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pwollstadt / IDTxl

The Information Dynamics Toolkit xl (IDTxl) is a comprehensive software package for efficient inference of networks and their node dynamics from multivariate time series data using information theory.
http://pwollstadt.github.io/IDTxl/
GNU General Public License v3.0
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setup_hde_fast_embedding.py trying to save to nonexistent folder #101

Open kdembny opened 1 year ago

kdembny commented 1 year ago

In order to use cython there are instructions available for using the code: python3 setup_hde_fast_embedding.py build_ext --inplace to achieve this. However, this script attempts to create a file that saves into a folder idtxl/, which does not exist in the folder you run the script from. The error reads as follows: error: could not create 'idtxl/hde_fast_embedding.cpython-39-x86_64-linux-gnu.so': No such file or directory As a patch, one can make a file within idtxl also called idtxl and move the file created by the script up one level after the conclusion of the script, but as the code exists, it can't complete.

pwollstadt commented 1 year ago

Hi, we are aware that there are some issues with the installation of the python module (there is also a Wiki page on this and see also issue #86). However, I could not replicate the error regarding the creation of the directory. Did you call python3 setup_hde_fast_embedding.py build_ext --inplace from within the IDTxl/idtxl folder?

kdembny commented 1 year ago

Yes, that's how I called it. I'm ran it from Ubuntu on Linux and had to create an idtxl folder within IDTxl/idtxl.

All the best,

Kate

On Sun, Sep 17, 2023 at 5:46 AM Patricia Wollstadt @.***> wrote:

Hi, we are aware that there are some issues with the installation of the python module (there is also a Wiki page https://github.com/pwollstadt/IDTxl/wiki/Installation-of-history-dependence-(HDE)-estimator on this and see also issue #86 https://github.com/pwollstadt/IDTxl/issues/86). However, I could not replicate the error regarding the creation of the directory. Did you call python3 setup_hde_fast_embedding.py build_ext --inplace from within the IDTxl/idtxl folder?

— Reply to this email directly, view it on GitHub https://github.com/pwollstadt/IDTxl/issues/101#issuecomment-1722448825, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFI5ZZHBO6PQ4WEOFT7DUYDX23IHHANCNFSM6AAAAAA42GFT4I . You are receiving this because you authored the thread.Message ID: @.***>

-- -- Kate Dembny (she/her/hers https://www.mypronouns.org/) MD/PhD Student | Entering Class of 2020 Netoff https://neuralnetoff.umn.edu/ and Herman-Darrow https://www.hermandarrowlab.com/ Labs Medical Scientist Training Program Department of Biomedical Engineering University of Minnesota