Got further with a simpler project that I own the rights too:
$ padne -d solve BP1.kicad_pro pdn.padne
2025-10-20 14:52:15,203 - padne.cli - DEBUG - Parsed arguments: Namespace(debug=True, command='solve', kicad_pro_file=PosixPath('BP1.kicad_pro'), output_file=PosixPath('pdn.padne'), mesh_angle=20.0, mesh_size=0.6, variable_density_min_distance=0.5, variable_density_max_distance=3.0, variable_size_maximum_factor=3.0, distance_map_quantization=1.0)
2025-10-20 14:52:15,203 - padne.cli - INFO - Loading KiCad project: BP1.kicad_pro
2025-10-20 14:52:15,203 - padne.kicad - INFO - Plotting layers to gerbers
2025-10-20 14:52:17,936 - padne.kicad - WARNING - Clipped geometry for layer F.Cu is empty after applying outline
2025-10-20 14:52:17,936 - padne.kicad - WARNING - Clipped geometry for layer B.Cu is empty after applying outline
2025-10-20 14:52:17,936 - padne.kicad - WARNING - Clipped geometry for layer In1.Cu is empty after applying outline
2025-10-20 14:52:17,936 - padne.kicad - WARNING - Clipped geometry for layer In2.Cu is empty after applying outline
2025-10-20 14:52:18,052 - padne.kicad - INFO - Processing vias and through hole pads
2025-10-20 14:52:18,081 - padne.kicad - WARNING - SMD pad Endpoint(designator='J1', pad='1') connection point at (156.25, 103.765) on layer F.Cu falls outside the layer geometry (likely in a hole). Skipping this connection point.
2025-10-20 14:52:18,081 - padne.kicad - WARNING - SMD pad Endpoint(designator='J1', pad='2') connection point at (156.25, 98.815) on layer F.Cu falls outside the layer geometry (likely in a hole). Skipping this connection point.
2025-10-20 14:52:18,081 - padne.kicad - WARNING - SMD pad Endpoint(designator='J1', pad='3') connection point at (153.71, 103.765) on layer F.Cu falls outside the layer geometry (likely in a hole). Skipping this connection point.
2025-10-20 14:52:18,081 - padne.kicad - WARNING - SMD pad Endpoint(designator='J1', pad='4') connection point at (153.71, 98.815) on layer F.Cu falls outside the layer geometry (likely in a hole). Skipping this connection point.
2025-10-20 14:52:18,081 - padne.kicad - WARNING - SMD pad Endpoint(designator='J1', pad='5') connection point at (151.17, 103.765) on layer F.Cu falls outside the layer geometry (likely in a hole). Skipping this connection point.
2025-10-20 14:52:18,081 - padne.kicad - WARNING - SMD pad Endpoint(designator='J1', pad='6') connection point at (151.17, 98.815) on layer F.Cu falls outside the layer geometry (likely in a hole). Skipping this connection point.
2025-10-20 14:52:18,082 - padne.kicad - WARNING - SMD pad Endpoint(designator='J1', pad='7') connection point at (153.71, 88.2625) on layer F.Cu falls outside the layer geometry (likely in a hole). Skipping this connection point.
2025-10-20 14:52:18,225 - padne.kicad - INFO - Creating networks from specifications
Traceback (most recent call last):
File "/home/ubuntu/.local/share/pipx/venvs/padne/lib/python3.13/site-packages/padne/cli.py", line 181, in wrapper
return func(*args, **kwargs)
File "/home/ubuntu/.local/share/pipx/venvs/padne/lib/python3.13/site-packages/padne/cli.py", line 221, in do_solve
prob = padne.kicad.load_kicad_project(args.kicad_pro_file)
File "/home/ubuntu/.local/share/pipx/venvs/padne/lib/python3.13/site-packages/padne/kicad.py", line 1698, in load_kicad_project
network = lumped_spec.construct(pad_index, layer_dict)
File "/home/ubuntu/.local/share/pipx/venvs/padne/lib/python3.13/site-packages/padne/kicad.py", line 685, in construct
main_source_elements = self._construct_source(p_connections[0], n_connections[0])
~~~~~~~~~~~~~^^^
IndexError: list index out of range
list index out of range
Let me know if you want to investigate. No dramas if you don’t.