Added initial setup file.

basesetup.py

@@ -0,0 +1,359 @@
+from __future__ import print_function, absolute_import
+import os
+import sys
+import imp
+import json
+import string
+import shutil
+import subprocess
+import tempfile
+from distutils.dep_util import newer_group
+from distutils.core import Extension
+from distutils.errors import DistutilsExecError
+from distutils.ccompiler import new_compiler
+from distutils.sysconfig import customize_compiler, get_config_vars
+from distutils.command.build_ext import build_ext as _build_ext
+
+
+def find_packages():
+    """Find all of mdtraj's python packages.
+    Adapted from IPython's setupbase.py. Copyright IPython
+    contributors, licensed under the BSD license.
+    """
+    packages = ['mdtraj.scripts']
+    for dir,subdirs,files in os.walk('MDTraj'):
+        package = dir.replace(os.path.sep, '.')
+        if '__init__.py' not in files:
+            # not a package
+            continue
+        packages.append(package.replace('MDTraj', 'mdtraj'))
+    return packages
+
+
+def check_dependencies(dependencies):
+    def module_exists(dep):
+        try:
+            imp.find_module(dep)
+            return True
+        except ImportError:
+            return False
+
+    for dep in dependencies:
+        if len(dep) == 1:
+            import_name, pkg_name = dep[0], dep[0]
+        elif len(dep) == 2:
+            import_name, pkg_name = dep
+        else:
+            raise ValueError(dep)
+
+        if not module_exists(import_name):
+            lines = [
+                '-' * 50,
+                'Warning: This package requires %r. Try' % import_name,
+                '',
+                '  $ conda install %s' % pkg_name,
+                '',
+                'or:',
+                '',
+                '  $ pip install %s' % pkg_name,
+                '-' * 50,
+            ]
+            print(os.linesep.join(lines), file=sys.stderr)
+
+
+################################################################################
+# Detection of compiler capabilities
+################################################################################
+
+class CompilerDetection(object):
+    # Necessary for OSX. See https://github.com/mdtraj/mdtraj/issues/576
+    # The problem is that distutils.sysconfig.customize_compiler()
+    # is necessary to properly invoke the correct compiler for this class
+    # (otherwise the CC env variable isn't respected). Unfortunately,
+    # distutils.sysconfig.customize_compiler() DIES on OSX unless some
+    # appropriate initialization routines have been called. This line
+    # has a side effect of calling those initialzation routes, and is therefor
+    # necessary for OSX, even though we don't use the result.
+    _DONT_REMOVE_ME = get_config_vars()
+
+    def __init__(self, disable_openmp):
+        cc = new_compiler()
+        customize_compiler(cc)
+
+        self.msvc = cc.compiler_type == 'msvc'
+        self._print_compiler_version(cc)
+
+        if disable_openmp:
+            self.openmp_enabled = False
+        else:
+            self.openmp_enabled, openmp_needs_gomp = self._detect_openmp()
+        self.sse3_enabled = self._detect_sse3() if not self.msvc else True
+        self.sse41_enabled = self._detect_sse41() if not self.msvc else True
+
+        self.compiler_args_sse2  = ['-msse2'] if not self.msvc else ['/arch:SSE2']
+        self.compiler_args_sse3  = ['-mssse3'] if (self.sse3_enabled and not self.msvc) else []
+
+        self.compiler_args_sse41, self.define_macros_sse41 = [], []
+        if self.sse41_enabled:
+            self.define_macros_sse41 = [('__SSE4__', 1), ('__SSE4_1__', 1)]
+            if not self.msvc:
+                self.compiler_args_sse41 = ['-msse4']
+
+        if self.openmp_enabled:
+            self.compiler_libraries_openmp = []
+
+            if self.msvc:
+                self.compiler_args_openmp = ['/openmp']
+            else:
+                self.compiler_args_openmp = ['-fopenmp']
