
       # Bind Docker volume on host for JupyterHub database and cookie secrets
-      - "data:${DATA_VOLUME_CONTAINER}"
+      - "data:/data"
       - "./jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py"
       - "/home/math/:/home/"
     ports:
-      - "8000:8000"
+      - "${PORT_NUM}:8000"
     links:
       - hub-db
     environment:
-      # All containers will join this network
+      HUB_NAME: ${HUB_NAME}
-      DOCKER_NETWORK_NAME: ${DOCKER_NETWORK_NAME}
-      # JupyterHub will spawn this Notebook image for users
-      DOCKER_NOTEBOOK_IMAGE: ${LOCAL_NOTEBOOK_IMAGE}
       # Notebook directory inside user image
       DOCKER_NOTEBOOK_DIR: ${DOCKER_NOTEBOOK_DIR}
       # Using this run command (optional)
       DOCKER_SPAWN_CMD: ${DOCKER_SPAWN_CMD}
       # Postgres db info
-      POSTGRES_DB: ${POSTGRES_DB}
+      POSTGRES_DB: ${HUB_NAME}
       POSTGRES_HOST: hub-db
     env_file:
       - secrets/postgres.env
@@ -61,12 +58,12 @@ services:
 volumes:
   data:
     external:
-      name: ${DATA_VOLUME_HOST}
+      name: ${HUB_NAME}-data
   db:
     external:
-      name: ${DB_VOLUME_HOST}
+      name: ${HUB_NAME}-db-data
 
 networks:
   default:
     external:
-      name: ${DOCKER_NETWORK_NAME}
+      name: ${HUB_NAME}-network

jupyterhub_config.py

@@ -8,7 +8,7 @@ from subprocess import check_call
 c = get_config()
 
 # Spawner dropdown menu?
-enable_options=True
+enable_options=False
 # We rely on environment variables to configure JupyterHub so that we
 # avoid having to rebuild the JupyterHub container every time we change a
 # configuration parameter.
@@ -20,10 +20,10 @@ c.JupyterHub.spawner_class = spawner = 'dockerspawner.DockerSpawner'
 
 # Spawn containers from this image (or a whitelist)
 #c.DockerSpawner.image = "jupyter/datascience-notebook:7254cdcfa22b"
-c.DockerSpawner.image = os.environ['DOCKER_NOTEBOOK_IMAGE']
+c.DockerSpawner.image = '%s-user'%os.environ['HUB_NAME']
 if enable_options:
     # if whitelist enabled, the .container_image will be ignored in favor of the options below:
-    c.DockerSpawner.image_whitelist = {'fenics': "jupyterhub-user", 
+    c.DockerSpawner.image_whitelist = {'default': c.DockerSpawner.image , 
                                      'scipy-notebook': "jupyter/scipy-notebook", 
                                      'datascience-notebook': "jupyter/datascience-notebook",
                                      'r-notebook': 'jupyter/r-notebook',
@@ -39,10 +39,11 @@ spawn_cmd = os.environ.get('DOCKER_SPAWN_CMD', "start-singleuser.sh")
 c.DockerSpawner.extra_create_kwargs.update({ 'command': spawn_cmd })
 
 # Memory limit
-c.Spawner.mem_limit = '1G'  # RAM limit
+c.Spawner.mem_limit = '2G'  # RAM limit
+#c.Spawner.cpu_limit = 0.1
 
 # Connect containers to this Docker network
-network_name = os.environ['DOCKER_NETWORK_NAME']
+network_name = '%s-network'%os.environ['HUB_NAME']
 c.DockerSpawner.use_internal_ip = True
 c.DockerSpawner.network_name = network_name
 # Pass the network name as argument to spawned containers
@@ -71,7 +72,9 @@ c.DockerSpawner.remove_containers = True
 c.DockerSpawner.debug = True
 
 # User containers will access hub by container name on the Docker network
-c.JupyterHub.hub_ip = 'jupyterhub'
+c.JupyterHub.hub_ip = os.environ['HUB_NAME']
+# The hub will be hosted at example.com/HUB_NAME/ 
+c.JupyterHub.base_url = u'/%s/'%os.environ['HUB_NAME']
 #c.JupyterHub.hub_port = 8001
 
 # TLS config
@@ -98,7 +101,7 @@ c.HashAuthenticator.show_logins = True            # Optional, defaults to False
 
 ### Database Interaction - cookies, db for jupyterhub
 # Persist hub data on volume mounted inside container
-data_dir = os.environ.get('DATA_VOLUME_CONTAINER', '/data')
+data_dir = '/data' # DATA_VOLUME_CONTAINER
 
 c.JupyterHub.cookie_secret_file = os.path.join(data_dir,
     'jupyterhub_cookie_secret')
@@ -106,7 +109,7 @@ c.JupyterHub.cookie_secret_file = os.path.join(data_dir,
 c.JupyterHub.db_url = 'postgresql://postgres:{password}@{host}/{db}'.format(
     host=os.environ['POSTGRES_HOST'],
     password=os.environ['POSTGRES_PASSWORD'],
-    db=os.environ['POSTGRES_DB'],
+    db=os.environ['HUB_NAME'],
 )
 
