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open2c / cooltools

The tools for your .cool's
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adaptive coarsegrain returns numpy attribute error #504

Closed danobaji closed 6 months ago

danobaji commented 8 months ago

hi i'm currently running into issues while trying to follow the visualization tutorial notebook with my own data at the "smoothing and interpolation" part. Here's what i'm running:

start,end = 15_850_000, 16_850_000

region=(chrom,start,end)

extents = (start, end, end, start)

cg = adaptive_coarsegrain(ca1200_rep2.matrix(balance=True).fetch(region),
                              ca1200_rep2.matrix(balance=False).fetch(region),
                              cutoff=3, max_levels=8)

cgi = interp_nan(cg)

and the error i get:

AttributeError: module 'numpy' has no attribute 'int'. np.int was a deprecated alias for the builtin int. To avoid this error in existing code, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at

since i'm not explicitly calling np.int, i assume it's been called by the adaptive_coarsegrain method, so i'm not sure how i can fix this. any help is appreciated!