Replace numpy.take with direct indexing for better performance and readability

[SaFE-APIOpt]

ecell4/ecell4/mca/cc.py

Line 12 in f38da95

reduced_matrix = numpy.take(stoichiometry, independent_list, 0)

Hi, I noticed the following line in your code:
reduced_matrix = numpy.take(stoichiometry, independent_list, 0)
This operation can be simplified and made more efficient by directly using NumPy's native indexing, which internally invokes NumPy's optimized getitem() method. Direct indexing is the most intuitive, common, and performant approach in NumPy.

Suggested replacement:
reduced_matrix = stoichiometry[independent_list, :]
Consider updating this line for improved code clarity and efficiency.

Thanks!