 # Whitlelist users and admins

singleuser/Dockerfile

@@ -15,8 +15,17 @@ USER jovyan
 RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse jupyter-rsession-proxy
 RUN conda install -c conda-forge fenics
 
+RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython ipykernel kernda numpy pandas matplotlib ipywidgets yaml && \
+    conda clean -tipsy
+
 USER root
 
+# Create a global kernelspec in the image and modify it so that it properly activates
+# the python2 conda environment.
+RUN $CONDA_DIR/envs/python2/bin/python -m ipykernel install && \
+$CONDA_DIR/envs/python2/bin/kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json
+
+
 # R pre-requisites
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -77,6 +86,7 @@ RUN apt-get clean && \
 
 RUN python3 -m pip install jupyterhub jupyter-rsession-proxy \
   && jupyter labextension install jupyterlab-server-proxy
+
 USER jovyan
 
 RUN python3 -m pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy

singleuser/Dockerfile-Fenics

@@ -1,244 +0,0 @@
-ARG DOCKER_NOTEBOOK_IMAGE
-FROM $DOCKER_NOTEBOOK_IMAGE
-
-ARG JUPYTERHUB_VERSION
-# Install vim in case someone wants to use the terminal
-
-USER root
-
-RUN apt-get update && \
-    apt-get install -y vim && \
-    apt-get install -y gcc && \
-    rm -rf /var/lib/apt/lists/*
-    
-    
-RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse
-#any additional installations go here.
-
-LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
-ARG NB_USER="student"
-ARG NB_UID="1001"
-ARG NB_GID="100"
-
-USER root
-
-# Install all OS dependencies for notebook server that starts but lacks all
-# features (e.g., download as all possible file formats)
-ENV DEBIAN_FRONTEND noninteractive
-RUN apt-get update && apt-get -yq dist-upgrade \
- && apt-get install -yq --no-install-recommends \
-    wget \
-    bzip2 \
-    ca-certificates \
-    sudo \
-    locales \
-    fonts-liberation \
- && rm -rf /var/lib/apt/lists/*
-
-RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
-    locale-gen
-
-# Configure environment
-ENV CONDA_DIR=/opt/conda \
-    SHELL=/bin/bash \
-    NB_USER=$NB_USER \
-    NB_UID=$NB_UID \
-    NB_GID=$NB_GID \
-    LC_ALL=en_US.UTF-8 \
-    LANG=en_US.UTF-8 \
-    LANGUAGE=en_US.UTF-8
-ENV PATH=$CONDA_DIR/bin:$PATH \
-    HOME=/home/$NB_USER
-
-
-ADD fix-permissions /usr/local/bin/fix-permissions
-# Create jovyan user with UID=1000 and in the 'users' group
-# and make sure these dirs are writable by the `users` group.
-RUN groupadd wheel -g 11 && \
-    echo "auth required pam_wheel.so use_uid" >> /etc/pam.d/su && \
-    useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
-    mkdir -p $CONDA_DIR && \
-    chown $NB_USER:$NB_GID $CONDA_DIR && \
-    chmod g+w /etc/passwd && \
-    fix-permissions $HOME && \
-    fix-permissions $CONDA_DIR
-
-USER $NB_UID
-
-# Setup work directory for backward-compatibility
-RUN mkdir /home/$NB_USER/work && \
-    fix-permissions /home/$NB_USER
-
-# Install conda as jovyan and check the md5 sum provided on the download site
-ENV MINICONDA_VERSION 4.5.11
-RUN cd /tmp && \
-    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
-    echo "e1045ee415162f944b6aebfe560b8fee *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
-    /bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
-    rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
-    $CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \
-    $CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
-    $CONDA_DIR/bin/conda config --system --set show_channel_urls true && \
-    $CONDA_DIR/bin/conda install --quiet --yes conda="${MINICONDA_VERSION%.*}.*" && \
-    $CONDA_DIR/bin/conda update --all --quiet --yes && \
-    conda clean -tipsy && \
-    rm -rf /home/$NB_USER/.cache/yarn && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-USER root
-RUN ln -s /usr/bin/python3 /usr/bin/python && \
-    mkdir /.symlinks && \
-    cd /.symlinks &&
-    ln -s $CONDA_DIR/conda conda && \
-    ln -s $CONDA_DIR/activate activate && \
-    ln -s $CONDA_DIR/deactivate deactivate && \
-    export PATH=/.symlinks:$PATH
-
-USER $NB_UID
-# Install Tini
-RUN conda install --quiet --yes 'tini=0.18.0' && \
-    conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
-    conda clean -tipsy && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-# Install Jupyter Notebook, Lab, and Hub
-# Generate a notebook server config
