Move code from boost.* to boost_adaptbx.*, #458

boost/__init__.py

@@ -1,2 +0,0 @@
-from __future__ import absolute_import, division, print_function
-import libtbx.forward_compatibility

boost/optional.py

@@ -1,4 +1,11 @@
 from __future__ import absolute_import, division, print_function
-import boost.python
-ext = boost.python.import_ext("boost_optional_ext")
-from boost_optional_ext import *
+from boost_adaptbx.optional import *
+import warnings
+
+warnings.warn(
+  "importing from boost.optional is deprecated; this module will be removed shortly. "
+  "import from boost_adaptbx.optional instead. "
+  "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
+  FutureWarning,
+  stacklevel=2
+)

boost/python.py

@@ -1,190 +1,14 @@
 from __future__ import absolute_import, division, print_function
-
-import inspect
-import os
-import re
-import sys
+from boost_adaptbx.python import *
 import warnings
 
-from libtbx import cpp_function_name
-
-symbol_not_found_pat = re.compile(
-  r"[Ss]ymbol[ ]not[ ]found: \s* (\w+) $", re.X | re.M | re.S)
-
-python_libstdcxx_so = None
-if (sys.platform.startswith("linux")):
-  from libtbx import easy_run
-  for line in easy_run.fully_buffered(
-                command='/usr/bin/ldd "%s"' % sys.executable).stdout_lines:
-    if (line.strip().startswith("libstdc++.so")):
-      python_libstdcxx_so = line.split()[0]
-      break
-
-def import_ext(name, optional=False):
-  components = name.split(".")
-  if (len(components) > 1):
-    __import__(".".join(components[:-1]))
-  previous_dlopenflags = None
-  if (sys.platform.startswith("linux")) :
-    previous_dlopenflags = sys.getdlopenflags()
-    sys.setdlopenflags(0x100|0x2)
-  try: mod = __import__(name)
-  except ImportError as e:
-    if (optional): return None
-    error_msg = str(e)
-    m = symbol_not_found_pat.search(error_msg)
-    if m:
-      error_msg = (  error_msg[:m.start(1)]
-                   + cpp_function_name.demangle(m.group(1))
-                   + error_msg[m.end(1):])
-    raise ImportError(
-      "\n  ".join(['__import__("%s"): %s' % (name, error_msg), "sys.path:"]
-      + ["  "+p for p in sys.path]))
-  for comp in components[1:]:
-    mod = getattr(mod, comp)
-  if (previous_dlopenflags is not None):
-    sys.setdlopenflags(previous_dlopenflags)
-  if (python_libstdcxx_so is not None):
-    mod_file = getattr(mod, "__file__", None)
-    if (mod_file is not None):
-      for line in easy_run.fully_buffered(
-                    command='/usr/bin/ldd "%s"' % mod_file).stdout_lines:
-        if (line.strip().startswith("libstdc++.so")):
-          mod_libstdcxx_so = line.split()[0]
-          if (mod_libstdcxx_so != python_libstdcxx_so):
-            raise SystemError("""\
-FATAL: libstdc++.so mismatch:
-  %s: %s
-  %s: %s""" % (sys.executable, python_libstdcxx_so,
-               mod_file, mod_libstdcxx_so))
-          break
-  return mod
-
-ext = import_ext("boost_python_meta_ext")
-
-try: streambuf = ext.streambuf
-except AttributeError: pass # XXX backward compatibility 2009-11-24
-try: ostream = ext.ostream
-except AttributeError: pass
-
-if os.getenv("BOOST_ADAPTBX_ENABLE_TRACE"):
-  ext.enable_signals_backtrace_if_possible()
-
-class floating_point_exceptions_type(object):
-  __shared_state = {'initialised': False}
-
-  def __init__(self):
-    self.__dict__ = self.__shared_state
-    if not self.initialised:
-      division_by_zero = bool(os.getenv("BOOST_ADAPTBX_TRAP_FPE", self.division_by_zero_trapped))
-      invalid = bool(os.getenv("BOOST_ADAPTBX_TRAP_INVALID",self.invalid_trapped))
-      overflow = bool(os.getenv("BOOST_ADAPTBX_TRAP_OVERFLOW",self.overflow_trapped))
-      ext.trap_exceptions(division_by_zero, invalid, overflow)
