def run_notebook():
app = NotebookApp.instance()
# Treat IPYTHON_ARGUMENTS from settings
ipython_arguments = self.get_ipython_arguments(options)
if "django_extensions.management.notebook_extension" not in ipython_arguments:
ipython_arguments.extend(["--ext", "django_extensions.management.notebook_extension"])
# Treat NOTEBOOK_ARGUMENTS from settings
notebook_arguments = self.get_notebook_arguments(options)
if no_browser and "--no-browser" not in notebook_arguments:
notebook_arguments.append("--no-browser")
if "--notebook-dir" not in notebook_arguments:
notebook_arguments.extend(["--notebook-dir", "."])
# IPython < 3 passes through kernel args from notebook CLI
if release.version_info[0] < 3:
notebook_arguments.extend(ipython_arguments)
app.initialize(notebook_arguments)
# IPython >= 3 uses kernelspecs to specify kernel CLI args
if release.version_info[0] >= 3:
display_name = getattr(settings, "IPYTHON_KERNEL_DISPLAY_NAME", "Django Shell-Plus")
install_kernel_spec(app, display_name, ipython_arguments)
app.start()
def get_nbextensions_path():
"""
Return the nbextensions search path
gets the search path for
- the current NotebookApp instance
or, if we can't instantiate one
- the default config used, found by spawning a subprocess
"""
# Attempt to get the path for the currently-running config, or the default
# if one isn't running.
# If there's already a non-NotebookApp traitlets app running, e.g. when
# we're inside an IPython kernel there's a KernelApp instantiated, then
# attempting to get a NotebookApp instance will raise a
# MultipleInstanceError.
try:
return NotebookApp.instance().nbextensions_path
except MultipleInstanceError:
# So, we spawn a new python process to get paths for the default config
cmd = "from {0} import {1}; [print(p) for p in {1}()]".format(
get_nbextensions_path.__module__, get_nbextensions_path.__name__)
return subprocess.check_output([
sys.executable, '-c', cmd
]).decode(sys.stdout.encoding).split('\n')
def run_notebook():
app = NotebookApp.instance()
# Treat IPYTHON_ARGUMENTS from settings
ipython_arguments = getattr(settings, 'IPYTHON_ARGUMENTS', [])
if 'django_extensions.management.notebook_extension' not in ipython_arguments:
ipython_arguments.extend(['--ext', 'django_extensions.management.notebook_extension'])
# Treat NOTEBOOK_ARGUMENTS from settings
notebook_arguments = getattr(settings, 'NOTEBOOK_ARGUMENTS', [])
if no_browser and '--no-browser' not in notebook_arguments:
notebook_arguments.append('--no-browser')
if '--notebook-dir' not in notebook_arguments:
notebook_arguments.extend(['--notebook-dir', '.'])
# IPython < 3 passes through kernel args from notebook CLI
if release.version_info[0] < 3:
notebook_arguments.extend(ipython_arguments)
app.initialize(notebook_arguments)
# IPython >= 3 uses kernelspecs to specify kernel CLI args
if release.version_info[0] >= 3:
display_name = getattr(settings, 'IPYTHON_KERNEL_DISPLAY_NAME', "Django Shell-Plus")
install_kernel_spec(app, display_name, ipython_arguments)
app.start()
def run_notebook():
app = NotebookApp.instance()
# Treat IPYTHON_ARGUMENTS from settings
ipython_arguments = self.get_ipython_arguments(options)
if 'django_extensions.management.notebook_extension' not in ipython_arguments:
ipython_arguments.extend([
'--ext',
'django_extensions.management.notebook_extension'
])
# Treat NOTEBOOK_ARGUMENTS from settings
notebook_arguments = self.get_notebook_arguments(options)
if no_browser and '--no-browser' not in notebook_arguments:
notebook_arguments.append('--no-browser')
if '--notebook-dir' not in notebook_arguments:
notebook_arguments.extend(['--notebook-dir', '.'])
