boost_adaptbx: change imports

- import boost_adaptbx.python -> import boost_adaptbx.boost.python as bp
- boost_adaptbx.optional -> boost_adaptbx.boost.optional
- boost_adaptbx.rational -> boost_adaptbx.boost.rational
- boost_adaptbx.std_pair -> boost_adaptbx.boost.std_pair
- boost_adaptbx.tuple -> boost_adaptbx.boost.tuple
- from boost_adaptbx import -> from boost_adaptbx.boost import (except for graph)

boost/optional.py

@@ -1,10 +1,10 @@
 from __future__ import absolute_import, division, print_function
-from boost_adaptbx.optional import *
+from boost_adaptbx.boost.optional import *
 import warnings
 
 warnings.warn(
   "importing from boost.optional is deprecated; this module will be removed shortly. "
-  "import from boost_adaptbx.optional instead. "
+  "import from boost_adaptbx.boost.optional instead. "
   "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
   FutureWarning,
   stacklevel=2

boost/python.py

@@ -1,10 +1,10 @@
 from __future__ import absolute_import, division, print_function
-from boost_adaptbx.python import *
+from boost_adaptbx.boost.python import *
 import warnings
 
 warnings.warn(
   "importing from boost.python is deprecated; this module will be removed shortly. "
-  "import from boost_adaptbx.python instead. "
+  "import from boost_adaptbx.boost.python instead. "
   "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
   FutureWarning,
   stacklevel=2
@@ -18,7 +18,7 @@ class CrystalExt(boost.python.injector, Crystal):
 
   please use
 
-  @boost_adaptbx.python.inject_into(Crystal)
+  @boost_adaptbx.boost.python.inject_into(Crystal)
   class _(object):
   '''
   class __metaclass__(meta_class):

boost/rational.py

@@ -1,10 +1,10 @@
 from __future__ import absolute_import, division, print_function
-from boost_adaptbx.rational import *
+from boost_adaptbx.boost.rational import *
 import warnings
 
 warnings.warn(
   "importing from boost.rational is deprecated; this module will be removed shortly. "
-  "import from boost_adaptbx.rational instead. "
+  "import from boost_adaptbx.boost.rational instead. "
   "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
   FutureWarning,
   stacklevel=2

boost/std_pair.py

@@ -1,10 +1,10 @@
 from __future__ import absolute_import, division, print_function
-from boost_adaptbx.std_pair import *
+from boost_adaptbx.boost.std_pair import *
 import warnings
 
 warnings.warn(
   "importing from boost.std_pair is deprecated; this module will be removed shortly. "
-  "import from boost_adaptbx.std_pair instead. "
+  "import from boost_adaptbx.boost.std_pair instead. "
   "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
   FutureWarning,
   stacklevel=2

boost/tuple.py

@@ -1,10 +1,10 @@
 from __future__ import absolute_import, division, print_function
-from boost_adaptbx.tuple import *
+from boost_adaptbx.boost.tuple import *
 import warnings
 
 warnings.warn(
   "importing from boost.tuple is deprecated; this module will be removed shortly. "
-  "import from boost_adaptbx.tuple instead. "
+  "import from boost_adaptbx.boost.tuple instead. "
   "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
   FutureWarning,
   stacklevel=2

boost_adaptbx/boost/optional.py

@@ -1,4 +1,4 @@
 from __future__ import absolute_import, division, print_function
-import boost_adaptbx.python
-ext = boost_adaptbx.python.import_ext("boost_optional_ext")
+import boost_adaptbx.boost.python as bp
+ext = bp.import_ext("boost_optional_ext")
 from boost_optional_ext import *

boost_adaptbx/boost/python.py

@@ -120,10 +120,10 @@ def fset(self, flag):
 class trapping(object):
   """ Synopsis:
 
