Remove np.matrix dependency#213
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Yenaled merged 3 commits intopachterlab:developmentfrom Mar 8, 2026
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As most of us may know,
numpyis slowly deprecating thenp.matrixclass. However, the package still has one dependency on this class inreport_matrix.ipynb, andscikit-learnis also in the process of doing it (see scikit-learn/scikit-learn#20165). This PR causes thepca.fit_transform's input to switch fromnp.matrix(the output ofcsr_matrix.todense()) tonp.ndarray(the output of csr_matrix.toarray()`)However, it must be noted that
pca.fit_transform()may have slightly different results depending on its input beingnp.matrixornp.ndarray, see scikit-learn/scikit-learn#18941. I guess the difference is small enough to matter, but I guess you may think about it a bit.This is my first PR in the past 5 years, so bear with me.