def install(kernel_spec_manager=None, user=False, kernel_name=None):
"""Install the IPython kernelspec for Jupyter
Parameters
----------
kernel_spec_manager: KernelSpecManager [optional]
A KernelSpecManager to use for installation.
If none provided, a default instance will be created.
user: bool [default: False]
Whether to do a user-only install, or system-wide.
kernel_name: str, optional
Specify a name for the kernelspec.
This is needed for having multiple IPython kernels for different environments.
Returns
-------
The path where the kernelspec was installed.
"""
if kernel_spec_manager is None:
kernel_spec_manager = KernelSpecManager()
if kernel_name is None:
kernel_name = KERNEL_NAME
path = write_kernel_spec()
dest = kernel_spec_manager.install_kernel_spec(path,
kernel_name=kernel_name, user=user)
# cleanup afterward
shutil.rmtree(path)
return dest
def install_kernelspec(self):
from ipykernel.kernelspec import write_kernel_spec
from jupyter_client.kernelspec import KernelSpecManager
kernel_spec_manager = KernelSpecManager()
log.info('Writing kernel spec')
kernel_spec_path = write_kernel_spec(overrides=kernel_json)
log.info('Installing kernel spec ' + kernel_spec_path)
try:
kernel_spec_manager.install_kernel_spec(
kernel_spec_path,
kernel_name=kernel_json['name'],
user=self.user)
except Exception as e:
log.error(str(e.args))
log.error('Failed to install kernel spec')
else:
return
# retry with not self.user
log.info('Retry install kernel spec')
try:
kernel_spec_manager.install_kernel_spec(
kernel_spec_path,
kernel_name=kernel_json['name'],
user=not self.user)
except Exception as e:
log.error(str(e.args))
log.error('Failed to install kernel spec')
def install(kernel_spec_manager=None, user=False, kernel_name=KERNEL_NAME, display_name=None,
prefix=None, profile=None):
"""Install the IPython kernelspec for Jupyter
Parameters
----------
kernel_spec_manager: KernelSpecManager [optional]
A KernelSpecManager to use for installation.
If none provided, a default instance will be created.
user: bool [default: False]
Whether to do a user-only install, or system-wide.
kernel_name: str, optional
Specify a name for the kernelspec.
This is needed for having multiple IPython kernels for different environments.
display_name: str, optional
Specify the display name for the kernelspec
profile: str, optional
Specify a custom profile to be loaded by the kernel.
prefix: str, optional
Specify an install prefix for the kernelspec.
This is needed to install into a non-default location, such as a conda/virtual-env.
Returns
-------
The path where the kernelspec was installed.
"""
if kernel_spec_manager is None:
kernel_spec_manager = KernelSpecManager()
if (kernel_name != KERNEL_NAME) and (display_name is None):
# kernel_name is specified and display_name is not
# default display_name to kernel_name
display_name = kernel_name
overrides = {}
if display_name:
overrides["display_name"] = display_name
if profile:
extra_arguments = ["--profile", profile]
if not display_name:
# add the profile to the default display name
overrides["display_name"] = 'Python %i [profile=%s]' % (sys.version_info[0], profile)
else:
extra_arguments = None
path = write_kernel_spec(overrides=overrides, extra_arguments=extra_arguments)
dest = kernel_spec_manager.install_kernel_spec(
path, kernel_name=kernel_name, user=user, prefix=prefix)
# cleanup afterward
shutil.rmtree(path)
return dest
def run(self):
# Regular installation
install.run(self)
# Now write the kernelspec
from jupyter_client.kernelspec import KernelSpecManager
from tempfile import TemporaryDirectory
kernel_spec = KernelSpecManager()
with TemporaryDirectory() as td:
os.chmod(td, 0o755) # Starts off as 700, not user readable
with open(os.path.join(td, 'kernel.json'), 'w') as f:
json.dump(kernel_json, f, sort_keys=True)
# TODO: Copy resources once they're specified
kernel_spec.install_kernel_spec(td, 'postgres', user=self.user)
def __init__(self, settings, document_language):
"""Initializes available kernel names"""
self.__settings = settings
self.__doc_lang = document_language
spec_manager = KernelSpecManager()
kernel_names = spec_manager.find_kernel_specs()
self.__available_kernel_names_mappings = {}
for name in kernel_names:
spec = spec_manager.get_kernel_spec(name)
self.__available_kernel_names_mappings[spec.display_name] = name
self.__manager = MultiKernelManager()
self.__client_managers = {}
def get_notebook_kernel(kernel_name, kernel_spec_manager=None):
"""
return a `KernelSpec <https://ipython.org/ipython-doc/dev/api/generated/IPython.kernel.kernelspec.html>`_
@param kernel_spec_manager see `KernelSpecManager <http://jupyter-client.readthedocs.org/en/latest/api/kernelspec.html#jupyter_client.kernelspec.KernelSpecManager>`_
A KernelSpecManager to use for installation.
If none provided, a default instance will be created.
@param kernel_name kernel name
@return KernelSpec
The function only works with Jupyter>=4.0.
.. versionadded:: 1.3
"""
if kernel_spec_manager is None:
from jupyter_client.kernelspec import KernelSpecManager
kernel_spec_manager = KernelSpecManager()
return kernel_spec_manager.get_kernel_spec(kernel_name)
def find_notebook_kernel(kernel_spec_manager=None):
"""
return a dict mapping kernel names to resource directories
@param kernel_spec_manager see `KernelSpecManager <http://jupyter-client.readthedocs.org/en/latest/api/kernelspec.html#jupyter_client.kernelspec.KernelSpecManager>`_
A KernelSpecManager to use for installation.
If none provided, a default instance will be created.
@return dict
The list of installed kernels is described at
`Making kernel for Jupyter <http://jupyter-client.readthedocs.org/en/latest/kernels.html#kernelspecs>`_.
The function only works with Jupyter>=4.0.
.. versionadded:: 1.3
"""
if kernel_spec_manager is None:
from jupyter_client.kernelspec import KernelSpecManager
kernel_spec_manager = KernelSpecManager()
return kernel_spec_manager.find_kernel_specs()
def install(kernel_spec_manager=None, user=False, kernel_name=None, display_name=None, prefix=None):
"""Install the IPython kernelspec for Jupyter
Parameters
----------
kernel_spec_manager: KernelSpecManager [optional]
A KernelSpecManager to use for installation.
If none provided, a default instance will be created.
user: bool [default: False]
Whether to do a user-only install, or system-wide.
kernel_name: str, optional
Specify a name for the kernelspec.
This is needed for having multiple IPython kernels for different environments.
prefix: str, optional
Specify an install prefix for the kernelspec.
This is needed to install into a non-default location, such as a conda/virtual-env.
display_name: str, optional
Specify the display name for the kernelspec
Returns
-------
The path where the kernelspec was installed.
