remove cython from setup.py (#504)

* remove cython from setup.py * remove six and xrange -> range * update changelog
choderalab · Mar 17, 2021 · 3f2cfc0 · 3f2cfc0
1 parent fa9e701
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diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -14,7 +14,6 @@ dependencies:
   - python
   - numpy
   - scipy
-  - six
   - parmed
   - mdtraj
   - netcdf4 >=1.4.2 # after bugfix: "always return masked array by default, even if there are no masked values"

diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
@@ -20,7 +20,6 @@ requirements:
     - python
     - numpy
     - scipy
-    - six
     - openmm >=7.3.1
     - parmed
     - mdtraj

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -9,7 +9,6 @@ dependencies:
     - cython
     - numpy
     - scipy
-    - six
     - parmed
     - mdtraj
     - numpydoc

diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -1,6 +1,10 @@
 Release History
 ***************
 
+0.20.2 - Remove leftover support for python 2.7
+
+- Remove leftover `six` imports and `xrange` (`#504 <https://github.com/choderalab/openmmtools/pull/504>`_)
+
 0.20.1 - Bugfix release
 ========================================
 

diff --git a/openmmtools/scripts/test_openmm_platforms.py b/openmmtools/scripts/test_openmm_platforms.py
@@ -91,7 +91,7 @@ def format(self, record):
     n_handlers = len(logging.root.handlers)
     if n_handlers > 0:
         root_logger = logging.root
-        for i in xrange(n_handlers):
+        for i in range(n_handlers):
             root_logger.removeHandler(root_logger.handlers[0])
 
     # If this is a worker node, don't save any log file
@@ -318,7 +318,7 @@ def get_all_subclasses(cls):
        List of all subclasses of `cls`.
 
     """
-       
+
     all_subclasses = []
 
     for subclass in cls.__subclasses__():
@@ -457,7 +457,7 @@ def main():
             xml_file.write(state_xml)
             xml_file.close()
 
-            
+
             # Place forces into different force groups.
             forces = [ system.getForce(force_index) for force_index in range(system.getNumForces()) ]
             force_group_names = dict()
@@ -490,7 +490,7 @@ def main():
                     try:
                         platform = openmm.Platform.getPlatform(platform_index)
                         platform_name = platform.getName()
-                        
+
                         # Define precision models to test.
                         if platform_name == 'Reference':
                             precision_models = ['double']
@@ -505,7 +505,7 @@ def main():
                                 platform.setPropertyDefaultValue('CudaPrecision', precision_model)
                             if platform_name == 'OpenCL':
                                 platform.setPropertyDefaultValue('OpenCLPrecision', precision_model)
-                                
+
                             # Compute potential and force.
                             [platform_potential, platform_force] = compute_potential_and_force_by_force_group(system, positions, platform, force_group)
 

diff --git a/openmmtools/sobol.py b/openmmtools/sobol.py
@@ -7,7 +7,6 @@
 """
 
 import math
-from six.moves import xrange
 from numpy import *
 
 def i4_bit_hi1 ( n ):
@@ -23,7 +22,7 @@ def i4_bit_hi1 ( n ):
 #       0           0     0
 #       1           1     1
 #       2          10     2
-#       3          11     2 
+#       3          11     2
 #       4         100     3
 #       5         101     3
 #       6         110     3
@@ -84,7 +83,7 @@ def i4_bit_lo0 ( n ):
 #       0           0     1
 #       1           1     2
 #       2          10     1
-#       3          11     3 
+#       3          11     3
 #       4         100     1
 #       5         101     2
 #       6         110     1
@@ -133,7 +132,7 @@ def i4_bit_lo0 ( n ):
 
                 i = i2
         return bit
-        
+
 def i4_sobol_generate ( m, n, skip ):
 
