cctbx-cvs Mailing List for Computational Crystallography Toolbox (Page 971)

Update of /cvsroot/cctbx/cctbx/cctbx/regression
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32507/cctbx/regression

Modified Files:
	tst_coordination_sequences.py tst_pair_asu_table.py 
Log Message:
major setpaths overhaul

Index: tst_coordination_sequences.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_coordination_sequences.py,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** tst_coordination_sequences.py	20 Feb 2005 04:10:44 -0000	1.11
--- tst_coordination_sequences.py	24 Feb 2005 23:33:36 -0000	1.12
***************
*** 72,77 ****
        dest="verbose")
    ).process(args=args)
!   atlas_file = libtbx.env.under_dist_root(
!     "regression/misc/strudat_zeolite_atlas")
    if (not os.path.isfile(atlas_file)):
      print "Skipping exercise(): input file not available"
--- 72,77 ----
        dest="verbose")
    ).process(args=args)
!   atlas_file = libtbx.env.under_dist(
!     "libtbx", "../regression/misc/strudat_zeolite_atlas")
    if (not os.path.isfile(atlas_file)):
      print "Skipping exercise(): input file not available"

Index: tst_pair_asu_table.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_pair_asu_table.py,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** tst_pair_asu_table.py	20 Feb 2005 04:10:44 -0000	1.7
--- tst_pair_asu_table.py	24 Feb 2005 23:33:36 -0000	1.8
***************
*** 201,205 ****
    exercise_icosahedron(verbose=verbose)
    default_distance_cutoff=3.5
!   regression_misc = libtbx.env.under_dist_root("regression/misc")
    file_names = []
    for file_name in ["strudat_zeolite_atlas", "strudat_special_bonds"]:
--- 201,205 ----
    exercise_icosahedron(verbose=verbose)
    default_distance_cutoff=3.5
!   regression_misc = libtbx.env.under_dist("libtbx", "../regression/misc")
    file_names = []
    for file_name in ["strudat_zeolite_atlas", "strudat_special_bonds"]:

Update of /cvsroot/cctbx/libtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31520

Added Files:
	windows_dispatcher.exe 
Log Message:
Initial version.

--- NEW FILE: windows_dispatcher.exe ---
(This appears to be a binary file; contents omitted.)

Update of /cvsroot/cctbx/libtbx/libtbx/bundle
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31275/libtbx/bundle

Modified Files:
	copy_build_libtbx.py copy_runtime_sources.py install_bat.py 
	install_csh.py 
Log Message:
major setpaths overhaul

Index: copy_runtime_sources.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/bundle/copy_runtime_sources.py,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** copy_runtime_sources.py	18 Nov 2004 10:18:40 -0000	1.9
--- copy_runtime_sources.py	24 Feb 2005 23:28:20 -0000	1.10
***************
*** 39,43 ****
      target_root)))
    libtbx_env = libtbx.config.env()
!   dist_root = libtbx_env.LIBTBX_DIST_ROOT
    for package in ["libtbx"] + libtbx_env.package_list:
      for package_suf in libtbx.config.package_pair(
--- 39,43 ----
      target_root)))
    libtbx_env = libtbx.config.env()
!   dist_root = libtbx_env.under_dist("libtbx", "..")
    for package in ["libtbx"] + libtbx_env.package_list:
      for package_suf in libtbx.config.package_pair(

Index: copy_build_libtbx.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/bundle/copy_build_libtbx.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** copy_build_libtbx.py	19 Feb 2005 01:50:13 -0000	1.4
--- copy_build_libtbx.py	24 Feb 2005 23:28:20 -0000	1.5
***************
*** 8,12 ****
  
    def __init__(self, libtbx_env):
!     self.dispatcher_front_end_exe = libtbx_env.dispatcher_front_end_exe()
  
    def __call__(self, target_root_dir, dirname, names):
--- 8,18 ----
  
    def __init__(self, libtbx_env):
!     windows_dispatcher = libtbx_env.windows_dispatcher(command_path=None)
!     if (windows_dispatcher is None):
!       self.windows_dispatcher_size = None
!     else:
!       self.windows_dispatcher_size = len(windows_dispatcher)
!       self.windows_dispatcher_unique_pattern = \
!         libtbx_env.windows_dispatcher_unique_pattern
  
    def __call__(self, target_root_dir, dirname, names):
***************
*** 34,41 ****
  
    def is_disposable_file(self, name, path):
!     if (    self.dispatcher_front_end_exe is not None
          and name.endswith(".exe")):
!       if (open(path, "rb").read(len(self.dispatcher_front_end_exe)+1)
!           == self.dispatcher_front_end_exe):
          return True
      else:
--- 40,49 ----
  
    def is_disposable_file(self, name, path):
!     if (self.windows_dispatcher_size is not None
          and name.endswith(".exe")):
!       binary_string = open(path, "rb").read(self.windows_dispatcher_size+1)
!       if (len(binary_string) > self.windows_dispatcher_size):
!         return True
!       if (binary_string.find(self.windows_dispatcher_unique_pattern) >= 0):
          return True
      else:

Index: install_bat.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/bundle/install_bat.py,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** install_bat.py	20 Jun 2004 13:06:28 -0000	1.10
--- install_bat.py	24 Feb 2005 23:28:20 -0000	1.11
***************
*** 43,47 ****
  cd ..
  if not %%el%% == 0 goto end
! call %(bundle)s_build\setpaths.bat
  
  if not exist "%%SCITBX_DIST%%\lbfgs\boost_python\tst_lbfgs.py" goto skip_test
--- 43,47 ----
  cd ..
  if not %%el%% == 0 goto end
! call %(bundle)s_build\setpaths.bat all
  
  if not exist "%%SCITBX_DIST%%\lbfgs\boost_python\tst_lbfgs.py" goto skip_test

Index: install_csh.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/bundle/install_csh.py,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** install_csh.py	22 Jan 2005 13:24:49 -0000	1.11
--- install_csh.py	24 Feb 2005 23:28:20 -0000	1.12
***************
*** 200,204 ****
  echo "Configuring $bundle build directory"
  "$python_exe" "$sources/libtbx/configure.py" --build="$build_mode" %(top_modules)s
! source setpaths.csh
  
  if ($have_sources != 0) then
--- 200,204 ----
  echo "Configuring $bundle build directory"
  "$python_exe" "$sources/libtbx/configure.py" --build="$build_mode" %(top_modules)s
! source setpaths.csh all
  
  if ($have_sources != 0) then

Update of /cvsroot/cctbx/libtbx/libtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31275/libtbx

Modified Files:
	config.py env.py path.py test_utils.py 
Log Message:
major setpaths overhaul

Index: test_utils.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/test_utils.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** test_utils.py	19 Jan 2005 12:17:45 -0000	1.4
--- test_utils.py	24 Feb 2005 23:28:19 -0000	1.5
***************
*** 4,8 ****
  def run_tests(build_dir, dist_dir, tst_list):
    import sys, os, os.path
!   python_exe = sys.executable
    for tst in tst_list:
      cmd_args = ""
--- 4,11 ----
  def run_tests(build_dir, dist_dir, tst_list):
    import sys, os, os.path
!   if (os.name == "nt"):
!     python_exe = sys.executable
!   else:
!     python_exe = "libtbx.python"
    for tst in tst_list:
      cmd_args = ""
***************
*** 22,31 ****
      assert tst_path.find("$") < 0
      tst_path = os.path.normpath(tst_path)
      if (tst_path.endswith(".py")):
!       cmd = python_exe + " " + tst_path
      else:
!       cmd = tst_path
!     if ("--valgrind" in sys.argv[1:]):
!       cmd = os.environ["LIBTBX_VALGRIND"] + " " + cmd
      cmd += cmd_args
      print cmd
--- 25,37 ----
      assert tst_path.find("$") < 0
      tst_path = os.path.normpath(tst_path)
+     cmd = ""
      if (tst_path.endswith(".py")):
!       if ("--valgrind" in sys.argv[1:]):
!         cmd = "libtbx.valgrind "
!       cmd += python_exe + " " + tst_path
      else:
!       if ("--valgrind" in sys.argv[1:]):
!         cmd = os.environ["LIBTBX_VALGRIND"] + " "
!       cmd += tst_path
      cmd += cmd_args
      print cmd

Index: config.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/config.py,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** config.py	20 Feb 2005 04:09:53 -0000	1.26
--- config.py	24 Feb 2005 23:28:19 -0000	1.27
***************
*** 1,9 ****
  from libtbx.path import norm_join
  import sys, os, pickle
  from os.path import normpath, join, abspath, dirname, isdir, isfile
  norm = normpath
  
- class UserError(Exception): pass
- 
  def full_path(command, search_first=[], search_last=[]):
    dirs = search_first + os.environ["PATH"].split(os.pathsep) + search_last
--- 1,8 ----
  from libtbx.path import norm_join
+ from libtbx.utils import UserError
  import sys, os, pickle
  from os.path import normpath, join, abspath, dirname, isdir, isfile
  norm = normpath
  
  def full_path(command, search_first=[], search_last=[]):
    dirs = search_first + os.environ["PATH"].split(os.pathsep) + search_last
***************
*** 113,121 ****
    return result
  
  class env:
  
!   def __init__(self, application_prefix="LIBTBX"):
!     self.application_prefix = application_prefix
!     libtbx_build = os.environ["LIBTBX_BUILD"] # XXX XXX XXX XXX XXX XXX XXX XXX
      file_name = join(libtbx_build, "libtbx_env")
      try:
--- 112,129 ----
    return result
  
+ def _windows_pathext():
+   result = os.environ.get("PATHEXT", "").lower().split(os.pathsep)
+   for ext in [".py", ".exe", ".bat"]:
+     if (ext not in result):
+       result.insert(0, ext)
+   return result
+ 
+ if (os.name == "nt"):
+   windows_pathext = _windows_pathext()
+ 
  class env:
  
!   def __init__(self):
!     libtbx_build = os.environ["LIBTBX_BUILD"]
      file_name = join(libtbx_build, "libtbx_env")
      try:
***************
*** 133,137 ****
         + " Version used to configure: %d.%d." % self.python_version_major_minor
         + " Version used now: %d.%d." % sys.version_info[:2])
!     self._dispatcher_front_end_exe = None
  
    def write_api_file(self):
--- 141,147 ----
         + " Version used to configure: %d.%d." % self.python_version_major_minor
         + " Version used now: %d.%d." % sys.version_info[:2])
!     self._dispatcher_precall_commands = None
!     self.partially_customized_windows_dispatcher = None
!     self.windows_dispatcher_unique_pattern = None
  
    def write_api_file(self):
***************
*** 146,151 ****
      return self.dist_name(package_name) in self.dist_paths
  
!   def dist_path(self, package_name):
!     return self.dist_paths[self.dist_name(package_name)]
  
    def effective_root(self, package_name):
--- 156,163 ----
      return self.dist_name(package_name) in self.dist_paths
  
!   def dist_path(self, package_name, default=KeyError):
!     if (default is KeyError):
!       return self.dist_paths[self.dist_name(package_name)]
!     return self.dist_paths.get(self.dist_name(package_name), default)
  
    def effective_root(self, package_name):
***************
*** 155,174 ****
      return norm(os.getcwd()) == self.LIBTBX_BUILD
  
!   def dispatcher_front_end_exe(self,
!        application_prefix_placeholder="3A7P0P0L4I8C3A5T5I6O3N490P0R7E6F8I6X4"):
!     if (    os.name == "nt"
!         and self._dispatcher_front_end_exe is None):
!       self._dispatcher_front_end_exe = open(join(
!         self.dist_path("libtbx"), "dispatcher_front_end.exe"), "rb").read()
!       application_prefix_index = self._dispatcher_front_end_exe.find(
!         application_prefix_placeholder)
!       assert application_prefix_index >= 0
!       assert len(self.application_prefix) <= len(application_prefix_placeholder)
!       self._dispatcher_front_end_exe \
!         = self._dispatcher_front_end_exe[:application_prefix_index] \
!         + self.application_prefix + "\0" \
!         + self._dispatcher_front_end_exe[
!             application_prefix_index+len(self.application_prefix)+1:]
!     return self._dispatcher_front_end_exe
  
  class include_registry:
--- 167,349 ----
      return norm(os.getcwd()) == self.LIBTBX_BUILD
  
