def test_nbextensionpy_uninstall_files(self):
self._inject_mock_extension()
install_nbextension_python('mockextension', user=True)
uninstall_nbextension_python('mockextension', user=True)
assert not check_nbextension('_mockdestination/index.js')
assert not check_nbextension(['_mockdestination/index.js'])
def test_nbextensionpy_uninstall_files(self):
self._inject_mock_extension()
install_nbextension_python('mockextension', user=True)
uninstall_nbextension_python('mockextension', user=True)
assert not check_nbextension('_mockdestination/index.js')
assert not check_nbextension(['_mockdestination/index.js'])
def test_check_nbextension(self):
with TemporaryDirectory() as d:
f = u'ƒ.js'
src = pjoin(d, f)
touch(src)
install_nbextension(src, user=True)
assert check_nbextension(f, user=True)
assert check_nbextension([f], user=True)
assert not check_nbextension([f, pjoin('dne', f)], user=True)
def test_check_nbextension(self):
with TemporaryDirectory() as d:
f = u'ƒ.js'
src = pjoin(d, f)
touch(src)
install_nbextension(src, user=True)
assert check_nbextension(f, user=True)
assert check_nbextension([f], user=True)
assert not check_nbextension([f, pjoin('dne', f)], user=True)
def nbinstall(overwrite=False, user=True):
"""
Copies javascript dependencies to the '/nbextensions' folder in
your IPython directory.
Parameters
----------
overwrite : bool
If True, always install the files, regardless of what may already be
installed. Defaults to False.
user : bool
Whether to install to the user's .ipython/nbextensions directory.
Otherwise do a system-wide install
(e.g. /usr/local/share/jupyter/nbextensions). Defaults to False.
"""
if (check_nbextension('matplotlib')
or check_nbextension('matplotlib', True)):
return
# Make a temporary directory so we can wrap mpl.js in a requirejs define().
tempdir = mkdtemp()
path = os.path.join(os.path.dirname(__file__), "web_backend")
shutil.copy2(os.path.join(path, "nbagg_mpl.js"), tempdir)
with open(os.path.join(path, 'mpl.js')) as fid:
contents = fid.read()
with open(os.path.join(tempdir, 'mpl.js'), 'w') as fid:
fid.write('define(["jquery"], function($) {\n')
fid.write(contents)
fid.write('\nreturn mpl;\n});')
install_nbextension(tempdir,
overwrite=overwrite,
symlink=False,
destination='matplotlib',
verbose=0,
**({
'user': user
} if version_info >= (3, 0, 0, '') else {}))
def nbinstall(overwrite=False, user=True):
"""
Copies javascript dependencies to the '/nbextensions' folder in
your IPython directory.
Parameters
----------
overwrite : bool
If True, always install the files, regardless of what may already be
installed. Defaults to False.
user : bool
Whether to install to the user's .ipython/nbextensions directory.
Otherwise do a system-wide install
(e.g. /usr/local/share/jupyter/nbextensions). Defaults to False.
"""
if (check_nbextension('matplotlib') or
check_nbextension('matplotlib', True)):
return
# Make a temporary directory so we can wrap mpl.js in a requirejs define().
tempdir = mkdtemp()
path = os.path.join(os.path.dirname(__file__), "web_backend")
shutil.copy2(os.path.join(path, "nbagg_mpl.js"), tempdir)
with open(os.path.join(path, 'mpl.js')) as fid:
contents = fid.read()
with open(os.path.join(tempdir, 'mpl.js'), 'w') as fid:
fid.write('define(["jquery"], function($) {\n')
fid.write(contents)
fid.write('\nreturn mpl;\n});')
install_nbextension(
tempdir,
overwrite=overwrite,
symlink=False,
destination='matplotlib',
verbose=0,
**({'user': user} if version_info >= (3, 0, 0, '') else {})
)
def get_installed_versions(pyname, getversion):
""" Check if the required NBExtensions are installed. If not, prompt user for action.
"""
import importlib
from notebook import nbextensions
spec = importlib.import_module(pyname)._jupyter_nbextension_paths()[0]
extname = spec['dest']
require = spec['require']
assert spec['section'] == 'notebook'
search_paths = nbextension_ordered_paths()
writable = location_writable()
installed = {
k: nbextensions.check_nbextension(extname, **EXTENSION_KWARGS[k])
for k in search_paths.keys()
}
config_dirs = jupyter_config_dirs()
paths = {}
versions = {}
enabled = {}
active = {}
found_active = False
for location in EXTENSION_KWARGS:
if not installed[location]:
active[location] = False
continue
active[location] = not found_active
found_active = True
paths[location] = os.path.join(search_paths[location], 'nbextensions',
extname)
config = nbextensions.BaseJSONConfigManager(
config_dir=config_dirs[location])
enabled[location] = require in config.get('notebook').get(
'load_extensions', {})
if getversion:
versionfile = os.path.join(paths[location], 'VERSION')
if installed[location] and os.path.exists(versionfile):
with open(versionfile, 'r') as pfile:
versions[location] = pfile.read().strip()
else:
versions[location] = 'pre-0.7'
return {
k: NbExtVersion(extname, installed[k], paths.get(k, None),
versions.get(k, None), enabled.get(k, False),
active[k], writable[k])
for k in installed
}
def get_installed_versions(pyname, getversion):
""" Check if the required NBExtensions are installed. If not, prompt user for action.
