msdnetInstructions.txt

Msdnet version 1.0.0 needs the following fix in store.py (when installed in a conda environment, this file can be found in miniconda3/envs/<NAMEOFENVIRONMENT>/lib/python3.7/site-packages/msdnet):

The function is:

def __store_grp_in_dict(grp, dct):
    for key, val in grp.attrs.items():
        dct[key] = val.item()
    
    for key, val in grp.items():
        if isinstance(val, h5py.Group):
            newdct = {}
            __store_grp_in_dict(val, newdct)
            dct[key] = newdct
        elif isinstance(val, h5py.Dataset):
            dct[key] = val[:]
            
but should become:

def __store_grp_in_dict(grp, dct):
    for key, val in grp.attrs.items():
        try:
            dct[key] = val.item()
        except ValueError: # Fix for old network files with python lists in attributes
            dct[key] = val
    
    for key, val in grp.items():
        if isinstance(val, h5py.Group):
            newdct = {}
            __store_grp_in_dict(val, newdct)
            dct[key] = newdct
        elif isinstance(val, h5py.Dataset):
            dct[key] = val[:]