Remove offset from the GMSH physical group ids
Description
Currently, the physical group ID in GMSH are integers starting from 1 while the ones in the ini file are starting by 0. This is strange to explain in the documentation, so it's easier if we just treat them as GMSH does.
Proposal
Use physical group ID as in GMSH for the parameter tree. Additionally, it will be good if we could remove the compartments
group and specify the phyisical id in the compartment subsection. For instance
Move from this
[model.compartments]
# nucleus corresponds to the physical group 1 in the gmsh file
nucleus = 0
# cytoplasm corresponds to the physical group 2 in the gmsh file
cytoplasm = 1
# They then become available as new compartment subsections
[model.nucleus]
# Parameters for the nucleus compartment
[model.cytoplasm]
# Parameters for the nucleus compartment
To this:
# They then become available as new compartment subsections
[model.nucleus]
physical_id = 1
# Parameters for the nucleus compartment
[model.cytoplasm]
physical_id = 2
# Parameters for the nucleus compartment
How to test the implementation?
System tests get the new format
Related issues
See #