!   def dispatcher_precall_commands(self):
!     if (self._dispatcher_precall_commands is None):
!       lines = []
!       if (    self.python_version_major_minor == (2,2)
!           and sys.platform == "linux2"
!           and os.path.isfile("/etc/redhat-release")):
!         try: red_hat_linux_release = open("/etc/redhat-release").readline()
!         except: pass
!         else:
!           if (    red_hat_linux_release.startswith("Red Hat Linux release")
!               and red_hat_linux_release.split()[4] == "9"):
!             lines.extend([
!               'if [ ! -n "$LD_ASSUME_KERNEL" ]; then',
!               '  LD_ASSUME_KERNEL=2.4.1',
!               '  export LD_ASSUME_KERNEL',
!               'fi'])
!       if (os.name == "posix" and self.compiler == "icc"):
!         addl_lines = self.create_posix_icc_ld_preload()
!         if (addl_lines is None):
!           raise UserError("Cannot determine LD_PRELOAD for icc.")
!         lines.extend(addl_lines)
!       self._dispatcher_precall_commands = lines
!     return self._dispatcher_precall_commands
! 
!   def create_posix_icc_ld_preload(self):
!     path_icc = full_path("icc")
!     if (path_icc is None): return None
!     path_lib = os.sep.join(path_icc.split(os.sep)[:-2] + ["lib"])
!     if (not isdir(path_lib)): return None
!     ld_preload = []
!     path_libirc_a = join(path_lib, "libirc.a")
!     path_libirc_so = join(path_lib, "libirc.so")
!     if (isfile(path_libirc_so)):
!       ld_preload.append(path_libirc_so)
!     else:
!       if (isfile(path_libirc_a)):
!         path_libirc_so = join(self.LIBTBX_BUILD, "libtbx/libirc.so")
!         if (not isfile(path_libirc_so)):
!           cmd = "%s -shared -o %s %s" % (
!             path_icc, path_libirc_so, path_libirc_a)
!           print cmd
!           sys.stdout.flush()
!           os.system(cmd)
!         ld_preload.append(path_libirc_so)
!     path_libunwind_so = None
!     best_version = None
!     for file_name in os.listdir(path_lib):
!       if (file_name.startswith("libunwind.so.")):
!         try: version = int(file_name.split(".")[2])
!         except: version = None
!         if (version is not None):
!           if (best_version is None or version > best_version):
!             path_libunwind_so = join(path_lib, file_name)
!             best_version = version
!     if (path_libunwind_so is not None):
!       ld_preload.append(path_libunwind_so)
!     if (len(ld_preload) == 0): return None
!     return [
!       'LD_PRELOAD="%s"' % os.pathsep.join(ld_preload),
!       'export LD_PRELOAD']
! 
!   def create_bin_sh_dispatcher(self, source_file, target_file):
!     f = open(target_file, "w")
!     print >> f, '#! /bin/sh'
!     print >> f, '# LIBTBX_DISPATCHER DO NOT EDIT'
!     print >> f, 'unset PYTHONHOME'
!     print >> f, 'LIBTBX_BUILD="%s"' % self.LIBTBX_BUILD
!     print >> f, 'export LIBTBX_BUILD'
!     essentials = [("PYTHONPATH", self.PYTHONPATH)]
!     if (sys.platform.startswith("darwin")):
!       ld_library_path = "DYLD_LIBRARY_PATH"
!     else:
!       ld_library_path = "LD_LIBRARY_PATH"
!     essentials.append((ld_library_path, self.LD_LIBRARY_PATH))
!     essentials.append(("PATH", self.PATH))
!     for n,v in essentials:
!       v = ":".join(v)
!       print >> f, 'if [ ! -n "$%s" ]; then' % n
!       print >> f, '  %s="%s"' % (n, v)
!       print >> f, 'else'
!       print >> f, '  %s="%s:$%s"' % (n, v, n)
!       print >> f, 'fi'
!       print >> f, 'export %s' % n
!     precall_commands = self.dispatcher_precall_commands()
!     if (precall_commands is not None):
!       for line in precall_commands:
!         print >> f, line
!     cmd = ""
!     if (source_file.lower().endswith(".py")):
!       cmd += " '"+self.LIBTBX_PYTHON_EXE+"'"
!     cmd += " '"+source_file+"'"
!     print >> f, 'if [ -n "$LIBTBX__VALGRIND_FLAG__" ]; then'
!     print >> f, "  exec $LIBTBX_VALGRIND"+cmd, '"$@"'
!     print >> f, "elif [ $# -eq 0 ]; then"
!     print >> f, "  exec"+cmd
!     print >> f, "else"
!     print >> f, "  exec"+cmd, '"$@"'
!     print >> f, "fi"
!     f.close()
!     os.chmod(target_file, 0755)
! 
!   def windows_dispatcher(self, command_path,
!         unique_pattern="0W6I0N6D0O2W8S5_0D0I8S1P4A3T6C4H9E4R7",
!         libtbx_build="3L0I2B2T9B4X2_8B5U5I5L2D4",
!         python_executable="5P2Y5T7H2O5N8_0E7X9E7C8U6T4A9B9L5E3",
!         pythonpath="2P0Y1T7H3O2N7P7A2T5H8",
!         main_path="1M5A1I0N4_8P7A0T9H9",
!         target_command="5T4A3R7G8E3T7_6C5O0M0M3A8N8D2",
!         dispatcher_exe_file_name="windows_dispatcher.exe"):
!     if (os.name == "nt"
!         and self.partially_customized_windows_dispatcher is None):
!       self.partially_customized_windows_dispatcher = open(join(
!         self.dist_path("libtbx"), dispatcher_exe_file_name), "rb").read()
!       if (self.partially_customized_windows_dispatcher.find(unique_pattern)<0):
!         raise RuntimeError('Unique pattern "%s" not found in file %s' % (
!           unique_pattern, dispatcher_exe_file_name))
!       self.windows_dispatcher_unique_pattern = unique_pattern
!       for place_holder,actual_value in [
!            (libtbx_build, self.LIBTBX_BUILD),
!            (python_executable, self.LIBTBX_PYTHON_EXE),
!            (pythonpath, os.pathsep.join(self.PYTHONPATH)),
!            (main_path, os.pathsep.join([
!                          norm(join(self.LIBTBX_BUILD, "libtbx/bin")),
!                          norm(join(self.LIBTBX_BUILD, "libtbx"))]))]:
!        self.partially_customized_windows_dispatcher = patch_windows_dispatcher(
!          dispatcher_exe_file_name=dispatcher_exe_file_name,
!          binary_string=self.partially_customized_windows_dispatcher,
!          place_holder=place_holder,
!          actual_value=actual_value)
!     if (command_path is None):
!       return self.partially_customized_windows_dispatcher
!     return patch_windows_dispatcher(
!       dispatcher_exe_file_name=dispatcher_exe_file_name,
!       binary_string=self.partially_customized_windows_dispatcher,
!       place_holder=target_command,
!       actual_value=command_path)
! 
!   def create_win32_dispatcher(self, source_file, target_file):
!     open(target_file+".exe", "wb").write(
!       self.windows_dispatcher(command_path=source_file))
! 
!   def create_dispatcher(self, source_file, target_file):
!     if (os.name == "nt"):
!       action = self.create_win32_dispatcher
!       ext = ".exe"
!     else:
!       action = self.create_bin_sh_dispatcher
!       ext = ""
!       try: os.chmod(source_file, 0755)
!       except OSError: pass
!     target_file_ext = target_file + ext
!     try: os.remove(target_file_ext)
!     except OSError:
!       try: os.remove(target_file_ext+".old")
!       except OSError: pass
!       try: os.rename(target_file_ext, target_file_ext+".old")
!       except OSError: pass
!     try: action(source_file, target_file)
!     except IOError, e: print "  Ignored:", e
! 
!   def create_dispatcher_in_bin(self, source_file, target_file):
!     self.create_dispatcher(
!       source_file=source_file,
!       target_file=norm(join(self.LIBTBX_BUILD, "libtbx/bin", target_file)))
! 
! def patch_windows_dispatcher(
!       dispatcher_exe_file_name,
!       binary_string,
!       place_holder,
!       actual_value):
!   place_holder_start = binary_string.find(place_holder)
!   if (place_holder_start < 0):
!     raise RuntimeError('Place holder "%s" not found in file %s' % (
!       place_holder, dispatcher_exe_file_name))
!   place_holder_end = binary_string.find("\0", place_holder_start)
!   assert len(actual_value) <= place_holder_end - place_holder_start
!   return binary_string[:place_holder_start] \
!        + actual_value + "\0" \
!        + binary_string[place_holder_start+len(actual_value)+1:]
  
  class include_registry:

Index: env.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/env.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** env.py	20 Feb 2005 04:09:53 -0000	1.1
--- env.py	24 Feb 2005 23:28:19 -0000	1.2
***************
*** 2,12 ****
  import os
  
! env_cache = libtbx.config.env()
! dist_root = env_cache.LIBTBX_DIST_ROOT
! dist_path = env_cache.dist_path
! build = env_cache.LIBTBX_BUILD
! 
! def under_dist_root(path):
!   return os.path.normpath(os.path.join(dist_root, path))
  
  def under_dist(package_name, path):
--- 2,8 ----
  import os
  
! cache = libtbx.config.env()
! dist_path = cache.dist_path
! build_path = cache.LIBTBX_BUILD
  
  def under_dist(package_name, path):
***************
*** 15,17 ****
  
  def under_build(path):
!   return os.path.normpath(os.path.join(build, path))
--- 11,13 ----
  
  def under_build(path):
!   return os.path.normpath(os.path.join(build_path, path))

Index: path.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/path.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** path.py	5 Jan 2005 00:49:12 -0000	1.4
--- path.py	24 Feb 2005 23:28:19 -0000	1.5
***************
*** 9,38 ****
      os.makedirs(target_dir)
  
- _shortpath_bat = None
- 
- def abs_path_short(abs_path):
-   if (os.name != "nt"): return abs_path
-   global _shortpath_bat
-   if (_shortpath_bat is None):
-     _shortpath_bat = "shortpath.bat"
-     libtbx_build = os.environ.get("LIBTBX_BUILD", None)
-     if (libtbx_build is not None):
-       _shortpath_bat = os.path.join(libtbx_build, _shortpath_bat)
-   assert os.path.exists(_shortpath_bat)
-   return os.popen('call "%s" "%s"' %
-     (_shortpath_bat, abs_path), "r").readline().rstrip()
- 
- def abs_path_clean(abs_path):
-   if (os.name != "nt"): return abs_path
-   short = abs_path_short(abs_path).split(os.sep)
-   orig = abs_path.split(os.sep)
-   clean = []
-   for o,s in zip(orig, short):
-     if (o.find(" ") < 0):
-       clean.append(o)
-     else:
-       clean.append(s)
-   return os.sep.join(clean)
- 
  def canonical_path(file_name, effective_current_working_directory=None):
    if (not os.path.isabs(file_name)):
--- 9,12 ----

Update of /cvsroot/cctbx/libtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31275

Modified Files:
	configure.py 
Added Files:
	windows_dispatcher.c 
Removed Files:
	dispatcher_front_end.c dispatcher_front_end.exe 
Log Message:
major setpaths overhaul

--- dispatcher_front_end.exe DELETED ---

--- NEW FILE: windows_dispatcher.c ---
#include <process.h>
#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

static const char* /* WINDOWS_DISPATCHER interleaved with random digits */
unique_pattern = "0W6I0N6D0O2W8S5_0D0I8S1P4A3T6C4H9E4R7";

static char* /* LIBTBX_BUILD interleaved with random digits */
libtbx_build = "LIBTBX_BUILD="
"3L0I2B2T9B4X2_8B5U5I5L2D4_3L0I2B2T9B4X2_8B5U5I5L2D4_3L0I2B2T9B4X2_8B5U5I5L2D4"
"_3L0I2B2T9B4X2_8B5U5I5L2D4_3L0I2B2T9B4X2_8B5U5I5L2D4_3L0I2B2T9B4X2_8B5U5I5L2D"
"4_3L0I2B2T9B4X2_8B5U5I5L2D4_3L0I2B2T9B4X2_8B5U5I5L2D4_3L0I2B2T9B4X2_8B5U5I5L2"
"D4_3L0I2B2T9B4X2_8B5U5I5";

static char* /* PYTHON_EXECUTABLE interleaved with random digits */
python_executable =
"5P2Y5T7H2O5N8_0E7X9E7C8U6T4A9B9L5E3_5P2Y5T7H2O5N8_0E7X9E7C8U6T4A9B9L5E3_5P2Y5"
"T7H2O5N8_0E7X9E7C8U6T4A9B9L5E3_5P2Y5T7H2O5N8_0E7X9E7C8U6T4A9B9L5E3_5P2Y5T7H2O"
"5N8_0E7X9E7C8U6T4A9B9L5E3_5P2Y5T7H2O5N8_0E7X9E7C8U6T4A9B9L5E3_5P2Y5T7H2O5N8_0"
"E7X9E7C8U6T4A9B9L5E3_5P2";

static char* /* PYTHONPATH interleaved with random digits */
pythonpath =
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2"
"N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_"
"2P0Y1T7H3O2N7P7A2T5H8_2P0Y1T7H3O2N7P7A2T5H8_2";

static char* /* MAIN_PATH interleaved with random digits */
main_path =
"1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9"
"H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A"
"0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8"
"P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N"
"4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1"
"I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M"
"5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P7A0T9H9_1M5A1I0N4_8P";

static char* /* TARGET_COMMAND interleaved with random digits */
target_command =
"5T4A3R7G8E3T7_6C5O0M0M3A8N8D2_5T4A3R7G8E3T7_6C5O0M0M3A8N8D2_5T4A3R7G8E3T7_6C5"
"O0M0M3A8N8D2_5T4A3R7G8E3T7_6C5O0M0M3A8N8D2_5T4A3R7G8E3T7_6C5O0M0M3A8N8D2_5T4A"
"3R7G8E3T7_6C5O0M0M3A8N8D2_5T4A3R7G8E3T7_6C5O0M0M3A8N8D2_5T4A3R7G8E3T7_6C5O0M0"
"M3A8N8D2_5T4A3R7G8E3T7_6";