+                if openmp_needs_gomp:
+                    self.compiler_libraries_openmp = ['gomp']
+        else:
+            self.compiler_libraries_openmp = []
+            self.compiler_args_openmp = []
+
+        if self.msvc:
+            self.compiler_args_opt = ['/O2']
+        else:
+            self.compiler_args_opt = ['-O3', '-funroll-loops']
+        print()
+
+    def _print_compiler_version(self, cc):
+        print("C compiler:")
+        try:
+            if self.msvc:
+                if not cc.initialized:
+                    cc.initialize()
+                cc.spawn([cc.cc])
+            else:
+                cc.spawn([cc.compiler[0]] + ['-v'])
+        except DistutilsExecError:
+            pass
+
+    def hasfunction(self, funcname, include=None, libraries=None, extra_postargs=None):
+        # running in a separate subshell lets us prevent unwanted stdout/stderr
+        part1 = '''
+from __future__ import print_function
+import os
+import json
+from distutils.ccompiler import new_compiler
+from distutils.sysconfig import customize_compiler, get_config_vars
+
+FUNCNAME = json.loads('%(funcname)s')
+INCLUDE = json.loads('%(include)s')
+LIBRARIES = json.loads('%(libraries)s')
+EXTRA_POSTARGS = json.loads('%(extra_postargs)s')
+        ''' % {
+            'funcname': json.dumps(funcname),
+            'include': json.dumps(include),
+            'libraries': json.dumps(libraries or []),
+            'extra_postargs': json.dumps(extra_postargs)}
+
+        part2 = '''
+get_config_vars()  # DON'T REMOVE ME
+cc = new_compiler()
+customize_compiler(cc)
+for library in LIBRARIES:
+    cc.add_library(library)
+
+status = 0
+try:
+    with open('func.c', 'w') as f:
+        if INCLUDE is not None:
+            f.write('#include %s\\n' % INCLUDE)
+        f.write('int main(void) {\\n')
+        f.write('    %s;\\n' % FUNCNAME)
+        f.write('}\\n')
+    objects = cc.compile(['func.c'], output_dir='.',
+                         extra_postargs=EXTRA_POSTARGS)
+    cc.link_executable(objects, 'a.out')
+except Exception as e:
+    status = 1
+exit(status)
+        '''
+        tmpdir = tempfile.mkdtemp(prefix='hasfunction-')
+        try:
+            curdir = os.path.abspath(os.curdir)
+            os.chdir(tmpdir)
+            with open('script.py', 'w') as f:
+                f.write(part1 + part2)
+            proc = subprocess.Popen(
+                [sys.executable, 'script.py'],
+                stderr=subprocess.PIPE, stdout=subprocess.PIPE)
+            proc.communicate()
+            status = proc.wait()
+        finally:
+            os.chdir(curdir)
+            shutil.rmtree(tmpdir)
+
+        return status == 0
+
+    def _print_support_start(self, feature):
+        print('Attempting to autodetect {0:6} support...'.format(feature), end=' ')
+
+    def _print_support_end(self, feature, status):
+        if status is True:
+            print('Compiler supports {0}'.format(feature))
+        else:
+            print('Did not detect {0} support'.format(feature))
+
+    def _detect_openmp(self):
+        self._print_support_start('OpenMP')
+        hasopenmp = self.hasfunction('omp_get_num_threads()', extra_postargs=['-fopenmp', '/openmp'])
+        needs_gomp = hasopenmp
+        if not hasopenmp:
+            hasopenmp = self.hasfunction('omp_get_num_threads()', libraries=['gomp'])
+            needs_gomp = hasopenmp
+        self._print_support_end('OpenMP', hasopenmp)
+        return hasopenmp, needs_gomp
+
+    def _detect_sse3(self):
+        "Does this compiler support SSE3 intrinsics?"
+        self._print_support_start('SSE3')
+        result = self.hasfunction('__m128 v; _mm_hadd_ps(v,v)',
+                           include='<pmmintrin.h>',
+                           extra_postargs=['-msse3'])
+        self._print_support_end('SSE3', result)
+        return result
+
+    def _detect_sse41(self):
+        "Does this compiler support SSE4.1 intrinsics?"
