repopulate MDANSE

setup.py

+import fnmatch
+import glob
+import os
+import sys
+
+import numpy
+
+from Cython.Distutils import build_ext
+
+from distutils.core import setup, Extension
+from distutils.command.build import build
+from distutils.command.build_py import build_py
+from distutils.command.build_scripts import build_scripts 
+from distutils.sysconfig import get_config_vars
+from distutils.util import convert_path
+
+#################################
+# Modules variables
+#################################
+EXCLUDE = ['*.py', '*.pyc', '*$py.class', '*~', '.*', '*.bak', '*.so', '*.pyd']
+
+EXCLUDE_DIRECTORIES = ('.*', 'CVS', '_darcs', './build','*svn','./dist', 'EGG-INFO', '*.egg-info')
+
+EXTENSIONS_PATH = "Extensions"
+
+INCLUDE_DIR = [numpy.get_include()]
+
+QHULL_DIR = os.path.join("Extensions","qhull_lib")
+
+QHULL_INCLUDE_DIR = INCLUDE_DIR + [EXTENSIONS_PATH] + [os.path.join(QHULL_DIR,"ext")] + [os.path.join(QHULL_DIR,"src")]
+
+SCRIPTS_PATH = "Scripts"
+
+#################################
+# Helper function
+#################################
+
+def is_package(path):
+    return (os.path.isdir(path) and os.path.isfile(os.path.join(path, '__init__.py')))
+
+def find_packages(path, base="", exclude=None):
+
+    packages = {}
+
+    for item in os.listdir(path):
+        d = os.path.join(path, item)
+        if exclude is not None and (os.path.abspath(d) == os.path.abspath(exclude)):
+            continue
+        if is_package(d):
+            if base:
+                module_name = "%(base)s.%(item)s" % vars()
+            else:
+                module_name = item
+            packages[module_name] = d
+            packages.update(find_packages(d, module_name, exclude))
+            
+    return packages
+
+def find_package_data(where='.', package='', exclude=EXCLUDE, exclude_directories=EXCLUDE_DIRECTORIES, only_in_packages=True, show_ignored=False):
+    
+    out = {}
+    stack = [(convert_path(where), '', package, only_in_packages)]
+    while stack:
+        where, prefix, package, only_in_packages = stack.pop(0)
+        for name in os.listdir(where):
+            fn = os.path.join(where, name)
+            if os.path.isdir(fn):
+                bad_name = False
+                for pattern in exclude_directories:
+                    if (fnmatch.fnmatchcase(name, pattern)
+                        or fn.lower() == pattern.lower()):
+                        bad_name = True
+                        if show_ignored:
+                            print >> sys.stderr, ("Directory %s ignored by pattern %s" % (fn, pattern))
+                        break
+                if bad_name:
+                    continue
+                if (os.path.isfile(os.path.join(fn, '__init__.py')) and not prefix):
+                    if not package:
+                        new_package = name
+                    else:
+                        new_package = package + '.' + name
+                    stack.append((fn, '', new_package, False))
+                else:
+                    stack.append((fn, prefix + name + '/', package, only_in_packages))
+            elif package or not only_in_packages:
+                # is a file
+                bad_name = False
+                for pattern in exclude:
+                    if (fnmatch.fnmatchcase(name, pattern)
+                        or fn.lower() == pattern.lower()):
+                        bad_name = True
+                        if show_ignored:
+                            print >> sys.stderr, ("File %s ignored by pattern %s" % (fn, pattern))
+                        break
+                if bad_name:
+                    continue
+                out.setdefault(package, []).append(prefix+name)
+    
+    return out
+
+
+def find_data(where=".", exclude=EXCLUDE, exclude_directories=EXCLUDE_DIRECTORIES, prefix=""):
+
+    out = {}
+    stack = [convert_path(where)]
+    while stack:
+        where = stack.pop(0)
+        for name in os.listdir(where):
+            fn = os.path.join(where, name)
+            d = os.path.join(prefix,os.path.dirname(fn))
+            if os.path.isdir(fn):
+                stack.append(fn)
+            else:
+                bad_name = False
+                for pattern in exclude:
+                    if (fnmatch.fnmatchcase(name, pattern) or fn.lower() == pattern.lower()):
+                        bad_name = True
+                        break
+                if bad_name:
+                    continue
+                out.setdefault(d, []).append(fn)
+            
+    out = [(k,v) for k, v in out.items()]
+    
+    return out
+
+
+#################################
+# Packages section
+#################################
+
+PACKAGE_INFO = {}
+execfile('nMOLDYN/__pkginfo__.py', PACKAGE_INFO)
+
+PACKAGES = find_packages(path=".", exclude=os.path.join("nMOLDYN","GUI"))
+PACKAGES = PACKAGES.keys()
+
+#################################
+# Package data section
+#################################
+
+# Retrieve all the data related to the nMoldyn package.
