danielballan · July 19, 2016 19:27
diff --git a/install.sh b/install.sh
 echo "deb http://mirror.cs.nsls2.local/debian wheezy-backports main" >> /etc/apt/sources.list.d/backports.list

 aptitude -t wheezy-backports install nodejs
 update-alternatives --install /usr/bin/node nodejs /usr/bin/nodejs 100
 wget https://www.npmjs.org/install.sh
 sh install.sh
 node -v
 npm -v

 npm config set proxy http://proxy:8888
 npm config set https-proxy http://proxy:8888  # N.B. http here, not https

 apt-get install python3

 pip3 install ipython
 pip3 install pyzmq
 pip3 install mistune
 pip3 install jinja2
 pip3 install pexpect  # not sure if this is actually required in the final configuration we use
 pip3 install jsonschema
 pip3 install terminado
 pip3 install jupyterhub  # We deployed v0.2.0

 # sudospawner is not yet on PyPI
 git clone https://github.com/jupyter/sudospawner
 cd sudospawner
 pip3 install -e .
 cd ..

 # remotekernel is not yet on PyPI
 git clone https://github.com/danielballan/remotekernel
 cd remotekernel
 pip3 install -e .
 cd ..
diff --git a/installing-node.md b/installing-node.md
diff --git a/jupyterhub_config.py b/jupyterhub_config.py
 # Configuration file for jupyterhub.

 #------------------------------------------------------------------------------
 # Configurable configuration
 #------------------------------------------------------------------------------

 #------------------------------------------------------------------------------
 # SingletonConfigurable configuration
 #------------------------------------------------------------------------------

 # A configurable that only allows one instance.
 # 
 # This class is for classes that should only have one instance of itself or
 # *any* subclass. To create and retrieve such a class use the
 # :meth:`SingletonConfigurable.instance` method.

 #------------------------------------------------------------------------------
 # Application configuration
 #------------------------------------------------------------------------------

 # This is an application.

 # The date format used by logging formatters for %(asctime)s
 # c.Application.log_datefmt = '%Y-%m-%d %H:%M:%S'

 # The Logging format template
 # c.Application.log_format = '[%(name)s]%(highlevel)s %(message)s'

 # Set the log level by value or name.
 # c.Application.log_level = 30

 #------------------------------------------------------------------------------
 # JupyterHub configuration
 #------------------------------------------------------------------------------

 # An Application for starting a Multi-User Jupyter Notebook server.

 # Interval (in seconds) at which to update last-activity timestamps.
 # c.JupyterHub.last_activity_interval = 300

 # File to write PID Useful for daemonizing jupyterhub.
 # c.JupyterHub.pid_file = ''

 # Grant admin users permission to access single-user servers.
 # 
 # Users should be properly informed if this is enabled.
 # c.JupyterHub.admin_access = False

 # url for the database. e.g. `sqlite:///jupyterhub.sqlite`
 c.JupyterHub.db_url = 'sqlite:////home/jupyter/jupyterhub.sqlite'

 # The ip for this process
 # c.JupyterHub.hub_ip = 'localhost'

 # Include any kwargs to pass to the database connection. See
 # sqlalchemy.create_engine for details.
 # c.JupyterHub.db_kwargs = traitlets.Undefined

 # Paths to search for jinja templates.
 # c.JupyterHub.template_paths = traitlets.Undefined

 # The class to use for spawning single-user servers.
 # 
 # Should be a subclass of Spawner.
 # c.JupyterHub.spawner_class = <class 'jupyterhub.spawner.LocalProcessSpawner'>
 c.JupyterHub.spawner_class='sudospawner.SudoSpawner'

 # Supply extra arguments that will be passed to Jinja environment.
 # c.JupyterHub.jinja_environment_options = traitlets.Undefined

 # Class for authenticating users.
 # 
 # This should be a class with the following form:
 # 
 # - constructor takes one kwarg: `config`, the IPython config object.
 # 
 # - is a tornado.gen.coroutine
 # - 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.
 # c.JupyterHub.authenticator_class = <class 'jupyterhub.auth.PAMAuthenticator'>

