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markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂
http://pyemma.org
GNU Lesser General Public License v3.0
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Errors in the pyemma jupyternotebook tutorials #1492

Closed e-richter closed 3 years ago

e-richter commented 3 years ago

Hi all, during my work with pyemma and looking into the documentation and jupyter notebook tutorials I've seen that there are error messages on the website. For example here: http://emma-project.org/latest/tutorials/notebooks/04-msm-analysis.html#, but also in later chapters.

Cheers, Emilius

clonker commented 3 years ago

Hi, thank you for reporting this! I need to check the serialization routines.

thempel commented 3 years ago

Does this error occur in the online version of the PyEMMA documentation (which is the topic of this issue) or just in your google colab?

If I understand this right, your error is ValueError: Object arrays cannot be loaded when allow_pickle=False. Have you tried just setting that flag?

data = np.load('adw_us.npz', encoding='latin1', allow_pickle=True)
clonker commented 3 years ago

Hi @andresilvapimentel, could you be a bit more specific than did not work? Also I suspect this is not really an issue related to PyEMMA but rather related to your general setup and NumPy(version). In any case, I could reproduce the error and subsequently fix it by adding the allow_pickle=True keyword argument. Please, try again and perhaps also restart your notebook kernel. For the future we would appreciate if you add a new issue rather than hijacking an existing one, helps us keeping everything organized :+1:

stale[bot] commented 3 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.