+PACKAGE_DATA = find_package_data(where='nMOLDYN',
+                                 package='nMOLDYN',
+                                 show_ignored=False)
+
+#################################
+# User data section
+#################################
+
+DATA_FILES = []
+
+#################################
+# Scripts section
+#################################
+
+SCRIPTS = []
+SCRIPTS.append(os.path.join(SCRIPTS_PATH,'nmoldyn_console'))
+
+#################################
+# Extensions section
+#################################
+
+if 'linux' in sys.platform:
+    (opt,) = get_config_vars('OPT')
+    os.environ['OPT'] = " ".join(flag for flag in opt.split() if flag != '-Wstrict-prototypes')
+
+EXTENSIONS = [Extension('nMOLDYN.Extensions.distance_histogram',
+                        include_dirs=INCLUDE_DIR,
+                        sources = [os.path.join("Extensions",'distance_histogram.pyx')]),
+              Extension('nMOLDYN.Extensions.fast_calculation',
+                        include_dirs=INCLUDE_DIR,
+                        sources = [os.path.join("Extensions",'fast_calculation.pyx')]),
+              Extension('nMOLDYN.Extensions.sas_fast_calc',
+                        include_dirs=INCLUDE_DIR,
+                        sources = [os.path.join("Extensions",'sas_fast_calc.pyx')]),
+              Extension('nMOLDYN.Extensions.mt_fast_calc',
+                        include_dirs=INCLUDE_DIR,
+                        sources = [os.path.join("Extensions",'mt_fast_calc.pyx')]),
+              Extension('nMOLDYN.Extensions.sd_fast_calc',
+                        include_dirs=INCLUDE_DIR,
+                        sources = [os.path.join("Extensions",'sd_fast_calc.pyx')]),
+              Extension('nMOLDYN.Extensions.mic_fast_calc', 
+                        include_dirs=INCLUDE_DIR,
+                        sources = [os.path.join("Extensions",'mic_fast_calc.pyx')],
+                        language="c++"),
+              Extension('nMOLDYN.Extensions.qhull',
+                        include_dirs  = QHULL_INCLUDE_DIR,
+                        sources =  glob.glob(os.path.join(QHULL_DIR, 'src','*.c')) + [os.path.join("Extensions",'qhull.pyx')],
+                        define_macros = [('qh_QHpointer','1')])
+              ]
+
+class ModifiedBuildScripts(build_scripts):
+    
+    def finalize_options (self):
+
+        build_scripts.finalize_options(self)
+
+        if self.distribution.command_obj['build'].gui:
+            self.scripts.append(os.path.join(SCRIPTS_PATH,'nmoldyn_gui'))
+                    
+
+class ModifiedBuildPy(build_py):
+
+    def finalize_options(self):
+
+        build_py.finalize_options(self)
+
+        if self.distribution.command_obj['build'].gui:
+            self.packages.append('nMOLDYN.GUI')
+            self.packages.extend(find_packages(path=os.path.join("nMOLDYN","GUI"), base="nMOLDYN.GUI").keys())
+             
+        self.data_files = self.get_data_files()
+
+
+class ModifiedBuild(build):
+    
+    user_options = build.user_options + [('gui',None,'Build nMOLDYN with GUI [default]'),
+                                         ('no-gui', None, "Build nMOLDYN without GUI")]
+    
+    boolean_options = build.boolean_options + ['gui']
+
+    negative_opt = {'no-gui' : 'gui'}
+
+    def initialize_options(self):
+        build.initialize_options(self)
+        self.gui = 1
+ 
+         
+#################################
+# The setup section
+#################################
+
+setup (name             = "nMOLDYN",
+       version          = PACKAGE_INFO["__version__"],
+       description      = "Analysis of Molecular Dynamics trajectories",
+       long_description =
+"""nMOLDYN is an interactive program for the analysis of Molecular
+Dynamics simulations. It is especially designed for the computation
+and decomposition of neutron scattering spectra. The structure and
+dynamics of the simulated systems can be characterized in terms of
+various space and time correlation functions. To analyze the dynamics
+of complex systems, rigid-body motions of arbitrarily chosen molecular
+subunits can be studied.
+""",
+       author           = "B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller",
+       author_email     = "aoun.ill.fr, goretg@ill.fr, pellegrini@ill.fr, kneller@cnrs-orleans.fr",
+       maintainer       = "B. Aoun, G. Goret, E. Pellegrini",
+       maintainer_email = "aoun.ill.fr, goretg.ill.fr, pellegrini@ill.fr",
+       url              = "https://forge.epn-campus.eu/projects/nmoldyn/",
+       license          = "CeCILL",
+       packages         = PACKAGES,
+       package_data     = PACKAGE_DATA,
+       data_files       = DATA_FILES,
+       platforms        = ['Unix','Windows'],
+       ext_modules      = EXTENSIONS,
+       scripts          = SCRIPTS,
+        cmdclass         = {'build_ext'     : build_ext,
+                            'build'         : ModifiedBuild,
+                            'build_py'      : ModifiedBuildPy,
+                            'build_scripts' : ModifiedBuildScripts}
+       )