# IPython < 3 passes through kernel args from notebook CLI
if release.version_info[0] < 3:
notebook_arguments.extend(ipython_arguments)
app.initialize(notebook_arguments)
# IPython >= 3 uses kernelspecs to specify kernel CLI args
if release.version_info[0] >= 3:
display_name = getattr(settings,
'IPYTHON_KERNEL_DISPLAY_NAME',
"Django Shell-Plus")
install_kernel_spec(app, display_name, ipython_arguments)
app.start()
def main():
"""Run main."""
opt = parse_cmd_line()
if opt.serve:
# pylint: disable=import-outside-toplevel
from imjoy.server import start_server
start_server(opt)
elif opt.jupyter:
sys.argv = sys.argv[:1]
sys.argc = 1
# pylint: disable=import-outside-toplevel
from notebook.notebookapp import NotebookApp
kwargs = {
"open_browser": False,
"allow_origin": opt.allow_origin,
"ip": opt.host,
"notebook_dir": opt.workspace,
"port": int(opt.port),
"tornado_settings": {
"headers": {
"Access-Control-Allow-Origin": opt.allow_origin,
"Content-Security-Policy": opt.content_security_policy,
}
},
}
if not opt.token:
if not opt.random_token:
opt.token = read_or_generate_token()
kwargs["token"] = opt.token
else:
kwargs["token"] = opt.token
if opt.insecure:
kwargs["token"] = ""
kwargs["disable_check_xsrf"] = True
logger.warning(
"Running Jupyter notebooks with --insecure flag, "
"please do not use it for production."
)
app = NotebookApp.instance(**kwargs)
app.initialize()
if app.port != int(opt.port):
print(f"\nWARNING: using a different port: {app.port}.\n")
write_token(app.token)
app._token_generated = True # pylint: disable=protected-access
app.start()
else:
print(
"\nNote: We have migrated the backend of the ImJoy Engine."
"You can start the Jupyter backend via`imjoy --jupyter`.\n\n"
"Or, you can start the socketio backend server via `imjoy --serve`\n"
)
def run_notebook():
app = NotebookApp.instance()
# Treat IPYTHON_ARGUMENTS from settings
ipython_arguments = self.get_ipython_arguments(options)
if 'django_extensions.management.notebook_extension' not in ipython_arguments:
ipython_arguments.extend([
'--ext', 'django_extensions.management.notebook_extension'
])
# Treat NOTEBOOK_ARGUMENTS from settings
notebook_arguments = self.get_notebook_arguments(options)
if no_browser and '--no-browser' not in notebook_arguments:
notebook_arguments.append('--no-browser')
if '--notebook-dir' not in notebook_arguments and not any(
e.startswith('--notebook-dir=')
for e in notebook_arguments):
notebook_arguments.extend(['--notebook-dir', '.'])
# IPython < 3 passes through kernel args from notebook CLI
if release.version_info[0] < 3:
notebook_arguments.extend(ipython_arguments)
app.initialize(notebook_arguments)
# IPython >= 3 uses kernelspecs to specify kernel CLI args
if release.version_info[0] >= 3:
ksm = app.kernel_spec_manager
for kid, ks in self.generate_kernel_specs(
app, ipython_arguments).items():
roots = [
os.path.dirname(ks.resource_dir), ksm.user_kernel_dir
]
success = False
for root in roots:
kernel_dir = os.path.join(root, kid)
try:
if not os.path.exists(kernel_dir):
os.makedirs(kernel_dir)
with open(os.path.join(kernel_dir, 'kernel.json'),
'w') as f:
f.write(ks.to_json())
success = True
break
except OSError:
continue
if not success:
raise CommandError(
"Could not write kernel %r in directories %r" %
(kid, roots))
app.start()
def project(self):
# 1. configuration option passed explicitly
# 2. from notebooks dir
# 3. from cwd
if self.ballet_yml_path:
return Project.from_path(self.ballet_yml_path)
path = NotebookApp.instance().notebook_dir
with fy.suppress(Exception):
return Project.from_path(path)
with fy.suppress(Exception):
return Project.from_cwd()
raise ConfigurationError('Could not detect Ballet project')
def _get_r_executable():
try:
# get notebook app
from notebook.notebookapp import NotebookApp
nbapp = NotebookApp.instance()
# get R executable:
kernel_name = nbapp.kernel_manager.default_kernel_name
if kernel_name:
kernel_spec = nbapp.kernel_spec_manager.get_kernel_spec(
kernel_name)
# nb_conda_kernels has conda env prefix at idx 4
return '{}/bin/R'.format(kernel_spec.argv[4])
except Exception:
nbapp.log.warning(
'Error when trying to get R executable from kernel')
return 'R'
def start_notebook(args, l, rc):
from notebook.notebookapp import NotebookApp
import sys
sys.argv = ['ambry']
app = NotebookApp.instance()
app._library = l
app.contents_manager_class = 'ambry_ui.jupyter.AmbryContentsManager'
app.open_browser = not args.no_browser
app.ip = args.host
if args.port is not None:
app.port = int(args.port)
app.initialize(None)
app.start()
def run_notebook(no_browser=False, display_name='notebook'):
app = NotebookApp.instance()
ipython_arguments = [] # Will implement to set specific IPython configs
notebook_arguments = [] # Will implement to set specific notebook configs
if no_browser is True:
notebook_arguments.append('--no-browser')
if '--notebook-dir' not in notebook_arguments:
notebook_arguments.extend(['--notebook-dir', '.'])