-      self.initialised = True
-
-  def division_by_zero_trapped():
-    def fget(self):
-      return ext.is_division_by_zero_trapped()
-    def fset(self, flag):
-      if flag == self.division_by_zero_trapped: return
-      ext.trap_exceptions(division_by_zero=flag,
-                          invalid=self.invalid_trapped,
-                          overflow=self.overflow_trapped)
-    return locals()
-  division_by_zero_trapped = property(**division_by_zero_trapped())
-
-  def invalid_trapped():
-    def fget(self):
-      return ext.is_invalid_trapped()
-    def fset(self, flag):
-      if flag == self.fget(): return
-      ext.trap_exceptions(division_by_zero=self.invalid_trapped,
-                          invalid=flag,
-                          overflow=self.overflow_trapped)
-    return locals()
-  invalid_trapped = property(**invalid_trapped())
-
-  def overflow_trapped():
-    def fget(self):
-      return ext.is_overflow_trapped()
-    def fset(self, flag):
-      if flag == self.fget(): return
-      ext.trap_exceptions(division_by_zero=self.overflow_trapped,
-                          invalid=self.invalid_trapped,
-                          overflow=flag)
-    return locals()
-  overflow_trapped = property(**overflow_trapped())
-
-floating_point_exceptions = floating_point_exceptions_type()
-
-
-class trapping(object):
-  """ Synopsis:
-
-      >>> import boost.python
-      >>> from scitbx.array_family import flex
-      >>> a = flex.double((0, 0, 0))
-      >>> with boost.python.trapping(division_by_zero=False):
-      >>>   b = 1/a
-      >>> tuple(b)
-      (inf, inf, inf)
-      >>> 1/a
-      ... CRASH ...
-  """
-  def __init__(self, division_by_zero=True, invalid=True, overflow=True):
-    self.division_by_zero = ext.is_division_by_zero_trapped()
-    self.invalid = ext.is_invalid_trapped()
-    self.overflow = ext.is_overflow_trapped()
-    ext.trap_exceptions(division_by_zero, invalid, overflow)
-
-
-  def __enter__(self):
-    return self
-
-  def __exit__(self, exc_type, exc_val, exc_tb):
-    ext.trap_exceptions(self.division_by_zero, self.invalid, self.overflow)
-
-
-meta_class = ext.holder.__class__
-platform_info = ext.platform_info()
-assert len(platform_info) > 0 # please disable this assertion and send email to cctbx@cci.lbl.gov
-
-def c_sizeof(typename):
-  pattern = "sizeof(%s) = " % typename
-  for line in platform_info.splitlines():
-    if (line.startswith(pattern)):
-      break
-  else:
-    raise RuntimeError('boost.python.platform_info: "%s" not found.' % pattern)
-  return int(line[len(pattern):])
-
-sizeof_void_ptr = c_sizeof("void*")
-
-
-class gcc_version(object):
-
-  def __init__(self):
-    pat = r" \s* = \s* (\d+) \s+"
-    m = re.search("__GNUC__ %s __GNUC_MINOR__ %s __GNUC_PATCHLEVEL__ %s"
-                  % ((pat,)*3),
-                  platform_info, re.X|re.M|re.S)
-    if not m:
-      self.major, self.minor, self.patchlevel = None, None, None
-    else:
-      self.major, self.minor, self.patchlevel = tuple(
-        [ int(x) for x in m.groups() ])
-
-  def __bool__(self):
-    return self.major is not None
-
-  __nonzero__ = __bool__
-
-  def __str__(self):
-    if self:
-      return "%i.%i.%i" % (self.major, self.minor, self.patchlevel)
-    else:
-      return "GCC, it is not"
-
+warnings.warn(
+  "importing from boost.python is deprecated; this module will be removed shortly. "
+  "import from boost_adaptbx.python instead. "
+  "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
+  FutureWarning,
+  stacklevel=2
+)
 
 _skip_warning = True
 class injector(object):
@@ -194,7 +18,7 @@ class CrystalExt(boost.python.injector, Crystal):
 
