TypeError: np.matrix is not supported. Please convert to a numpy array with np.asarray.

[PengleiGao]

Hi, when I use the package, I have the following issues:
code is:
d1 = np.random.rand(100,10)
d2 = np.random.rand(100,10)
d3 = np.random.rand(100,10)
data = [d1,d2,d3]
params = pyrea.parea_2_genetic(data, k_min=2, k_max=5)

it returns the error:
TypeError Traceback (most recent call last)
Cell In[14], line 1
----> 1 params_hierarchical = pyrea.parea_1_genetic(data, k_min=2, k_max=5, k_final=3, n_generations=10, n_population=10)

File ~/anaconda3/envs/eval/lib/python3.10/site-packages/pyrea/core.py:833, in parea_1_genetic(data, k_min, k_max, k_final, n_population, n_generations)
830 stats.register("max", np.max)
832 # Run the genetic algorithm
--> 833 pop, log = algorithms.eaSimple(population, toolbox, cxpb=0.7, mutpb=0.2, ngen=n_generations, stats=stats, halloffame=hall_of_fame, verbose=True)
835 print(f"\nSummary:\n{log}")
837 return hall_of_fame[0]

File ~/anaconda3/envs/eval/lib/python3.10/site-packages/deap/algorithms.py:151, in eaSimple(population, toolbox, cxpb, mutpb, ngen, stats, halloffame, verbose)
149 invalid_ind = [ind for ind in population if not ind.fitness.valid]
150 fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
--> 151 for ind, fit in zip(invalid_ind, fitnesses):
152 ind.fitness.values = fit
154 if halloffame is not None:

File ~/anaconda3/envs/eval/lib/python3.10/site-packages/pyrea/core.py:795, in parea_1_genetic..evaluate(individual)
792 with warnings.catch_warnings():
793 warnings.simplefilter("ignore")
--> 795 sil = parea_1(data,
796 individual[0],
797 individual[1],
...
839 xp, is_array_api_compliant = get_namespace(array)
841 # store reference to original array to check if copy is needed when
842 # function returns
TypeError: np.matrix is not supported. Please convert to a numpy array with np.asarray.

Do you know how to fix it?
Thanks.

[mdbloice]

Hi @PengleiGao

yeah this is because I used the numpy.matrix class and this now deprecated in newer versions of NumPy. I would need to change Pyrea's code to use the numpy.array class instead. Which is on the agenda, and I will do so in the coming days actually. Once I have made the changes, I will update the package and let you know.