"""
import importlib
from notebook import nbextensions
spec = importlib.import_module(pyname)._jupyter_nbextension_paths()[0]
extname = spec['dest']
require = spec['require']
assert spec['section'] == 'notebook'
search_paths = nbextension_ordered_paths()
writable = location_writable()
installed = {k: nbextensions.check_nbextension(extname, **EXTENSION_KWARGS[k])
for k in search_paths.keys()}
config_dirs = jupyter_config_dirs()
paths = {}
versions = {}
enabled = {}
active = {}
found_active = False
for location in EXTENSION_KWARGS:
if not installed[location]:
active[location] = False
continue
active[location] = not found_active
found_active = True
paths[location] = os.path.join(search_paths[location], 'nbextensions', extname)
config = nbextensions.BaseJSONConfigManager(config_dir=config_dirs[location])
enabled[location] = require in config.get('notebook').get('load_extensions', {})
if getversion:
versionfile = os.path.join(paths[location], 'VERSION')
if installed[location] and os.path.exists(versionfile):
with open(versionfile, 'r') as pfile:
versions[location] = pfile.read().strip()
else:
versions[location] = 'pre-0.7'
return {k: NbExtVersion(extname,
installed[k],
paths.get(k, None),
versions.get(k, None),
enabled.get(k, False),
active[k],
writable[k])
for k in installed}
def install_static(local_path=None, target_name=None, overwrite=False):
"""
Write the javascript libraries to the given location.
This utility is used by the IPython notebook tools to enable easy use
of pyLDAvis with no web connection.
Parameters
----------
local_path: string (optional)
the path to a file or a directory
target_name: string (optional)
the name of the target file or directory
overwrite: boolean (optional)
whether to overwrite if existing file or directory exists
Returns
-------
The urls of the local_files
"""
if IPYTHON_VERSION is None or IPYTHON_VERSION[0] < '2':
raise ModuleNotFoundError(
'IPython with version larger than 2.0 need to be installed!')
if IPYTHON_VERSION[0] > '3':
from notebook.nbextensions import install_nbextension, check_nbextension
else:
from IPython.html.nbextensions import install_nbextension, check_nbextension
if local_path is None:
local_path = STATIC_DIR
target_name = VERSIONED_NAME
if target_name is None:
target_name = os.path.basename(local_path)
if not os.path.exists(local_path):
raise ValueError('%s not found at %s' % (target_name, local_path))
if check_nbextension([target_name]):
if overwrite:
warnings.warn("Extension %s already exists. Overwriting..." %
target_name)
else:
# skipping
return '/nbextensions/' + target_name
else:
full_url = install_nbextension(local_path,
overwrite=overwrite,
destination=target_name)
print(full_url)
return '/nbextensions/' + target_name
def valid_arborist_or_exception(**kwargs):
from notebook import __version__ as notebook_version
if notebook_version < '4.2.0':
print(
"Version of notebook package should be atleast 4.2.0 for Arborist, consider:"
)
print(" $ pip3 install --upgrade notebook")
raise RuntimeError("Notebook too old for Arborist.")
from notebook.serverextensions import validate_serverextension
from notebook.nbextensions import check_nbextension
warnings = validate_serverextension('tmtk.arborist')
if warnings or not check_nbextension('transmart-arborist', **kwargs):
print(
'For the Arborist to work you need to install a jupyter serverextension using something like:'
)
print(' $ jupyter nbextension install --py tmtk.arborist')
print(' $ jupyter serverextension enable --py tmtk.arborist')
print('Then to verify installation run:')
print(' $ jupyter serverextension list')
raise RuntimeError('Transmart-arborist extension not found.')
from rdkit.Chem import AllChem as Chem
if TYPE_CHECKING:
from rdkit.Chem import Mol
# Named tuple for storing serialized JSME widget value in several
# popular formats
JsmeValue = namedtuple("JsmeValue", ["jme", "molblock", "smiles"])
# Rel file path for Javascript source
JS_SOURCE = "jsme/jsme.nocache.js"
# Base URL for widget source javascript
BASE_URL = "/nbextensions/jupyter_jsme"
if check_nbextension("jupyter_jsme") is False:
# Fallback option in case user didn't install Jupyter extension
BASE_URL = "https://peter-ertl.com/jsme/JSME_2020-06-11"
_HTML_STR_FORMAT = '''
<script type="text/javascript" src="{base_url}/{js_source}"></script>
<script type="text/javascript">
function jsmeOnLoad() {{
jsmeApp_{uid} = new JSApplet.JSME("JSApp_{uid}", \
"{width}px", "{height}px", {{
"options" : "{options}",
"{data_type}": "{data}"
}});
}}
function saveAs_{uid}(var_name) {{
