Re: [cctbxbb] [git/cctbx] master: Python 3 syntax changes (790d9e315)

Folks, I expressed some surprise at this & friends however - - this is necessary to make the bootstrap process Python 3 compatible - the timetable for which said this should have been finished 9 months ago (https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap https://github.com/cctbx/cctbx_project/wiki/Python-3-roadmap) - these changes were discussed and agreed (https://github.com/cctbx/cctbx_project/pull/199 https://github.com/cctbx/cctbx_project/pull/199) The only part of this which was not approved was reverted before the request was merged (I felt that this annotation was helpful as the changes themselves go back ~6 months so people have possibly forgotten the context) Best wishes Graeme

On 21 Sep 2018, at 14:25, CCTBX commit wrote:

Repository : ssh://ws133.diamond.ac.uk/cctbx On branch : master

commit 790d9e315a2a6ae5a875ba86b461ed570c77280d Author: Markus Gerstel Date: Thu May 24 12:16:38 2018 +0100

Python 3 syntax changes

Replace the reduce(add, ...) function by sum(). reduce() is no longer in the global namespace in python 3.

790d9e315a2a6ae5a875ba86b461ed570c77280d scitbx/math/__init__.py | 34 ++++++++++++++++------------------ 1 file changed, 16 insertions(+), 18 deletions(-)

diff --git a/scitbx/math/__init__.py b/scitbx/math/__init__.py index a13405f92..49e295eb0 100644 --- a/scitbx/math/__init__.py +++ b/scitbx/math/__init__.py @@ -1,11 +1,13 @@ -from __future__ import division, absolute_import +from __future__ import absolute_import, division, print_function + +import math + from scitbx.math.ext import * import scitbx.linalg.eigensystem import scitbx.math.gaussian # implicit import from scitbx import matrix from scitbx.array_family import flex from boost import rational # implicit import -import math

gaussian_fit_1d_analytical.__doc__ = """ Fits a gaussian function to a list of points. @@ -88,16 +90,14 @@ def r3_rotation_average_rotation_matrix_from_matrices(*matrices): """

if not matrices: - raise TypeError, "Average of empty sequence" + raise TypeError("Average of empty sequence")

- import operator import scitbx.matrix

- average = reduce( - operator.add, - [ scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) - for e in matrices ] - ) + average = sum( + scitbx.matrix.col( r3_rotation_matrix_as_unit_quaternion( e ) ) + for e in matrices + )

return r3_rotation_unit_quaternion_as_matrix( average.normalize() )

@@ -111,13 +111,12 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver """

if not matrices: - raise TypeError, "Average of empty sequence" + raise TypeError("Average of empty sequence")

if maxiter < 0 or convergence <= 0: - raise ValueError, "Invalid iteration parameters" + raise ValueError("Invalid iteration parameters")

from scitbx.math import so3_lie_algebra - import operator

conv_sq = convergence * convergence norm = 1.0 / len( matrices ) @@ -125,10 +124,9 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver

for i in range( maxiter ): inverse = current.inverse() - log_diff = norm * reduce( - operator.add, - [ so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) - for m in matrices ] + log_diff = norm * sum( + so3_lie_algebra.element.from_rotation_matrix( matrix = inverse * m ) + for m in matrices )

if log_diff.norm_sq() < conv_sq: @@ -136,7 +134,7 @@ def r3_rotation_average_rotation_via_lie_algebra(matrices, maxiter = 100, conver

current *= log_diff.exponential()

- raise RuntimeError, "Iteration limit exceeded" + raise RuntimeError("Iteration limit exceeded")

def euler_angles_as_matrix(angles, deg=False): if (deg): @@ -174,7 +172,7 @@ class erf_verification(object): if (self.max_delta < delta): self.max_delta = delta if (delta > self.tolerance): - print x, expected_result, result, delta + print(x, expected_result, result, delta)

class minimum_covering_sphere_nd(object):

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