MAINT: cluster: clean up the use of malloc() in the function identify_swaps(). #10027
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In the function identify_swaps() in _optimal_leaf_ordering.pyx, the variables u_clusters, m_clusters, w_clusters and k_clusters are each malloc'ed as malloc(sizeof(int) * 2). For small fixed-size arrays such as these, it makes more sense to declare them as arrays on the stack and avoid malloc() completely.
Changes in the function identify_swaps() in _optimal_leaf_ordering.pyx: * The code was malloc'ing and freeing arrays in an inner loop, but the size of the arrays was the same in each iteration of the inner loop. The malloc() and free() calls have been moved out to the level where the variables that define the size are set. * A MemoryError is raised if any of the malloc() calls fail. * The types of the numpy arrays used to create the memoryviews `swap_status` and `must_swap` was changed from np.int32 to np.intc, to match the declaration of the memoryviews (int[:, :, :] and int[:], respectively).
WarrenWeckesser
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LGTM, merged. Thanks @WarrenWeckesser |
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This addresses one of the modules with unchecked malloc() calls listed in #9999.
The commit messages explain the details of the changes.