Closed jvanhoefer closed 2 years ago
Here comes a full Error Log:
NBMAKE INTERNAL ERROR
cannot import name 'secure_write' from 'jupyter_core.paths' (/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/jupyter_core/paths.py)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/_pytest/runner.py", line 244, in from_call
result = func()
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/_pytest/runner.py", line 217, in <lambda>
lambda: ihook(item=item, **kwds), when=when, reraise=reraise
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pluggy/manager.py", line 87, in <lambda>
firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pluggy/callers.py", line 208, in _multicall
return outcome.get_result()
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
raise ex[1].with_traceback(ex[2])
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/_pytest/runner.py", line 143, in pytest_runtest_call
raise e
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/_pytest/runner.py", line 135, in pytest_runtest_call
item.runtest()
File "/Users/jvanhoefer/Library/Python/3.7/lib/python/site-packages/nbmake/pytest_items.py", line 50, in runtest
res: NotebookResult = run.execute()
File "/Users/jvanhoefer/Library/Python/3.7/lib/python/site-packages/nbmake/nb_run.py", line 73, in execute
raise err
File "/Users/jvanhoefer/Library/Python/3.7/lib/python/site-packages/nbmake/nb_run.py", line 55, in execute
c.execute(cwd=self.filename.parent)
File "/Users/jvanhoefer/Library/Python/3.7/lib/python/site-packages/nbclient/util.py", line 37, in wrapped
result = loop.run_until_complete(coro(self, *args, **kwargs))
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/asyncio/base_events.py", line 573, in run_until_complete
return future.result()
File "/Users/jvanhoefer/Library/Python/3.7/lib/python/site-packages/nbclient/client.py", line 474, in async_execute
async with self.async_setup_kernel(**kwargs):
File "/Users/jvanhoefer/Library/Python/3.7/lib/python/site-packages/async_generator/_util.py", line 34, in __aenter__
return await self._agen.asend(None)
File "/Users/jvanhoefer/Library/Python/3.7/lib/python/site-packages/nbclient/client.py", line 440, in async_setup_kernel
self.start_kernel_manager()
File "/Users/jvanhoefer/Library/Python/3.7/lib/python/site-packages/nbclient/client.py", line 327, in start_kernel_manager
self.km = self.kernel_manager_class(kernel_name=self.kernel_name, config=self.config)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/traitlets/traitlets.py", line 556, in __get__
return self.get(obj, cls)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/traitlets/traitlets.py", line 535, in get
value = self._validate(obj, dynamic_default())
File "/Users/jvanhoefer/Library/Python/3.7/lib/python/site-packages/nbclient/client.py", line 240, in _kernel_manager_class_default
from jupyter_client import AsyncKernelManager
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/jupyter_client/__init__.py", line 4, in <module>
from .connect import *
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/jupyter_client/connect.py", line 32, in <module>
from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write
This happens consistently over all three notebooks in the repository... :)
When googling, I found this answer to a related question
https://github.com/jupyter/notebook/issues/5014#issuecomment-581556926
Generally speaking, ensure that jupyter_client >= 5.3.4 and jupyter_core >= 4.6.1 for issues surrounding
secure_write()
.
Updating both repositories solved my problem, so it might be a good idea to have them as requirement in setup.py
? :)
Thank you for providing this anyhow! Looks awesome and I will definitely use this in future projects :)
@jvanhoefer thanks for the report! My notifications are all messed up so I missed this unfortunately.
I'm glad you managed to solve this and get things running. The dependency tree around nbclient has been a little painful for me and I'd rather not touch it until I get a bit more feedback.
Best to just pin this issue/fix for now.
closing this one as stale, nbclient has gone through a few updates since, so likely this is solved.
Describe the bug As suggested in https://github.com/yaml2sbml-dev/yaml2sbml/issues/34, I tried to use
nbmake
to add the notebooks in the repo, to the unit tests. I received the error message:To Reproduce Run
pytest --nbmake
in yaml2sbml. (I guess)Desktop (please complete the following information):
Additional context If you need any further information or anything, that I can help to identify the problem, please let me know :)