kanzure · kanzure · Sep 19, 2012
diff --git a/cad/plugins/NanoDynamics-1/TranslateStruts.py b/cad/plugins/NanoDynamics-1/TranslateStruts.py
@@ -32,7 +32,7 @@
 import sys
 import math
 
-from Numeric import array
+from numpy.oldnumeric import array
 from LinearAlgebra import inverse
 
 # a nice upgrade would be to read values selected from the NE1 history

diff --git a/cad/src/atombase.pyx b/cad/src/atombase.pyx
@@ -9,7 +9,7 @@ make atombase.so ; valgrind python atombasetests.py >& OUCH; less OUCH
 __author__ = "Will"
 
 import types
-import Numeric
+import numpy.oldnumeric
 from foundation.inval import InvalMixin
 
 cdef extern from "atombasehelp.c":

diff --git a/cad/src/cnt/commands/EditNanotube/EditNanotube_GraphicsMode.py b/cad/src/cnt/commands/EditNanotube/EditNanotube_GraphicsMode.py
@@ -18,7 +18,7 @@
 Created 2008-03-10 from copy of DnaSegment_GraphicsMode.py
 Recreated 2008-04-02 from copy of DnaSegment_GraphicsMode.py
 """
-from Numeric import dot
+from numpy.oldnumeric import dot
 from PyQt4.Qt import QMouseEvent
 
 from cnt.commands.BuildNanotube.BuildNanotube_GraphicsMode import BuildNanotube_GraphicsMode

diff --git a/cad/src/cnt/model/NanotubeParameters.py b/cad/src/cnt/model/NanotubeParameters.py
@@ -16,7 +16,7 @@
 
 from math import sin, cos, pi
 from math import atan2
-from Numeric import dot, argmax, argmin, sqrt
+from numpy.oldnumeric import dot, argmax, argmin, sqrt
 
 from model.chem import Atom
 from model.bonds import bond_atoms

diff --git a/cad/src/command_support/GraphicsMode.py b/cad/src/command_support/GraphicsMode.py
@@ -23,7 +23,7 @@
 """
 
 import math # just for pi
-from Numeric import exp
+from numpy.oldnumeric import exp
 
 from PyQt4.Qt import Qt
 from PyQt4.Qt import QMenu

diff --git a/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py b/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py
@@ -29,7 +29,7 @@
 
 
 import math
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from OpenGL.GL import GL_FALSE
 from OpenGL.GL import glDepthMask

diff --git a/cad/src/commands/BuildCrystal/BuildCrystal_Command.py b/cad/src/commands/BuildCrystal/BuildCrystal_Command.py
@@ -17,7 +17,7 @@
 """
 
 import math # only for pi
-from Numeric import size, dot, sqrt, floor
+from numpy.oldnumeric import size, dot, sqrt, floor
 
 from OpenGL.GL import GL_COLOR_LOGIC_OP
 from OpenGL.GL import GL_DEPTH_TEST

diff --git a/cad/src/commands/BuildCrystal/CrystalShape.py b/cad/src/commands/BuildCrystal/CrystalShape.py
@@ -39,7 +39,7 @@
 keep that member around in CSDL.
 """
 
-from Numeric import dot, floor
+from numpy.oldnumeric import dot, floor
 
 from geometry.VQT import vlen, V
 from OpenGL.GL import glNewList, glEndList, glCallList

diff --git a/cad/src/commands/Extrude/extrudeMode.py b/cad/src/commands/Extrude/extrudeMode.py
@@ -38,7 +38,7 @@
 import foundation.env as env
 import foundation.changes as changes
 
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from OpenGL.GL import GL_CW
 from OpenGL.GL import glFrontFace

diff --git a/cad/src/commands/Move/Move_GraphicsMode.py b/cad/src/commands/Move/Move_GraphicsMode.py
@@ -12,7 +12,7 @@
 """
 
 import math
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from PyQt4.Qt import QMouseEvent
 from PyQt4.Qt import Qt

diff --git a/cad/src/commands/Rotate/RotateChunks_GraphicsMode.py b/cad/src/commands/Rotate/RotateChunks_GraphicsMode.py
@@ -19,7 +19,7 @@
 """
 from utilities import debug_flags
 import math
-from Numeric import dot, sign
+from numpy.oldnumeric import dot, sign
 import foundation.env as env
 from utilities.Log import redmsg
 from utilities.debug import print_compact_stack

diff --git a/cad/src/commands/Select/Select_GraphicsMode.py b/cad/src/commands/Select/Select_GraphicsMode.py
@@ -50,7 +50,7 @@
                           related methods into this class from selectMode.py
 
