automatic naming to make deploying hubs easier.
This commit is contained in:
mathematicalmichael
parent
ec9ecbe628
commit
389d934f40
30
.env
30
.env
@ -6,43 +6,41 @@
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# values for environment variables in the configuration file IF the variables
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# are not set in the shell environment.
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EMAIL=consistentbayes@gmail.com
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DOMAIN_NAME=consistentbayes.com
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# To override these values, set the shell environment variables.
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JUPYTERHUB_VERSION=0.9.4
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# Name of Docker machine
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DOCKER_MACHINE_NAME=jupyterhub
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# Assign a port for the hub to be hosted on.
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# To check the ports that are in use, run `docker ps`.
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# Generally, picking a random number between 8000-9999 won't be an issue.
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PORT_NUM=8001
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HUB_NAME=vcarey
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# Name of Docker network
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DOCKER_NETWORK_NAME=jupyterhub-network
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#DOCKER_NETWORK_NAME=stathub-network
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# Single-user Jupyter Notebook server container image
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DOCKER_NOTEBOOK_IMAGE=jupyter/datascience-notebook
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DOCKER_NOTEBOOK_IMAGE=jupyter/scipy-notebook
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# the local image we use, after pinning jupyterhub version
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LOCAL_NOTEBOOK_IMAGE=jupyterhub-user
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#LOCAL_NOTEBOOK_IMAGE=jupyterhub-user
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# Notebook directory in the container.
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# This will be /home/jovyan/work if the default
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# This directory is stored as a docker volume for each user
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# This directory is mapped to a docker volume for each user
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DOCKER_NOTEBOOK_DIR=/home/jovyan/work
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# Docker run command to use when spawning single-user containers
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# DO NOT CHANGE THIS. It is how the docker-stacks notebooks launch the single-user servers.
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DOCKER_SPAWN_CMD=start-singleuser.sh
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# Name of JupyterHub container data volume
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DATA_VOLUME_HOST=jupyterhub-data
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#DATA_VOLUME_HOST=stathub-data
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# Data volume container mount point
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DATA_VOLUME_CONTAINER=/data
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#DATA_VOLUME_CONTAINER=/data
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# Name of JupyterHub postgres database data volume
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DB_VOLUME_HOST=jupyterhub-db-data
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# Postgres volume container mount point
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DB_VOLUME_CONTAINER=/var/lib/postgresql/data
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#DB_VOLUME_HOST=stathub-db-data
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# The name of the postgres database containing JupyterHub state
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POSTGRES_DB=jupyterhub
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#POSTGRES_DB=stathub
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16
Makefile
16
Makefile
@ -6,13 +6,11 @@ include .env
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.DEFAULT_GOAL=build
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network:
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@docker network inspect $(DOCKER_NETWORK_NAME) >/dev/null 2>&1 || docker network create $(DOCKER_NETWORK_NAME)
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@docker network inspect $(HUB_NAME)-network >/dev/null 2>&1 || docker network create $(HUB_NAME)-network
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volumes:
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@docker volume inspect $(DATA_VOLUME_HOST) >/dev/null 2>&1 || docker volume create --name $(DATA_VOLUME_HOST)
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@docker volume inspect $(DB_VOLUME_HOST) >/dev/null 2>&1 || docker volume create --name $(DB_VOLUME_HOST)
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@docker volume inspect ro_shared_volume >/dev/null 2>&1 || docker volume create --name ro_shared_volume
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@docker volume inspect rw_shared_volume >/dev/null 2>&1 || docker volume create --name rw_shared_volume
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@docker volume inspect $(HUB_NAME)-data >/dev/null 2>&1 || docker volume create --name $(HUB_NAME)-data
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@docker volume inspect $(HUB_NAME)-db-data >/dev/null 2>&1 || docker volume create --name $(HUB_NAME)-db-data
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secrets/postgres.env:
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@echo "Generating postgres password in $@"
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@ -30,10 +28,6 @@ secrets/jupyterhub.key:
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@echo "Need an SSL key in secrets/jupyterhub.key"
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@exit 1
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secrets/acme.json:
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@chmod 600 secrets/acme.json
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@exit 1
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userlist:
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@echo "Add usernames, one per line, to ./userlist, such as:"
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@echo " zoe admin"
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@ -48,13 +42,13 @@ userlist:
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# cert_files=
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#endif
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check-files: userlist secrets/acme.json secrets/oauth.env secrets/postgres.env
