PendingDeprecationWarning: numpy matrix

[Allen Lawrence]

Having just updated to numpy 1.15, `canonInterface.format_matrix` now triggers the following error:

PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.

  return matrix(data, dtype=dtype, copy=False)

This is caused by a numpy.matrix conversion in `format_matrix`:

def format_matrix(matrix, format='dense'):

    ''' Returns the matrix in the appropriate form,

        so that it can be efficiently loaded with our swig wrapper

    '''

    if (format == 'dense'):

        # Ensure is 2D.

        matrix = np.atleast_2d(matrix)

        return np.asfortranarray(matrix)

    elif(format == 'sparse'):

        return scipy.sparse.coo_matrix(matrix)

    elif(format == 'scalar'):

        return np.asfortranarray(np.matrix(matrix))

    else:

        raise NotImplementedError()

This doesn't break anything (only a warning), I just mention I should post it here as a heads up.

[Steven Diamond]

I appreciate the heads up! It's good to know we need to take care of this.