 """
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from OpenGL.GL import GL_CLIP_PLANE0
 from OpenGL.GL import GL_DEPTH_COMPONENT

diff --git a/cad/src/commands/Translate/TranslateChunks_GraphicsMode.py b/cad/src/commands/Translate/TranslateChunks_GraphicsMode.py
@@ -16,7 +16,7 @@
 """
 from utilities import debug_flags
 import math
-from Numeric import dot
+from numpy.oldnumeric import dot
 import foundation.env as env
 from utilities.debug import print_compact_traceback
 from geometry.VQT import V, A, vlen, norm

diff --git a/cad/src/dna/commands/BuildDna/BuildDna_GraphicsMode.py b/cad/src/dna/commands/BuildDna/BuildDna_GraphicsMode.py
@@ -13,7 +13,7 @@
 from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
 from model.chem import Atom
 from model.bonds import Bond
-from Numeric import dot
+from numpy.oldnumeric import dot
 from PyQt4.Qt import QMouseEvent
 from geometry.VQT import V, Q, A, norm, vlen
 from commands.Select.Select_GraphicsMode import DRAG_STICKINESS_LIMIT

diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py b/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py
@@ -41,7 +41,7 @@
 
 from geometry.VQT import V, Veq, vlen
 from geometry.VQT import cross, norm
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from utilities.constants  import gensym
 from utilities.Log        import redmsg

diff --git a/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py b/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py
@@ -26,7 +26,7 @@
 from geometry.VQT import  V
 from geometry.VQT import  vlen
 from geometry.VQT import  norm
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from exprs.State_preMixin import State_preMixin
 from exprs.attr_decl_macros import Instance, State

diff --git a/cad/src/dna/commands/MakeCrossovers/CrossoverSite_Marker.py b/cad/src/dna/commands/MakeCrossovers/CrossoverSite_Marker.py
@@ -38,7 +38,7 @@
 from dna.commands.MakeCrossovers.MakeCrossovers_Handle import MakeCrossovers_Handle
 
 from geometry.VQT import orthodist, norm, vlen, angleBetween
-from Numeric import dot
+from numpy.oldnumeric import dot
 from model.bonds import bond_direction
 
 
@@ -552,4 +552,4 @@ def get_final_crossover_atoms_dict(self):
         return self._final_crossover_atoms_dict
 
     def get_final_crossover_pairs(self):
-        return self.final_crossover_pairs_dict.values()
+        return self.final_crossover_pairs_dict.values()
diff --git a/cad/src/dna/commands/MultipleDnaSegmentResize/MultipleDnaSegmentResize_EditCommand.py b/cad/src/dna/commands/MultipleDnaSegmentResize/MultipleDnaSegmentResize_EditCommand.py
@@ -15,7 +15,7 @@
 2008-05-09 - 2008-05-14 Created / modified.
 
 """
-from Numeric import dot
+from numpy.oldnumeric import dot
 from geometry.VQT import V, norm, vlen
 from utilities.constants import applegreen
 
@@ -656,4 +656,4 @@ def _determine_numberOfBasePairs_to_change(self):
 
         return numberOfBasesToAddOrRemove
 
-
+
diff --git a/cad/src/dna/generators/B_Dna_PAM3_Generator.py b/cad/src/dna/generators/B_Dna_PAM3_Generator.py
@@ -30,7 +30,7 @@
 LEFT_HANDED  =  1
 
 from geometry.VQT import norm
-from Numeric import dot
+from numpy.oldnumeric import dot
 from dna.generators.B_Dna_Generator import B_Dna_Generator
 
 class B_Dna_PAM3_Generator(B_Dna_Generator):
@@ -375,4 +375,4 @@ def _create_atomLists_for_regrouping(self, dnaGroup):
                 elif atom.element.symbol in ('Ax3', 'Ae3'):
                     _axis_list.append(atom)
 
