JOSS Review: Example Notebook 10_2D_Underworld_conversion.ipynb

[kujaku11]

Running Jupyter notebook from examples/10_2D_Underworld_Conversion.ipynb produces the following error in the 3rd cell from the bottom [using pip install --> v0.3 and notebooks from main branch]:

The deformation related conductivity for the material Sediment_0 is calculated.
The deformation related conductivity for the material Sediment_1 is calculated.
The deformation related conductivity for the material Sediment_1 is calculated.
The deformation related conductivity for the material Sediment_1 is calculated.
The deformation related conductivity for the material Sediment_1 is calculated.
The deformation related conductivity for the material Sediment_1 is calculated.
The deformation related conductivity for the material Sediment_1 is calculated.

RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "\Anaconda3\envs\pide\lib\multiprocessing\pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "\Anaconda3\envs\pide\lib\multiprocessing\pool.py", line 48, in mapstar
return list(map(*args))
File "k\Anaconda3\envs\pide\lib\site-packages\pide\model.py", line 287, in run_deform2cond
c, str_dcy, cnd_dcy, msft = plastic_strain_2_conductivity(strain = p_strain[index_number[0],index_number[1]],low_cond = background_cond[index_number[0],index_number[1]],
File "\Anaconda3\envs\pide\lib\site-packages\pide\geodyn\deform_cond.py", line 184, in plastic_strain_2_conductivity
cond_calced,strain_decay_factor,conductivity_decay_factor,misfit = fit(method = scipy_methods[0], init_start = True, run_idx = 0,
File "\Anaconda3\envs\pide\lib\site-packages\pide\geodyn\deform_cond.py", line 127, in fit
params, params_cov = curve_fit(func, strains, conds, method = method, sigma = cond_err)
File "\Anaconda3\envs\pide\lib\site-packages\scipy\optimize_minpack_py.py", line 925, in curve_fit
ydata = np.asarray_chkfinite(ydata, float)
File "\Anaconda3\envs\pide\lib\site-packages\numpy\lib\function_base.py", line 630, in asarray_chkfinite
raise ValueError(
ValueError: array must not contain infs or NaNs

[sinanozaydin]

The issues should be resolved in the latest version at the github repo (post-joss branch).