Replace np.flatnonzero with np.nonzero()[0] for faster 1-D index retrieval

[SaFE-APIOpt]

RefiNA/mnc.py

Line 33 in 532dd7e

one_hop_neighbor = np.flatnonzero(a)

Current code:

a = np.array(adj1[i, :])
one_hop_neighbor = np.flatnonzero(a)

Proposed replacement:

a = np.array(adj1[i, :])
one_hop_neighbor = np.nonzero(a)[0]

np.flatnonzero(a) is essentially a convenience wrapper that calls np.nonzero(a) and then flattens the result with .ravel(). When a is already a 1-D array, this extra flattening step is unnecessary. In contrast, np.nonzero(a)[0] directly returns the non-zero indices for the 1-D case, making it more efficient. Benchmarks confirm that np.nonzero(a)[0] runs faster while producing exactly the same output as np.flatnonzero(a) in this context.