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check-files: userlist secrets/postgres.env
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pull:
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docker pull $(DOCKER_NOTEBOOK_IMAGE)
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notebook_image: pull singleuser/Dockerfile
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docker build -t $(LOCAL_NOTEBOOK_IMAGE) \
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docker build -t $(HUB_NAME)-user:latest \
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--build-arg JUPYTERHUB_VERSION=$(JUPYTERHUB_VERSION) \
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--build-arg DOCKER_NOTEBOOK_IMAGE=$(DOCKER_NOTEBOOK_IMAGE) \
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singleuser
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@ -7,15 +7,15 @@ version: "3"
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services:
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hub-db:
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image: postgres:9.5
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container_name: jupyterhub-db
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container_name: ${HUB_NAME}-db
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restart: always
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environment:
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POSTGRES_DB: ${POSTGRES_DB}
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PGDATA: ${DB_VOLUME_CONTAINER}
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POSTGRES_DB: ${HUB_NAME}
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PGDATA: "/var/lib/postgresql/data"
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env_file:
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- secrets/postgres.env
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volumes:
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- "db:${DB_VOLUME_CONTAINER}"
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- "db:/var/lib/postgresql/data"
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hub:
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depends_on:
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@ -26,31 +26,28 @@ services:
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args:
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JUPYTERHUB_VERSION: ${JUPYTERHUB_VERSION}
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restart: always
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image: jupyterhub
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container_name: jupyterhub
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image: ${HUB_NAME}
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container_name: ${HUB_NAME}
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volumes:
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# Bind Docker socket on the host so we can connect to the daemon from
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# within the container
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- "/var/run/docker.sock:/var/run/docker.sock:rw"
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# Bind Docker volume on host for JupyterHub database and cookie secrets
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- "data:${DATA_VOLUME_CONTAINER}"
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- "data:/data"
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- "./jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py"
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- "/home/math/:/home/"
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ports:
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- "8000:8000"
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- "${PORT_NUM}:8000"
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links:
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- hub-db
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environment:
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# All containers will join this network
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DOCKER_NETWORK_NAME: ${DOCKER_NETWORK_NAME}
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# JupyterHub will spawn this Notebook image for users
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DOCKER_NOTEBOOK_IMAGE: ${LOCAL_NOTEBOOK_IMAGE}
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HUB_NAME: ${HUB_NAME}
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# Notebook directory inside user image
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DOCKER_NOTEBOOK_DIR: ${DOCKER_NOTEBOOK_DIR}
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# Using this run command (optional)
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DOCKER_SPAWN_CMD: ${DOCKER_SPAWN_CMD}
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# Postgres db info
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POSTGRES_DB: ${POSTGRES_DB}
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POSTGRES_DB: ${HUB_NAME}
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POSTGRES_HOST: hub-db
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env_file:
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- secrets/postgres.env
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@ -61,12 +58,12 @@ services:
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volumes:
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data:
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external:
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name: ${DATA_VOLUME_HOST}
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name: ${HUB_NAME}-data
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db:
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external:
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name: ${DB_VOLUME_HOST}
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name: ${HUB_NAME}-db-data
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networks:
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default:
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external:
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name: ${DOCKER_NETWORK_NAME}
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name: ${HUB_NAME}-network
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@ -8,7 +8,7 @@ from subprocess import check_call
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c = get_config()
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# Spawner dropdown menu?
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enable_options=True
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enable_options=False
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# We rely on environment variables to configure JupyterHub so that we
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# avoid having to rebuild the JupyterHub container every time we change a
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# configuration parameter.