"""
if kernel_spec_manager is None:
kernel_spec_manager = KernelSpecManager()
if kernel_name is None:
kernel_name = KERNEL_NAME
elif display_name is None:
# kernel_name is specified and display_name is not
# default display_name to kernel_name
display_name = kernel_name
if display_name:
overrides = dict(display_name=display_name)
else:
overrides = None
path = write_kernel_spec(overrides=overrides)
dest = kernel_spec_manager.install_kernel_spec(path,
kernel_name=kernel_name, user=user, prefix=prefix)
# cleanup afterward
shutil.rmtree(path)
return dest
def install(kernel_spec_manager=None, user=False):
"""Install the IPython kernelspec for Jupyter
Parameters
----------
kernel_spec_manager: KernelSpecManager [optional]
A KernelSpecManager to use for installation.
If none provided, a default instance will be created.
user: bool [default: False]
Whether to do a user-only install, or system-wide.
"""
if kernel_spec_manager is None:
kernel_spec_manager = KernelSpecManager()
path = write_kernel_spec()
kernel_spec_manager.install_kernel_spec(path,
kernel_name=KERNEL_NAME, user=user, replace=True)
# cleanup afterward
shutil.rmtree(path)
def setup(self):
ipydir = TemporaryDirectory()
self.dirs.append(ipydir)
self.env['IPYTHONDIR'] = ipydir.name
# FIXME: install IPython kernel in temporary IPython dir
# remove after big split
try:
from jupyter_client.kernelspec import KernelSpecManager
except ImportError:
pass
else:
ksm = KernelSpecManager(ipython_dir=ipydir.name)
ksm.install_native_kernel_spec(user=True)
self.workingdir = workingdir = TemporaryDirectory()
self.dirs.append(workingdir)
self.env['IPTEST_WORKING_DIR'] = workingdir.name
# This means we won't get odd effects from our own matplotlib config
self.env['MPLCONFIGDIR'] = workingdir.name
# For security reasons (http://bugs.python.org/issue16202), use
# a temporary directory to which other users have no access.
self.env['TMPDIR'] = workingdir.name
# Add a non-accessible directory to PATH (see gh-7053)
noaccess = os.path.join(self.workingdir.name, "_no_access_")
self.noaccess = noaccess
os.mkdir(noaccess, 0)
PATH = os.environ.get('PATH', '')
if PATH:
PATH = noaccess + os.pathsep + PATH
else:
PATH = noaccess
self.env['PATH'] = PATH
# From options:
if self.options.xunit:
self.add_xunit()
if self.options.coverage:
self.add_coverage()
self.env['IPTEST_SUBPROC_STREAMS'] = self.options.subproc_streams
self.cmd.extend(self.options.extra_args)
def test_kernelspec_installed(self):
"""Test that the jupyter kernelspec installations work, and that
all the examples can be installed as expected."""
manager = KernelSpecManager()
# Remove all kernelspecs first.
subprocess.check_call(["jupyter", "kernelspec", "remove", "-f",
"basic", "calculator", "stdin"])
# Check that kernelspec installation works, the kernel exists after
# it has been installed, and the executable file is found.
subprocess.check_call(["kernel-basic", "install"])
kernelspec = manager.get_kernel_spec("basic")
self.assertTrue(os.path.isfile(kernelspec.argv[0]))
subprocess.check_call(["kernel-calculator", "install"])
kernelspec = manager.get_kernel_spec("calculator")
self.assertTrue(os.path.isfile(kernelspec.argv[0]))
subprocess.check_call(["kernel-stdin", "install"])
kernelspec = manager.get_kernel_spec("stdin")
self.assertTrue(os.path.isfile(kernelspec.argv[0]))
def install_kernel():
from jupyter_client.kernelspec import KernelSpecManager
logging.info('Installing Qudi kernel.')
try:
# prepare temporary kernelspec folder
tempdir = tempfile.mkdtemp(suffix='_kernels')
path = os.path.join(tempdir, 'qudi')
resourcepath = os.path.join(path, 'resources')
kernelpath = os.path.abspath(__file__)
os.mkdir(path)
os.mkdir(resourcepath)
kernel_dict = {
'argv': [sys.executable, kernelpath, '{connection_file}'],
'display_name': 'Qudi',
'language': 'python',
}
# write the kernelspe file
with open(os.path.join(path, 'kernel.json'), 'w') as f:
json.dump(kernel_dict, f, indent=1)
# copy logo
logopath = os.path.abspath(os.path.join(os.path.dirname(kernelpath), '..', 'artwork', 'logo'))
shutil.copy(os.path.join(logopath, 'logo-qudi-32x32.png'), os.path.join(resourcepath, 'logo-32x32.png'))
shutil.copy(os.path.join(logopath, 'logo-qudi-32x32.png'), os.path.join(resourcepath, 'logo-32x32.png'))
# install kernelspec folder
kernel_spec_manager = KernelSpecManager()
dest = kernel_spec_manager.install_kernel_spec(path, kernel_name='qudi', user=True)
logging.info('Installed kernelspec qudi in {}'.format(dest))
except OSError as e:
if e.errno == errno.EACCES:
print(e, file=sys.stderr)
sys.exit(1)
finally:
if os.path.isdir(tempdir):
shutil.rmtree(tempdir)
def get_kernel_specs(self):
return KernelSpecManager().get_all_specs()
import jupyter_client
import time
from jupyter_client.kernelspec import KernelSpecManager, NoSuchKernel, NATIVE_KERNEL_NAME
from IPython.utils.capture import capture_output
from ipython_genutils.tempdir import TemporaryDirectory
TIMEOUT = 30
td = TemporaryDirectory()
km, kc = jupyter_client.manager.start_new_kernel(kernel_name='python3')
KernelSpecManager().get_kernel_spec('python3')
with capture_output() as io:
reply = kc.execute_interactive("print('hello')", timeout=TIMEOUT)
print(reply)
print(io.stdout)
# assert 'hello' in io.stdout
# assert reply['content']['status'] == 'ok'
kc.execute("print('hello world')")
kc.get_shell_msg()
time.sleep(10)
from jupyter_client.kernelspec import KernelSpecManager
manager = KernelSpecManager()
kernels = manager.get_all_specs().keys()
assert "scijava" in kernels
print("Scijava kernel correctly installed.")
def get(self):
self.write(json.dumps(KernelSpecManager().get_all_specs()))
class TestExecute(PreprocessorTestsBase):
"""Contains test functions for execute.py"""
maxDiff = None
def test_constructor(self):
"""Can a ExecutePreprocessor be constructed?"""
build_preprocessor({})
def test_populate_language_info(self):
preprocessor = build_preprocessor(opts=dict(kernel_name="python"))
nb = nbformat.v4.new_notebook() # Certainly has no language_info.
nb, _ = preprocessor.preprocess(nb, resources={})
assert 'language_info' in nb.metadata
def test_empty_path(self):
"""Can the kernel be started when the path is empty?"""
filename = os.path.join(current_dir, 'files', 'HelloWorld.ipynb')
res = self.build_resources()
res['metadata']['path'] = ''
input_nb, output_nb = run_notebook(filename, {}, res)
assert_notebooks_equal(input_nb, output_nb)
@pytest.mark.xfail("python3" not in KernelSpecManager().find_kernel_specs(),
reason="requires a python3 kernelspec")
def test_empty_kernel_name(self):
"""Can kernel in nb metadata be found when an empty string is passed?