 # The Proxy Auth token.
 # 
 # Loaded from the CONFIGPROXY_AUTH_TOKEN env variable by default.
 # c.JupyterHub.proxy_auth_token = ''

 # The ip for the proxy API handlers
 # c.JupyterHub.proxy_api_ip = 'localhost'

 # The port for this process
 # c.JupyterHub.hub_port = 8081

 # The location of jupyterhub data files (e.g. /usr/local/share/jupyter/hub)
 # c.JupyterHub.data_files_path = '/etc/jupyterhub/jupyterhub/share/jupyter/hub'

 # Interval (in seconds) at which to check if the proxy is running.
 # c.JupyterHub.proxy_check_interval = 30

 # DEPRECATED, use Authenticator.admin_users instead.
 # c.JupyterHub.admin_users = traitlets.Undefined

 # Extra log handlers to set on JupyterHub logger
 # c.JupyterHub.extra_log_handlers = traitlets.Undefined

 # Path to SSL certificate file for the public facing interface of the proxy
 # 
 # Use with ssl_key
 c.JupyterHub.ssl_cert = '/etc/certificates/cs_nsls2_local.crt'

 # log all database transactions. This has A LOT of output
 # c.JupyterHub.debug_db = False

 # The cookie secret to use to encrypt cookies.
 # 
 # Loaded from the JPY_COOKIE_SECRET env variable by default.
 # c.JupyterHub.cookie_secret = b''

 # Set a logging.FileHandler on this file.
 # c.JupyterHub.extra_log_file = ''

 # Answer yes to any questions (e.g. confirm overwrite)
 # c.JupyterHub.answer_yes = False

 # Number of days for a login cookie to be valid. Default is two weeks.
 # c.JupyterHub.cookie_max_age_days = 14

 # Purge and reset the database.
 # c.JupyterHub.reset_db = False

 # Path to SSL key file for the public facing interface of the proxy
 # 
 # Use with ssl_cert
 c.JupyterHub.ssl_key = '/etc/certificates/cs_nsls2_local.key'

 # File in which to store the cookie secret.
 c.JupyterHub.cookie_secret_file = '/home/jupyter/jupyterhub_cookie_secret'

 # The command to start the http proxy.
 # 
 # Only override if configurable-http-proxy is not on your PATH
 # c.JupyterHub.proxy_cmd = traitlets.Undefined

 # The base URL of the entire application
 # c.JupyterHub.base_url = '/'

 # The public facing ip of the proxy
 # c.JupyterHub.ip = ''

 # The public facing port of the proxy
 c.JupyterHub.port = 7777

 # Whether to shutdown the proxy when the Hub shuts down.
 # 
 # Disable if you want to be able to teardown the Hub while leaving the proxy
 # running.
 # 
 # Only valid if the proxy was starting by the Hub process.
 # 
 # If both this and cleanup_servers are False, sending SIGINT to the Hub will
 # only shutdown the Hub, leaving everything else running.
 # 
 # The Hub should be able to resume from database state.
 # c.JupyterHub.cleanup_proxy = True

 # Whether to shutdown single-user servers when the Hub shuts down.
 # 
 # Disable if you want to be able to teardown the Hub while leaving the single-
 # user servers running.
 # 
 # If both this and cleanup_proxy are False, sending SIGINT to the Hub will only
 # shutdown the Hub, leaving everything else running.
 # 
 # The Hub should be able to resume from database state.
 # c.JupyterHub.cleanup_servers = True

 # The prefix for the hub server. Must not be '/'
 # c.JupyterHub.hub_prefix = '/hub/'

 # 
 # c.JupyterHub.tornado_settings = traitlets.Undefined

 # show debug output in configurable-http-proxy
 # c.JupyterHub.debug_proxy = False

 # Generate default config file
 # c.JupyterHub.generate_config = False

 # The port for the proxy API handlers
 # c.JupyterHub.proxy_api_port = 0

 # The config file to load
 # c.JupyterHub.config_file = 'jupyterhub_config.py'

 #------------------------------------------------------------------------------
 # LoggingConfigurable configuration
 #------------------------------------------------------------------------------

 # A parent class for Configurables that log.
 # 
 # Subclasses have a log trait, and the default behavior is to get the logger
 # from the currently running Application.

