search

wiheto / teneto

Temporal Network Tools
GNU General Public License v3.0
85 stars 26 forks source link

AttributeError: module 'sqlalchemy.util' has no attribute 'dependencies' after importing TemporalNetworks() #77

Open Son17 opened 3 years ago

Son17 commented 3 years ago

Hi,

I am getting the below error when running the following:

!pip install teneto (on Google Cloud Platform JupyterLab in a Python 3 environment) from teneto import TemporalNetwork tnet = TemporalNetwork()

image

Any idea how to resolve this? Many thanks!

wiheto commented 3 years ago

This related to us wanting to remove the neuroimaging dependencies but havn't done so yet.

For now, if you install pybids, i.e. pip install pybids this should go away. Let me know if it does not.

Son17 commented 3 years ago

Thank you for the fast response. Unfortunately, I continue to get the same error, even after installing pybids. I should also add that this only happens in JupyterLabs on GCP. It does not happen in Google Colab or on my local machine (all Python 3 environments), and for the latter two, I do not need to install pybids for teneto to work.

I was hoping to make teneto work on JupyterLabs as I need a high-RAM machine.

Is there anything else I could try? Many thanks.

wiheto commented 3 years ago

You'll have to look up configuring sqlalchemy on GCP, as the issue is there.

However, if you are not using the neuroimaging functions, you can remove the importing of TenetoBIDS in the relevant places.

74 Also please note that there is currently a big speed problem with teneto that I am trying to solve. This is about any function that uses the shortest paths especially (and will be even with high ram).

And fixing the importing structure to not import bids is on the todo list.