Note: this pattern should be discouraged in practice.
Passing in no kernel_name to ExecutePreprocessor is recommended instead.
"""
filename = os.path.join(current_dir, 'files', 'UnicodePy3.ipynb')
res = self.build_resources()
input_nb, output_nb = run_notebook(filename, {"kernel_name": ""}, res)
assert_notebooks_equal(input_nb, output_nb)
with pytest.raises(TraitError):
input_nb, output_nb = run_notebook(filename, {"kernel_name": None}, res)
def test_disable_stdin(self):
"""Test disabling standard input"""
filename = os.path.join(current_dir, 'files', 'Disable Stdin.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
input_nb, output_nb = run_notebook(filename, dict(allow_errors=True), res)
# We need to special-case this particular notebook, because the
# traceback contains machine-specific stuff like where IPython
# is installed. It is sufficient here to just check that an error
# was thrown, and that it was a StdinNotImplementedError
self.assertEqual(len(output_nb['cells']), 1)
self.assertEqual(len(output_nb['cells'][0]['outputs']), 1)
output = output_nb['cells'][0]['outputs'][0]
self.assertEqual(output['output_type'], 'error')
self.assertEqual(output['ename'], 'StdinNotImplementedError')
self.assertEqual(output['evalue'], 'raw_input was called, but this frontend does not support input requests.')
def test_timeout(self):
"""Check that an error is raised when a computation times out"""
filename = os.path.join(current_dir, 'files', 'Interrupt.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
with pytest.raises(TimeoutError):
run_notebook(filename, dict(timeout=1), res)
def test_timeout_func(self):
"""Check that an error is raised when a computation times out"""
filename = os.path.join(current_dir, 'files', 'Interrupt.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
def timeout_func(source):
return 10
with pytest.raises(TimeoutError):
run_notebook(filename, dict(timeout_func=timeout_func), res)
def test_kernel_death(self):
"""Check that an error is raised when the kernel is_alive is false"""
filename = os.path.join(current_dir, 'files', 'Interrupt.ipynb')
with io.open(filename, 'r') as f:
input_nb = nbformat.read(f, 4)
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
preprocessor = build_preprocessor({"timeout": 5})
try:
input_nb, output_nb = preprocessor(input_nb, {})
except TimeoutError:
pass
km, kc = preprocessor.start_new_kernel()
with patch.object(km, "is_alive") as alive_mock:
alive_mock.return_value = False
with pytest.raises(DeadKernelError):
input_nb, output_nb = preprocessor.preprocess(input_nb, {}, km=km)
def test_allow_errors(self):
"""
Check that conversion halts if ``allow_errors`` is False.
"""
filename = os.path.join(current_dir, 'files', 'Skip Exceptions.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
with pytest.raises(CellExecutionError) as exc:
run_notebook(filename, dict(allow_errors=False), res)
self.assertIsInstance(str(exc.value), str)
if sys.version_info >= (3, 0):
assert u"# üñîçø∂é" in str(exc.value)
else:
assert u"# üñîçø∂é".encode('utf8', 'replace') in str(exc.value)
def test_force_raise_errors(self):
"""
Check that conversion halts if the ``force_raise_errors`` traitlet on
ExecutePreprocessor is set to True.
"""
filename = os.path.join(current_dir, 'files',
'Skip Exceptions with Cell Tags.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
with pytest.raises(CellExecutionError) as exc:
run_notebook(filename, dict(force_raise_errors=True), res)
self.assertIsInstance(str(exc.value), str)
if sys.version_info >= (3, 0):
assert u"# üñîçø∂é" in str(exc.value)
else:
assert u"# üñîçø∂é".encode('utf8', 'replace') in str(exc.value)
def test_custom_kernel_manager(self):
from .fake_kernelmanager import FakeCustomKernelManager
filename = os.path.join(current_dir, 'files', 'HelloWorld.ipynb')
with io.open(filename) as f:
input_nb = nbformat.read(f, 4)
preprocessor = build_preprocessor({
'kernel_manager_class': FakeCustomKernelManager
})
cleaned_input_nb = copy.deepcopy(input_nb)
for cell in cleaned_input_nb.cells:
if 'execution_count' in cell:
del cell['execution_count']
cell['outputs'] = []
# Override terminal size to standardise traceback format
with modified_env({'COLUMNS': '80', 'LINES': '24'}):
output_nb, _ = preprocessor(cleaned_input_nb,
self.build_resources())
expected = FakeCustomKernelManager.expected_methods.items()
for method, call_count in expected:
self.assertNotEqual(call_count, 0, '{} was called'.format(method))
def test_process_message_wrapper(self):
outputs = []
class WrappedPreProc(ExecutePreprocessor):
def process_message(self, msg, cell, cell_index):
result = super(WrappedPreProc, self).process_message(msg, cell, cell_index)
if result:
outputs.append(result)
return result
current_dir = os.path.dirname(__file__)
filename = os.path.join(current_dir, 'files', 'HelloWorld.ipynb')
with io.open(filename) as f:
input_nb = nbformat.read(f, 4)
original = copy.deepcopy(input_nb)
wpp = WrappedPreProc()
executed = wpp.preprocess(input_nb, {})[0]
assert outputs == [
{'name': 'stdout', 'output_type': 'stream', 'text': 'Hello World\n'}
]
assert_notebooks_equal(original, executed)
def test_execute_function(self):
# Test the executenb() convenience API
filename = os.path.join(current_dir, 'files', 'HelloWorld.ipynb')
with io.open(filename) as f:
input_nb = nbformat.read(f, 4)
original = copy.deepcopy(input_nb)
executed = executenb(original, os.path.dirname(filename))
assert_notebooks_equal(original, executed)
def test_widgets(self):
"""Runs a test notebook with widgets and checks the widget state is saved."""
input_file = os.path.join(current_dir, 'files', 'JupyterWidgets.ipynb')
opts = dict(kernel_name="python")
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(input_file)
input_nb, output_nb = run_notebook(input_file, opts, res)
output_data = [
output.get('data', {})
for cell in output_nb['cells']
for output in cell['outputs']
]
model_ids = [
data['application/vnd.jupyter.widget-view+json']['model_id']
for data in output_data
if 'application/vnd.jupyter.widget-view+json' in data
]
wdata = output_nb['metadata']['widgets'] \
['application/vnd.jupyter.widget-state+json']
for k in model_ids:
d = wdata['state'][k]
assert 'model_name' in d
assert 'model_module' in d
assert 'state' in d
assert 'version_major' in wdata
assert 'version_minor' in wdata
def get_kernelspec(name):
ksm = KernelSpecManager()
kernelspec = ksm.get_kernel_spec(name).to_dict()
kernelspec['name'] = name
kernelspec.pop('argv')
return kernelspec
import os
import unittest
import pytest
import nbformat
from nbconvert.preprocessors import ExecutePreprocessor
from nbconvert.preprocessors.execute import CellExecutionError
from popmon import resources
from jupyter_client.kernelspec import KernelSpecManager, NoSuchKernel
kernel_name = 'python3'
# check if jupyter python3 kernel can be opened. if kernel not found, skip unit tests below.
try:
km = KernelSpecManager()
km.get_kernel_spec(kernel_name)
kernel_found = True
except NoSuchKernel:
kernel_found = False
class NotebookTest(unittest.TestCase):
"""Unit test notebook"""
def run_notebook(self, notebook):
""" Test notebook """
# load notebook
with open(notebook) as f:
nb = nbformat.read(f, as_version=4)
def uninstall_kernel():
""" Uninstall the kernel.
