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

[Graeme.Winter@Diamond.ac.uk]

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)
 - these changes were discussed and agreed (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

Begin forwarded message:

From: CCTBX commit <diamondlightsource.jenkins at GMAIL.COM<mailto:diamondlightsource.jenkins at GMAIL.COM>>
Subject: [git/cctbx] master: Python 3 syntax changes (790d9e315)
Date: 21 September 2018 at 14:25:29 BST
To: <CCTBX-COMMIT at JISCMAIL.AC.UK<mailto:CCTBX-COMMIT at JISCMAIL.AC.UK>>
Reply-To: <cctbxbb at PHENIX-ONLINE.ORG<mailto:cctbxbb at PHENIX-ONLINE.ORG>>

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

________________________________


commit 790d9e315a2a6ae5a875ba86b461ed570c77280d
Author: Markus Gerstel <markus.gerstel at diamond.ac.uk<mailto: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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