Merge pull request #34 from yambottle/DEV-221-djlabhub-chain-breaker

Dev 221 djlabhub chain breaker

.github/workflows/singleuser-release.yaml

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+name: singleuser-relase-wip
+on:
+  workflow_dispatch:
+    inputs:
+      jupyterhub_version:
+        required: true
+        default: '4.0.2'
+        type: choice
+        options:
+          - '4.0.2'
+          - '1.4.2'
+jobs:
+  release-image:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          # following python version end of life: https://devguide.python.org/versions/
+          - py_ver: '3.10'
+          - py_ver: '3.9'
+          - py_ver: '3.8'
+    env:
+      PY_VER: ${{matrix.py_ver}}
+      JUPYTERHUB_VER: ${{github.event.inputs.jupyterhub_version}}
+    steps:
+      - uses: actions/checkout@v4
+      # TODO - use docker build action
+      # TODO - use conventional commit action to make release and changelog

.gitignore

@@ -1,6 +1 @@
-.vscode
-*.tar.gz
-docs/_build
-sphinx-validator.yaml
-common
-home_user
+.env

README.md

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+TODO - will make this a proper README.md later
+
+Pro
+- Break the chain of dependencies of self-managed base images
+  - Reduce image maintenance hell
+  - Use jupyter/minimal-notebook as base image instead
+- Compatible with previous supported feature as many as possible
+- Provide simpler way for mainteners to manage system dependencies and for users to install packages
+- Provide a way to config jupyter through environment variables
+- This can be used as jupyter lab, so we can archive djlab-docker and only focus on this repo
+- Add jupyterhub docker for single user image testing at local
+
+Con
+- Username if jovyan by default, consider this is a minor issue, since it's only visible in the terminal
+- Larger image size, this can be optimized when it becomes a problem

hub/Dockerfile

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+ARG JUPYTERHUB_VERSION
+FROM jupyterhub/jupyterhub:${JUPYTERHUB_VERSION}
+
+COPY ./config/jupyterhub_config.py /etc/jupyterhub/jupyterhub_config.py
+RUN pip install dockerspawner oauthenticator