int
is_py(const char* path)
{
  int n, i;
  n = strlen(path);
  if (n < 3) return 0;
  n -= 3;
  for(i=0;i<3;i++,n++) {
    if (tolower(path[n]) != ".py"[i]) return 0;
  }
  return 1;
}

void*
malloc_certain(const char* argv0, unsigned long n)
{
  void* ptr;
  errno = 0;
  ptr = malloc(n);
  if (ptr == NULL) {
    fprintf(stderr, "%s: error allocating %lu bytes", argv0, n);
    if (errno) {
      fprintf(stderr, ": %s", strerror(errno));
    }
    fprintf(stderr, "\n");
    exit(2);
  }
  return ptr;
}

void
prepend_path_element(
  const char* argv0,
  const char* var_name,
  const char* additional_element)
{
  const char* original_value;
  char* buffer;
  size_t sz;
  original_value = getenv(var_name);
  sz = strlen(var_name) + 1 + strlen(additional_element) + 1;
  if (original_value != NULL) sz += 1 + strlen(original_value);
  buffer = malloc_certain(argv0, sz);
  strcpy(buffer, var_name);
  strcat(buffer, "=");
  strcat(buffer, additional_element);
  if (original_value != NULL) {
    strcat(buffer, ";");
    strcat(buffer, original_value);
  }
  _putenv(buffer);
}

int
main(int argc, char *const argv[])
{
  char** extended_argv;
  int n, i;
  _putenv("PYTHONHOME=");
  _putenv(libtbx_build);
  prepend_path_element(argv[0], "PYTHONPATH", pythonpath);
  prepend_path_element(argv[0], "PATH", main_path);
  extended_argv = malloc_certain(argv[0], (argc + 2) * sizeof(char*));
  n = 0;
  if (is_py(target_command)) {
    extended_argv[n++] = python_executable;
  }
  extended_argv[n++] = target_command;
  for(i=1;i<argc;i++,n++) {
    extended_argv[n] = malloc_certain(argv[0], strlen(argv[i]) + 3);
    strcpy(extended_argv[n], "\"");
    strcat(extended_argv[n], argv[i]);
    strcat(extended_argv[n], "\"");
  }
  extended_argv[n] = NULL;
  _flushall();
  _fileinfo = 1;
  _spawnv(_P_WAIT, extended_argv[0], extended_argv);
  if (errno) {
    fprintf(stderr, "%s: error starting %s: %s\n",
      argv[0], extended_argv[0], strerror(errno));
    exit(3);
  }
  return 0;
}

--- dispatcher_front_end.c DELETED ---

Index: configure.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/configure.py,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** configure.py	13 Jun 2004 03:50:09 -0000	1.19
--- configure.py	24 Feb 2005 23:28:19 -0000	1.20
***************
*** 14,20 ****
    if (os.name == "nt"):
      open("shortpath.bat", "w").write("@echo off\necho %~s1\n")
-   from os.path import normpath, join, dirname
-   libtbx_libtbx = normpath(join(dirname(sys.argv[0]), "libtbx"))
-   sys.path.insert(0, libtbx_libtbx)
    from libtbx.command_line import configure
    configure.cold_start(sys.argv)
--- 14,17 ----

Update of /cvsroot/cctbx/libtbx/libtbx/command_line
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31275/libtbx/command_line

Modified Files:
	configure.py path_utility.py refresh.py scons.py 
Added Files:
	printenv.bat printenv.sh show_bin_path.py show_build_path.py 
	show_dist_paths.py show_lib_path.py valgrind.sh 
Removed Files:
	env_run.py 
Log Message:
major setpaths overhaul

--- NEW FILE: show_dist_paths.py ---
import libtbx.env
import sys
if (len(sys.argv) == 1):
  for path in libtbx.env.cache.dist_paths.values():
    print path
else:
  for arg in sys.argv[1:]:
    print libtbx.env.cache.dist_path(arg, None)

Index: scons.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/command_line/scons.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** scons.py	20 Feb 2005 04:09:53 -0000	1.4
--- scons.py	24 Feb 2005 23:28:20 -0000	1.5
***************
*** 2,8 ****
  import sys, os
  
! engine = libtbx.env.under_dist_root("scons/engine")
  if (not os.path.isdir(engine)):
!   engine = libtbx.env.under_dist_root("scons/src/engine")
  sys.path.insert(0, engine)
  try: import SCons
--- 2,8 ----
  import sys, os
  
! engine = libtbx.env.under_dist("libtbx", "../scons/engine")
  if (not os.path.isdir(engine)):
!   engine = libtbx.env.under_dist("libtbx", "../scons/src/engine")
  sys.path.insert(0, engine)
  try: import SCons

Index: path_utility.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/command_line/path_utility.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** path_utility.py	10 Dec 2003 19:37:20 -0000	1.3
--- path_utility.py	24 Feb 2005 23:28:20 -0000	1.4
***************
*** 1,4 ****
- #! /usr/bin/env python
- 
  import sys, os
  
--- 1,2 ----
***************
*** 36,39 ****
--- 34,39 ----
          remaining_env_paths.append(path)
          remaining_env_paths_norm.append(norm(path))
+   if (os.name == "nt" and len(remaining_env_paths) == 0):
+     return "E_M_P_T_Y"
    return os.pathsep.join(remaining_env_paths)
  

--- NEW FILE: printenv.bat ---
@echo off
call %LIBTBX_BUILD%\setpaths.bat all
set

--- NEW FILE: show_build_path.py ---
import libtbx.env
print libtbx.env.build_path

--- NEW FILE: printenv.sh ---
#! /bin/sh
. $LIBTBX_BUILD/setpaths.sh all
printenv

--- env_run.py DELETED ---

--- NEW FILE: valgrind.sh ---
#! /bin/sh
if [ ! -n "$LIBTBX_VALGRIND" ]; then
  echo 'Error: $LIBTBX_VALGRIND is not defined.'
  exit 1
fi
valgrind --version
if [ $? -eq 0 ]; then
  LIBTBX__VALGRIND_FLAG__=1
  export LIBTBX__VALGRIND_FLAG__
  exec "$@"
fi

--- NEW FILE: show_lib_path.py ---
import libtbx.env
print libtbx.env.under_build("libtbx")

--- NEW FILE: show_bin_path.py ---
import libtbx.env
print libtbx.env.under_build("libtbx/bin")

Index: refresh.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/command_line/refresh.py,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** refresh.py	20 Feb 2005 04:09:53 -0000	1.24
--- refresh.py	24 Feb 2005 23:28:20 -0000	1.25
***************
*** 1,64 ****
! #! /usr/bin/env python
! 
  import libtbx.config
! import sys, os
! from os.path import normpath, join, split, isdir, isfile, islink, splitext
  norm = normpath
  
! class create_bin_sh_dispatcher:
! 
!   def __init__(self, python_exe, precall_commands):
!     self.python_exe = python_exe
!     self.precall_commands = precall_commands
! 
!   def __call__(self, source_file, target_file):
!     f = open(target_file, "w")
!     print >> f, '#! /bin/sh'
!     print >> f, '# LIBTBX_DISPATCHER DO NOT EDIT'
!     print >> f, 'unset PYTHONHOME'
!     essentials = ["PYTHONPATH"]
!     if (sys.platform.startswith("darwin")):
!       essentials.append("DYLD_LIBRARY_PATH")
!     else:
!       essentials.append("LD_LIBRARY_PATH")
!     for v in essentials:
!       print >> f, 'if [ -n "$LIBTBX0%s" ]; then' % v
!       print >> f, '  if [ ! -n "$%s" ]; then' % v
!       print >> f, '    %s="$LIBTBX0%s"' % (v, v)
!       print >> f, '    export %s' % v
!       print >> f, '  elif [ "$%s" != "$LIBTBX0%s" ]; then' % (v, v)
!       print >> f, '    x=`echo "$%s" | grep libtbx`' % v
!       print >> f, '    if [ ! -n "$x" ]; then'
!       print >> f, '      %s="$LIBTBX0%s:$%s"' % (v, v, v)
!       print >> f, '      export %s' % v
!       print >> f, '    fi'
!       print >> f, '  fi'
!       print >> f, 'fi'
!     if (self.precall_commands is not None):
!       for line in self.precall_commands:
!         print >> f, line
!     cmd = "  exec"
!     if (    source_file != self.python_exe
!         and source_file.lower().endswith(".py")):
!       cmd += " '"+self.python_exe+"'"
!     print >> f, "if [ $# -eq 0 ]; then"
!     print >> f, cmd, "'"+source_file+"'"
!     print >> f, "else"
!     print >> f, cmd, "'"+source_file+"'", '"$@"'
!     print >> f, "fi"
!     f.close()
!     os.chmod(target_file, 0755)
! 
! class create_win32_dispatcher:
! 
!   def __init__(self, dispatcher_front_end_exe):
!     self.dispatcher_front_end_exe = dispatcher_front_end_exe
! 
!   def __call__(self, source_file, target_file):
!     open(target_file+".exe", "wb").write(self.dispatcher_front_end_exe)
! 
! def create_driver(libtbx_env, precall_commands,
!                   target_dir, package_name, source_dir, file_name,
!                   dispatcher_dict):
    source_file = norm(join(source_dir, file_name))
    if (not isfile(source_file)): return
--- 1,9 ----
! import libtbx.env
  import libtbx.config
! import os
! from os.path import normpath, join, isdir, isfile, splitext
  norm = normpath
  
! def create_dispatcher(target_dir, package_name, source_dir, file_name):
    source_file = norm(join(source_dir, file_name))
    if (not isfile(source_file)): return
***************
*** 66,225 ****
    if (file_name.lower().endswith(".pyc")): return
    if (file_name[0] == "."): return
    target_file = norm(join(target_dir, package_name))
    if (file_name.lower() != "main.py"):
      target_file += "." + splitext(file_name)[0]
!   if (os.name == "nt"):
!     if (not file_name.lower().endswith(".py")): return
!     action = create_win32_dispatcher(
!       dispatcher_front_end_exe=libtbx_env.dispatcher_front_end_exe())
!   else:
!     action = create_bin_sh_dispatcher(
!       python_exe=libtbx_env.LIBTBX_PYTHON_EXE,
!       precall_commands=precall_commands)
!     try: os.chmod(source_file, 0755)
!     except: pass
!   if (isfile(target_file) or islink(target_file)):
!     try: os.remove(target_file)
!     except OSError: pass
!     else: action(source_file, target_file)
!   else:
!     action(source_file, target_file)
!   dispatcher_dict[os.path.basename(target_file).lower()] = source_file
  
