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dekoning-lab / slim-tree

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Numpy update - deprecated names #65

Closed johnpatramanis closed 1 year ago

johnpatramanis commented 1 year ago

When using -w False -fc False options, some python scripts are called. Newer versions of numpy however have changed how they name things a bit, so the scritps need to be updated in order for slim tree to run with the current versions of numpy.

I've encountered two occurances of this:

slim-tree/contactmaps/utils.py", line 93, in residue_array; a = numpy.zeros(count_residues(chain), numpy.object)

where numpy.object needs to change to numpy.object_

and

/slim-tree/contactmaps/ContactMap.py, , line 32, in calc_matrix

where numpy.bool needs to change to numpy.bool_

ebrintn commented 1 year ago

Closing for now as in protein contact maps which have been removed