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@ -20,10 +20,10 @@ c.JupyterHub.spawner_class = spawner = 'dockerspawner.DockerSpawner'
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# Spawn containers from this image (or a whitelist)
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#c.DockerSpawner.image = "jupyter/datascience-notebook:7254cdcfa22b"
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c.DockerSpawner.image = os.environ['DOCKER_NOTEBOOK_IMAGE']
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c.DockerSpawner.image = '%s-user'%os.environ['HUB_NAME']
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if enable_options:
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# if whitelist enabled, the .container_image will be ignored in favor of the options below:
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c.DockerSpawner.image_whitelist = {'fenics': "jupyterhub-user",
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c.DockerSpawner.image_whitelist = {'default': c.DockerSpawner.image ,
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'scipy-notebook': "jupyter/scipy-notebook",
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'datascience-notebook': "jupyter/datascience-notebook",
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'r-notebook': 'jupyter/r-notebook',
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@ -39,10 +39,11 @@ spawn_cmd = os.environ.get('DOCKER_SPAWN_CMD', "start-singleuser.sh")
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c.DockerSpawner.extra_create_kwargs.update({ 'command': spawn_cmd })
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# Memory limit
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c.Spawner.mem_limit = '1G' # RAM limit
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c.Spawner.mem_limit = '2G' # RAM limit
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#c.Spawner.cpu_limit = 0.1
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# Connect containers to this Docker network
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network_name = os.environ['DOCKER_NETWORK_NAME']
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network_name = '%s-network'%os.environ['HUB_NAME']
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c.DockerSpawner.use_internal_ip = True
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c.DockerSpawner.network_name = network_name
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# Pass the network name as argument to spawned containers
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@ -71,7 +72,9 @@ c.DockerSpawner.remove_containers = True
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c.DockerSpawner.debug = True
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# User containers will access hub by container name on the Docker network
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c.JupyterHub.hub_ip = 'jupyterhub'
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c.JupyterHub.hub_ip = os.environ['HUB_NAME']
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# The hub will be hosted at example.com/HUB_NAME/
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c.JupyterHub.base_url = u'/%s/'%os.environ['HUB_NAME']
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#c.JupyterHub.hub_port = 8001
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# TLS config
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@ -98,7 +101,7 @@ c.HashAuthenticator.show_logins = True # Optional, defaults to False
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### Database Interaction - cookies, db for jupyterhub
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# Persist hub data on volume mounted inside container
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data_dir = os.environ.get('DATA_VOLUME_CONTAINER', '/data')
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data_dir = '/data' # DATA_VOLUME_CONTAINER
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c.JupyterHub.cookie_secret_file = os.path.join(data_dir,
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'jupyterhub_cookie_secret')
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@ -106,7 +109,7 @@ c.JupyterHub.cookie_secret_file = os.path.join(data_dir,
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c.JupyterHub.db_url = 'postgresql://postgres:{password}@{host}/{db}'.format(
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host=os.environ['POSTGRES_HOST'],
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password=os.environ['POSTGRES_PASSWORD'],
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db=os.environ['POSTGRES_DB'],
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db=os.environ['HUB_NAME'],
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)
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# Whitlelist users and admins
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@ -15,8 +15,17 @@ USER jovyan
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RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse jupyter-rsession-proxy
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RUN conda install -c conda-forge fenics
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RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython ipykernel kernda numpy pandas matplotlib ipywidgets yaml && \
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conda clean -tipsy
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USER root
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# Create a global kernelspec in the image and modify it so that it properly activates
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# the python2 conda environment.
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RUN $CONDA_DIR/envs/python2/bin/python -m ipykernel install && \
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$CONDA_DIR/envs/python2/bin/kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json
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# R pre-requisites
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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@ -77,6 +86,7 @@ RUN apt-get clean && \
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RUN python3 -m pip install jupyterhub jupyter-rsession-proxy \
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&& jupyter labextension install jupyterlab-server-proxy
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USER jovyan
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RUN python3 -m pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy
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@ -1,244 +0,0 @@
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ARG DOCKER_NOTEBOOK_IMAGE
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FROM $DOCKER_NOTEBOOK_IMAGE
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ARG JUPYTERHUB_VERSION
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# Install vim in case someone wants to use the terminal
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USER root
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RUN apt-get update && \
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apt-get install -y vim && \
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apt-get install -y gcc && \
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rm -rf /var/lib/apt/lists/*
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RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse
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#any additional installations go here.