! def create_drivers(libtbx_env, precall_commands,
!                    target_dir, package_name, source_dir,
!                    dispatcher_dict):
    if (not isdir(source_dir)): return
    print "Processing:", source_dir
    for file_name in os.listdir(source_dir):
!     create_driver(
!       libtbx_env=libtbx_env,
!       precall_commands=precall_commands,
        target_dir=target_dir,
        package_name=package_name,
        source_dir=source_dir,
!       file_name=file_name,
!       dispatcher_dict=dispatcher_dict)
! 
! def create_dispatcher_back_end(libtbx_env, dispatcher_dict):
!   dispatcher_path = norm(join(libtbx_env.LIBTBX_BUILD, "dispatcher"))
!   f = open(dispatcher_path, "w")
!   print >> f, "import sys, os"
!   print >> f, "scripts = {"
!   for item in dispatcher_dict.items():
!     print >> f, '"%s": r"%s",' % item
!   print >> f, "}"
!   print >> f, """\
! cmd = os.path.basename(sys.argv[1]).lower()
! if (cmd.endswith(".exe")):
!   cmd = cmd[:-4]
! script = scripts.get(cmd, None)
! if (script is None):
!   raise RuntimeError("Unknown script: %s" % cmd)
! sys.argv = sys.argv[1:]
! execfile(script)
!   """
!   f.close()
! 
! def create_posix_icc_ld_preload(libtbx_env):
!   path_icc = libtbx.config.full_path("icc")
!   if (path_icc is None): return None
!   path_lib = os.sep.join(path_icc.split(os.sep)[:-2] + ["lib"])
!   if (not os.path.isdir(path_lib)): return None
!   ld_preload = []
!   path_libirc_a = os.path.join(path_lib, "libirc.a")
!   path_libirc_so = os.path.join(path_lib, "libirc.so")
!   if (os.path.isfile(path_libirc_so)):
!     ld_preload.append(path_libirc_so)
!   else:
!     if (os.path.isfile(path_libirc_a)):
!       path_libirc_so = os.path.join(
!         libtbx_env.LIBTBX_BUILD, "libtbx", "libirc.so")
!       cmd = "%(path_icc)s -shared -o %(path_libirc_so)s %(path_libirc_a)s" \
!         % vars()
!       print cmd
!       sys.stdout.flush()
!       os.system(cmd)
!       ld_preload.append(path_libirc_so)
!   path_libunwind_so = None
!   best_version = None
!   for file_name in os.listdir(path_lib):
!     if (file_name.startswith("libunwind.so.")):
!       try: version = int(file_name.split(".")[2])
!       except: version = None
!       if (version is not None):
!         if (best_version is None or version > best_version):
!           path_libunwind_so = os.path.join(path_lib, file_name)
!           best_version = version
!   if (path_libunwind_so is not None):
!     ld_preload.append(path_libunwind_so)
!   if (len(ld_preload) == 0): return None
!   return [
!     'LD_PRELOAD="%s"' % os.pathsep.join(ld_preload),
!     'export LD_PRELOAD']
! 
! def assemble_dispatcher_precall_commands(libtbx_env):
!   lines = []
!   if (    libtbx_env.python_version_major_minor == (2,2)
!       and sys.platform == "linux2"
!       and os.path.isfile("/etc/redhat-release")):
!     try: red_hat_linux_release = open("/etc/redhat-release").readline()
!     except: pass
!     else:
!       if (    red_hat_linux_release.startswith("Red Hat Linux release")
!           and red_hat_linux_release.split()[4] == "9"):
!         lines.extend([
!           'if [ ! -n "$LD_ASSUME_KERNEL" ]; then',
!           '  LD_ASSUME_KERNEL=2.4.1',
!           '  export LD_ASSUME_KERNEL',
!           'fi'])
!   if (os.name == "posix" and libtbx_env.compiler == "icc"):
!     addl_lines = create_posix_icc_ld_preload(libtbx_env)
!     if (addl_lines is None):
!       raise libtbx.config.UserError("Cannot determine LD_PRELOAD for icc.")
!     lines.extend(addl_lines)
!   return lines
! 
! def create_python_dispatchers(libtbx_env, target_dir, precall_commands):
!   python_exe = libtbx_env.LIBTBX_PYTHON_EXE
!   for file_name in ("libtbx.python", "python"):
!     target_file = norm(join(target_dir, file_name))
!     if (os.name == "nt"):
!       action = create_win32_dispatcher(
!         dispatcher_front_end_exe=libtbx_env.dispatcher_front_end_exe())
!     else:
!       action = create_bin_sh_dispatcher(
!         python_exe=python_exe,
!         precall_commands=precall_commands)
!       try: os.chmod(source_file, 0755)
!       except: pass
!     if (isfile(target_file) or islink(target_file)):
!       try: os.remove(target_file)
!       except OSError: pass
!       else: action(python_exe, target_file)
!     else:
!       action(python_exe, target_file)
! 
! def create_show_build_path(libtbx_env, target_dir):
!   target_file = os.path.join(target_dir, "libtbx.show_build_path")
!   f = open(target_file, "w")
!   print >> f, '#! /bin/sh'
!   print >> f, '# LIBTBX_DISPATCHER DO NOT EDIT'
!   print >> f, 'echo "%s"' % libtbx_env.LIBTBX_BUILD
!   f.close()
!   os.chmod(target_file, 0755)
  
  def run():
!   libtbx_env = libtbx.config.env()
!   target_dir = norm(join(libtbx_env.LIBTBX_BUILD, "libtbx/bin"))
    if (not isdir(target_dir)):
      os.makedirs(target_dir)
!   precall_commands = assemble_dispatcher_precall_commands(libtbx_env)
!   create_python_dispatchers(
!     libtbx_env=libtbx_env,
!     target_dir=target_dir,
!     precall_commands=precall_commands)
!   dispatcher_dict = {}
!   for dist_path in libtbx_env.dist_paths.values():
      dist_root = os.path.dirname(dist_path)
      package_name = os.path.basename(dist_path)
--- 11,43 ----
    if (file_name.lower().endswith(".pyc")): return
    if (file_name[0] == "."): return
+   if (os.name == "nt"):
+     ext = splitext(file_name)[1].lower()
+     if (ext not in libtbx.config.windows_pathext): return
    target_file = norm(join(target_dir, package_name))
    if (file_name.lower() != "main.py"):
      target_file += "." + splitext(file_name)[0]
!   libtbx.env.cache.create_dispatcher(
!     source_file=source_file,
!     target_file=target_file)
  
! def create_dispatchers(target_dir, package_name, source_dir):
    if (not isdir(source_dir)): return
    print "Processing:", source_dir
    for file_name in os.listdir(source_dir):
!     create_dispatcher(
        target_dir=target_dir,
        package_name=package_name,
        source_dir=source_dir,
!       file_name=file_name)
  
  def run():
!   target_dir = libtbx.env.under_build("libtbx/bin")
    if (not isdir(target_dir)):
      os.makedirs(target_dir)
!   for file_name in ("libtbx.python", "python"):
!     libtbx.env.cache.create_dispatcher(
!       source_file=libtbx.env.cache.LIBTBX_PYTHON_EXE,
!       target_file=norm(join(target_dir, file_name)))
!   for dist_path in libtbx.env.cache.dist_paths.values():
      dist_root = os.path.dirname(dist_path)
      package_name = os.path.basename(dist_path)
***************
*** 227,243 ****
                             name=package_name,
                             dist_root=dist_root).primary_first():
!       create_drivers(
!         libtbx_env=libtbx_env,
!         precall_commands=precall_commands,
          target_dir=target_dir,
          package_name=package_name,
!         source_dir=norm(join(dist_path_suf, package_name, "command_line")),
!         dispatcher_dict=dispatcher_dict)
!   if (os.name == "nt"):
!     create_dispatcher_back_end(
!       libtbx_env=libtbx_env,
!       dispatcher_dict=dispatcher_dict)
!   else:
!     create_show_build_path(libtbx_env=libtbx_env, target_dir=target_dir)
  
  if (__name__ == "__main__"):
--- 45,60 ----
                             name=package_name,
                             dist_root=dist_root).primary_first():
!       create_dispatchers(
          target_dir=target_dir,
          package_name=package_name,
!         source_dir=norm(join(dist_path_suf, package_name, "command_line")))
!   exe_path = norm(join(libtbx.env.cache.LIBTBX_BUILD, "exe"))
!   if (os.path.isdir(exe_path)):
!     print "Processing:", exe_path
!     for file_name in os.listdir(exe_path):
!       if (file_name[0] == "."): continue
!       libtbx.env.cache.create_dispatcher(
!         source_file=norm(join(exe_path, file_name)),
!         target_file=norm(join(target_dir, file_name)))
  
  if (__name__ == "__main__"):

Index: configure.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/command_line/configure.py,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** configure.py	20 Feb 2005 04:09:53 -0000	1.50
--- configure.py	24 Feb 2005 23:28:20 -0000	1.51
***************
*** 7,11 ****
  import libtbx.config
  import libtbx.path
! from libtbx.config import UserError
  
  class registry:
--- 7,11 ----
  import libtbx.config
  import libtbx.path
! from libtbx.utils import UserError
  
  class registry:
***************
*** 102,107 ****
          try:
            p = package(self.dist_root, package_name)
!         except UserError:
!           pass
          else:
            if (p.dist_path is not None):
--- 102,107 ----
          try:
            p = package(self.dist_root, package_name)
!         except UserError, e:
!           e.reset_tracebacklimit()
          else:
            if (p.dist_path is not None):
***************
*** 122,140 ****
  
    def __init__(self, cwd, libtbx_dist):
      self.python_version_major_minor = sys.version_info[:2]
      if (os.name == "nt"):
!       self.LIBTBX_PYTHON_EXE = norm(abspath(join(sys.prefix, "python.exe")))
      else:
!       self.LIBTBX_PYTHON_EXE = norm(abspath(join(sys.prefix, "bin", "python")))
!     self.LIBTBX_BUILD = norm(abspath(os.getcwd()))
!     self.LIBTBX_DIST_ROOT = norm(dirname(libtbx_dist))
      self.LD_LIBRARY_PATH = [norm(join(self.LIBTBX_BUILD, "libtbx"))]
      self.PYTHONPATH = [norm(join(self.LIBTBX_BUILD, "libtbx")), libtbx_dist]
      self.PATH = [norm(join(self.LIBTBX_BUILD, "libtbx/bin"))]
      self.package_list = []
      self.effective_roots = []
      self.dist_paths = {"LIBTBX_DIST": libtbx_dist}
      self.scons_in_dist_root = False
!     if (os.path.isdir(join(self.LIBTBX_DIST_ROOT, "scons"))):
        self.scons_in_dist_root = True
  
--- 122,149 ----
  
    def __init__(self, cwd, libtbx_dist):
+     self.LIBTBX_BUILD = norm(abspath(os.getcwd()))
+     self._shortpath_bat = None
+     self.LIBTBX_BUILD = self.abs_path_clean(self.LIBTBX_BUILD)
+     libtbx_dist = self.abs_path_clean(libtbx_dist)
      self.python_version_major_minor = sys.version_info[:2]
      if (os.name == "nt"):
!       self.LIBTBX_PYTHON_EXE = self.abs_path_clean(join(
!         sys.prefix, "python.exe"))
      else:
!       self.LIBTBX_PYTHON_EXE = self.abs_path_clean(join(
!         sys.prefix, "bin/python"))
      self.LD_LIBRARY_PATH = [norm(join(self.LIBTBX_BUILD, "libtbx"))]
      self.PYTHONPATH = [norm(join(self.LIBTBX_BUILD, "libtbx")), libtbx_dist]
      self.PATH = [norm(join(self.LIBTBX_BUILD, "libtbx/bin"))]
+     self.libtbx_dist_root = dirname(libtbx_dist)
+     self.libtbx_python = norm(join(
+       self.LIBTBX_BUILD,"libtbx","bin","libtbx.python"))
+     self.libtbx_path_utility = norm(join(
+       libtbx_dist, "libtbx/command_line/path_utility.py"))
      self.package_list = []
      self.effective_roots = []
      self.dist_paths = {"LIBTBX_DIST": libtbx_dist}
      self.scons_in_dist_root = False
!     if (os.path.isdir(join(self.libtbx_dist_root, "scons"))):
        self.scons_in_dist_root = True
  
***************
*** 146,150 ****
          and package.effective_root_adaptbx not in self.effective_roots):
        self.effective_roots.append(package.effective_root_adaptbx)
!     self.dist_paths[package.name.upper() + "_DIST"] = package.dist_path
      if (not explicit_adaptbx):
        ppn = libtbx.config.package_pair(name=package.name)
--- 155,160 ----
          and package.effective_root_adaptbx not in self.effective_roots):
        self.effective_roots.append(package.effective_root_adaptbx)
!     self.dist_paths[package.name.upper() + "_DIST"] = self.abs_path_clean(
!       package.dist_path)
      if (not explicit_adaptbx):
        ppn = libtbx.config.package_pair(name=package.name)
***************
*** 153,157 ****
            name=package.name,
            dist_root=package.dist_root)
!         self.dist_paths[ppn.adaptbx.upper() + "_DIST"] = ppd.adaptbx
      if (package.python_path is not None):
        insert_normed_path(self.PYTHONPATH, package.python_path)
--- 163,168 ----
            name=package.name,
            dist_root=package.dist_root)
!         self.dist_paths[ppn.adaptbx.upper() + "_DIST"] = self.abs_path_clean(
!           ppd.adaptbx)
      if (package.python_path is not None):
        insert_normed_path(self.PYTHONPATH, package.python_path)
***************
*** 182,258 ****
          + " used to build binaries: %s") % (api_from_process, api_from_build))
  
