munichpavel
commented
2 years ago I get a permissions error when running test for notebooks:
___________________________________________________________ test_ipynb[notebook_path0] ____________________________________________________________
notebook_path = PosixPath('/Users/pauldev/delo/projects/fake-data-for-learning/notebooks/bayesian-network.ipynb')
@pytest.mark.parametrize(
'notebook_path',
[
notebook_dir / 'bayesian-network.ipynb',
notebook_dir / 'conditional-probability-tables-with-constraints.ipynb'
]
)
def test_ipynb(notebook_path):
> nb, errors = _notebook_run(notebook_path)
tests/test_demo_notebooks.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_demo_notebooks.py:40: in _notebook_run
subprocess.check_call(args)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['python', '-m', 'nbconvert', '--to', 'notebook', '--execute', ...],), kwargs = {}, retcode = 1
cmd = ['python', '-m', 'nbconvert', '--to', 'notebook', '--execute', ...]
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['python', '-m', 'nbconvert', '--to', 'notebook', '--execute', '--ExecutePreprocessor.timeout=60', '--output', '/var/folders/xf/jv1nj4vd0lb05xfnp6gly8n40000gq/T/tmpyrm5g5q9.ipynb', PosixPath('/Users/pauldev/delo/projects/fake-data-for-learning/notebooks/bayesian-network.ipynb')]' returned non-zero exit status 1.
../../../miniconda3/lib/python3.7/subprocess.py:363: CalledProcessError
-------------------------------------------------------------- Captured stderr call ---------------------------------------------------------------
Traceback (most recent call last):
File "/Users/pauldev/miniconda3/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/Users/pauldev/miniconda3/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/Users/pauldev/.virtualenvs/fake-data/lib/python3.7/site-packages/nbconvert/__main__.py", line 1, in <module>
from .nbconvertapp import main
File "/Users/pauldev/.virtualenvs/fake-data/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 156, in <module>
class NbConvertApp(JupyterApp):
File "/Users/pauldev/.virtualenvs/fake-data/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 241, in NbConvertApp
""".format(formats=get_export_names()))
File "/Users/pauldev/.virtualenvs/fake-data/lib/python3.7/site-packages/nbconvert/exporters/base.py", line 146, in get_export_names
e = get_exporter(exporter_name)(config=config)
File "/Users/pauldev/.virtualenvs/fake-data/lib/python3.7/site-packages/nbconvert/exporters/base.py", line 103, in get_exporter
if getattr(exporter(config=config), 'enabled', True):
File "/Users/pauldev/.virtualenvs/fake-data/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 332, in __init__
super().__init__(config=config, **kw)
File "/Users/pauldev/.virtualenvs/fake-data/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 114, in __init__
self._init_preprocessors()
File "/Users/pauldev/.virtualenvs/fake-data/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 499, in _init_preprocessors
conf = self._get_conf()
File "/Users/pauldev/.virtualenvs/fake-data/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 519, in _get_conf
if conf_path.exists():
File "/Users/pauldev/miniconda3/lib/python3.7/pathlib.py", line 1356, in exists
self.stat()
File "/Users/pauldev/miniconda3/lib/python3.7/pathlib.py", line 1178, in stat
return self._accessor.stat(self)
PermissionError: [Errno 13] Permission denied: '/usr/local/share/jupyter/nbconvert/templates/conf.json'Perhaps related to https://discourse.jupyter.org/t/500-internal-server-error-while-trying-to-open-python-notebook-on-jupyterhub/9738/6.
Will try downgrading nbconvert as per above chat.
NOPE, no help. Not surprising. It is a permissions error, so I would expect the solution involves fixing some broken permissions, and not changing package versions.
This seems clearly a local issue, so will trouble-shoot elsewhere.
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