-# Cleanup temporary files
-# Correct permissions
-# Do all this in a single RUN command to avoid duplicating all of the
-# files across image layers when the permissions change
-RUN conda install --quiet --yes \
-    'notebook=5.7.2' \
-    'jupyterhub=0.9.4' \
-    'jupyterlab=0.35.4' && \
-    conda clean -tipsy && \
-    jupyter labextension install @jupyterlab/hub-extension@^0.12.0 && \
-    npm cache clean --force && \
-    jupyter notebook --generate-config && \
-    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
-    rm -rf /home/$NB_USER/.cache/yarn && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-USER root
-
-EXPOSE 8888
-WORKDIR $HOME
-
-# Configure container startup
-ENTRYPOINT ["tini", "-g", "--"]
-CMD ["start-notebook.sh"]
-
-### Minimal Notebook:
-
-USER root
-
-# Install all OS dependencies for fully functional notebook server
-RUN apt-get update && apt-get install -yq --no-install-recommends \
-    build-essential \
-    emacs \
-    git \
-    inkscape \
-    jed \
-    libsm6 \
-    libxext-dev \
-    libxrender1 \
-    lmodern \
-    netcat \
-    pandoc \
-    python-dev \
-    texlive-fonts-extra \
-    texlive-fonts-recommended \
-    texlive-generic-recommended \
-    texlive-latex-base \
-    texlive-latex-extra \
-    texlive-xetex \
-    unzip \
-    nano \
-    && rm -rf /var/lib/apt/lists/*
-
-
-
-
-### Now onto scipy-notebook
-
-
-# ffmpeg for matplotlib anim
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ffmpeg && \
-    rm -rf /var/lib/apt/lists/*
-
-
-USER $NB_UID
-
-# Install Python 3 packages
-# Remove pyqt and qt pulled in for matplotlib since we're only ever going to
-# use notebook-friendly backends in these images
-RUN conda install --quiet --yes \
-    'conda-forge::blas=*=openblas' \
-    'ipywidgets=7.2*' \
-    'pandas=0.23*' \
-    'numexpr=2.6*' \
-    'matplotlib=2.2*' \
-    'scipy=1.1*' \
-    'seaborn=0.9*' \
-    'scikit-learn=0.20*' \
-    'scikit-image=0.14*' \
-    'sympy=1.1*' \
-    'cython=0.28*' \
-    'patsy=0.5*' \
-    'statsmodels=0.9*' \
-    'cloudpickle=0.5*' \
-    'dill=0.2*' \
-    'numba=0.38*' \
-    'bokeh=0.13*' \
-    'sqlalchemy=1.2*' \
-    'hdf5=1.10*' \
-    'h5py=2.7*' \
-    'vincent=0.4.*' \
-    'beautifulsoup4=4.6.*' \
-    'protobuf=3.*' \
-    'xlrd'  && \
-    conda remove --quiet --yes --force qt pyqt && \
-    conda clean -tipsy && \
-    # Activate ipywidgets extension in the environment that runs the notebook server
-    jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
-    # Also activate ipywidgets extension for JupyterLab
-    # Check this URL for most recent compatibilities
-    # https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
-    jupyter labextension install @jupyter-widgets/jupyterlab-manager@^0.38.1 && \
-    jupyter labextension install jupyterlab_bokeh@0.6.3 && \
-    npm cache clean --force && \
-    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
-    rm -rf /home/$NB_USER/.cache/yarn && \
-    rm -rf /home/$NB_USER/.node-gyp && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-# Install facets which does not have a pip or conda package at the moment
-RUN cd /tmp && \
-    git clone https://github.com/PAIR-code/facets.git && \
-    cd facets && \
-    jupyter nbextension install facets-dist/ --sys-prefix && \
-    cd && \
-    rm -rf /tmp/facets && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-# Import matplotlib the first time to build the font cache.
-ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
-RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
-    fix-permissions /home/$NB_USER
-
-USER $NB_UID
-
-# Add local files as late as possible to avoid cache busting
-
-COPY start.sh /usr/local/bin/
-COPY start-notebook.sh /usr/local/bin/
-COPY start-singleuser.sh /usr/local/bin/
-COPY jupyter_notebook_config.py /etc/jupyter/
-RUN fix-permissions /etc/jupyter/
-

singleuser/Dockerfile-R

@@ -1,4 +1,6 @@
-FROM jupyter/r-notebook
+ARG DOCKER_NOTEBOOK_IMAGE
+FROM $DOCKER_NOTEBOOK_IMAGE
+ARG JUPYTERHUB_VERSION
 
 USER root
 
@@ -23,7 +25,8 @@ RUN apt-get clean && \
 
 USER $NB_USER
 
-RUN pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy
+RUN pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy \
+  && jupyter labextension install jupyterlab-server-proxy
 
 # The desktop package uses /usr/lib/rstudio/bin
 ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"