! def emit_setpaths_sh(env):
!   for file_name in ("setpaths.sh", "env_run.sh"):
!     full_path = norm(join(env.LIBTBX_BUILD, file_name))
!     f = open_info(full_path)
!     for var_name, values in env.items():
!       if (var_name.upper() != var_name): continue
!       if (var_name == "LD_LIBRARY_PATH" and sys.platform.startswith("darwin")):
!         var_name = "DYLD_LIBRARY_PATH"
!       if (type(values) == type([])):
!         val = os.pathsep.join(values)
!         print >> f, 'LIBTBX_%s="%s"' % (var_name, val)
!         print >> f, 'export LIBTBX_%s' % var_name
!         val = "$LIBTBX_%s" % var_name
!         print >> f, 'if [ ! -n "$%s" ]; then' % (var_name,)
!         print >> f, '  %s="%s"' % (var_name, val)
!         print >> f, 'else'
!         print >> f, '  %s="%s%s$%s"' % (var_name, val, os.pathsep, var_name)
!         print >> f, 'fi'
!         print >> f, 'LIBTBX0%s="$%s"' % (var_name, var_name)
!         print >> f, 'export LIBTBX0%s' % var_name
        else:
!         print >> f, '%s="%s"' % (var_name, values)
!       print >> f, 'export %s' % (var_name,)
!     if (file_name == "env_run.sh"):
!       print >> f, '"%s" "%s" "$@"' % (
!         "$LIBTBX_BUILD/libtbx/bin/libtbx.python",
!         "$LIBTBX_DIST/libtbx/command_line/env_run.py")
!     f.close()
!     os.chmod(full_path, 0755)
  
  def emit_setpaths_csh(env):
-   libtbx_python = norm(join(
-     env.LIBTBX_BUILD, "libtbx","bin","libtbx.python"))
-   libtbx_path_utility = norm(join(
-     env.LIBTBX_DIST_ROOT, "libtbx","libtbx","command_line","path_utility.py"))
    setpaths_csh_path = norm(join(env.LIBTBX_BUILD, "setpaths.csh"))
    unsetpaths_csh_path = norm(join(env.LIBTBX_BUILD, "unsetpaths.csh"))
    s = open_info(setpaths_csh_path)
    u = open_info(unsetpaths_csh_path)
    for f in s, u:
!     print >> f, '"%s" -V >& /dev/null' % libtbx_python
!     print >> f, 'if ($status != 0 || ! -f "%s") then' % libtbx_path_utility
!     print >> f, '  echo "*******************************************"'
!     print >> f, '  echo "Fatal Error: Incomplete libtbx environment!"'
!     print >> f, '  echo "*******************************************"'
!     print >> f, '  echo "Please re-run the libtbx/configure.py command."'
!     print >> f, '  echo ""'
!     if (f is s):
!       print >> f, 'else if ($#argv != 0 && $#argv != 1'\
!                   ' || $#argv && "$1" != "minimal") then'
!       print >> f, '  echo "usage: source $0 [minimal]"'
      print >> f, 'else'
    for var_name, values in env.items():
!     if (var_name.upper() != var_name): continue
!     if (var_name == "LD_LIBRARY_PATH" and sys.platform.startswith("darwin")):
!       var_name = "DYLD_LIBRARY_PATH"
!     if (type(values) == type([])):
!       val = os.pathsep.join(values)
!       print >> s, '  setenv LIBTBX_%s "%s"' % (var_name, val)
!       print >> u, '  unsetenv LIBTBX_%s' % var_name
!       fmt_args = (var_name, libtbx_python, libtbx_path_utility, var_name, val)
!       print >> s, '''  setenv %s "`'%s' '%s' prepend %s '%s'`"''' % fmt_args
!       print >> u, '''  setenv %s "`'%s' '%s' delete %s '%s'`"''' % fmt_args
!       print >> s, '  setenv LIBTBX0%s "$%s"' % (var_name, var_name)
!       print >> u, '  unsetenv LIBTBX0%s' % var_name
!     else:
!       if (   var_name.endswith("_DIST")
!           or var_name.endswith("_DIST_ROOT")):
!         condition = "if ($#argv == 0) "
!       else:
!         condition = ""
!       print >> s, '  %ssetenv %s "%s"' % (condition, var_name, values)
!       print >> u, '  unsetenv %s' % var_name
    for f in s, u:
      print >> f, 'endif'
--- 193,379 ----
          + " used to build binaries: %s") % (api_from_process, api_from_build))
  
!   def abs_path_short(self, abs_path):
!     if (os.name != "nt"): return abs_path
!     if (self._shortpath_bat is None):
!       self._shortpath_bat = "shortpath.bat"
!       libtbx_build = self.LIBTBX_BUILD
!       if (libtbx_build is not None):
!         self._shortpath_bat = os.path.join(libtbx_build, self._shortpath_bat)
!     assert os.path.exists(self._shortpath_bat)
!     return os.popen('call "%s" "%s"' %
!       (self._shortpath_bat, abs_path), "r").readline().rstrip()
! 
!   def abs_path_clean(self, path):
!     abs_path = norm(abspath(path))
!     if (os.name != "nt"): return abs_path
!     short = self.abs_path_short(abs_path).split(os.sep)
!     orig = abs_path.split(os.sep)
!     clean = []
!     for o,s in zip(orig, short):
!       if (o.find(" ") < 0):
!         clean.append(o)
        else:
!         clean.append(s)
!     return os.sep.join(clean)
! 
! def write_incomplete_libtbx_environment(f):
!   message = [
!     "*******************************************",
!     "Fatal Error: Incomplete libtbx environment!",
!     "*******************************************",
!     "Please re-run the libtbx/configure.py command."]
!   if (os.name != "nt"):
!     for line in message: print >> f, '  echo "%s"' % line
!     print >> f, '  echo ""'
!   else:
!     for line in message: print >> f, '  echo %s' % line
!     print >> f, '  echo.'
! 
! class unix_update_path:
! 
!   def __init__(self, env, shell, s, u):
!     assert shell in ["sh", "csh"]
!     self.shell = shell
!     self.env = env
!     self.s = s
!     self.u = u
!     if (self.shell == "sh"):
!       self.setenv = "%s="
!     else:
!       self.setenv = "setenv %s "
! 
!   def write(self, prefixes, var_name, val):
!     val = os.pathsep.join(val)
!     for f,prefix,action in [(self.s, prefixes[0], "prepend"),
!                             (self.u, prefixes[1], "delete")]:
!       print >> f, '''%s%s"`'%s' '%s' %s %s '%s'`"''' % (
!         prefix,
!         self.setenv % var_name,
!         self.env.LIBTBX_PYTHON_EXE,
!         self.env.libtbx_path_utility,
!         action,
!         var_name,
!         val)
!       if (f is self.s and self.shell == "sh"):
!         print >> f, '%sexport %s' % (prefixes[0], var_name)
! 
! class windows_update_path:
! 
!   def __init__(self, env, s, u):
!     self.env = env
!     self.s = s
!     self.u = u
! 
!   def write(self, prefixes, var_name, val):
!     val = os.pathsep.join(val)
!     fmt = '''%sfor /F %%%%i in ('%s "%s" %s %s "%s"') do set %s=%%%%i'''
!     for f,prefix,action in [(self.s, prefixes[0], "prepend"),
!                             (self.u, prefixes[1], "delete")]:
!       print >> f, fmt % (
!         prefix,
!         self.env.LIBTBX_PYTHON_EXE,
!         self.env.libtbx_path_utility,
!         action,
!         var_name,
!         val,
!         var_name)
!       print >> f, '%sif "%%%s%%" == "E_M_P_T_Y" set %s=' % (
!         prefix, var_name, var_name)
! 
! def emit_setpaths_sh(env):
!   setpaths_path = norm(join(env.LIBTBX_BUILD, "setpaths.sh"))
!   unsetpaths_path = norm(join(env.LIBTBX_BUILD, "unsetpaths.sh"))
!   s = open_info(setpaths_path)
!   u = open_info(unsetpaths_path)
!   update_path = unix_update_path(env, "sh", s, u)
!   for f in s, u:
!     print >> f, '"%s" -V > /dev/null 2>&1' % env.libtbx_python
!     print >> f, \
!       'if [ $? -ne 0 -o ! -f "%s" ]; then' % env.libtbx_path_utility
!     write_incomplete_libtbx_environment(f)
!     print >> f, 'else'
!   update_path.write(("  ", "  "), "PATH", env.PATH)
!   for un in ["", "un"]:
!     print >> s, \
!       """  alias libtbx.%ssetpaths='source "%s/%ssetpaths.sh"'""" % (
!         un, env.LIBTBX_BUILD, un)
!   print >> u, '  unalias libtbx.unsetpaths > /dev/null 2>&1'
!   print >> s, '  if [ $# -ne 0 ]; then'
!   print >> s, \
!     '    if [ $# -ne 1 -o \( "$1" != "all" -a "$1" != "debug" \) ]; then'
!   print >> s, '      echo "usage: source setpaths.sh [all|debug]"'
!   print >> s, '    else'
!   print >> s, '      %s="%s"' % ("LIBTBX_BUILD", env.LIBTBX_BUILD)
!   print >> s, '      export %s' % "LIBTBX_BUILD"
!   print >> u, '  unset %s' % "LIBTBX_BUILD"
!   for var_name, values in env.items():
!     if (not var_name.endswith("_DIST")): continue
!     print >> s, '      %s="%s"' % (var_name, values)
!     print >> s, '      export %s' % var_name
!     print >> u, '  unset %s' % var_name
!   print >> s, '      if [ "$1" == "debug" ]; then'
!   update_path.write(("        ", "  "), "PYTHONPATH", env.PYTHONPATH)
!   if (sys.platform.startswith("darwin")):
!     ld_library_path = "DYLD_LIBRARY_PATH"
!   else:
!     ld_library_path = "LD_LIBRARY_PATH"
!   update_path.write(("        ", "  "), ld_library_path, env.LD_LIBRARY_PATH)
!   print >> s, '      fi'
!   print >> s, '    fi'
!   print >> s, '  fi'
!   for f in s, u:
!     print >> f, 'fi'
!   s.close()
!   u.close()
! 
! def emit_env_run_sh(env):
!   env_run_sh = norm(join(env.LIBTBX_BUILD, "env_run.sh"))
!   f = open_info(env_run_sh)
!   print >> f, '. "%s" all' % (os.path.join(env.LIBTBX_BUILD, "setpaths.sh"))
!   print >> f, '"%s" "%s" "$@"' % (
!     "$LIBTBX_BUILD/libtbx/bin/python",
!     "$LIBTBX_DIST/libtbx/command_line/env_run.py")
!   f.close()
!   os.chmod(env_run_sh, 0755)
  
  def emit_setpaths_csh(env):
    setpaths_csh_path = norm(join(env.LIBTBX_BUILD, "setpaths.csh"))
    unsetpaths_csh_path = norm(join(env.LIBTBX_BUILD, "unsetpaths.csh"))
    s = open_info(setpaths_csh_path)
    u = open_info(unsetpaths_csh_path)
+   update_path = unix_update_path(env, "csh", s, u)
    for f in s, u:
!     print >> f, '"%s" -V >& /dev/null' % env.libtbx_python
!     print >> f, \
!       'if ($status != 0 || ! -f "%s") then' % env.libtbx_path_utility
!     write_incomplete_libtbx_environment(f)
      print >> f, 'else'
+   update_path.write(("  ", "  "), "PATH", env.PATH)
+   for un in ["", "un"]:
+     print >> s, \
+       """  alias libtbx.%ssetpaths 'source "%s/%ssetpaths.csh"'""" % (
+         un, env.LIBTBX_BUILD, un)
+   print >> u, '  unalias libtbx.unsetpaths'
+   print >> s, '  if ($#argv != 0) then'
+   print >> s, \
+     '    if ($#argv != 1 || ("$1" != "all" && "$1" != "debug")) then'
+   print >> s, '      echo "usage: source setpaths.csh [all|debug]"'
+   print >> s, '    else'
+   print >> s, '      setenv %s "%s"' % ("LIBTBX_BUILD", env.LIBTBX_BUILD)
+   print >> u, '  unsetenv %s' % "LIBTBX_BUILD"
    for var_name, values in env.items():
!     if (not var_name.endswith("_DIST")): continue
!     print >> s, '      setenv %s "%s"' % (var_name, values)
!     print >> u, '  unsetenv %s' % var_name
!   print >> s, '      if ("$1" == "debug") then'
!   update_path.write(("        ", "  "), "PYTHONPATH", env.PYTHONPATH)
!   if (sys.platform.startswith("darwin")):
!     ld_library_path = "DYLD_LIBRARY_PATH"
!   else:
!     ld_library_path = "LD_LIBRARY_PATH"
!   update_path.write(("        ", "  "), ld_library_path, env.LD_LIBRARY_PATH)
!   print >> s, '      endif'
!   print >> s, '    endif'
!   print >> s, '  endif'
    for f in s, u:
      print >> f, 'endif'
***************
*** 260,286 ****
    u.close()
  
- def join_path_ld_library_path(env):
-   joined_path = list(env.PATH)
-   for path in env.LD_LIBRARY_PATH:
-     if (not path in joined_path):
-       joined_path.append(path)
-   return joined_path
- 
  def emit_setpaths_bat(env):
!   setpaths_bat_path = norm(join(env.LIBTBX_BUILD, "setpaths.bat"))
!   f = open_info(setpaths_bat_path)
!   print >> f, '@ECHO off'
    for var_name, values in env.items():
!     if (var_name.upper() != var_name): continue
!     if (type(values) == type([])):
!       if (var_name == "LD_LIBRARY_PATH"): continue
!       if (var_name == "PATH"):
!         values = join_path_ld_library_path(env)
!       val = os.pathsep.join([libtbx.path.abs_path_clean(v) for v in values])
!       print >> f, 'if not defined %s set %s=' % (var_name, var_name)
!       print >> f, 'set %s=%s%s%%%s%%' % (var_name, val, os.pathsep, var_name)
!     else:
!       print >> f, 'set %s=%s' % (var_name, libtbx.path.abs_path_clean(values))
!   f.close()
  
  class build_options_t:
--- 381,424 ----
    u.close()
  