-      >>> import boost_adaptbx.python
+      >>> import boost_adaptbx.boost.python as bp
       >>> from scitbx.array_family import flex
       >>> a = flex.double((0, 0, 0))
-      >>> with boost_adaptbx.python.trapping(division_by_zero=False):
+      >>> with bp.trapping(division_by_zero=False):
       >>>   b = 1/a
       >>> tuple(b)
       (inf, inf, inf)
@@ -154,7 +154,7 @@ def c_sizeof(typename):
     if (line.startswith(pattern)):
       break
   else:
-    raise RuntimeError('boost_adaptbx.python.platform_info: "%s" not found.' % pattern)
+    raise RuntimeError('bp.platform_info: "%s" not found.' % pattern)
   return int(line[len(pattern):])
 
 sizeof_void_ptr = c_sizeof("void*")
@@ -193,11 +193,11 @@ def inject(target_class, *mixin_classes):
             class _():
               def method(...):
                 ...
-            boost_adaptbx.python.inject(extension_class, _)
+            bp.inject(extension_class, _)
 
       instead of the previous mechanism of
 
-            class _(boost_adaptbx.python.injector, extension_class):
+            class _(bp.injector, extension_class):
               def method(...):
                 ...
 
@@ -217,7 +217,7 @@ def inject_into(target_class, *mixin_classes):
 
      It is used as follows:
 
-           @boost_adaptbx.python.inject_into(extension_class)
+           @bp.inject_into(extension_class)
            class _():
              def method(...):
                ...

boost_adaptbx/boost/rational.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import, division, print_function
-import boost_adaptbx.python
+import boost_adaptbx.boost.python as bp
 from six.moves import range
-ext = boost_adaptbx.python.import_ext("boost_rational_ext")
+ext = bp.import_ext("boost_rational_ext")
 from boost_rational_ext import *
 
 builtin_int = __builtins__["int"]

boost_adaptbx/boost/std_pair.py

@@ -1,4 +1,4 @@
 from __future__ import absolute_import, division, print_function
-import boost_adaptbx.python
-ext = boost_adaptbx.python.import_ext("std_pair_ext")
+import boost_adaptbx.boost.python as bp
+ext = bp.import_ext("std_pair_ext")
 from std_pair_ext import *

boost_adaptbx/boost/tuple.py

@@ -1,4 +1,4 @@
 from __future__ import absolute_import, division, print_function
-import boost_adaptbx.python
-ext = boost_adaptbx.python.import_ext("boost_tuple_ext")
+import boost_adaptbx.boost.python as bp
+ext = bp.import_ext("boost_tuple_ext")
 from boost_tuple_ext import *

boost_adaptbx/command_line/divide_by_zero.py

@@ -2,26 +2,26 @@
 
 # LIBTBX_SET_DISPATCHER_NAME boost_adaptbx.divide_by_zero
 
-import boost_adaptbx.python
+import boost_adaptbx.boost.python as bp
 import sys
 
 def run(args):
   assert len(args) <= 1
   if len(args) == 0:
     print("Now dividing by zero (in C++) ...")
     sys.stdout.flush()
-    result = boost_adaptbx.python.ext.divide_doubles(1, 0)
+    result = bp.ext.divide_doubles(1, 0)
     print("Result:", result)
   else:
-    boost_adaptbx.python.floating_point_exceptions.division_by_zero_trapped = False
+    bp.floating_point_exceptions.division_by_zero_trapped = False
     print("Dividing by zero in C++: not gonna be caught")
-    result = boost_adaptbx.python.ext.divide_doubles(1, 0)
+    result = bp.ext.divide_doubles(1, 0)
     print("Result:", result)
-    boost_adaptbx.python.floating_point_exceptions.division_by_zero_trapped = True
+    bp.floating_point_exceptions.division_by_zero_trapped = True
     print()
     print("Dividing by zero in C++: gonna crash")
     sys.stdout.flush()
-    result = boost_adaptbx.python.ext.divide_doubles(1, 0)
+    result = bp.ext.divide_doubles(1, 0)
     print("Result:", result)
 
 if (__name__ == "__main__"):

boost_adaptbx/command_line/double_overflow.py

@@ -2,18 +2,18 @@
 
 # LIBTBX_SET_DISPATCHER_NAME boost_adaptbx.double_overflow
 
-import boost_adaptbx.python
+import boost_adaptbx.boost.python as bp
 import sys
 
 def run(args):
   assert len(args) == 0
-  sizeof_double = boost_adaptbx.python.c_sizeof("double")
+  sizeof_double = bp.c_sizeof("double")
   assert sizeof_double == 8
   x = 1.e300
   y = 1.e200
   print("Now multiplying double values %g * %g ..." % (x, y))
   sys.stdout.flush()
-  result = boost_adaptbx.python.ext.multiply_doubles(x, y)
+  result = bp.ext.multiply_doubles(x, y)
   print("Result:", result)
 
 if (__name__ == "__main__"):

boost_adaptbx/command_line/gcd.py

@@ -1,6 +1,6 @@
 from __future__ import absolute_import, division, print_function
 