-        return (_strandA_list, _strandB_list, _axis_list)
+        return (_strandA_list, _strandB_list, _axis_list)
diff --git a/cad/src/dna/generators/B_Dna_PAM3_SingleStrand_Generator.py b/cad/src/dna/generators/B_Dna_PAM3_SingleStrand_Generator.py
@@ -29,7 +29,7 @@
 """
 
 from geometry.VQT import Q, norm, vlen, cross
-from Numeric import dot
+from numpy.oldnumeric import dot
 from utilities.debug import print_compact_stack
 from model.bonds import bond_at_singlets
 

diff --git a/cad/src/dna/generators/B_Dna_PAM5_Generator.py b/cad/src/dna/generators/B_Dna_PAM5_Generator.py
@@ -51,7 +51,7 @@
 
 from geometry.VQT import V, Q, norm, cross  
 from geometry.VQT import  vlen
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from utilities.debug import print_compact_stack
 from model.bonds import bond_at_singlets

diff --git a/cad/src/dna/generators/Dna_Generator.py b/cad/src/dna/generators/Dna_Generator.py
@@ -52,7 +52,7 @@
 
 from geometry.VQT import V, Q, norm, cross  
 from geometry.VQT import  vlen
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from utilities.debug import print_compact_stack
 from model.bonds import bond_at_singlets

diff --git a/cad/src/dna/generators/Z_Dna_Atomistic_Generator.py b/cad/src/dna/generators/Z_Dna_Atomistic_Generator.py
@@ -51,7 +51,7 @@
 
 from geometry.VQT import V, Q, norm, cross  
 from geometry.VQT import  vlen
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from utilities.debug import print_compact_stack
 from model.bonds import bond_at_singlets

diff --git a/cad/src/dna/generators/Z_Dna_Generator.py b/cad/src/dna/generators/Z_Dna_Generator.py
@@ -51,7 +51,7 @@
 
 from geometry.VQT import V, Q, norm, cross  
 from geometry.VQT import  vlen
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from utilities.debug import print_compact_stack
 from model.bonds import bond_at_singlets

diff --git a/cad/src/dna/generators/Z_Dna_PAM5_Generator.py b/cad/src/dna/generators/Z_Dna_PAM5_Generator.py
@@ -51,7 +51,7 @@
 
 from geometry.VQT import V, Q, norm, cross  
 from geometry.VQT import  vlen
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from utilities.debug import print_compact_stack
 from model.bonds import bond_at_singlets

diff --git a/cad/src/dna/model/DnaLadder.py b/cad/src/dna/model/DnaLadder.py
@@ -46,7 +46,7 @@
 undoable state), and is not stored in the mmp file.
 """
 
-from Numeric import dot
+from numpy.oldnumeric import dot
 from geometry.VQT import cross
 
 from model.elements import Pl5

diff --git a/cad/src/dna/model/outtakes/PositionInWholeChain-outtakes.py b/cad/src/dna/model/outtakes/PositionInWholeChain-outtakes.py
@@ -1,4 +1,4 @@
-from Numeric import sign
+from numpy.oldnumeric import sign
 
 class PositionInWholeChain(object):
     """

diff --git a/cad/src/experimental/LearningOpenGL/Craft.py b/cad/src/experimental/LearningOpenGL/Craft.py
@@ -10,7 +10,7 @@
 from qtcanvas import *
 from qtgl import *
 from OpenGL.GL import *
-import Numeric
+import numpy.oldnumeric
 import sys
 import random
 import time

diff --git a/cad/src/experimental/LearningOpenGL/Cruft.py b/cad/src/experimental/LearningOpenGL/Cruft.py
@@ -34,7 +34,7 @@ def mypaintGL(): bla
 from qtcanvas import *
 from qtgl import *
 from OpenGL.GL import *
-import Numeric
+import numpy.oldnumeric
 import sys
 import random
 import time

diff --git a/cad/src/experimental/pyrex-atoms-bonds/prototype.py b/cad/src/experimental/pyrex-atoms-bonds/prototype.py
@@ -6,7 +6,7 @@
 import unittest
 import time
 import types
-import Numeric
+import numpy.oldnumeric
 
 # This is a prototype of the desired API for Pyrex atoms, bonds, and
 # atom sets. See "Pyrex atoms and bonds" page on the wiki.

diff --git a/cad/src/experimental/pyrex-atoms-bonds/smallerFootprint.py b/cad/src/experimental/pyrex-atoms-bonds/smallerFootprint.py
@@ -4,7 +4,7 @@
 
 import time
 import unittest
-import Numeric
+import numpy.oldnumeric
 
 stuff = None
 #stuff = [ ]

diff --git a/cad/src/experimental/pyrex-atoms-bonds/tryit.py b/cad/src/experimental/pyrex-atoms-bonds/tryit.py
@@ -2,7 +2,7 @@
 import time
 import unittest
 import random
-import Numeric
+import numpy.oldnumeric
 from bases import *
 
