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Fix Numpy-related deprecation warnings

Viacheslav Ostroukh requested to merge fix/ndarray_deprecation_warnings into stable

In several places of code, Numpy arrays are created from lists of arrays with mismatched shape. This is a deprecated behaviour and will be a failure in future. This MR aligns the shape, so that warnings are not emitted.

Part of this MR is a fixer for master by @anton-akhmerov

Edited by Viacheslav Ostroukh

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