"""
KernelSpecManager().remove_kernel_spec(KERNEL_NAME)
def init_kernel_manager(self):
self._km = MultiKernelManager(log=self.log, parent=self)
self._ksm = KernelSpecManager(log=self.log, parent=self)
self._kernels = {}
def _jupyter_kernel(
user=False,
prefix=None,
root=None,
):
"""Generate xonsh kernel for jupyter.
Parameters
----------
user : -u, --user
Install kernel spec in user config directory.
prefix : -p, --prefix
Installation prefix for bin, lib, etc.
root : -r, --root
Install relative to this alternate root directory.
"""
try:
from jupyter_client.kernelspec import KernelSpecManager, NoSuchKernel
except ImportError as e:
raise ImportError("Jupyter not found in current Python environment") from e
ksm = KernelSpecManager()
prefix = prefix or sys.prefix
spec = {
"argv": [
sys.executable,
"-m",
"xonsh.jupyter_kernel",
"-f",
"{connection_file}",
],
"display_name": "Xonsh",
"language": "xonsh",
"codemirror_mode": "shell",
}
if root and prefix:
# os.path.join isn't used since prefix is probably absolute
prefix = root + prefix
try:
old_jup_kernel = ksm.get_kernel_spec(XONSH_JUPYTER_KERNEL)
if not old_jup_kernel.resource_dir.startswith(prefix):
print(
"Removing existing Jupyter kernel found at {}".format(
old_jup_kernel.resource_dir
)
)
ksm.remove_kernel_spec(XONSH_JUPYTER_KERNEL)
except NoSuchKernel:
pass
if sys.platform == "win32":
# Ensure that conda-build detects the hard coded prefix
spec["argv"][0] = spec["argv"][0].replace(os.sep, os.altsep)
prefix = prefix.replace(os.sep, os.altsep)
with tempfile.TemporaryDirectory() as d:
os.chmod(d, 0o755) # Starts off as 700, not user readable
with open(os.path.join(d, "kernel.json"), "w") as f:
json.dump(spec, f, sort_keys=True)
print("Installing Jupyter kernel spec:")
print(f" root: {root!r}")
if user:
print(f" as user: {user}")
elif root and prefix:
print(f" combined prefix {prefix!r}")
else:
print(f" prefix: {prefix!r}")
ksm.install_kernel_spec(
d, XONSH_JUPYTER_KERNEL, user=user, prefix=(None if user else prefix)
)
return 0
def _info(
to_json=False,
) -> str:
"""Displays configuration information
Parameters
----------
to_json : -j, --json
reports results as json
"""
env = XSH.env
data: tp.List[tp.Any] = [("xonsh", XONSH_VERSION)]
hash_, date_ = githash()
if hash_:
data.append(("Git SHA", hash_))
data.append(("Commit Date", date_))
data.extend(
[
("Python", "{}.{}.{}".format(*PYTHON_VERSION_INFO)),
("PLY", ply.__version__),
("have readline", is_readline_available()),
("prompt toolkit", ptk_version() or None),
("shell type", env.get("SHELL_TYPE")),
("history backend", env.get("XONSH_HISTORY_BACKEND")),
("pygments", pygments_version()),
("on posix", bool(ON_POSIX)),
("on linux", bool(ON_LINUX)),
]
)
if ON_LINUX:
data.append(("distro", linux_distro()))
data.append(("on wsl", bool(ON_WSL)))
if ON_WSL:
data.append(("wsl version", 1 if ON_WSL1 else 2))
data.extend(
[
("on darwin", bool(ON_DARWIN)),
("on windows", bool(ON_WINDOWS)),
("on cygwin", bool(ON_CYGWIN)),
("on msys2", bool(ON_MSYS)),
("is superuser", is_superuser()),
("default encoding", DEFAULT_ENCODING),
("xonsh encoding", env.get("XONSH_ENCODING")),
("encoding errors", env.get("XONSH_ENCODING_ERRORS")),
]
)
jup_ksm = jup_kernel = None
try:
from jupyter_client.kernelspec import KernelSpecManager
jup_ksm = KernelSpecManager()
jup_kernel = jup_ksm.find_kernel_specs().get(XONSH_JUPYTER_KERNEL)
except Exception:
pass
data.extend([("on jupyter", jup_ksm is not None), ("jupyter kernel", jup_kernel)])
data.extend([("xontrib", xontribs_loaded())])
data.extend([("RC file", XSH.rc_files)])
formatter = _xonfig_format_json if to_json else _xonfig_format_human
s = formatter(data)
return s
# The great "support IPython 2, 3, 4" strat begins
if not TEST:
try:
import jupyter
except ImportError:
jupyter_era = False
else:
jupyter_era = True
if jupyter_era:
# Jupyter / IPython 4.x
from jupyter_client import KernelManager
from jupyter_client.kernelspec import KernelSpecManager
from jupyter_client import MultiKernelManager
kernelSpecManager = KernelSpecManager()
multiKernelManager = MultiKernelManager()
else:
from IPython.kernel import KernelManager
from IPython.kernel.kernelspec import KernelSpecManager
from IPython.kernel.multikernelmanager import MultiKernelManager
kernelSpecManager = KernelSpecManager()
multiKernelManager = MultiKernelManager()
# End of the great "support IPython 2, 3, 4" strat
def _debug_write(out):
if DEBUG:
sys.__stdout__.write(out)
sys.__stdout__.write("\n")
def _jupyter_kernel(args):
"""Make xonsh available as a Jupyter kernel."""