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LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
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ARG NB_USER="student"
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ARG NB_UID="1001"
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ARG NB_GID="100"
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USER root
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# Install all OS dependencies for notebook server that starts but lacks all
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# features (e.g., download as all possible file formats)
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt-get update && apt-get -yq dist-upgrade \
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&& apt-get install -yq --no-install-recommends \
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wget \
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bzip2 \
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ca-certificates \
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sudo \
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locales \
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fonts-liberation \
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&& rm -rf /var/lib/apt/lists/*
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RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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# Configure environment
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ENV CONDA_DIR=/opt/conda \
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SHELL=/bin/bash \
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NB_USER=$NB_USER \
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NB_UID=$NB_UID \
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NB_GID=$NB_GID \
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LC_ALL=en_US.UTF-8 \
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LANG=en_US.UTF-8 \
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LANGUAGE=en_US.UTF-8
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ENV PATH=$CONDA_DIR/bin:$PATH \
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HOME=/home/$NB_USER
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ADD fix-permissions /usr/local/bin/fix-permissions
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# Create jovyan user with UID=1000 and in the 'users' group
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# and make sure these dirs are writable by the `users` group.
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RUN groupadd wheel -g 11 && \
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echo "auth required pam_wheel.so use_uid" >> /etc/pam.d/su && \
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useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
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mkdir -p $CONDA_DIR && \
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chown $NB_USER:$NB_GID $CONDA_DIR && \
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chmod g+w /etc/passwd && \
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fix-permissions $HOME && \
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fix-permissions $CONDA_DIR
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USER $NB_UID
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# Setup work directory for backward-compatibility
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RUN mkdir /home/$NB_USER/work && \
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fix-permissions /home/$NB_USER
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# Install conda as jovyan and check the md5 sum provided on the download site
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ENV MINICONDA_VERSION 4.5.11
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RUN cd /tmp && \
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wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
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echo "e1045ee415162f944b6aebfe560b8fee *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
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/bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
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rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
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$CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \
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$CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
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$CONDA_DIR/bin/conda config --system --set show_channel_urls true && \
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$CONDA_DIR/bin/conda install --quiet --yes conda="${MINICONDA_VERSION%.*}.*" && \
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$CONDA_DIR/bin/conda update --all --quiet --yes && \
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conda clean -tipsy && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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USER root
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RUN ln -s /usr/bin/python3 /usr/bin/python && \
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mkdir /.symlinks && \
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cd /.symlinks &&
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ln -s $CONDA_DIR/conda conda && \
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ln -s $CONDA_DIR/activate activate && \
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ln -s $CONDA_DIR/deactivate deactivate && \
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export PATH=/.symlinks:$PATH
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USER $NB_UID
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# Install Tini
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RUN conda install --quiet --yes 'tini=0.18.0' && \
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conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
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conda clean -tipsy && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Install Jupyter Notebook, Lab, and Hub
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# Generate a notebook server config
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# Cleanup temporary files
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# Correct permissions
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# Do all this in a single RUN command to avoid duplicating all of the
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# files across image layers when the permissions change
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RUN conda install --quiet --yes \
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'notebook=5.7.2' \
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'jupyterhub=0.9.4' \
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'jupyterlab=0.35.4' && \
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conda clean -tipsy && \
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jupyter labextension install @jupyterlab/hub-extension@^0.12.0 && \
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npm cache clean --force && \
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jupyter notebook --generate-config && \
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rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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USER root
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EXPOSE 8888
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WORKDIR $HOME
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# Configure container startup
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ENTRYPOINT ["tini", "-g", "--"]
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CMD ["start-notebook.sh"]
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### Minimal Notebook:
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USER root
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# Install all OS dependencies for fully functional notebook server
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RUN apt-get update && apt-get install -yq --no-install-recommends \
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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/
|
||||
|
||||
@ -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"
|
||||
|
||||
Loading…
Reference in New Issue
Block a user