install_kernel_spec(app, display_name, ipython_arguments)
app.initialize(notebook_arguments)
app.start()
def run_notebook(no_browser=False, display_name='notebook'):
app = NotebookApp.instance()
ipython_arguments = [
] # Will implement to set specific IPython configs
notebook_arguments = [
] # Will implement to set specific notebook configs
if no_browser is True:
notebook_arguments.append('--no-browser')
if '--notebook-dir' not in notebook_arguments:
notebook_arguments.extend(['--notebook-dir', '.'])
install_kernel_spec(app, display_name, ipython_arguments)
app.initialize(notebook_arguments)
app.start()
def test_basic(self):
from notebook.notebookapp import NotebookApp
import sys
l = self.library()
b = l.new_bundle(source='example.com', dataset='test', assignment_class='self')
l.commit()
sys.argv = ['ambry']
app = NotebookApp.instance()
app._library = l
app.contents_manager_class = 'ambry_ui.jupyter.AmbryContentsManager'
app.initialize(None)
cm = app.contents_manager
self.assertEqual('example.com', cm.get('')['content'][0]['path'])
self.assertEqual('/example.com/test-0.0.1/bundle.yaml', cm.get(b.identity.cache_key)['content'][0]['path'])
def handle(self, arguments):
try:
from notebook.notebookapp import NotebookApp
except ImportError: # pragma: no cover
self.parser.error("notebook not found. Please install it")
else:
extension = "corral.libs.notebook_extension"
pipeline = setup.load_pipeline_setup()
app = NotebookApp.instance()
dir_name = conf.PACKAGE
display_name = pipeline.name
settings_module = conf.CORRAL_SETTINGS_MODULE
ipython_arguments = ['--ext', extension]
app.initialize(arguments)
self.install_kernel_spec(app, dir_name, display_name,
settings_module, ipython_arguments)
app.start()
def handle(self, arguments):
try:
from notebook.notebookapp import NotebookApp
except ImportError:
self.parser.error("notebook not found. Please install it")
else:
extension = "corral.libs.notebook_extension"
pipeline = setup.load_pipeline_setup()
app = NotebookApp.instance()
dir_name = conf.PACKAGE
display_name = pipeline.name
settings_module = conf.CORRAL_SETTINGS_MODULE
ipython_arguments = ['--ext', extension]
app.initialize(arguments)
self.install_kernel_spec(
app, dir_name, display_name,
settings_module, ipython_arguments)
app.start()
def get_nbextensions_path():
"""
Return the nbextensions search path
gets the search path for
- the current NotebookApp instance
or, if we can't instantiate one
- the default config used, found by spawning a subprocess
"""