try:
from jupyter_client.kernelspec import KernelSpecManager, NoSuchKernel
except ImportError as e:
raise ImportError("Jupyter not found in current Python environment") from e
ksm = KernelSpecManager()
root = args.root
prefix = args.prefix if args.prefix else sys.prefix
user = args.user
spec = {
"argv": [
sys.executable,
"-m",
"xonsh.jupyter_kernel",
"-f",
"{connection_file}",
],
"display_name": "Xonsh",
"language": "xonsh",
"codemirror_mode": "shell",
}
if root and prefix:
# os.path.join isn't used since prefix is probably absolute
prefix = root + prefix
try:
old_jup_kernel = ksm.get_kernel_spec(XONSH_JUPYTER_KERNEL)
if not old_jup_kernel.resource_dir.startswith(prefix):
print(
"Removing existing Jupyter kernel found at {0}".format(
old_jup_kernel.resource_dir
)
)
ksm.remove_kernel_spec(XONSH_JUPYTER_KERNEL)
except NoSuchKernel:
pass
if sys.platform == "win32":
# Ensure that conda-build detects the hard coded prefix
spec["argv"][0] = spec["argv"][0].replace(os.sep, os.altsep)
prefix = prefix.replace(os.sep, os.altsep)
with tempfile.TemporaryDirectory() as d:
os.chmod(d, 0o755) # Starts off as 700, not user readable
with open(os.path.join(d, "kernel.json"), "w") as f:
json.dump(spec, f, sort_keys=True)
print("Installing Jupyter kernel spec:")
print(" root: {0!r}".format(root))
if user:
print(" as user: {0}".format(user))
elif root and prefix:
print(" combined prefix {0!r}".format(prefix))
else:
print(" prefix: {0!r}".format(prefix))
ksm.install_kernel_spec(
d, XONSH_JUPYTER_KERNEL, user=user, prefix=(None if user else prefix)
)
return 0
class TestExecute(ExecuteTestBase):
"""Contains test functions for execute.py"""
maxDiff = None
@staticmethod
def normalize_output(output):
"""
Normalizes outputs for comparison.
"""
output = dict(output)
if 'metadata' in output:
del output['metadata']
if 'text' in output:
output['text'] = re.sub(addr_pat, '<HEXADDR>', output['text'])
if 'text/plain' in output.get('data', {}):
output['data']['text/plain'] = \
re.sub(addr_pat, '<HEXADDR>', output['data']['text/plain'])
if 'application/vnd.jupyter.widget-view+json' in output.get(
'data', {}):
output['data']['application/vnd.jupyter.widget-view+json'] \
['model_id'] = '<MODEL_ID>'
for key, value in output.get('data', {}).items():
if isinstance(value, string_types):
if sys.version_info.major == 2:
value = value.replace('u\'', '\'')
output['data'][key] = _normalize_base64(value)
if 'traceback' in output:
tb = [
re.sub(ipython_input_pat, '<IPY-INPUT>', strip_ansi(line))
for line in output['traceback']
]
output['traceback'] = tb
return output
def assert_notebooks_equal(self, expected, actual):
expected_cells = expected['cells']
actual_cells = actual['cells']
assert len(expected_cells) == len(actual_cells)
for expected_cell, actual_cell in zip(expected_cells, actual_cells):
expected_outputs = expected_cell.get('outputs', [])
actual_outputs = actual_cell.get('outputs', [])
normalized_expected_outputs = list(
map(self.normalize_output, expected_outputs))
normalized_actual_outputs = list(
map(self.normalize_output, actual_outputs))
assert normalized_expected_outputs == normalized_actual_outputs
expected_execution_count = expected_cell.get(
'execution_count', None)
actual_execution_count = actual_cell.get('execution_count', None)
assert expected_execution_count == actual_execution_count
def test_constructor(self):
"""Can a ExecutePreprocessor be constructed?"""
self.build_preprocessor({})
def run_notebook(self, filename, opts, resources):
"""Loads and runs a notebook, returning both the version prior to
running it and the version after running it.
"""
with io.open(filename) as f:
input_nb = nbformat.read(f, 4)
preprocessor = self.build_preprocessor(opts)
cleaned_input_nb = copy.deepcopy(input_nb)
for cell in cleaned_input_nb.cells:
if 'execution_count' in cell:
del cell['execution_count']
cell['outputs'] = []
# Override terminal size to standardise traceback format
with modified_env({'COLUMNS': '80', 'LINES': '24'}):
output_nb, _ = preprocessor(cleaned_input_nb, resources)
return input_nb, output_nb
def test_run_notebooks(self):
"""Runs a series of test notebooks and compares them to their actual output"""
input_files = glob.glob(os.path.join(current_dir, 'files', '*.ipynb'))
shared_opts = dict(kernel_name="python")
for filename in input_files:
# There is some slight differences between the output in IPython 6 and IPython 7.
IPY_MAJOR = IPython.version_info[0]
if os.path.basename(filename).endswith("-IPY6.ipynb"):
print(filename, IPY_MAJOR)
if IPY_MAJOR >= 7:
continue
elif os.path.basename(filename) in (
"Interrupt.ipynb", "Skip Exceptions with Cell Tags.ipynb",
"Skip Exceptions.ipynb"):
if IPY_MAJOR < 7:
continue
# Special arguments for the notebooks
if os.path.basename(filename) == "Disable Stdin.ipynb":
continue
elif os.path.basename(filename) in ("Interrupt.ipynb",
"Interrupt-IPY6.ipynb"):
opts = dict(timeout=1,
interrupt_on_timeout=True,
allow_errors=True)
elif os.path.basename(filename) in ("Skip Exceptions.ipynb",
"Skip Exceptions-IPY6.ipynb"):
opts = dict(allow_errors=True)
else:
opts = dict()
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
opts.update(shared_opts)
input_nb, output_nb = self.run_notebook(filename, opts, res)
self.assert_notebooks_equal(input_nb, output_nb)
def test_populate_language_info(self):
preprocessor = self.build_preprocessor(opts=dict(kernel_name="python"))
nb = nbformat.v4.new_notebook() # Certainly has no language_info.
nb, _ = preprocessor.preprocess(nb, resources={})
assert 'language_info' in nb.metadata
def test_empty_path(self):
"""Can the kernel be started when the path is empty?"""
filename = os.path.join(current_dir, 'files', 'HelloWorld.ipynb')
res = self.build_resources()
res['metadata']['path'] = ''
input_nb, output_nb = self.run_notebook(filename, {}, res)
self.assert_notebooks_equal(input_nb, output_nb)
@pytest.mark.xfail("python3"
not in KernelSpecManager().find_kernel_specs(),
reason="requires a python3 kernelspec")
def test_empty_kernel_name(self):
"""Can kernel in nb metadata be found when an empty string is passed?
Note: this pattern should be discouraged in practice.
Passing in no kernel_name to ExecutePreprocessor is recommended instead.
"""
filename = os.path.join(current_dir, 'files', 'UnicodePy3.ipynb')
res = self.build_resources()
input_nb, output_nb = self.run_notebook(filename, {"kernel_name": ""},
res)
self.assert_notebooks_equal(input_nb, output_nb)
with pytest.raises(TraitError):
input_nb, output_nb = self.run_notebook(filename,
{"kernel_name": None}, res)
def test_disable_stdin(self):
"""Test disabling standard input"""
filename = os.path.join(current_dir, 'files', 'Disable Stdin.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
input_nb, output_nb = self.run_notebook(filename,
dict(allow_errors=True), res)
# We need to special-case this particular notebook, because the
# traceback contains machine-specific stuff like where IPython
# is installed. It is sufficient here to just check that an error
# was thrown, and that it was a StdinNotImplementedError
self.assertEqual(len(output_nb['cells']), 1)
self.assertEqual(len(output_nb['cells'][0]['outputs']), 1)
output = output_nb['cells'][0]['outputs'][0]
self.assertEqual(output['output_type'], 'error')
self.assertEqual(output['ename'], 'StdinNotImplementedError')
self.assertEqual(
output['evalue'],
'raw_input was called, but this frontend does not support input requests.'