-from boost_adaptbx.rational import gcd
+from boost_adaptbx.boost.rational import gcd
 from libtbx.utils import Usage
 import libtbx.load_env
 import sys

boost_adaptbx/command_line/inexact.py

@@ -2,14 +2,14 @@
 
 # LIBTBX_SET_DISPATCHER_NAME boost_adaptbx.inexact
 
-import boost_adaptbx.python
+import boost_adaptbx.boost.python as bp
 import sys
 
 def run(args):
   assert len(args) == 0
   print("Now creating a NaN in C++ as 0/0 ...")
   sys.stdout.flush()
-  result = boost_adaptbx.python.ext.divide_doubles(0, 0)
+  result = bp.ext.divide_doubles(0, 0)
   print("Result:", result)
 
 if (__name__ == "__main__"):

boost_adaptbx/command_line/int_overflow.py

@@ -2,17 +2,17 @@
 
 # LIBTBX_SET_DISPATCHER_NAME boost_adaptbx.int_overflow
 
-import boost_adaptbx.python
+import boost_adaptbx.boost.python as bp
 import sys
 
 def run(args):
   assert len(args) == 0
   for itype in ["int", "long"]:
-    sizeof_itype = boost_adaptbx.python.c_sizeof(itype)
+    sizeof_itype = bp.c_sizeof(itype)
     imax = 2**(8*sizeof_itype-1)-1
     print("Now adding %s values %d + 1 ..." % (itype, imax))
     sys.stdout.flush()
-    result = getattr(boost_adaptbx.python.ext, "add_%ss" % itype)(imax, 1)
+    result = getattr(bp.ext, "add_%ss" % itype)(imax, 1)
     print("Result:", result)
 
 if (__name__ == "__main__"):

boost_adaptbx/command_line/lcm.py

@@ -1,6 +1,6 @@
 from __future__ import absolute_import, division, print_function
 import gcd
-from boost_adaptbx.rational import lcm
+from boost_adaptbx.boost.rational import lcm
 import sys
 
 def run(args):

boost_adaptbx/command_line/nested_cpp_loops_with_check_signals.py

@@ -4,8 +4,8 @@
 
 def run(args):
   assert len(args) == 2, "iterations_outer, iterations_inner"
-  import boost_adaptbx.python
-  count = boost_adaptbx.python.ext.nested_cpp_loops_with_check_signals(
+  import boost_adaptbx.boost.python as bp
+  count = bp.ext.nested_cpp_loops_with_check_signals(
     iterations_outer=int(args[0]),
     iterations_inner=int(args[1]))
   print("actual iterations outer:", count)

boost_adaptbx/command_line/segmentation_fault.py

@@ -2,14 +2,14 @@
 
 # LIBTBX_SET_DISPATCHER_NAME boost_adaptbx.segmentation_fault
 
-import boost_adaptbx.python
+import boost_adaptbx.boost.python as bp
 import sys
 
 def run(args):
   assert len(args) == 0
   print("Now dereferencing null-pointer ...")
   sys.stdout.flush()
-  result = boost_adaptbx.python.ext.dereference_char_pointer(None)
+  result = bp.ext.dereference_char_pointer(None)
   print("Result:", result)
 
 if (__name__ == "__main__"):

boost_adaptbx/command_line/show_platform_info.py

@@ -2,7 +2,7 @@
 
 # LIBTBX_SET_DISPATCHER_NAME boost_adaptbx.show_platform_info
 
-import boost_adaptbx.python
+import boost_adaptbx.boost.python as bp
 from libtbx import introspection
 import libtbx.load_env
 import platform
@@ -15,7 +15,7 @@ def __truediv__(O, other): return "true"
 