   please use
 
-  @boost.python.inject_into(Crystal)
+  @boost_adaptbx.python.inject_into(Crystal)
   class _(object):
   '''
   class __metaclass__(meta_class):
@@ -204,7 +28,7 @@ def __init__(self, name, bases, dict):
         warnings.warn(
           "boost.python.injector is deprecated and does not work on Python 3. "
           "Please see https://github.com/cctbx/cctbx_project/pull/386 for more information.",
-          DeprecationWarning,
+          FutureWarning,
           stacklevel=2
         )
       if (len(bases) > 1):
@@ -225,73 +49,3 @@ def setattr_from_dict(d):
           setattr_from_dict(b.__dict__)
       return type.__init__(self, name, (), {})
 _skip_warning = False
-
-def inject(target_class, *mixin_classes):
-   '''Add entries from python class dictionaries to a boost extension class.
-
-      It is used as follows:
-
-            class _():
-              def method(...):
-                ...
-            boost.python.inject(extension_class, _)
-
-      instead of the previous mechanism of
-
-            class _(boost.python.injector, extension_class):
-              def method(...):
-                ...
-
-      which does not work in python 3.
-   '''
-   for m in mixin_classes:
-     for key, value in m.__dict__.items():
-       if key not in ("__init__",
-                      "__del__",
-                      "__module__",
-                      "__file__",
-                      "__dict__") and (key != '__doc__' or value):
-         setattr(target_class, key, value)
-
-def inject_into(target_class, *mixin_classes):
-  '''Add entries from python class dictionaries to a boost extension class.
-
-     It is used as follows:
-
-           @boost.python.inject_into(extension_class)
-           class _():
-             def method(...):
-               ...
-  '''
-  def _inject(c):
-    if inspect.isclass(c):
-      inject(target_class, c, *mixin_classes)
-    else:
-      setattr(target_class, c.__name__, c)
-      class empty_class:
-        pass
-      inject(target_class, empty_class, *mixin_classes)
-  return _inject
-
-def process_docstring_options(env_var="BOOST_ADAPTBX_DOCSTRING_OPTIONS"):
-  from_env = os.environ.get(env_var)
-  if (from_env is None): return None
-  try:
-    return eval(
-      "docstring_options(%s)" % from_env,
-      {},
-      {"docstring_options": ext.docstring_options})
-  except KeyboardInterrupt: raise
-  except Exception as e:
-    from libtbx.str_utils import show_string
-    raise RuntimeError(
-      "Error processing %s=%s\n" % (env_var, show_string(from_env))
-      + "  Exception: %s\n" % str(e)
-      + "  Valid example:\n"
-      + '    %s="show_user_defined=True,show_signatures=False"' % env_var)
-
-docstring_options = process_docstring_options()
-
-class py3_make_iterator:
-  def __next__(obj):
-    return obj.next()

boost/rational.py

@@ -1,30 +1,11 @@
 from __future__ import absolute_import, division, print_function
-import boost.python
-from six.moves import range
-ext = boost.python.import_ext("boost_rational_ext")
-from boost_rational_ext import *
-
-builtin_int = __builtins__["int"]
-
-def from_string(s):
-  flds = [builtin_int(i) for i in s.split("/")]
-  assert len(flds) in (1,2)
-  if (len(flds) == 1):
-    return int(flds[0])
-  return int(flds[0], flds[1])
-
-def vector(numerators, denominators):
-  if (isinstance(denominators, builtin_int)):
-    denominators = [denominators] * len(numerators)
-  else:
-    assert len(numerators) == len(denominators)
-  result = []
-  for i in range(len(numerators)):
-    result.append(int(numerators[i], denominators[i]))
-  return result
-
-def lcm_denominators(array):
-  l = 1
-  for r in array:
-    l = lcm(l, r.denominator())
-  return l
+from boost_adaptbx.rational import *
+import warnings
+
+warnings.warn(
+  "importing from boost.rational is deprecated; this module will be removed shortly. "
+  "import from boost_adaptbx.rational instead. "
+  "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
+  FutureWarning,
+  stacklevel=2
+)

boost/std_pair.py

@@ -1,4 +1,11 @@
 from __future__ import absolute_import, division, print_function
-import boost.python
-ext = boost.python.import_ext("std_pair_ext")
-from std_pair_ext import *
+from boost_adaptbx.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. "
+  "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
+  FutureWarning,
+  stacklevel=2
+)

boost/tuple.py

@@ -1,4 +1,11 @@
 from __future__ import absolute_import, division, print_function
-import boost.python
-ext = boost.python.import_ext("boost_tuple_ext")
-from boost_tuple_ext import *
+from boost_adaptbx.tuple import *
+import warnings
+
+warnings.warn(
+  "importing from boost.tuple is deprecated; this module will be removed shortly. "
+  "import from boost_adaptbx.tuple instead. "
+  "Please see https://github.com/cctbx/cctbx_project/issues/458 for more information.",
+  FutureWarning,
+  stacklevel=2
+)

boost_adaptbx/__init__.py

@@ -0,0 +1,2 @@
+from __future__ import absolute_import, division, print_function
+import libtbx.forward_compatibility