 #------------------------------------------------------------------------------
 # Spawner configuration
 #------------------------------------------------------------------------------

 # Base class for spawning single-user notebook servers.
 # 
 # Subclass this, and override the following methods:
 # 
 # - load_state - get_state - start - stop - poll

 # Timeout (in seconds) before giving up on a spawned HTTP server
 # 
 # Once a server has successfully been spawned, this is the amount of time we
 # wait before assuming that the server is unable to accept connections.
 # c.Spawner.http_timeout = 30

 # Extra arguments to be passed to the single-user server
 c.Spawner.args = ['--MappingKernelManager.kernel_manager_class=remotekernel.manager.RemoteIOLoopKernelManager']

 # Enable debug-logging of the single-user server
 # c.Spawner.debug = False

 # Whitelist of environment variables for the subprocess to inherit
 # c.Spawner.env_keep = traitlets.Undefined

 # The notebook directory for the single-user server
 # 
 # `~` will be expanded to the user's home directory
 # c.Spawner.notebook_dir = ''

 # The IP address (or hostname) the single-user server should listen on
 # c.Spawner.ip = 'localhost'

 # The command used for starting notebooks.
 # c.Spawner.cmd = ['jupyterhub-singleuser', '--MappingKernelManager.kernel_manager_class=remotekernel.manager.RemoteIOLoopKernelManager']

 # Timeout (in seconds) before giving up on the spawner.
 # 
 # This is the timeout for start to return, not the timeout for the server to
 # respond. Callers of spawner.start will assume that startup has failed if it
 # takes longer than this. start should return when the server process is started
 # and its location is known.
 # c.Spawner.start_timeout = 60

 # Interval (in seconds) on which to poll the spawner.
 # c.Spawner.poll_interval = 30

 #------------------------------------------------------------------------------
 # LocalProcessSpawner configuration
 #------------------------------------------------------------------------------

 # A Spawner that just uses Popen to start local processes.

 # Seconds to wait for process to halt after SIGKILL before giving up
 # c.LocalProcessSpawner.KILL_TIMEOUT = 5

 # Seconds to wait for process to halt after SIGTERM before proceeding to SIGKILL
 # c.LocalProcessSpawner.TERM_TIMEOUT = 5

 # Seconds to wait for process to halt after SIGINT before proceeding to SIGTERM
 # c.LocalProcessSpawner.INTERRUPT_TIMEOUT = 10

 #------------------------------------------------------------------------------
 # Authenticator configuration
 #------------------------------------------------------------------------------

 # A class for authentication.
 # 
 # The API is one method, `authenticate`, a tornado gen.coroutine.

 # set of usernames of admin users
 # 
 # If unspecified, only the user that launches the server will be admin.
 # c.Authenticator.admin_users = traitlets.Undefined

 # Username whitelist.
 # 
 # Use this to restrict which users can login. If empty, allow any user to
 # attempt login.
 # c.Authenticator.whitelist = traitlets.Undefined

 #------------------------------------------------------------------------------
 # LocalAuthenticator configuration
 #------------------------------------------------------------------------------

 # Base class for Authenticators that work with local *ix users
 # 
 # Checks for local users, and can attempt to create them if they exist.