 def run(out=None, omit_unicode_experiment=False):
   if (out is None): out = sys.stdout
-  out.write(boost_adaptbx.python.platform_info)
+  out.write(bp.platform_info)
   tag = libtbx.env.under_dist("boost", "TAG")
   if (op.isfile(tag)):
     tag = open(tag).read().strip()
@@ -29,15 +29,15 @@ def run(out=None, omit_unicode_experiment=False):
   print("platform.architecture():", platform.architecture(), file=out)
   for attr in ["division_by_zero", "invalid", "overflow"]:
     attr = "floating_point_exceptions.%s_trapped" % attr
-    print("%s:" % attr, eval("boost_adaptbx.python.%s" % attr), file=out)
+    print("%s:" % attr, eval("bp.%s" % attr), file=out)
   print("number of processors:", introspection.number_of_processors(
     return_value_if_unknown="unknown"), file=out)
   introspection.machine_memory_info().show(out=out)
   try: import thread
   except ImportError: print("import thread: NO", file=out)
   else: print("import thread: OK", file=out)
   print("Division operator semantics: %s division" % (div_probe() / 0))
-  c = getattr(boost_adaptbx.python.ext, "str_or_unicode_as_char_list", None)
+  c = getattr(bp.ext, "str_or_unicode_as_char_list", None)
   if (c is not None and not omit_unicode_experiment):
     print('"hello" =', c("hello"), file=out)
     print('u"hello" =', c(u"hello"), file=out)

boost_adaptbx/graph/__init__.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import, division, print_function
 
-import boost_adaptbx.python
-ext = boost_adaptbx.python.import_ext( "boost_adaptbx_graph_ext" )
+import boost_adaptbx.boost.python as bp
+ext = bp.import_ext( "boost_adaptbx_graph_ext" )
 from boost_adaptbx_graph_ext import *
 
 _abbreviation_for_component = {
@@ -42,4 +42,3 @@ def adjacency_list(
 
   except AttributeError:
     raise NotImplementedError
-

boost_adaptbx/graph/breadth_first_search.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import, division, print_function
 
-import boost_adaptbx.python
-ext = boost_adaptbx.python.import_ext( "boost_adaptbx_graph_breadth_first_search_ext" )
+import boost_adaptbx.boost.python as bp
+ext = bp.import_ext( "boost_adaptbx_graph_breadth_first_search_ext" )
 from boost_adaptbx_graph_breadth_first_search_ext import *
 
 class visitor(object):
@@ -121,4 +121,3 @@ def tree_edge(self, edge, graph):
     source = graph.source( edge )
     target = graph.target( edge )
     self.distance_for[ target ] = self.distance_for[ source ] + 1
-

boost_adaptbx/graph/clustering_algorithm.py

@@ -1,6 +1,6 @@
 from __future__ import absolute_import, division, print_function
 
-import boost_adaptbx.python
-ext = boost_adaptbx.python.import_ext( "boost_adaptbx_graph_clustering_algorithm_ext" )
+import boost_adaptbx.boost.python as bp
+ext = bp.import_ext( "boost_adaptbx_graph_clustering_algorithm_ext" )
 
 from boost_adaptbx_graph_clustering_algorithm_ext import *

boost_adaptbx/graph/connected_component_algorithm.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import, division, print_function
 
-import boost_adaptbx.python
-ext = boost_adaptbx.python.import_ext( "boost_adaptbx_graph_connected_component_algorithm_ext" )
+import boost_adaptbx.boost.python as bp
+ext = bp.import_ext( "boost_adaptbx_graph_connected_component_algorithm_ext" )
 
 
 def connected_components(graph):
@@ -12,4 +12,3 @@ def connected_components(graph):
     result.setdefault( component, [] ).append( desc )
 
   return list(result.values())
-

boost_adaptbx/graph/graph_structure_comparison.py

@@ -1,6 +1,5 @@
 from __future__ import absolute_import, division, print_function
 
-import boost_adaptbx.python
-ext = boost_adaptbx.python.import_ext( "boost_adaptbx_graph_graph_structure_comparison_ext" )
+import boost_adaptbx.boost.python as bp
+ext = bp.import_ext( "boost_adaptbx_graph_graph_structure_comparison_ext" )
 from boost_adaptbx_graph_graph_structure_comparison_ext import *
-