 N = int(10**6)

diff --git a/cad/src/experimental/pyrex-opengl/bearing_data.py b/cad/src/experimental/pyrex-opengl/bearing_data.py
diff --git a/cad/src/experimental/pyrex-opengl/quux.pyx b/cad/src/experimental/pyrex-opengl/quux.pyx
@@ -1,5 +1,5 @@
 # Copyright 2006-2007 Nanorex, Inc.  See LICENSE file for details. 
-import Numeric
+import numpy.oldnumeric
 import types
 import unittest
 import random

diff --git a/cad/src/exprs/Exprs.py b/cad/src/exprs/Exprs.py
@@ -806,7 +806,7 @@ def _e_make_argval(self, argval, env, i, ipath):
     pass
 
 # same as in basic.py:
-from Numeric import dot
+from numpy.oldnumeric import dot
 from geometry.VQT import V, norm, vlen
 
 class V_expr(OpExpr):
@@ -1259,7 +1259,7 @@ def _e_make_in(self, env, ipath):
 ##from VQT import V ###e replace with a type constant -- probably there's one already in state_utils
 ##V_expr = tuple_Expr ### kluge; even once this is defined, in formulas you may have to use V_expr instead of V,
     # unless we redefine V to not try to use float() on exprs inside it -- right now it's def V(*v): return array(v, Float)
-    # (note: that Float is from Numeric and equals 'd')
+    # (note: that Float is from numpy.oldnumeric and equals 'd')
     ##e (maybe we could make a new V def try to use old def, make __float__ asfail so that would fail, then use V_expr if any expr arg)
 
 def canon_expr(subexpr):###CALL ME FROM MORE PLACES -- a comment in Column.py says that env.understand_expr should call this...

diff --git a/cad/src/exprs/dna_ribbon_view.py b/cad/src/exprs/dna_ribbon_view.py
@@ -81,7 +81,7 @@
 """
 
 from math import pi
-from Numeric import dot, cos, sin
+from numpy.oldnumeric import dot, cos, sin
 
 from OpenGL.GL import GL_LIGHTING
 from OpenGL.GL import glDisable

diff --git a/cad/src/exprs/draw_utils.py b/cad/src/exprs/draw_utils.py
@@ -25,7 +25,7 @@
 from OpenGL.GLU import gluUnProject
 
 from geometry.VQT import norm, A
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from array import array
 # ==

diff --git a/cad/src/exprs/geometry_exprs.py b/cad/src/exprs/geometry_exprs.py
@@ -104,7 +104,7 @@
 
 """
 
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 from geometry.VQT import planeXline
 from geometry.VQT import norm

diff --git a/cad/src/exprs/outtakes/basic.py b/cad/src/exprs/outtakes/basic.py
@@ -35,7 +35,7 @@
 # == imports from python itself
 
 import sys, os
-from Numeric import dot
+from numpy.oldnumeric import dot
 
 sys.setrecursionlimit(650) # 5000 is set in startup_funcs.py; this will ease debugging, but REMOVE WHEN DEVEL IS DONE [061121]
 

diff --git a/cad/src/files/dpb_trajectory/moviefile.py b/cad/src/files/dpb_trajectory/moviefile.py
@@ -17,7 +17,7 @@
 import os, sys
 from struct import unpack # fyi: used for old-format header, no longer for delta frames
 ## from VQT import A
-from Numeric import array, Int8
+from numpy.oldnumeric import array, Int8
 from utilities import debug_flags
 from utilities.debug import print_compact_stack, print_compact_traceback
 import foundation.env as env

diff --git a/cad/src/foundation/state_utils.py b/cad/src/foundation/state_utils.py
@@ -1136,7 +1136,7 @@ def scan_Numeric_array(obj, func):
     return
 
 try:
-    from Numeric import array, PyObject
+    from nompy.oldnumeric import array, PyObject
 except:
     if env.debug() or DEBUG_PYREX_ATOMS:
         print "fyi: can't import array, PyObject from Numeric, so not registering its copy & scan functions"
@@ -2321,7 +2321,7 @@ def __ne__(self, other):
 
 def _test():
     print "testing some simple cases of copy_val"
-    from Numeric import array
+    from numpy.oldnumeric import array
     map( _test1, [2,
                   3,
                   "string",