 # If a user is added that doesn't exist on the system, should I try to create
 # the system user?
 # c.LocalAuthenticator.create_system_users = False

 # Automatically whitelist anyone in this group.
 # c.LocalAuthenticator.group_whitelist = traitlets.Undefined

 #------------------------------------------------------------------------------
 # PAMAuthenticator configuration
 #------------------------------------------------------------------------------

 # Authenticate local *ix users with PAM

 # The PAM service to use for authentication.
 # c.PAMAuthenticator.service = 'login'

 # The encoding to use for PAM
 # c.PAMAuthenticator.encoding = 'utf8'
diff --git a/overview.md b/overview.md
	echo "deb http://mirror.cs.nsls2.local/debian wheezy-backports main" >> /etc/apt/sources.list.d/backports.list

	aptitude -t wheezy-backports install nodejs
	update-alternatives --install /usr/bin/node nodejs /usr/bin/nodejs 100
	wget https://www.npmjs.org/install.sh
	sh install.sh
	node -v
	npm -v

	npm config set proxy http://proxy:8888
	npm config set https-proxy http://proxy:8888 # N.B. http here, not https

	apt-get install python3

	pip3 install ipython
	pip3 install pyzmq
	pip3 install mistune
	pip3 install jinja2
	pip3 install pexpect # not sure if this is actually required in the final configuration we use
	pip3 install jsonschema
	pip3 install terminado
	pip3 install jupyterhub # We deployed v0.2.0

	# sudospawner is not yet on PyPI
	git clone https://github.com/jupyter/sudospawner
	cd sudospawner
	pip3 install -e .
	cd ..

	# remotekernel is not yet on PyPI
	git clone https://github.com/danielballan/remotekernel
	cd remotekernel
	pip3 install -e .
	cd ..
	# Configuration file for jupyterhub.

	#------------------------------------------------------------------------------
	# Configurable configuration
	#------------------------------------------------------------------------------

	#------------------------------------------------------------------------------
	# SingletonConfigurable configuration
	#------------------------------------------------------------------------------

	# A configurable that only allows one instance.
	#
	# This class is for classes that should only have one instance of itself or
	# any subclass. To create and retrieve such a class use the
	# :meth:`SingletonConfigurable.instance` method.

	#------------------------------------------------------------------------------
	# Application configuration
	#------------------------------------------------------------------------------

	# This is an application.

	# The date format used by logging formatters for %(asctime)s
	# c.Application.log_datefmt = '%Y-%m-%d %H:%M:%S'

	# The Logging format template
	# c.Application.log_format = '[%(name)s]%(highlevel)s %(message)s'

	# Set the log level by value or name.
	# c.Application.log_level = 30

	#------------------------------------------------------------------------------
	# JupyterHub configuration
	#------------------------------------------------------------------------------

	# An Application for starting a Multi-User Jupyter Notebook server.

	# Interval (in seconds) at which to update last-activity timestamps.
	# c.JupyterHub.last_activity_interval = 300

	# File to write PID Useful for daemonizing jupyterhub.
	# c.JupyterHub.pid_file = ''

	# Grant admin users permission to access single-user servers.
	#
	# Users should be properly informed if this is enabled.
	# c.JupyterHub.admin_access = False

	# url for the database. e.g. `sqlite:///jupyterhub.sqlite`
	c.JupyterHub.db_url = 'sqlite:////home/jupyter/jupyterhub.sqlite'

	# The ip for this process
	# c.JupyterHub.hub_ip = 'localhost'

	# Include any kwargs to pass to the database connection. See
	# sqlalchemy.create_engine for details.
	# c.JupyterHub.db_kwargs = traitlets.Undefined

	# Paths to search for jinja templates.
	# c.JupyterHub.template_paths = traitlets.Undefined

	# The class to use for spawning single-user servers.
	#
	# Should be a subclass of Spawner.
	# c.JupyterHub.spawner_class = <class 'jupyterhub.spawner.LocalProcessSpawner'>
	c.JupyterHub.spawner_class='sudospawner.SudoSpawner'

	# Supply extra arguments that will be passed to Jinja environment.
	# c.JupyterHub.jinja_environment_options = traitlets.Undefined

	# Class for authenticating users.
	#
	# This should be a class with the following form:
	#
	# - constructor takes one kwarg: `config`, the IPython config object.
	#
	# - is a tornado.gen.coroutine
	# - 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.
	# c.JupyterHub.authenticator_class = <class 'jupyterhub.auth.PAMAuthenticator'>

