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

[Graeme Winter]

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 <diamondlightsource.jenkins at GMAIL.COM> wrote:
> 
> Repository : ssh://ws133.diamond.ac.uk/cctbx
> On branch  : master
> 
> 
> 
> commit 790d9e315a2a6ae5a875ba86b461ed570c77280d
> Author: Markus Gerstel <markus.gerstel at diamond.ac.uk>
> 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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