  def emit_setpaths_bat(env):
!   setpaths_path = norm(join(env.LIBTBX_BUILD, "setpaths.bat"))
!   unsetpaths_path = norm(join(env.LIBTBX_BUILD, "unsetpaths.bat"))
!   s = open_info(setpaths_path)
!   u = open_info(unsetpaths_path)
!   update_path = windows_update_path(env, s, u)
!   for f in s, u:
!     print >> f, '@ECHO off'
!     print >> f, 'if not exist "%s" goto fatal_error' % env.LIBTBX_PYTHON_EXE
!     print >> f, 'if not exist "%s" goto fatal_error' % env.libtbx_path_utility
!     print >> f, 'if exist "%s.exe" goto update_path' % env.libtbx_python
!     write_incomplete_libtbx_environment(f)
!     print >> f, '  goto end_of_script'
!     print >> f, ':update_path'
!   update_path.write(("  ", "  "), "PATH", env.PATH)
!   for un in ["", "un"]:
!     print >> s, '  doskey libtbx.%ssetpaths="%s\\%ssetpaths.bat" $*' % (
!       un, env.LIBTBX_BUILD, un)
!   print >> u, '  doskey libtbx.unsetpaths='
!   print >> s, '  if "%1" == "" goto end_of_script'
!   print >> s, '  if not "%2" == "" goto show_usage'
!   print >> s, '  if "%1" == "all" goto set_all'
!   print >> s, '  if "%1" == "debug" goto set_all'
!   print >> s, ':show_usage'
!   print >> s, '  echo usage: setpaths [all^|debug]'
!   print >> s, '  goto end_of_script'
!   print >> s, ':set_all'
!   print >> s, '  set %s="%s"' % ("LIBTBX_BUILD", env.LIBTBX_BUILD)
!   print >> u, '  set %s=' % "LIBTBX_BUILD"
    for var_name, values in env.items():
!     if (not var_name.endswith("_DIST")): continue
!     print >> s, '  set %s="%s"' % (var_name, values)
!     print >> u, '  set %s=' % var_name
!   print >> s, '  if not "%1" == "debug" goto end_of_script'
!   update_path.write(("    ", "  "), "PYTHONPATH", env.PYTHONPATH)
!   update_path.write(("    ", "  "), "PATH", env.LD_LIBRARY_PATH)
!   for f in s, u:
!     print >> f, ':end_of_script'
!   s.close()
!   u.close()
  
  class build_options_t:
***************
*** 436,443 ****
    packages = registry()
    for arg in args:
!     packages.merge(package(env.LIBTBX_DIST_ROOT, arg).dependency_registry)
    if (len(packages.list) == 0):
      show_help(old_env)
      raise UserError("At least one package must be specified.")
    if (len(packages.missing_for_build) == 0):
      build_options.report()
--- 574,582 ----
    packages = registry()
    for arg in args:
!     packages.merge(package(env.libtbx_dist_root, arg).dependency_registry)
    if (len(packages.list) == 0):
      show_help(old_env)
      raise UserError("At least one package must be specified.")
+   print "Python:", sys.version.split()[0], sys.executable
    if (len(packages.missing_for_build) == 0):
      build_options.report()
***************
*** 465,468 ****
--- 604,608 ----
    if (hasattr(os, "symlink")):
      emit_setpaths_sh(env)
+     emit_env_run_sh(env)
      emit_setpaths_csh(env)
    else:
***************
*** 481,485 ****
      print "Error:", e
    else:
-     sys.path.insert(0, norm(join(env.dist_paths["LIBTBX_DIST"], "libtbx")))
      os.environ["LIBTBX_BUILD"] = env.LIBTBX_BUILD
      from libtbx.command_line import refresh
--- 621,624 ----
***************
*** 494,498 ****
          "Current working directory must be: " + old_env.LIBTBX_BUILD)
      run(
!       libtbx_dist=old_env.dist_paths["LIBTBX_DIST"],
        args=args[1:],
        old_env=old_env)
--- 633,637 ----
          "Current working directory must be: " + old_env.LIBTBX_BUILD)
      run(
!       libtbx_dist=old_env.dist_path("libtbx"),
        args=args[1:],
        old_env=old_env)

Update of /cvsroot/cctbx/cctbx/cctbx/xray
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31376

Modified Files:
	target_functors.py 
Log Message:
new ls targets

Index: target_functors.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/xray/target_functors.py,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** target_functors.py	28 Jan 2005 16:38:36 -0000	1.15
--- target_functors.py	24 Feb 2005 00:55:22 -0000	1.16
***************
*** 29,33 ****
                       scale_factor           = 0):
      adopt_init_args(self, locals())
!     assert self.target_name in ("ml","ls","mlhl")
      assert self.f_obs.data().size() == self.flags.size()
      if(self.flags.count(True) > 0):
--- 29,37 ----
                       scale_factor           = 0):
      adopt_init_args(self, locals())
!     assert self.target_name in ("ls_wunit_k1","ls_wunit_k2","ls_wunit_kunit",
!                                 "ls_wexp_k1" ,"ls_wexp_k2" ,"ls_wexp_kunit",
!                                 "ls_wff_k1"  ,"ls_wff_k2"  ,"ls_wff_kunit",
!                                 "lsm_k1"     ,"lsm_k2"     ,"lsm_kunit",
!                                 "ml","mlhl")
      assert self.f_obs.data().size() == self.flags.size()
      if(self.flags.count(True) > 0):
***************
*** 52,56 ****
        self.abcd_w, self.abcd_t = None, None
      if(self.weights is not None):
!       assert self.target_name == "ls"
        if(self.flags.count(True) > 0):
          self.weights_w = self.weights.select(~self.flags)
--- 56,60 ----
        self.abcd_w, self.abcd_t = None, None
      if(self.weights is not None):
!       assert self.target_name.count("ls")+self.target_name.count("k") == 2
        if(self.flags.count(True) > 0):
          self.weights_w = self.weights.select(~self.flags)
***************
*** 74,83 ****
        if(self.abcd_w is not None): abcd = self.abcd_w.select(selection)
        else:                        abcd = self.abcd_w
!     if(self.target_name == "ls"):
!       return least_squares_residual(
!                             f_obs                 = f_obs,
!                             weights               = weights,
!                             use_sigmas_as_weights = self.use_sigmas_as_weights,
!                             scale_factor          = self.scale_factor)
      if(self.target_name == "ml"):
        return maximum_likelihood_criterion(f_obs = f_obs)
--- 78,99 ----
        if(self.abcd_w is not None): abcd = self.abcd_w.select(selection)
        else:                        abcd = self.abcd_w
!     if(self.target_name.count("k1") == 1):
!        assert self.scale_factor == 0
!        return ls_k1(f_obs            = f_obs,
!                     weights          = weights,
!                     scale_factor     = self.scale_factor,
!                     fix_scale_factor = False)
!     if(self.target_name.count("k2") == 1):
!        assert self.scale_factor == 0
!        return ls_k2(f_obs            = f_obs,
!                     weights          = weights,
!                     scale_factor     = self.scale_factor,
!                     fix_scale_factor = False)
!     if(self.target_name.count("kunit") == 1):
!        assert self.scale_factor == 1
!        return ls_k1(f_obs            = f_obs,
!                     weights          = weights,
!                     scale_factor     = self.scale_factor,
!                     fix_scale_factor = True)
      if(self.target_name == "ml"):
        return maximum_likelihood_criterion(f_obs = f_obs)
***************
*** 99,108 ****
        if(self.abcd_t is not None): abcd = self.abcd_t.select(selection)
        else:                        abcd = self.abcd_t
!     if(self.target_name == "ls"):
!       return least_squares_residual(
!                             f_obs                 = f_obs,
!                             weights               = weights,
!                             use_sigmas_as_weights = self.use_sigmas_as_weights,
!                             scale_factor          = self.scale_factor)
      if(self.target_name == "ml"):
        return maximum_likelihood_criterion(f_obs = f_obs)
--- 115,136 ----
        if(self.abcd_t is not None): abcd = self.abcd_t.select(selection)
        else:                        abcd = self.abcd_t
!     if(self.target_name.count("k1") == 1):
!        assert self.scale_factor == 0
!        return ls_k1(f_obs            = f_obs,
!                     weights          = weights,
!                     scale_factor     = self.scale_factor,
!                     fix_scale_factor = False)
!     if(self.target_name.count("k2") == 1):
!        assert self.scale_factor == 0
!        return ls_k2(f_obs            = f_obs,
!                     weights          = weights,
!                     scale_factor     = self.scale_factor,
!                     fix_scale_factor = False)
!     if(self.target_name.count("kunit") == 1):
!        assert self.scale_factor == 1
!        return ls_k1(f_obs            = f_obs,
!                     weights          = weights,
!                     scale_factor     = self.scale_factor,
!                     fix_scale_factor = True)
      if(self.target_name == "ml"):
        return maximum_likelihood_criterion(f_obs = f_obs)
***************
*** 112,115 ****
--- 140,206 ----
                                abcd                 = abcd.data())
  
+ class ls_k1:
+ 
+   def __init__(self, f_obs,
+                      weights,
+                      scale_factor,
+                      fix_scale_factor):
+     adopt_init_args(self, locals(), hide=True)
+     if(self._fix_scale_factor == True):
+        assert self._scale_factor > 0.0
+ 
+   def f_obs(self):
+     return self._f_obs
+ 
+   def weights(self):
+     return self._weights
+ 
+   def scale_factor(self):
+     return self._scale_factor
+ 
+   def __call__(self, f_calc, compute_derivatives):
+     assert f_calc.unit_cell().is_similar_to(
+            self.f_obs().unit_cell())
+     assert f_calc.space_group() == self.f_obs().space_group()
+     assert f_calc.data().size() == self.f_obs().data().size()
+     return ext.ls_target_with_scale_k1(
+                                   f_obs               = self.f_obs().data(),
+                                   weights             = self.weights(),
+                                   f_calc              = f_calc.data(),
+                                   compute_derivatives = compute_derivatives,
+                                   fix_scale           = self._fix_scale_factor,
+                                   scale               = self._scale_factor)
+ 
+ class ls_k2:
+ 
+   def __init__(self, f_obs,
+                      weights,
+                      scale_factor,
+                      fix_scale_factor):
+     adopt_init_args(self, locals(), hide=True)
+     if(self._fix_scale_factor == True):
+        assert self._scale_factor > 0.0
+ 
+   def f_obs(self):
+     return self._f_obs
+ 
+   def weights(self):
+     return self._weights
+ 
+   def scale_factor(self):
+     return self._scale_factor
+ 
+   def __call__(self, f_calc, compute_derivatives):
+     assert f_calc.unit_cell().is_similar_to(
+            self.f_obs().unit_cell())
+     assert f_calc.space_group() == self.f_obs().space_group()
+     assert f_calc.data().size() == self.f_obs().data().size()
+     return ext.ls_target_with_scale_k2(
+                                   f_obs               = self.f_obs().data(),
+                                   weights             = self.weights(),
+                                   f_calc              = f_calc.data(),
+                                   compute_derivatives = compute_derivatives,
+                                   fix_scale           = self._fix_scale_factor,
+                                   scale               = self._scale_factor)
  
  class least_squares_residual:

Update of /cvsroot/cctbx/iotbx/iotbx/xplor
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23122/iotbx/xplor

Modified Files:
	tst_xplormap.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: tst_xplormap.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/xplor/tst_xplormap.py,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** tst_xplormap.py	22 Jan 2005 14:18:26 -0000	1.14
--- tst_xplormap.py	20 Feb 2005 04:10:57 -0000	1.15
***************
*** 7,10 ****
--- 7,11 ----
  from scitbx.python_utils.math_utils import iround
  from libtbx.test_utils import approx_equal, eps_eq
+ import libtbx.env
  import sys, os
  
***************
*** 37,42 ****
  end
    """
!   return os.path.join(os.environ["LIBTBX_DIST_ROOT"],
!     "regression", "misc", "cns.map")
  
  def read_xplor(file_name):
--- 38,42 ----
  end
    """
!   return libtbx.env.under_dist_root("regression/misc/cns.map")
  
  def read_xplor(file_name):

Update of /cvsroot/cctbx/iotbx/iotbx/pdb
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23122/iotbx/pdb

Modified Files:
	tst_pdb.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: tst_pdb.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/pdb/tst_pdb.py,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** tst_pdb.py	4 Feb 2005 02:58:51 -0000	1.28
--- tst_pdb.py	20 Feb 2005 04:10:57 -0000	1.29
***************
*** 10,13 ****
--- 10,14 ----
  from cctbx.array_family import flex
  import scitbx.math
+ import libtbx.env
  from cStringIO import StringIO
  import sys, os
***************
*** 145,150 ****
  
  def exercise_interpretation(verbose=0, quick=True):
!   pdb_dir = os.path.join(os.environ["LIBTBX_DIST_ROOT"],
!     "regression", "pdb")
    if (not os.path.isdir(pdb_dir)):
      print "Skipping exercise_interpretation(): input file not available"
--- 146,150 ----
  
  def exercise_interpretation(verbose=0, quick=True):
!   pdb_dir = libtbx.env.under_dist_root("regression/pdb")
    if (not os.path.isdir(pdb_dir)):
      print "Skipping exercise_interpretation(): input file not available"

Update of /cvsroot/cctbx/iotbx/iotbx/mtz
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23122/iotbx/mtz

Modified Files:
	extract_from_symop_lib.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: extract_from_symop_lib.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/mtz/extract_from_symop_lib.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** extract_from_symop_lib.py	20 Oct 2004 20:00:08 -0000	1.5
--- extract_from_symop_lib.py	20 Feb 2005 04:10:56 -0000	1.6
***************
*** 1,17 ****
  from cctbx import sgtbx
  import os
  