	# The Proxy Auth token.
	#
	# Loaded from the CONFIGPROXY_AUTH_TOKEN env variable by default.
	# c.JupyterHub.proxy_auth_token = ''

	# The ip for the proxy API handlers
	# c.JupyterHub.proxy_api_ip = 'localhost'

	# The port for this process
	# c.JupyterHub.hub_port = 8081

	# The location of jupyterhub data files (e.g. /usr/local/share/jupyter/hub)
	# c.JupyterHub.data_files_path = '/etc/jupyterhub/jupyterhub/share/jupyter/hub'

	# Interval (in seconds) at which to check if the proxy is running.
	# c.JupyterHub.proxy_check_interval = 30

	# DEPRECATED, use Authenticator.admin_users instead.
	# c.JupyterHub.admin_users = traitlets.Undefined

	# Extra log handlers to set on JupyterHub logger
	# c.JupyterHub.extra_log_handlers = traitlets.Undefined

	# Path to SSL certificate file for the public facing interface of the proxy
	#
	# Use with ssl_key
	c.JupyterHub.ssl_cert = '/etc/certificates/cs_nsls2_local.crt'

	# log all database transactions. This has A LOT of output
	# c.JupyterHub.debug_db = False

	# The cookie secret to use to encrypt cookies.
	#
	# Loaded from the JPY_COOKIE_SECRET env variable by default.
	# c.JupyterHub.cookie_secret = b''

	# Set a logging.FileHandler on this file.
	# c.JupyterHub.extra_log_file = ''

	# Answer yes to any questions (e.g. confirm overwrite)
	# c.JupyterHub.answer_yes = False

	# Number of days for a login cookie to be valid. Default is two weeks.
	# c.JupyterHub.cookie_max_age_days = 14

	# Purge and reset the database.
	# c.JupyterHub.reset_db = False

	# Path to SSL key file for the public facing interface of the proxy
	#
	# Use with ssl_cert
	c.JupyterHub.ssl_key = '/etc/certificates/cs_nsls2_local.key'

	# File in which to store the cookie secret.
	c.JupyterHub.cookie_secret_file = '/home/jupyter/jupyterhub_cookie_secret'

	# The command to start the http proxy.
	#
	# Only override if configurable-http-proxy is not on your PATH
	# c.JupyterHub.proxy_cmd = traitlets.Undefined

	# The base URL of the entire application
	# c.JupyterHub.base_url = '/'

	# The public facing ip of the proxy
	# c.JupyterHub.ip = ''

	# The public facing port of the proxy
	c.JupyterHub.port = 7777

	# Whether to shutdown the proxy when the Hub shuts down.
	#
	# Disable if you want to be able to teardown the Hub while leaving the proxy
	# running.
	#
	# Only valid if the proxy was starting by the Hub process.
	#
	# If both this and cleanup_servers are False, sending SIGINT to the Hub will
	# only shutdown the Hub, leaving everything else running.
	#
	# The Hub should be able to resume from database state.
	# c.JupyterHub.cleanup_proxy = True

	# Whether to shutdown single-user servers when the Hub shuts down.
	#
	# Disable if you want to be able to teardown the Hub while leaving the single-
	# user servers running.
	#
	# If both this and cleanup_proxy are False, sending SIGINT to the Hub will only
	# shutdown the Hub, leaving everything else running.
	#
	# The Hub should be able to resume from database state.
	# c.JupyterHub.cleanup_servers = True

	# The prefix for the hub server. Must not be '/'
	# c.JupyterHub.hub_prefix = '/hub/'

	#
	# c.JupyterHub.tornado_settings = traitlets.Undefined

	# show debug output in configurable-http-proxy
	# c.JupyterHub.debug_proxy = False

	# Generate default config file
	# c.JupyterHub.generate_config = False

	# The port for the proxy API handlers
	# c.JupyterHub.proxy_api_port = 0

	# The config file to load
	# c.JupyterHub.config_file = 'jupyterhub_config.py'

	#------------------------------------------------------------------------------
	# LoggingConfigurable configuration
	#------------------------------------------------------------------------------

	# A parent class for Configurables that log.
	#
	# Subclasses have a log trait, and the default behavior is to get the logger
	# from the currently running Application.

