multinetlab-amsterdam / network_tda_tutorial Goto Github PK

Describe the bug
Use the requirements.txt from the GitHub, inside the anaconda environment with python version 3.10.9, during the installation, encountered many "subprocess-exited-with-error" during pip install -r requirements.txt.

So I created a new requirements.txt file only use the libraries list in the suggested requirements inside the README file as below.
But still encountered the same installation errors.
numpy==1.18.5
matplotlib==3.3.2
meshio==4.0.16
seaborn==0.11.0
pandas==1.1.3
networkx==2.4
nxviz==0.6.2
community==0.13
gudhi==3.4.1
plotly==4.6.0
scikit-learn==0.24.1
scipy==1.5.0
jupyterlab==1.2.0

Screenshots

Desktop (please complete the following information):
system:
Distributor ID: Ubuntu
Description: Ubuntu 20.04.3 LTS
Release: 20.04
Codename: focal

Please help me on the installation issues and looking forward to your reply. Thank you very much.

Xin

I got the following error while running HCP_Data_Vis.py of 2-visualization-3d Jupyter notebook, on my macbook with macOS High Sierra 10.13.6

3. Creating 3D visualisations with Plotly
   First, we need to import the necessary backup script. Then, it is possible to use a list of values for most of the nodal metrics, e.g., centralities, etc.
    
   %run "/Users/oswaldoartiles/networkTDA/network_TDA_tutorial/Background Scripts/HCP_Data_Vis.py"

ValueError Traceback (most recent call last)
~/networkTDA/network_TDA_tutorial/Background Scripts/HCP_Data_Vis.py in
1397
1398 ## Create gray shell
-> 1399 brain_mesh = meshio.read(path_brainobj) # Reading a brain.obj file
1400 brain_trace = shell_brain(brain_mesh)
1401 trace1, _, _, _ = dictpos(areas, path_pos) # Transparent shell

~/anaconda3/lib/python3.7/site-packages/meshio/_helpers.py in read(filename, file_format)
67 raise ReadError(msg)
68
---> 69 return reader_mapfile_format
70
71

~/anaconda3/lib/python3.7/site-packages/meshio/obj/_obj.py in read(filename)
17 def read(filename):
18 with open_file(filename, "r") as f:
---> 19 mesh = read_buffer(f)
20 return mesh
21

~/anaconda3/lib/python3.7/site-packages/meshio/obj/_obj.py in read_buffer(f)
91 )
92
---> 93 return Mesh(points, cells, point_data=point_data)
94
95

~/anaconda3/lib/python3.7/site-packages/meshio/_mesh.py in init(self, points, cells, point_data, cell_data, field_data, point_sets, cell_sets, gmsh_periodic, info)
60 if len(self.point_data[key]) != len(self.points):
61 raise ValueError(
---> 62 f"len(points) = {len(points)}, "
63 f'but len(point_data["{key}"]) = {len(point_data[key])}'
64 )

ValueError: len(points) = 54284, but len(point_data["obj:vn"]) = 48585