)
def test_timeout(self):
"""Check that an error is raised when a computation times out"""
filename = os.path.join(current_dir, 'files', 'Interrupt.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
with pytest.raises(TimeoutError):
self.run_notebook(filename, dict(timeout=1), res)
def test_timeout_func(self):
"""Check that an error is raised when a computation times out"""
filename = os.path.join(current_dir, 'files', 'Interrupt.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
def timeout_func(source):
return 10
with pytest.raises(TimeoutError):
self.run_notebook(filename, dict(timeout_func=timeout_func), res)
def test_kernel_death(self):
"""Check that an error is raised when the kernel is_alive is false"""
filename = os.path.join(current_dir, 'files', 'Interrupt.ipynb')
with io.open(filename, 'r') as f:
input_nb = nbformat.read(f, 4)
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
preprocessor = self.build_preprocessor({"timeout": 5})
try:
input_nb, output_nb = preprocessor(input_nb, {})
except TimeoutError:
pass
km, kc = preprocessor.start_new_kernel()
with patch.object(km, "is_alive") as alive_mock:
alive_mock.return_value = False
with pytest.raises(DeadKernelError):
input_nb, output_nb = preprocessor.preprocess(input_nb, {},
km=km)
def test_allow_errors(self):
"""
Check that conversion halts if ``allow_errors`` is False.
"""
filename = os.path.join(current_dir, 'files', 'Skip Exceptions.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
with pytest.raises(CellExecutionError) as exc:
self.run_notebook(filename, dict(allow_errors=False), res)
self.assertIsInstance(str(exc.value), str)
if sys.version_info >= (3, 0):
assert u"# üñîçø∂é" in str(exc.value)
else:
assert u"# üñîçø∂é".encode('utf8', 'replace') in str(exc.value)
def test_force_raise_errors(self):
"""
Check that conversion halts if the ``force_raise_errors`` traitlet on
ExecutePreprocessor is set to True.
"""
filename = os.path.join(current_dir, 'files',
'Skip Exceptions with Cell Tags.ipynb')
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(filename)
with pytest.raises(CellExecutionError) as exc:
self.run_notebook(filename, dict(force_raise_errors=True), res)
self.assertIsInstance(str(exc.value), str)
if sys.version_info >= (3, 0):
assert u"# üñîçø∂é" in str(exc.value)
else:
assert u"# üñîçø∂é".encode('utf8', 'replace') in str(exc.value)
def test_custom_kernel_manager(self):
from .fake_kernelmanager import FakeCustomKernelManager
filename = os.path.join(current_dir, 'files', 'HelloWorld.ipynb')
with io.open(filename) as f:
input_nb = nbformat.read(f, 4)
preprocessor = self.build_preprocessor(
{'kernel_manager_class': FakeCustomKernelManager})
cleaned_input_nb = copy.deepcopy(input_nb)
for cell in cleaned_input_nb.cells:
if 'execution_count' in cell:
del cell['execution_count']
cell['outputs'] = []
# Override terminal size to standardise traceback format
with modified_env({'COLUMNS': '80', 'LINES': '24'}):
output_nb, _ = preprocessor(cleaned_input_nb,
self.build_resources())
expected = FakeCustomKernelManager.expected_methods.items()
for method, call_count in expected:
self.assertNotEqual(call_count, 0, '{} was called'.format(method))
def test_process_message_wrapper(self):
outputs = []
class WrappedPreProc(ExecutePreprocessor):
def process_message(self, msg, cell, cell_index):
result = super(WrappedPreProc,
self).process_message(msg, cell, cell_index)
if result:
outputs.append(result)
return result
current_dir = os.path.dirname(__file__)
filename = os.path.join(current_dir, 'files', 'HelloWorld.ipynb')
with io.open(filename) as f:
input_nb = nbformat.read(f, 4)
original = copy.deepcopy(input_nb)
wpp = WrappedPreProc()
executed = wpp.preprocess(input_nb, {})[0]
assert outputs == [{
'name': 'stdout',
'output_type': 'stream',
'text': 'Hello World\n'
}]
self.assert_notebooks_equal(original, executed)
def test_execute_function(self):
# Test the executenb() convenience API
filename = os.path.join(current_dir, 'files', 'HelloWorld.ipynb')
with io.open(filename) as f:
input_nb = nbformat.read(f, 4)
original = copy.deepcopy(input_nb)
executed = executenb(original, os.path.dirname(filename))
self.assert_notebooks_equal(original, executed)
def test_widgets(self):
"""Runs a test notebook with widgets and checks the widget state is saved."""
input_file = os.path.join(current_dir, 'files', 'JupyterWidgets.ipynb')
opts = dict(kernel_name="python")
res = self.build_resources()
res['metadata']['path'] = os.path.dirname(input_file)
input_nb, output_nb = self.run_notebook(input_file, opts, res)
output_data = [
output.get('data', {}) for cell in output_nb['cells']
for output in cell['outputs']
]
model_ids = [
data['application/vnd.jupyter.widget-view+json']['model_id']
for data in output_data
if 'application/vnd.jupyter.widget-view+json' in data
]
wdata = output_nb['metadata']['widgets'] \
['application/vnd.jupyter.widget-state+json']
for k in model_ids:
d = wdata['state'][k]
assert 'model_name' in d
assert 'model_module' in d
assert 'state' in d
assert 'version_major' in wdata
assert 'version_minor' in wdata
def install(kernel_spec_manager=None,
user=False,
kernel_name=KERNEL_NAME,
display_name=None,
prefix=None,
profile=None,
env=None):
"""Install the IPython kernelspec for Jupyter
Parameters
----------
kernel_spec_manager : KernelSpecManager [optional]
A KernelSpecManager to use for installation.
If none provided, a default instance will be created.
user : bool [default: False]
Whether to do a user-only install, or system-wide.
kernel_name : str, optional
Specify a name for the kernelspec.
This is needed for having multiple IPython kernels for different environments.
display_name : str, optional
Specify the display name for the kernelspec
profile : str, optional
Specify a custom profile to be loaded by the kernel.
prefix : str, optional
Specify an install prefix for the kernelspec.
This is needed to install into a non-default location, such as a conda/virtual-env.
env : dict, optional
A dictionary of extra environment variables for the kernel.
These will be added to the current environment variables before the
kernel is started
Returns
-------
The path where the kernelspec was installed.
