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ysig / GraKeL

A scikit-learn compatible library for graph kernels
https://ysig.github.io/GraKeL/
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GraphHopper error #45

Closed paulamartingonzalez closed 4 years ago

paulamartingonzalez commented 4 years ago

While running your library in a HPC (I have a singularity image with the required python packages) I am encountering the following error:

Traceback (most recent call last): File "MI.py", line 163, in K_GH = gh_kernel.fit_transform(Gs) File "/opt/conda/lib/python3.6/site-packages/grakel/kernels/kernel.py", line 194, in fit_transform self.fit(X) File "/opt/conda/lib/python3.6/site-packages/grakel/kernels/kernel.py", line 123, in fit self.X = self.parse_input(X) File "/opt/conda/lib/python3.6/site-packages/grakel/kernels/graph_hopper.py", line 206, in parse_input occ_p, des_p = od_vectors_dag(A_cc, D_cc) File "/opt/conda/lib/python3.6/site-packages/grakel/kernels/graph_hopper.py", line 407, in od_vectors_dag np.matlib.repmat(np.hstack([0, occ[i, :-1]]), edges_starting_at_ith.shape[0], AttributeError: module 'numpy' has no attribute 'matlib'

Doing a quick search in stack overflow I wonder if there is the need to explicitly import numpy.matlib? I haven't had this issue while running the file locally. Thanks in advance!

paulamartingonzalez commented 4 years ago

After some time debugging, just realised that the correct way to install it is pip install grakel (I was using pip install grakel-dev) so I assume you already fixed this in the later editions. Thanks!