! def environ_based_path(path_elements):
!   if (os.environ.has_key(path_elements[0])):
!     return os.path.normpath(os.sep.join(
!       [os.environ[path_elements[0]]] + path_elements[1:]))
!   return None
  
  def ccp4_symbol(space_group_info):
    found_at_least_one_symop_lib = False
!   for symop_lib_path in (
!         environ_based_path(["CCP4_LIB", "data", "symop.lib"]),
!         environ_based_path(["CCP4IO_DIST", "lib", "data", "symop.lib"])):
!     if (symop_lib_path is not None):
        found_at_least_one_symop_lib = True
        file_iter = iter(open(symop_lib_path, "r"))
--- 1,19 ----
  from cctbx import sgtbx
+ import libtbx.env
  import os
  
! try:
!   ccp4io_dist = libtbx.env.dist_path("ccp4io")
! except KeyError:
!   ccp4io_dist = None
  
  def ccp4_symbol(space_group_info):
+   symop_lib_paths = [os.path.expandvars("$CCP4_LIB/data/symop.lib")]
+   if (ccp4io_dist is not None):
+     symop_lib_paths.append(os.path.normpath(os.path.join(
+       ccp4io_dist, "lib/data/symop.lib")))
    found_at_least_one_symop_lib = False
!   for symop_lib_path in symop_lib_paths:
!     if (os.path.isfile(symop_lib_path)):
        found_at_least_one_symop_lib = True
        file_iter = iter(open(symop_lib_path, "r"))

Update of /cvsroot/cctbx/iotbx/include/iotbx/mtz
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23122/include/iotbx/mtz

Modified Files:
	tst_ext.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: tst_ext.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/include/iotbx/mtz/tst_ext.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** tst_ext.py	22 Jan 2005 14:18:25 -0000	1.5
--- tst_ext.py	20 Feb 2005 04:10:56 -0000	1.6
***************
*** 6,9 ****
--- 6,10 ----
  from libtbx.itertbx import count
  from libtbx.test_utils import approx_equal
+ import libtbx.env
  from cStringIO import StringIO
  import sys, os
***************
*** 41,46 ****
    assert mtz_object.n_crystals() == 0
    assert mtz_object.n_active_crystals() == 0
!   file_name = os.path.expandvars(
!     "$LIBTBX_DIST_ROOT/regression/reflection_files/dano.mtz")
    if (not os.path.isfile(file_name)):
      print "Skipping dano.mtz test: input file not available"
--- 42,47 ----
    assert mtz_object.n_crystals() == 0
    assert mtz_object.n_active_crystals() == 0
!   file_name = libtbx.env.under_dist_root(
!     "regression/reflection_files/dano.mtz")
    if (not os.path.isfile(file_name)):
      print "Skipping dano.mtz test: input file not available"

Update of /cvsroot/cctbx/iotbx/iotbx/kriber
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23122/iotbx/kriber

Modified Files:
	tst_strudat.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: tst_strudat.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/iotbx/kriber/tst_strudat.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** tst_strudat.py	22 Jan 2005 14:18:25 -0000	1.6
--- tst_strudat.py	20 Feb 2005 04:10:56 -0000	1.7
***************
*** 4,7 ****
--- 4,8 ----
  from cctbx import uctbx
  from cctbx.array_family import flex
+ import libtbx.env
  from cStringIO import StringIO
  import sys, os
***************
*** 130,135 ****
  
  def exercise_zeolite_atlas(distance_cutoff=3.5):
!   atlas_file = os.path.join(os.environ["LIBTBX_DIST_ROOT"],
!     "regression", "misc", "strudat_zeolite_atlas")
    if (not os.path.isfile(atlas_file)):
      print "Skipping exercise_zeolite_atlas(): input file not available"
--- 131,136 ----
  
  def exercise_zeolite_atlas(distance_cutoff=3.5):
!   atlas_file = libtbx.env.under_dist_root(
!     "regression/misc/strudat_zeolite_atlas")
    if (not os.path.isfile(atlas_file)):
      print "Skipping exercise_zeolite_atlas(): input file not available"

Update of /cvsroot/cctbx/iotbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23122

Modified Files:
	run_tests.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: run_tests.py
===================================================================
RCS file: /cvsroot/cctbx/iotbx/run_tests.py,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** run_tests.py	13 Jan 2005 19:41:05 -0000	1.21
--- run_tests.py	20 Feb 2005 04:10:55 -0000	1.22
***************
*** 1,4 ****
- import os, os.path
  from libtbx import test_utils
  
  def run():
--- 1,4 ----
  from libtbx import test_utils
+ import libtbx.env
  
  def run():
***************
*** 21,26 ****
    )
  
!   build_dir = os.path.join(os.environ["LIBTBX_BUILD"], "iotbx")
!   dist_dir = os.environ["IOTBX_DIST"]
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)
--- 21,26 ----
    )
  
!   build_dir = libtbx.env.under_build("iotbx")
!   dist_dir = libtbx.env.dist_path("iotbx")
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)

Update of /cvsroot/cctbx/cctbx/cctbx/regression
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23020/cctbx/regression

Modified Files:
	tst_coordination_sequences.py tst_pair_asu_table.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: tst_coordination_sequences.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_coordination_sequences.py,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** tst_coordination_sequences.py	4 Feb 2005 02:57:56 -0000	1.10
--- tst_coordination_sequences.py	20 Feb 2005 04:10:44 -0000	1.11
***************
*** 4,7 ****
--- 4,8 ----
  from cctbx import xray
  from iotbx.option_parser import iotbx_option_parser
+ import libtbx.env
  import sys, os
  
***************
*** 71,76 ****
        dest="verbose")
    ).process(args=args)
!   atlas_file = os.path.join(os.environ["LIBTBX_DIST_ROOT"],
!     "regression", "misc", "strudat_zeolite_atlas")
    if (not os.path.isfile(atlas_file)):
      print "Skipping exercise(): input file not available"
--- 72,77 ----
        dest="verbose")
    ).process(args=args)
!   atlas_file = libtbx.env.under_dist_root(
!     "regression/misc/strudat_zeolite_atlas")
    if (not os.path.isfile(atlas_file)):
      print "Skipping exercise(): input file not available"

Index: tst_pair_asu_table.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/regression/tst_pair_asu_table.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** tst_pair_asu_table.py	4 Feb 2005 02:57:56 -0000	1.6
--- tst_pair_asu_table.py	20 Feb 2005 04:10:44 -0000	1.7
***************
*** 6,9 ****
--- 6,10 ----
  import scitbx.math
  from libtbx.test_utils import approx_equal
+ import libtbx.env
  from cStringIO import StringIO
  import math
***************
*** 200,205 ****
    exercise_icosahedron(verbose=verbose)
    default_distance_cutoff=3.5
!   regression_misc = os.path.join(
!     os.environ["LIBTBX_DIST_ROOT"], "regression", "misc")
    file_names = []
    for file_name in ["strudat_zeolite_atlas", "strudat_special_bonds"]:
--- 201,205 ----
    exercise_icosahedron(verbose=verbose)
    default_distance_cutoff=3.5
!   regression_misc = libtbx.env.under_dist_root("regression/misc")
    file_names = []
    for file_name in ["strudat_zeolite_atlas", "strudat_special_bonds"]:

Update of /cvsroot/cctbx/cctbx/cctbx/source_generators/eltbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23020/cctbx/source_generators/eltbx

Modified Files:
	generate_henke_cpp.py generate_sasaki_cpp.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: generate_sasaki_cpp.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/source_generators/eltbx/generate_sasaki_cpp.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** generate_sasaki_cpp.py	14 Nov 2003 16:55:24 -0000	1.3
--- generate_sasaki_cpp.py	20 Feb 2005 04:10:44 -0000	1.4
***************
*** 1,4 ****
--- 1,5 ----
  from scitbx.source_generators.utils import join_open
  from scitbx.source_generators.utils import write_this_is_auto_generated
+ import libtbx.env
  import string
  import sys, os
***************
*** 268,272 ****
  
  def run(target_dir):
!   cctbx_dist = os.environ["CCTBX_DIST"]
    f = join_open(cctbx_dist, "reference/sasaki/fpwide.tbl", "r")
    tables_wide = collect_tables(f, 0)
--- 269,273 ----
  
  def run(target_dir):
!   cctbx_dist = libtbx.env.dist_path("cctbx")
    f = join_open(cctbx_dist, "reference/sasaki/fpwide.tbl", "r")
    tables_wide = collect_tables(f, 0)

Index: generate_henke_cpp.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/source_generators/eltbx/generate_henke_cpp.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** generate_henke_cpp.py	14 Nov 2003 16:55:24 -0000	1.3
--- generate_henke_cpp.py	20 Feb 2005 04:10:44 -0000	1.4
***************
*** 1,4 ****
--- 1,5 ----
  from scitbx.source_generators.utils import norm_join, join_open
  from scitbx.source_generators.utils import write_this_is_auto_generated
+ import libtbx.env
  import string
  import sys, os
***************
*** 39,43 ****
  
  def collect_tables():
!   cctbx_dist = os.environ["CCTBX_DIST"]
    henke_tables_dir = norm_join(cctbx_dist, "reference/henke/tables")
    nff_files = []
--- 40,44 ----
  
  def collect_tables():
!   cctbx_dist = libtbx.env.dist_path("cctbx")
    henke_tables_dir = norm_join(cctbx_dist, "reference/henke/tables")
    nff_files = []

Update of /cvsroot/cctbx/cctbx/include/cctbx/adp_restraints
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23020/include/cctbx/adp_restraints

Modified Files:
	tst_ext.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: tst_ext.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/include/cctbx/adp_restraints/tst_ext.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** tst_ext.py	22 Jan 2005 13:35:01 -0000	1.4
--- tst_ext.py	20 Feb 2005 04:10:44 -0000	1.5
***************
*** 3,6 ****
--- 3,7 ----
  from cctbx.array_family import flex
  from cctbx import adp_restraints
+ import libtbx.env
  import math, os
  
***************
*** 69,73 ****
    System for Windows)
    """
!   ins_file = os.path.expandvars('$LIBTBX_DIST_ROOT/regression/pdb/enk_11i.res')
    if (not os.path.isfile(ins_file)):
      print "Skipping exercise_rigid_bond_test(): input file not available"
--- 70,74 ----
    System for Windows)
    """
!   ins_file = libtbx.env.under_dist_root("regression/pdb/enk_11i.res")
    if (not os.path.isfile(ins_file)):
      print "Skipping exercise_rigid_bond_test(): input file not available"

Update of /cvsroot/cctbx/cctbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23020

Modified Files:
	SConscript run_examples.py run_tests.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: run_examples.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/run_examples.py,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** run_examples.py	19 Dec 2003 06:00:50 -0000	1.6
--- run_examples.py	20 Feb 2005 04:10:43 -0000	1.7
***************
*** 1,4 ****
- import os, os.path
  from libtbx import test_utils
  
  def run():
--- 1,4 ----
  from libtbx import test_utils
+ import libtbx.env
  
  def run():
***************
*** 12,17 ****
    )
  
!   build_dir = os.path.join(os.environ["LIBTBX_BUILD"], "cctbx")
!   dist_dir = os.environ["CCTBX_DIST"]
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)
--- 12,17 ----
    )
  
!   build_dir = libtbx.env.under_build("cctbx")
!   dist_dir = libtbx.env.dist_path("cctbx")
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)

Index: SConscript
===================================================================
RCS file: /cvsroot/cctbx/cctbx/SConscript,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** SConscript	1 Oct 2004 22:03:34 -0000	1.21
--- SConscript	20 Feb 2005 04:10:43 -0000	1.22
***************
*** 1,6 ****
- import os
  Import("env_base", "env_etc")
  
! env_etc.cctbx_dist = os.environ["CCTBX_DIST"]
  env_etc.cctbx_include = env_etc.norm_join(env_etc.cctbx_dist, "include")
  env_etc.cctbx_common_includes = [
--- 1,5 ----
  Import("env_base", "env_etc")
  
! env_etc.cctbx_dist = env_etc.libtbx_env.dist_path("cctbx")
  env_etc.cctbx_include = env_etc.norm_join(env_etc.cctbx_dist, "include")
  env_etc.cctbx_common_includes = [

Index: run_tests.py
===================================================================
RCS file: /cvsroot/cctbx/cctbx/run_tests.py,v
retrieving revision 1.41
retrieving revision 1.42
diff -C2 -d -r1.41 -r1.42
*** run_tests.py	22 Dec 2004 00:24:40 -0000	1.41
--- run_tests.py	20 Feb 2005 04:10:43 -0000	1.42
***************
*** 1,4 ****
- import os, os.path
  from libtbx import test_utils
  
  def run():
--- 1,4 ----
  from libtbx import test_utils
+ import libtbx.env
  
  def run():
***************
*** 66,71 ****
    )
  
!   build_dir = os.path.join(os.environ["LIBTBX_BUILD"], "cctbx")
!   dist_dir = os.environ["CCTBX_DIST"]
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)
--- 66,71 ----
    )
  
!   build_dir = libtbx.env.under_build("cctbx")
!   dist_dir = libtbx.env.dist_path("cctbx")
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)

Update of /cvsroot/cctbx/cctbx/cctbx/command_line
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23020/cctbx/command_line

Modified Files:
	web.install.csh 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: web.install.csh
===================================================================
RCS file: /cvsroot/cctbx/cctbx/cctbx/command_line/web.install.csh,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** web.install.csh	16 Dec 2004 23:03:53 -0000	1.6
--- web.install.csh	20 Feb 2005 04:10:43 -0000	1.7
***************
*** 1,4 ****
--- 1,5 ----
  #! /bin/csh -f
  