"""
if kernel_spec_manager is None:
kernel_spec_manager = KernelSpecManager()
if (kernel_name != KERNEL_NAME) and (display_name is None):
# kernel_name is specified and display_name is not
# default display_name to kernel_name
display_name = kernel_name
overrides = {}
if display_name:
overrides["display_name"] = display_name
if profile:
extra_arguments = ["--profile", profile]
if not display_name:
# add the profile to the default display name
overrides["display_name"] = 'Python %i [profile=%s]' % (
sys.version_info[0], profile)
else:
extra_arguments = None
if env:
overrides['env'] = env
path = write_kernel_spec(overrides=overrides,
extra_arguments=extra_arguments)
dest = kernel_spec_manager.install_kernel_spec(path,
kernel_name=kernel_name,
user=user,
prefix=prefix)
# cleanup afterward
shutil.rmtree(path)
return dest
def install(self):
with TemporaryDirectory() as td:
os.chmod(td, 0o755) # check if this is needed
with open(os.path.join(td, 'kernel.json'), 'w') as file:
json.dump(self.kernel_spec, file, sort_keys=True)
return KernelSpecManager().install_kernel_spec(td, self.kernel_name, replace=True)
# from jinja2 import FileSystemLoader
# from notebook.base.handlers import IPythonHandler, FileFindHandler
import logging
from tornado import web, ioloop
from notebook.services.kernels.kernelmanager import MappingKernelManager
import os
from jupyter_client.kernelspec import KernelSpecManager
from .handlers import pages_handler, kernels_handler, kernelspecs_handler, content_handeler
logger = logging.getLogger("lab_dash")
settings = dict(kernel_manager=MappingKernelManager(),
kernel_spec_manager=KernelSpecManager(),
logger=logger)
default_handlers = (pages_handler.default_handlers +
kernels_handler.default_handlers +
kernelspecs_handler.default_handlers +
content_handeler.default_handlers)
static_handler = (r'/(.*)', web.StaticFileHandler, {
'path':
os.path.join(os.path.dirname(__file__), '..', '..', 'build')
})
default_handlers += [static_handler]
def main():
logger.setLevel(logging.INFO)
ch = logging.StreamHandler()
def install_my_kernel_javascript():
seq_js_file = os.path.join(os.environ['SEQ_PATH'][:-7], 'jupyter',
'seq_kernel', 'kernel.js')
kernel_js_file = os.path.join(
KernelSpecManager().get_kernel_spec('seq').resource_dir, 'kernel.js')
os.system(f'cp {seq_js_file} {kernel_js_file}')
'--replace',
help='Replace any existing kernel spec with this name.',
action='store_true'
)
@/s/GENERATED_ARGS@
args = parser.parse_args()
@/s/GENERATED_DEFAULT_REPLACEMENT@
# Install the kernel
install_dest = KernelSpecManager().install_kernel_spec(
os.path.join(os.path.dirname(os.path.abspath(__file__)), '@KERNEL_DIRECTORY@'),
kernel_name='@KERNEL_NAME@',
user=args.user,
prefix=sys.prefix if args.sys_prefix else args.prefix,
replace=args.replace
)
# Connect the self referencing token left in the kernel.json to point to it's install location.
# Prepare the token replacement string which should be properly escaped for use in a JSON string
# The [1:-1] trims the first and last " json.dumps adds for strings.
install_dest_json_fragment = json.dumps(install_dest)[1:-1]
# Prepare the paths to the installed kernel.json and the one bundled with this installer.
local_kernel_json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), '@KERNEL_DIRECTORY@', 'kernel.json')
installed_kernel_json_path = os.path.join(install_dest, 'kernel.json')
# Replace the @KERNEL_INSTALL_DIRECTORY@ token with the path to where the kernel was installed
def uninstall_kernel():
print("Uninstalling", kernel_name, "kernel...")
KernelSpecManager().remove_kernel_spec(kernel_name)
print(kernel_name.capitalize(), "kernel uninstallation complete")
def init_configurables(self):
"""Initializes all configurable objects including a kernel manager, kernel
spec manager, session manager, and personality.
Any kernel pool configured by the personality will be its responsibility
to shut down.
Optionally, loads a notebook and pre-spawns the configured number of
kernels.
"""
self.kernel_spec_manager = KernelSpecManager(parent=self)
self.seed_notebook = None
if self.seed_uri is not None:
# Note: must be set before instantiating a SeedingMappingKernelManager
self.seed_notebook = self._load_notebook(self.seed_uri)
# Only pass a default kernel name when one is provided. Otherwise,
# adopt whatever default the kernel manager wants to use.
kwargs = {}
if self.default_kernel_name:
kwargs['default_kernel_name'] = self.default_kernel_name
self.kernel_spec_manager = self.kernel_spec_manager_class(
parent=self,
)
self.kernel_manager = self.kernel_manager_class(
parent=self,
log=self.log,
connection_dir=self.runtime_dir,
kernel_spec_manager=self.kernel_spec_manager,
**kwargs
)
# Detect older version of notebook
func = getattr(self.kernel_manager, 'initialize_culler', None)
if not func:
self.log.warning("Older version of Notebook detected - idle kernels will not be culled. "
"Culling requires Notebook >= 5.1.0.")
self.session_manager = SessionManager(
log=self.log,
kernel_manager=self.kernel_manager
)
self.kernel_session_manager = self.kernel_session_manager_class(
parent=self,
log=self.log,
kernel_manager=self.kernel_manager,
config=self.config, # required to get command-line options visible
**kwargs
)
# Attempt to start persisted sessions
self.kernel_session_manager.start_sessions()
self.contents_manager = None # Gateways don't use contents manager
if self.prespawn_count:
if self.max_kernels and self.prespawn_count > self.max_kernels:
raise RuntimeError('cannot prespawn {}; more than max kernels {}'.format(
self.prespawn_count, self.max_kernels)
)
api_module = self._load_api_module(self.api)
func = getattr(api_module, 'create_personality')
self.personality = func(parent=self, log=self.log)
self.personality.init_configurables()
def run_notebook(nb_path, output_dir):
"""Run a notebook tests
executes the notebook and stores the output in a file
"""
import nbformat
from jupyter_client.kernelspec import KernelSpecManager
from nbconvert.preprocessors.execute import executenb
log.info(f"Testing notebook {nb_path}")
with open(nb_path) as f:
nb = nbformat.read(f, as_version=4)
kernel_specs = KernelSpecManager().get_all_specs()
kernel_info = nb.metadata.get("kernelspec") or {}
kernel_name = kernel_info.get("name", "")
kernel_language = kernel_info.get("language") or ""
if kernel_name in kernel_specs:
log.info(f"Found kernel {kernel_name}")
elif kernel_language:
log.warning(
f"No such kernel {kernel_name}, falling back on kernel language={kernel_language}"
)
kernel_language = kernel_language.lower()
# no exact name match, re-implement js notebook fallback,
# using kernel language instead
# nbconvert does not implement this, but it should
for kernel_spec_name, kernel_info in kernel_specs.items():
if (kernel_info.get("spec",
{}).get("language",
"").lower() == kernel_language):
log.warning(
f"Using kernel {kernel_spec_name} to provide language: {kernel_language}"
)
kernel_name = kernel_spec_name