# Attempt to get the path for the currently-running config, or the default
# if one isn't running.
# If there's already a non-NotebookApp traitlets app running, e.g. when
# we're inside an IPython kernel there's a KernelApp instantiated, then
# attempting to get a NotebookApp instance will raise a
# MultipleInstanceError.
try:
return NotebookApp.instance().nbextensions_path
except MultipleInstanceError:
# So, we spawn a new python process to get paths for the default config
cmd = "from {0} import {1}; [print(p) for p in {1}()]".format(
get_nbextensions_path.__module__, get_nbextensions_path.__name__)
return subprocess.check_output([sys.executable, '-c', cmd]).decode(
sys.stdout.encoding).split('\n')
def app_init(*args, **kwargs):
app = NotebookApp.instance()
app.initialize(*args, **kwargs)
return app
def run_notebook():
app = NotebookApp.instance()
self.run_notebookapp(app, options, use_kernel_specs)
"""
Run this to debug
"""
import sys
import os
from notebook.notebookapp import NotebookApp
from jupyter_geppetto import settings
os.environ['JUPYTER_CONFIG_DIR'] = os.path.join(
os.path.dirname(os.path.abspath(__file__)), '.jupyter-config')
settings.debug = True
if __name__ == '__main__':
sys.argv.append('--NotebookApp.default_url=/geppetto')
sys.argv.append("--NotebookApp.token=''")
sys.argv.append('--library=netpyne_ui')
sys.argv.append('--NotebookApp.disable_check_xsrf=True')
app = NotebookApp.instance()
app.initialize(sys.argv)
app.file_to_run = ''
sys.exit(app.start())
# Init the Jupyter app
kwargs = {}
argv = ['--no-browser']
jupyterlab = False
if len(sys.argv) > 1:
jupyterlab = sys.argv[1] == 'lab'
if jupyterlab:
from jupyterlab.labapp import LabApp
app = LabApp.instance(**kwargs)
else:
from notebook.notebookapp import NotebookApp
app = NotebookApp.instance(**kwargs)
# import logging
# app.log_level = logging.DEBUG
app.initialize(argv)
with stdoutlock:
print(json.dumps({'sys.path': sys.path}))
print(json.dumps({'sys.executable': sys.executable}))
print(json.dumps({'os.environ': dict(os.environ)}))
print(json.dumps({'server_info': app.server_info()}))
sys.stdout.flush()
inthread = threading.Thread(target=read_stdin, args=(
def main():
"""Run main."""
opt = parse_cmd_line()
background_task = None
if opt.plugin_file and (opt.plugin_server or opt.serve):
async def start_plugin(app):
default_config.update({
"name":
"ImJoy Plugin",
"plugin_server":
opt.plugin_server or "http://127.0.0.1:{}".format(opt.serve),
})
load_plugin(opt.plugin_file)
background_task = start_plugin
if opt.serve:
try:
from imjoy.socketio_server import create_socketio_server
except:
logger.error(
"It appears that your ImJoy installation is not complete, please reinstall it with 'pip install imjoy[socketio]'"
)
raise SystemExit
if opt.plugin_server and not opt.plugin_server.endswith(opt.serve):
print(
"WARNING: the specified port ({}) does not match the one in the url ({})"
.format(opt.serve, opt.plugin_server))
app = create_socketio_server()
if background_task:
app.on_startup.append(background_task)
web.run_app(app, port=opt.serve)
elif opt.plugin_file:
loop = asyncio.get_event_loop()
loop.create_task(background_task(app))
loop.run_forever()
elif opt.jupyter:
sys.argv = sys.argv[:1]
sys.argc = 1
from notebook.notebookapp import NotebookApp
kwargs = {
"open_browser": False,
"allow_origin": opt.allow_origin,
"ip": opt.host,
"notebook_dir": opt.workspace,
"port": int(opt.port),
"tornado_settings": {
"headers": {
"Access-Control-Allow-Origin": opt.allow_origin,
"Content-Security-Policy": opt.content_security_policy,
}
},
}
if not opt.token:
if not opt.random_token:
opt.token = read_or_generate_token()
kwargs["token"] = opt.token
else:
kwargs["token"] = opt.token
app = NotebookApp.instance(**kwargs)
app.initialize()
if app.port != int(opt.port):
print("\nWARNING: using a different port: {}.\n".format(app.port))
write_token(app.token)
app._token_generated = True
app.start()
elif not opt.legacy:
print(
"\nNote: We are migrating the backend of the ImJoy Engine to Jupyter, to use it please run `imjoy --jupyter`.\n\nIf you want to use the previous engine, run `imjoy --legacy`, however, please note that it maybe removed soon.\n"
)