hub/config/jupyterhub_config.py

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+import os
+import pwd
+from traitlets.config import Config
+
+c = Config() if "c" not in locals() else c
+
+# get the current user
+user = [u for u in pwd.getpwall() if u.pw_uid == os.getuid()][0]
+
+## Class for authenticating users.
+#
+#          This should be a subclass of :class:`jupyterhub.auth.Authenticator`
+#
+#          with an :meth:`authenticate` method that:
+#
+#          - is a coroutine (asyncio or tornado)
+#          - returns username on success, None on failure
+#          - takes two arguments: (handler, data),
+#            where `handler` is the calling web.RequestHandler,
+#            and `data` is the POST form data from the login page.
+#
+#          .. versionchanged:: 1.0
+#              authenticators may be registered via entry points,
+#              e.g. `c.JupyterHub.authenticator_class = 'pam'`
+#
+#  Currently installed:
+#    - default: jupyterhub.auth.PAMAuthenticator
+#    - dummy: jupyterhub.auth.DummyAuthenticator
+#    - null: jupyterhub.auth.NullAuthenticator
+#    - pam: jupyterhub.auth.PAMAuthenticator
+#  Default: 'jupyterhub.auth.PAMAuthenticator'
+c.JupyterHub.authenticator_class = "jupyterhub.auth.DummyAuthenticator"
+
+# ## TODO - callback_url needs to enable ssl
+# c.JupyterHub.authenticator_class = "oauthenticator.generic.GenericOAuthenticator"
+# c.GenericOAuthenticator.client_id = os.getenv("OAUTH2_CLIENT_ID")
+# c.GenericOAuthenticator.client_secret = os.getenv("OAUTH2_CLIENT_SECRET")
+# c.GenericOAuthenticator.oauth_callback_url = "https://127.0.0.1:8000/hub/oauth_callback"
+# c.GenericOAuthenticator.authorize_url = "https://keycloak-qa.datajoint.io/realms/datajoint/protocol/openid-connect/auth"
+# c.GenericOAuthenticator.token_url = "https://keycloak-qa.datajoint.io/realms/datajoint/protocol/openid-connect/token"
+# c.GenericOAuthenticator.userdata_url = "https://keycloak-qa.datajoint.io/realms/datajoint/protocol/openid-connect/userinfo"
+# c.GenericOAuthenticator.login_service = "Datajoint"
+# c.GenericOAuthenticator.username_claim = "preferred_username"
+# c.GenericOAuthenticator.enable_auth_state = True
+# c.GenericOAuthenticator.scope = ["openid"]
+# c.GenericOAuthenticator.claim_groups_key = "groups"
+# c.GenericOAuthenticator.admin_groups = ["datajoint"]
+
+## The class to use for spawning single-user servers.
+#
+#          Should be a subclass of :class:`jupyterhub.spawner.Spawner`.
+#
+#          .. versionchanged:: 1.0
+#              spawners may be registered via entry points,
+#              e.g. `c.JupyterHub.spawner_class = 'localprocess'`
+#
+#  Currently installed:
+#    - default: jupyterhub.spawner.LocalProcessSpawner
+#    - localprocess: jupyterhub.spawner.LocalProcessSpawner
+#    - simple: jupyterhub.spawner.SimpleLocalProcessSpawner
+#  Default: 'jupyterhub.spawner.LocalProcessSpawner'
+c.JupyterHub.spawner_class = "dockerspawner.DockerSpawner"
+
+## The ip address for the Hub process to *bind* to.
+#
+#          By default, the hub listens on localhost only. This address must be accessible from
+#          the proxy and user servers. You may need to set this to a public ip or '' for all
+#          interfaces if the proxy or user servers are in containers or on a different host.
+#
+#          See `hub_connect_ip` for cases where the bind and connect address should differ,
+#          or `hub_bind_url` for setting the full bind URL.
+#  Default: '127.0.0.1'
+c.JupyterHub.hub_ip = ""
+
+c.DockerSpawner.network_name = os.getenv("DOCKER_NETWORK_NAME", "jupyterhub_network")
+c.DockerSpawner.start_timeout = 60
+# https://github.com/jupyterhub/jupyterhub/issues/2913#issuecomment-580535422
+c.Spawner.http_timeout = 60
+c.Spawner.start_timeout = 60
+c.DockerSpawner.container_image = "datajoint/djlabhub:singleuser-4.0.2-py3.10-qa"
+
+c.DockerSpawner.environment = {
+    ## Jupyter Official Environment Variables
+    "DOCKER_STACKS_JUPYTER_CMD": "lab",
+    ## Extended by Datajoint
+    ## Before Start Hook
+    "DJLABHUB_REPO": "https://github.com/datajoint/datajoint-tutorials.git",
+    "DJLABHUB_REPO_BRANCH": "main",
+    "DJLABHUB_REPO_INSTALL": "TRUE",
+    ## Jupyter Config
+    # "JUPYTER_SERVER_APP_IP": "0.0.0.0",
+    # "JUPYTER_SERVER_APP_PASSWORD": "",
+    # "JUPYTER_SERVER_APP_PORT": "8889",
+    # "JUPYTER_SERVER_APP_ROOT_DIR": "/home/jovyan",
+    "JUPYTER_FILE_CONTENTS_MANAGER_ROOT_DIR": "/home/jovyan",
+    "JUPYTER_YDOCEXTENSION_DISABLE_RTC": "TRUE",
+}

hub/docker-compose.yaml

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+version: '3.7'
+services:
+  hub:
+    build:
+      context: .
+      dockerfile: Dockerfile
+      args:
+        - JUPYTERHUB_VERSION
+    image: datajoint/djlabhub:hub-${JUPYTERHUB_VERSION}
+    container_name: djlabhub-hub
+    user: root
+    env_file: .env
+    # network to connect the hub and singleusers
+    networks:
+      - jupyterhub_network
+    environment:
+      - DOCKER_NETWORK_NAME=jupyterhub_network
+    command: jupyterhub -f /etc/jupyterhub/jupyterhub_config.py
+    ports:
+      - 8000:8000
+    volumes:
+      - ./config/jupyterhub_config.py:/etc/jupyterhub/jupyterhub_config.py
+      - /var/run/docker.sock:/var/run/docker.sock
+
+networks:
+  jupyterhub_network:
+    name: jupyterhub_network
+    driver: bridge
+

hub/example.env

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+# build
+JUPYTERHUB_VERSION=4.0.2
+
+OAUTH2_CLIENT_ID=
+OAUTH2_CLIENT_SECRET=
+# Need to generate by `openssl rand -hex 32`
+JUPYTERHUB_CRYPT_KEY=

.github/workflows/development.yaml → legacy/.github/workflows/development.yaml

@@ -1,7 +1,8 @@
 name: Development
 on:
-  push:
-  pull_request:
+  # push:
+  # pull_request:
+  workflow_dispatch:
 jobs:
   build:
     runs-on: ubuntu-latest

legacy/.gitignore

@@ -0,0 +1,6 @@
+.vscode
+*.tar.gz
+docs/_build
+sphinx-validator.yaml
+common
+home_user