break
else:
log.warning(
"Found no matching kernel for name={kernel_name}, language={kernel_language}"
)
summary_specs = [
f"name={name}, language={info['spec'].get('language')}"
for name, info in kernel_specs.items()
]
log.warning(f"Found kernel specs: {'; '.join(summary_specs)}")
exported = executenb(nb,
cwd=os.path.dirname(nb_path),
kernel_name=kernel_name,
timeout=600)
rel_path = os.path.relpath(nb_path, os.getcwd())
dest_path = os.path.join(output_dir, "notebooks", rel_path)
log.info(f"Saving exported notebook to {dest_path}")
try:
os.makedirs(os.path.dirname(dest_path))
except FileExistsError:
pass
with open(dest_path, "w") as f:
nbformat.write(exported, f)
def start(self):
self.connection_dir = tempfile.mkdtemp(prefix='voila_',
dir=self.connection_dir_root)
self.log.info('Storing connection files in %s.' % self.connection_dir)
self.log.info('Serving static files from %s.' % self.static_root)
self.kernel_spec_manager = KernelSpecManager(parent=self)
self.kernel_manager = MappingKernelManager(
parent=self,
connection_dir=self.connection_dir,
kernel_spec_manager=self.kernel_spec_manager,
allowed_message_types=[
'comm_msg', 'comm_info_request', 'kernel_info_request',
'shutdown_request'
])
jenv_opt = {
"autoescape": True
} # we might want extra options via cmd line like notebook server
env = jinja2.Environment(loader=jinja2.FileSystemLoader(
self.template_paths),
extensions=['jinja2.ext.i18n'],
**jenv_opt)
nbui = gettext.translation('nbui',
localedir=os.path.join(ROOT, 'i18n'),
fallback=True)
env.install_gettext_translations(nbui, newstyle=False)
self.contents_manager = LargeFileManager(parent=self)
# we create a config manager that load both the serverconfig and nbconfig (classical notebook)
read_config_path = [
os.path.join(p, 'serverconfig') for p in jupyter_config_path()
]
read_config_path += [
os.path.join(p, 'nbconfig') for p in jupyter_config_path()
]
self.config_manager = ConfigManager(parent=self,
read_config_path=read_config_path)
# default server_url to base_url
self.server_url = self.server_url or self.base_url
self.app = tornado.web.Application(
base_url=self.base_url,
server_url=self.server_url or self.base_url,
kernel_manager=self.kernel_manager,
kernel_spec_manager=self.kernel_spec_manager,
allow_remote_access=True,
autoreload=self.autoreload,
voila_jinja2_env=env,
jinja2_env=env,
static_path='/',
server_root_dir='/',
contents_manager=self.contents_manager,
config_manager=self.config_manager)
self.app.settings.update(self.tornado_settings)
handlers = []
handlers.extend([
(url_path_join(self.server_url,
r'/api/kernels/%s' % _kernel_id_regex),
KernelHandler),
(url_path_join(self.server_url,
r'/api/kernels/%s/channels' % _kernel_id_regex),
ZMQChannelsHandler),
(url_path_join(self.server_url,
r'/voila/static/(.*)'), MultiStaticFileHandler, {
'paths': self.static_paths,
'default_filename': 'index.html'
})
])
# Serving notebook extensions
if self.voila_configuration.enable_nbextensions:
handlers.append((
url_path_join(self.server_url, r'/voila/nbextensions/(.*)'),
FileFindHandler,
{
'path': self.nbextensions_path,
'no_cache_paths':
['/'], # don't cache anything in nbextensions
},
))
handlers.append((
url_path_join(self.server_url, r'/voila/files/(.*)'),
WhiteListFileHandler,
{
'whitelist': self.voila_configuration.file_whitelist,
'blacklist': self.voila_configuration.file_blacklist,
'path': self.root_dir,
},
))
tree_handler_conf = {'voila_configuration': self.voila_configuration}
if self.notebook_path:
handlers.append(
(url_path_join(self.server_url, r'/(.*)'), VoilaHandler, {
'notebook_path':
os.path.relpath(self.notebook_path, self.root_dir),
'nbconvert_template_paths':
self.nbconvert_template_paths,
'config':
self.config,
'voila_configuration':
self.voila_configuration
}))
else:
self.log.debug('serving directory: %r', self.root_dir)
handlers.extend([
(self.server_url, VoilaTreeHandler, tree_handler_conf),
(url_path_join(self.server_url, r'/voila/tree' + path_regex),
VoilaTreeHandler, tree_handler_conf),
(url_path_join(self.server_url, r'/voila/render/(.*)'),
VoilaHandler, {
'nbconvert_template_paths': self.nbconvert_template_paths,
'config': self.config,
'voila_configuration': self.voila_configuration
}),
])
self.app.add_handlers('.*$', handlers)
self.listen()
from jupyter_client.kernelspec import KernelSpecManager
from setuptools import setup
name = 'cwlkernel'
setup(
name=name,
version='0.1',
py_modules=['cwlkernel'],
url='https://github.com/giannisdoukas/CWLJNIKernel',
author='Yannis Doukas',
author_email='',
description='',
classifiers=[
"Programming Language :: Python :: 3",
"License :: OSI Approved :: Apache Software License",
"Operating System :: OS Independent",
"Development Status :: 2 - Pre-Alpha"
],
)
import sys
import os
kernel_requirements_directory = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'kernelmeta')
print('Installing IPython kernel spec')
KernelSpecManager().install_kernel_spec(kernel_requirements_directory,
name,
user=False,
prefix=sys.prefix)
def get_kernelspec(name):
ksm = KernelSpecManager()
kernelspec = ksm.get_kernel_spec(name).to_dict()
kernelspec['name'] = name
kernelspec.pop('argv')
return kernelspec
def kernel_spec_manager(environ, setup_kernelspecs):
yield KernelSpecManager(ensure_native_kernel=False)
def remove(_ctx) -> None:
kernel_spec = KernelSpecManager()
kernel_spec.remove_kernel_spec('michelson')
def uninstall(self):
return KernelSpecManager().remove_kernel_spec(self.kernel_name.lower())
aliases=ALIASES,
name_map=NAME_MAP,
help=
"The path to the Graphviz dot executable that is used for the %viz magic command.",
type=type_assertion("graphviz-path", str),
)
args = parser.parse_args()
if not hasattr(args, "env") or getattr(args, "env") is None:
setattr(args, "env", {})
# Install the kernel
install_dest = KernelSpecManager().install_kernel_spec(
os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sysml'),
kernel_name='sysml',
user=args.user,
prefix=sys.prefix if args.sys_prefix else args.prefix,
replace=args.replace)
# Connect the self referencing token left in the kernel.json to point to it's install location.
# Prepare the token replacement string which should be properly escaped for use in a JSON string
# The [1:-1] trims the first and last " json.dumps adds for strings.
install_dest_json_fragment = json.dumps(install_dest)[1:-1]
# Prepare the paths to the installed kernel.json and the one bundled with this installer.
local_kernel_json_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'sysml', 'kernel.json')
installed_kernel_json_path = os.path.join(install_dest, 'kernel.json')
# Replace the @KERNEL_INSTALL_DIRECTORY@ token with the path to where the kernel was installed
def __init__(self):
self.args = self.parse_arguments()
self.connection = self.parse_connection_file(self.args.connection_file)
self.spawn = eval(f"self._spawn_{self.args.scheduler}")
self.kernel_spec = KernelSpecManager().get_kernel_spec(self.args.kernel)