+ source "`libtbx.show_build_path`/setpaths.csh"
  set echo
  

Update of /cvsroot/cctbx/scitbx/array_family/boost_python
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22956/array_family/boost_python

Modified Files:
	regression_test.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: regression_test.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/array_family/boost_python/regression_test.py,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** regression_test.py	7 Aug 2003 02:15:48 -0000	1.10
--- regression_test.py	20 Feb 2005 04:10:34 -0000	1.11
***************
*** 1,9 ****
  from scitbx.array_family import flex
  
  def extend_sys_path():
!   import sys, os.path
!   libtbx_build = os.environ["LIBTBX_BUILD"]
!   sys.path.insert(0, os.path.normpath(os.path.join(libtbx_build,
!     "scitbx/array_family/boost_python")))
  
  def exercise_std_vector_conversions(verbose=0):
--- 1,9 ----
  from scitbx.array_family import flex
+ import libtbx.env
+ import sys
  
  def extend_sys_path():
!   sys.path.insert(0,
!     libtbx.env.under_build("scitbx/array_family/boost_python"))
  
  def exercise_std_vector_conversions(verbose=0):

Update of /cvsroot/cctbx/scitbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22956

Modified Files:
	SConscript run_tests.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: SConscript
===================================================================
RCS file: /cvsroot/cctbx/scitbx/SConscript,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** SConscript	5 Jul 2004 07:16:43 -0000	1.23
--- SConscript	20 Feb 2005 04:10:34 -0000	1.24
***************
*** 1,6 ****
- import os
  Import("env_etc")
  
! env_etc.scitbx_dist = os.environ["SCITBX_DIST"]
  env_etc.scitbx_include = env_etc.norm_join(env_etc.scitbx_dist, "include")
  env_etc.scitbx_common_includes = [
--- 1,5 ----
  Import("env_etc")
  
! env_etc.scitbx_dist = env_etc.libtbx_env.dist_path("scitbx")
  env_etc.scitbx_include = env_etc.norm_join(env_etc.scitbx_dist, "include")
  env_etc.scitbx_common_includes = [

Index: run_tests.py
===================================================================
RCS file: /cvsroot/cctbx/scitbx/run_tests.py,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** run_tests.py	25 Jan 2005 01:34:05 -0000	1.24
--- run_tests.py	20 Feb 2005 04:10:34 -0000	1.25
***************
*** 1,4 ****
- import os, os.path
  from libtbx import test_utils
  
  def run():
--- 1,4 ----
  from libtbx import test_utils
+ import libtbx.env
  
  def run():
***************
*** 30,35 ****
    )
  
!   build_dir = os.path.join(os.environ["LIBTBX_BUILD"], "scitbx")
!   dist_dir = os.environ["SCITBX_DIST"]
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)
--- 30,35 ----
    )
  
!   build_dir = libtbx.env.under_build("scitbx")
!   dist_dir = libtbx.env.dist_path("scitbx")
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)

Update of /cvsroot/cctbx/boost_adaptbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22881

Modified Files:
	SConscript run_tests.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: SConscript
===================================================================
RCS file: /cvsroot/cctbx/boost_adaptbx/SConscript,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** SConscript	16 Feb 2005 08:32:28 -0000	1.33
--- SConscript	20 Feb 2005 04:10:24 -0000	1.34
***************
*** 206,209 ****
--- 206,211 ----
          source=["#boost/libs/python/test/%s.cpp" % s for s in src.split(";")],
        )
+     test_dir = os.path.normpath(os.path.join(
+       env_etc.boost_dist, "libs/python/test"))
      if (sys.platform == "win32"):
        boost_python_run_tests = \
***************
*** 211,215 ****
        f = open(boost_python_run_tests, "w")
        for tst in all_tst:
!         print >> f, "call python %%BOOST_DIST%%/libs/python/test/%s.py" % tst
        f.close()
      else:
--- 213,217 ----
        f = open(boost_python_run_tests, "w")
        for tst in all_tst:
!         print >> f, 'call python "%s"' % (os.path.join(test_dir, tst+".py"))
        f.close()
      else:
***************
*** 220,224 ****
        print >> f, "set verbose"
        for tst in all_tst:
!         print >> f, "python $BOOST_DIST/libs/python/test/%s.py" % tst
        f.close()
        os.chmod(boost_python_run_tests, 0755)
--- 222,226 ----
        print >> f, "set verbose"
        for tst in all_tst:
!         print >> f, 'python "%s"' % (os.path.join(test_dir, tst+".py"))
        f.close()
        os.chmod(boost_python_run_tests, 0755)

Index: run_tests.py
===================================================================
RCS file: /cvsroot/cctbx/boost_adaptbx/run_tests.py,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** run_tests.py	19 Dec 2003 05:58:31 -0000	1.1
--- run_tests.py	20 Feb 2005 04:10:24 -0000	1.2
***************
*** 1,4 ****
  from libtbx import test_utils
! import os
  
  def run():
--- 1,4 ----
  from libtbx import test_utils
! import libtbx.env
  
  def run():
***************
*** 7,12 ****
    )
  
!   build_dir = os.path.join(os.environ["LIBTBX_BUILD"], "boost_adaptbx")
!   dist_dir = os.environ["BOOST_ADAPTBX_DIST"]
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)
--- 7,12 ----
    )
  
!   build_dir = libtbx.env.under_build("boost_adaptbx")
!   dist_dir = libtbx.env.dist_path("boost_adaptbx")
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)

Update of /cvsroot/cctbx/libtbx/libtbx/server
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22638/libtbx/server

Modified Files:
	FileClient.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: FileClient.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/server/FileClient.py,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** FileClient.py	21 Jan 2005 19:38:55 -0000	1.5
--- FileClient.py	20 Feb 2005 04:09:53 -0000	1.6
***************
*** 176,181 ****
    import FileServer
    import time
  
!   cmd = os.path.expandvars('$LIBTBX_DIST/libtbx/server/StartServer.py')
    python_path = sys.executable
  
--- 176,182 ----
    import FileServer
    import time
+   import libtbx.env
  
!   cmd = libtbx.env.under_dist("libtbx", "libtbx/server/StartServer.py")
    python_path = sys.executable
  

Update of /cvsroot/cctbx/libtbx/libtbx/command_line
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22638/libtbx/command_line

Modified Files:
	configure.py refresh.py scons.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: scons.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/command_line/scons.py,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** scons.py	11 Dec 2004 01:12:50 -0000	1.3
--- scons.py	20 Feb 2005 04:09:53 -0000	1.4
***************
*** 1,8 ****
  import sys, os
  
! dist_root = os.environ["LIBTBX_DIST_ROOT"]
! engine = os.path.normpath(os.path.join(dist_root, "scons/engine"))
  if (not os.path.isdir(engine)):
!   engine = os.path.normpath(os.path.join(dist_root, "scons/src/engine"))
  sys.path.insert(0, engine)
  try: import SCons
--- 1,8 ----
+ import libtbx.env
  import sys, os
  
! engine = libtbx.env.under_dist_root("scons/engine")
  if (not os.path.isdir(engine)):
!   engine = libtbx.env.under_dist_root("scons/src/engine")
  sys.path.insert(0, engine)
  try: import SCons

Index: refresh.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/command_line/refresh.py,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** refresh.py	20 Oct 2004 06:50:33 -0000	1.23
--- refresh.py	20 Feb 2005 04:09:53 -0000	1.24
***************
*** 201,204 ****
--- 201,213 ----
        action(python_exe, target_file)
  
+ def create_show_build_path(libtbx_env, target_dir):
+   target_file = os.path.join(target_dir, "libtbx.show_build_path")
+   f = open(target_file, "w")
+   print >> f, '#! /bin/sh'
+   print >> f, '# LIBTBX_DISPATCHER DO NOT EDIT'
+   print >> f, 'echo "%s"' % libtbx_env.LIBTBX_BUILD
+   f.close()
+   os.chmod(target_file, 0755)
+ 
  def run():
    libtbx_env = libtbx.config.env()
***************
*** 229,232 ****
--- 238,243 ----
        libtbx_env=libtbx_env,
        dispatcher_dict=dispatcher_dict)
+   else:
+     create_show_build_path(libtbx_env=libtbx_env, target_dir=target_dir)
  
  if (__name__ == "__main__"):

Index: configure.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/command_line/configure.py,v
retrieving revision 1.49
retrieving revision 1.50
diff -C2 -d -r1.49 -r1.50
*** configure.py	22 Jan 2005 15:48:15 -0000	1.49
--- configure.py	20 Feb 2005 04:09:53 -0000	1.50
***************
*** 229,232 ****
--- 229,236 ----
      print >> f, '  echo "Please re-run the libtbx/configure.py command."'
      print >> f, '  echo ""'
+     if (f is s):
+       print >> f, 'else if ($#argv != 0 && $#argv != 1'\
+                   ' || $#argv && "$1" != "minimal") then'
+       print >> f, '  echo "usage: source $0 [minimal]"'
      print >> f, 'else'
    for var_name, values in env.items():
***************
*** 244,248 ****
        print >> u, '  unsetenv LIBTBX0%s' % var_name
      else:
!       print >> s, '  setenv %s "%s"' % (var_name, values)
        print >> u, '  unsetenv %s' % var_name
    for f in s, u:
--- 248,257 ----
        print >> u, '  unsetenv LIBTBX0%s' % var_name
      else:
!       if (   var_name.endswith("_DIST")
!           or var_name.endswith("_DIST_ROOT")):
!         condition = "if ($#argv == 0) "
!       else:
!         condition = ""
!       print >> s, '  %ssetenv %s "%s"' % (condition, var_name, values)
        print >> u, '  unsetenv %s' % var_name
    for f in s, u:

Update of /cvsroot/cctbx/libtbx/libtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22638/libtbx

Modified Files:
	config.py optparse_wrapper.py 
Added Files:
	env.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: optparse_wrapper.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/optparse_wrapper.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** optparse_wrapper.py	13 Jan 2005 19:24:32 -0000	1.2
--- optparse_wrapper.py	20 Feb 2005 04:09:53 -0000	1.3
***************
*** 2,10 ****
  # mv lib optik
  import sys, os
! if (sys.version_info[0] < 3 or sys.version_info[1] < 3):
!   sys.path.insert(0, os.path.join(os.environ["LIBTBX_DIST"], "optik141"))
    from optik import *
  else:
    from optparse import *
  
  class option_parser(OptionParser):
--- 2,14 ----
  # mv lib optik
  import sys, os
! if (sys.version_info[0] < 3 and sys.version_info[1] < 3):
!   import libtbx.config
!   sys.path.insert(0, os.path.join(
!     libtbx.config.env().dist_path("libtbx"),
!     "optik141"))
    from optik import *
  else:
    from optparse import *
+   from optparse import make_option
  
  class option_parser(OptionParser):

Index: config.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/libtbx/config.py,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** config.py	19 Feb 2005 01:50:13 -0000	1.25
--- config.py	20 Feb 2005 04:09:53 -0000	1.26
***************
*** 117,121 ****
    def __init__(self, application_prefix="LIBTBX"):
      self.application_prefix = application_prefix
!     libtbx_build = os.environ["LIBTBX_BUILD"]
      file_name = join(libtbx_build, "libtbx_env")
      try:
--- 117,121 ----
    def __init__(self, application_prefix="LIBTBX"):
      self.application_prefix = application_prefix
!     libtbx_build = os.environ["LIBTBX_BUILD"] # XXX XXX XXX XXX XXX XXX XXX XXX
      file_name = join(libtbx_build, "libtbx_env")
      try:

--- NEW FILE: env.py ---
import libtbx.config
import os

env_cache = libtbx.config.env()
dist_root = env_cache.LIBTBX_DIST_ROOT
dist_path = env_cache.dist_path
build = env_cache.LIBTBX_BUILD

def under_dist_root(path):
  return os.path.normpath(os.path.join(dist_root, path))

def under_dist(package_name, path):
  return os.path.normpath(os.path.join(
    dist_path(package_name=package_name), path))

def under_build(path):
  return os.path.normpath(os.path.join(build, path))

Update of /cvsroot/cctbx/libtbx
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22638

Modified Files:
	run_tests.py 
Log Message:
eliminaton of os.environ["*_DIST"] and os.path.expandvars("*_DIST/*") from SConscripts and regresstion tests

Index: run_tests.py
===================================================================
RCS file: /cvsroot/cctbx/libtbx/run_tests.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** run_tests.py	13 Jan 2005 19:23:52 -0000	1.2
--- run_tests.py	20 Feb 2005 04:09:36 -0000	1.3
***************
*** 1,4 ****
  from libtbx import test_utils
! import os, os.path
  
  def run():
--- 1,4 ----
  from libtbx import test_utils
! import libtbx.env
  
  def run():
***************
*** 10,14 ****
  
    build_dir = None
!   dist_dir = os.environ["LIBTBX_DIST"]
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)
--- 10,14 ----
  
    build_dir = None
!   dist_dir = libtbx.env.dist_path("libtbx")
  
    test_utils.run_tests(build_dir, dist_dir, tst_list)