Make separate (standalone) modules for each of the model types
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AuguB commented
For example, our tree could look something like this:
pcntoolkit
|----__init__.py
|----normative.py
|----normative_utils.py
|----model
| |----__init__.py
| |----BLR <--- Each model module is standalone
| |----__init__.py
| |----blr.py
| |----blr_utils.py
| |----GPR
| |----__init__.py
| |----gpr.py
| |----gpr_utils.py
| |----cov.py
| |----HBR
| |----__init__.py
| |----hbr.py
| |----hbr_utils.py
| |----parambuilder.py
| |----prior.py
| |----parameterization.py
| |----...
|----normative_model
| |----__init__.py
| |----norm_base.py
| |----norm_blr.py
| |----norm_gpr.py
| |----norm_hbr.py
| |----...
|----dataio
| |----__init__.py
| |----dataloader.py
| |----dataloader_utils.py
|----preprocessing
| |----basis_expansion.py
| |----scaler.py