 #*****************************************************************************80
@@ -164,7 +163,7 @@ def i4_sobol_generate ( m, n, skip ):
 #    Output, real R(M,N), the points.
 #
         r=zeros((m,n))
-        for j in xrange (1, n+1):
+        for j in range (1, n+1):
                 seed = skip + j - 2
                 [ r[0:m,j-1], seed ] = i4_sobol ( m, seed )
         return r
@@ -207,7 +206,7 @@ def i4_sobol ( dim_num, seed ):
 #
 #    Bennett Fox,
 #    Algorithm 647:
-#    Implementation and Relative Efficiency of Quasirandom 
+#    Implementation and Relative Efficiency of Quasirandom
 #    Sequence Generators,
 #    ACM Transactions on Mathematical Software,
 #    Volume 12, Number 4, pages 362-376, 1986.
@@ -216,10 +215,10 @@ def i4_sobol ( dim_num, seed ):
 #    USSR Computational Mathematics and Mathematical Physics,
 #    Volume 16, pages 236-242, 1977.
 #
-#    Ilya Sobol, Levitan, 
-#    The Production of Points Uniformly Distributed in a Multidimensional 
+#    Ilya Sobol, Levitan,
+#    The Production of Points Uniformly Distributed in a Multidimensional
 #    Cube (in Russian),
-#    Preprint IPM Akad. Nauk SSSR, 
+#    Preprint IPM Akad. Nauk SSSR,
 #    Number 40, Moscow 1976.
 #
 #  Parameters:
@@ -274,7 +273,7 @@ def i4_sobol ( dim_num, seed ):
                         1, 3, 7, 9, 5,13,13,11, 3,15, \
                         5, 3,15, 7, 9,13, 9, 1,11, 7, \
                         5,15, 1,15,11, 5, 3, 1, 7, 9 ])
-        
+
                 v[7:40,4] = transpose([ \
                         9, 3,27, \
                         15,29,21,23,19,11,25, 7,13,17, \
@@ -331,7 +330,7 @@ def i4_sobol ( dim_num, seed ):
 #
 #       Initialize the remaining rows of V.
 #
-                for i in xrange(2 , dim_num+1):
+                for i in range(2 , dim_num+1):
 #
 #       The bits of the integer POLY(I) gives the form of polynomial I.
 #
@@ -349,18 +348,18 @@ def i4_sobol ( dim_num, seed ):
 #
                         j = self.poly[i-1]
                         includ=zeros(m)
-                        for k in xrange(m, 0, -1):
+                        for k in range(m, 0, -1):
                                 j2 = math.floor ( j / 2. )
                                 includ[k-1] =  (j != 2 * j2 )
                                 j = j2
 #
 #       Calculate the remaining elements of row I as explained
 #       in Bratley and Fox, section 2.
 #
-                        for j in xrange( m+1, self.maxcol+1 ):
+                        for j in range( m+1, self.maxcol+1 ):
                                 newv = self.v[i-1,j-m-1]
                                 l = 1
-                                for k in xrange(1, m+1):
+                                for k in range(1, m+1):
                                         l = 2 * l
                                         if ( includ[k-1] ):
                                                 newv = bitwise_xor ( int(newv), int(l * self.v[i-1,j-k-1]) )
@@ -369,7 +368,7 @@ def i4_sobol ( dim_num, seed ):
 #       Multiply columns of V by appropriate power of 2.
 #
                 l = 1
-                for j in xrange( self.maxcol-1, 0, -1):
+                for j in range( self.maxcol-1, 0, -1):
                         l = 2 * l
                         self.v[0:dim_num,j-1] = self.v[0:dim_num,j-1] * l
 #
@@ -399,18 +398,18 @@ def i4_sobol ( dim_num, seed ):
                 l = 1
                 self.lastq=zeros(dim_num)
 
-                for seed_temp in xrange( int(self.seed_save), int(seed)):
+                for seed_temp in range( int(self.seed_save), int(seed)):
                         l = i4_bit_lo0 ( seed_temp )
-                        for i in xrange(1 , dim_num+1):
+                        for i in range(1 , dim_num+1):
                                 self.lastq[i-1] = bitwise_xor ( int(self.lastq[i-1]), int(self.v[i-1,l-1]) )
 
                 l = i4_bit_lo0 ( seed )
 
         elif ( self.seed_save + 1 < seed ):
 
-                for seed_temp in xrange( int(self.seed_save + 1), int(seed) ):
+                for seed_temp in range( int(self.seed_save + 1), int(seed) ):
                         l = i4_bit_lo0 ( seed_temp )
-                        for i in xrange(1, dim_num+1):
+                        for i in range(1, dim_num+1):
                                 self.lastq[i-1] = bitwise_xor ( int(self.lastq[i-1]), int(self.v[i-1,l-1]) )
 
                 l = i4_bit_lo0 ( seed )
@@ -427,7 +426,7 @@ def i4_sobol ( dim_num, seed ):
 #       Calculate the new components of QUASI.
 #
         quasi=zeros(dim_num)
-        for i in xrange( 1, dim_num+1):
+        for i in range( 1, dim_num+1):
                 quasi[i-1] = self.lastq[i-1] * self.recipd
                 self.lastq[i-1] = bitwise_xor ( int(self.lastq[i-1]), int(self.v[i-1,l-1]) )
 
@@ -571,7 +570,7 @@ def prime_ge ( n ):
 #    Input, integer N, the number to be bounded.
 #
 #    Output, integer P, the smallest prime number that is greater
-#    than or equal to N.        
+#    than or equal to N.
 #
         p = max ( math.ceil ( n ), 2 )
         while ( not isprime ( p ) ):

diff --git a/setup.py b/setup.py
@@ -1,9 +1,6 @@
 """
 Various Python tools for OpenMM.
 """
-import distutils.extension
-from Cython.Build import cythonize
-
 import sys
 from setuptools import setup, find_packages
 import versioneer