	#------------------------------------------------------------------------------
	# Spawner configuration
	#------------------------------------------------------------------------------

	# Base class for spawning single-user notebook servers.
	#
	# Subclass this, and override the following methods:
	#
	# - load_state - get_state - start - stop - poll

	# Timeout (in seconds) before giving up on a spawned HTTP server
	#
	# Once a server has successfully been spawned, this is the amount of time we
	# wait before assuming that the server is unable to accept connections.
	# c.Spawner.http_timeout = 30

	# Extra arguments to be passed to the single-user server
	c.Spawner.args = ['--MappingKernelManager.kernel_manager_class=remotekernel.manager.RemoteIOLoopKernelManager']

	# Enable debug-logging of the single-user server
	# c.Spawner.debug = False

	# Whitelist of environment variables for the subprocess to inherit
	# c.Spawner.env_keep = traitlets.Undefined

	# The notebook directory for the single-user server
	#
	# `~` will be expanded to the user's home directory
	# c.Spawner.notebook_dir = ''

	# The IP address (or hostname) the single-user server should listen on
	# c.Spawner.ip = 'localhost'

	# The command used for starting notebooks.
	# c.Spawner.cmd = ['jupyterhub-singleuser', '--MappingKernelManager.kernel_manager_class=remotekernel.manager.RemoteIOLoopKernelManager']

	# Timeout (in seconds) before giving up on the spawner.
	#
	# This is the timeout for start to return, not the timeout for the server to
	# respond. Callers of spawner.start will assume that startup has failed if it
	# takes longer than this. start should return when the server process is started
	# and its location is known.
	# c.Spawner.start_timeout = 60

	# Interval (in seconds) on which to poll the spawner.
	# c.Spawner.poll_interval = 30

	#------------------------------------------------------------------------------
	# LocalProcessSpawner configuration
	#------------------------------------------------------------------------------

	# A Spawner that just uses Popen to start local processes.

	# Seconds to wait for process to halt after SIGKILL before giving up
	# c.LocalProcessSpawner.KILL_TIMEOUT = 5

	# Seconds to wait for process to halt after SIGTERM before proceeding to SIGKILL
	# c.LocalProcessSpawner.TERM_TIMEOUT = 5

	# Seconds to wait for process to halt after SIGINT before proceeding to SIGTERM
	# c.LocalProcessSpawner.INTERRUPT_TIMEOUT = 10

	#------------------------------------------------------------------------------
	# Authenticator configuration
	#------------------------------------------------------------------------------

	# A class for authentication.
	#
	# The API is one method, `authenticate`, a tornado gen.coroutine.

	# set of usernames of admin users
	#
	# If unspecified, only the user that launches the server will be admin.
	# c.Authenticator.admin_users = traitlets.Undefined

	# Username whitelist.
	#
	# Use this to restrict which users can login. If empty, allow any user to
	# attempt login.
	# c.Authenticator.whitelist = traitlets.Undefined

	#------------------------------------------------------------------------------
	# LocalAuthenticator configuration
	#------------------------------------------------------------------------------

	# Base class for Authenticators that work with local *ix users
	#
	# Checks for local users, and can attempt to create them if they exist.

	# If a user is added that doesn't exist on the system, should I try to create
	# the system user?
	# c.LocalAuthenticator.create_system_users = False

	# Automatically whitelist anyone in this group.
	# c.LocalAuthenticator.group_whitelist = traitlets.Undefined

	#------------------------------------------------------------------------------
	# PAMAuthenticator configuration
	#------------------------------------------------------------------------------

	# Authenticate local *ix users with PAM

	# The PAM service to use for authentication.
	# c.PAMAuthenticator.service = 'login'

	# The encoding to use for PAM
	# c.PAMAuthenticator.encoding = 'utf8'