Comments (11)
takluyver
commented on June 12, 2024
It looks like all the warnings are coming from jupyter, so there's probably nothing for pyemma to do. I think we were over-eager with issuing deprecation warnings.
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stefdoerr
commented on June 12, 2024
Okay, I just thought that since importing jupyter_core did not throw any messages it might be related to pyemma, but yes they all come from the core code.
If you need it I can provide you the full list of warnings
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Carreau
commented on June 12, 2024
still unsure why it would do that at pyemma import...
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Carreau
commented on June 12, 2024
Hum, PyEmme is definitively inderectly maybe doing stuff it should not.
Traceback (most recent call last):
File "/Users/bussonniermatthias/dev/ipython/IPython/core/interactiveshell.py", line 2885, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-1-e542aa3daeae>", line 1, in <module>
import pyemma
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/pyemma/__init__.py", line 28, in <module>
from . import msm
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/pyemma/msm/__init__.py", line 91, in <module>
from msmtools import analysis, estimation, generation, dtraj, flux
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/msmtools/__init__.py", line 41, in <module>
from . import analysis
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/msmtools/analysis/__init__.py", line 113, in <module>
from .api import *
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/msmtools/analysis/api.py", line 92, in <module>
@shortcut('is_tmatrix')
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/msmtools/util/annotators.py", line 155, in shortcut
frame = inspect.stack()[1][0]
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/inspect.py", line 1464, in stack
return getouterframes(sys._getframe(1), context)
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/inspect.py", line 1441, in getouterframes
frameinfo = (frame,) + getframeinfo(frame, context)
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/inspect.py", line 1414, in getframeinfo
lines, lnum = findsource(frame)
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/inspect.py", line 756, in findsource
module = getmodule(object, file)
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/inspect.py", line 709, in getmodule
if ismodule(module) and hasattr(module, '__file__'):
File "/Users/bussonniermatthias/dev/ipython/IPython/utils/shimmodule.py", line 90, in __getattr__
return import_item(name)
File "/Users/bussonniermatthias/dev/ipython/IPython/utils/importstring.py", line 31, in import_item
module = __import__(package, fromlist=[obj])
File "/Users/bussonniermatthias/dev/notebook/notebook/__init__.py", line 25, in <module>
from .nbextensions import install_nbextension
File "/Users/bussonniermatthias/dev/notebook/notebook/nbextensions.py", line 227, in <module>
from jupyter_core.application import JupyterApp
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/jupyter_core/application.py", line 61, in <module>
class JupyterApp(Application):
File "/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/jupyter_core/application.py", line 105, in JupyterApp
raise DeprecationWarning('Foo')
DeprecationWarning: Foo
It also for some reason disable warnigns filters:
In [1]: import warnings
In [2]: warnings.simplefilter('error')
In [3]: import pyemma
/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/mdtraj/formats/hdf5.py:91: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
setattr(wrapper, '__argspec__', inspect.getargspec(f))
/Users/bussonniermatthias/anaconda3/lib/python3.5/site-packages/mdtraj/formats/hdf5.py:91: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() instead
<... no execeptions>
And most of errors are not from jupyter_core (mdtraj/formats/hdf5.py:91:),
The reason is that the hacks provided by msmtools are so horrible (well, they do what they have to do), that they end up importing our shims, which raise deprecation warnings.
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stefdoerr
commented on June 12, 2024
@franknoe @marscher Can you check this?
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franknoe
commented on June 12, 2024
@Carreau , could you be more specific which msmtools hacks are horrible / what should be avoided?
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takluyver
commented on June 12, 2024
I think he's referring to the stack inspection in msmtools.util.annotators. Looking up the caller is generally a dubious thing to do, but it does mostly work. However, we monkeypatch something in inspect to work around a critical bug, so it's triggering some of our code, and something is doing something odd with warning filters that makes normally hidden warnings visible.
I'll try to dig into this a bit more to understand what's going on.
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Carreau
commented on June 12, 2024
could you be more specific which msmtools hacks are horrible / what should be avoided
the "horrible" was partially written in a sarcastic way, but yes I am referring to looking up the caller.
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marscher
commented on June 12, 2024
Thanks a lot for the explanation! I think the warnings filter got mistreated and finally fixed by mdtraj/mdtraj#1030. So we can close this one now.
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franknoe
commented on June 12, 2024
I agree.
Am 09/02/16 um 17:55 schrieb Martin K. Scherer:
Thanks a lot for the explanation! I think the warnings filter got
mistreated and finally fixed by mdtraj/mdtraj#1030
mdtraj/mdtraj#1030. So we can close this one
now.—
Reply to this email directly or view it on GitHub
#71 (comment).
Prof. Dr. Frank Noe
Head of Computational Molecular Biology group
Freie Universitaet Berlin
Phone: (+49) (0)30 838 75354
Web: research.franknoe.de
Mail: Arnimallee 6, 14195 Berlin, Germany
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takluyver
commented on June 12, 2024
Great, thanks!
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Related Issues (20)
- 5.0 changelog HOT 1
- ModuleNotFoundError: No module named 'jupyter_core' HOT 3
- Current working directory not anymore in config_dir HOT 1
- 6.0: Change Default for JUPYTER_PLATFORM_DIRS to "true" HOT 3
- Deprecation warning for platform dirs affecting downstream CI tests HOT 1
- Feature request: do not prefer env path if it is not writeable HOT 6
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- FAILED tests/test_troubleshoot.py::test_troubleshoot HOT 1
- Draft7Validator(TyperError: create.<locals>.Validator.__init__() got an unexpected keyword argument 'registry' HOT 23
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- 0.5.6 causes "This event loop is already running" Error HOT 2
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