+        self._print_support_start('SSE4.1')
+        result = self.hasfunction( '__m128 v; _mm_round_ps(v,0x00)',
+                           include='<smmintrin.h>',
+                           extra_postargs=['-msse4'])
+        self._print_support_end('SSE4.1', result)
+        return result
+
+################################################################################
+# Writing version control information to the module
+################################################################################
+
+def git_version():
+    # Return the git revision as a string
+    # copied from numpy setup.py
+    def _minimal_ext_cmd(cmd):
+        # construct minimal environment
+        env = {}
+        for k in ['SYSTEMROOT', 'PATH']:
+            v = os.environ.get(k)
+            if v is not None:
+                env[k] = v
+        # LANGUAGE is used on win32
+        env['LANGUAGE'] = 'C'
+        env['LANG'] = 'C'
+        env['LC_ALL'] = 'C'
+        out = subprocess.Popen(
+            cmd, stdout=subprocess.PIPE, env=env).communicate()[0]
+        return out
+
+    try:
+        out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
+        GIT_REVISION = out.strip().decode('ascii')
+    except OSError:
+        GIT_REVISION = 'Unknown'
+
+    return GIT_REVISION
+
+
+def write_version_py(VERSION, ISRELEASED, filename='MDTraj/version.py'):
+    cnt = """
+# THIS FILE IS GENERATED FROM MDTRAJ SETUP.PY
+short_version = '%(version)s'
+version = '%(version)s'
+full_version = '%(full_version)s'
+git_revision = '%(git_revision)s'
+release = %(isrelease)s
+
+if not release:
+    version = full_version
+"""
+    # Adding the git rev number needs to be done inside write_version_py(),
+    # otherwise the import of numpy.version messes up the build under Python 3.
+    FULLVERSION = VERSION
+    if os.path.exists('.git'):
+        GIT_REVISION = git_version()
+    else:
+        GIT_REVISION = 'Unknown'
+
+    if not ISRELEASED:
+        FULLVERSION += '.dev-' + GIT_REVISION[:7]
+
+    a = open(filename, 'w')
+    try:
+        a.write(cnt % {'version': VERSION,
+                       'full_version': FULLVERSION,
+                       'git_revision': GIT_REVISION,
+                       'isrelease': str(ISRELEASED)})
+    finally:
+        a.close()
+
+
+class StaticLibrary(Extension):
+    def __init__(self, *args, **kwargs):
+        self.export_include = kwargs.pop('export_include', [])
+        Extension.__init__(self, *args, **kwargs)
+
+
+class build_ext(_build_ext):
+
+    def build_extension(self, ext):
+        if isinstance(ext, StaticLibrary):
+            self.build_static_extension(ext)
+        else:
+            _build_ext.build_extension(self, ext)
+
+    def build_static_extension(self, ext):
+        from distutils import log
+
+        sources = ext.sources
+        if sources is None or not isinstance(sources, (list, tuple)):
+            raise DistutilsSetupError(
+                  ("in 'ext_modules' option (extension '%s'), " +
+                   "'sources' must be present and must be " +
+                   "a list of source filenames") % ext.name)
+        sources = list(sources)
+
+        ext_path = self.get_ext_fullpath(ext.name)
+        depends = sources + ext.depends
+        if not (self.force or newer_group(depends, ext_path, 'newer')):
+            log.debug("skipping '%s' extension (up-to-date)", ext.name)
+            return
+        else:
+            log.info("building '%s' extension", ext.name)
+
+        extra_args = ext.extra_compile_args or []
+        macros = ext.define_macros[:]
+        for undef in ext.undef_macros:
+            macros.append((undef,))
+        objects = self.compiler.compile(sources,
+                                         output_dir=self.build_temp,
+                                         macros=macros,
+                                         include_dirs=ext.include_dirs,
+                                         debug=self.debug,
+                                         extra_postargs=extra_args,
+                                         depends=ext.depends)
+        self._built_objects = objects[:]
+        if ext.extra_objects:
+            objects.extend(ext.extra_objects)
+        extra_args = ext.extra_link_args or []
+
+        language = ext.language or self.compiler.detect_language(sources)
+
+        libname = os.path.splitext(os.path.basename(ext_path))[0]
+        output_dir = os.path.dirname(ext_path)
+        if (self.compiler.static_lib_format.startswith('lib') and
+            libname.startswith('lib')):
+            libname = libname[3:]
+
+        if not os.path.exists(output_dir):
+            # necessary for windows
+            os.makedirs(output_dir)
+
+        self.compiler.create_static_lib(objects,
+            output_libname=libname,
+            output_dir=output_dir,
+            target_lang=language)
+
+        for item in ext.export_include:
+            shutil.copy(item, output_dir)