restore

scripts/install_libcpptraj.py

@@ -8,74 +8,86 @@
 from check_openmp import get_openmp_flag
 from find_lib import find_lib
 
+# DEFAULT_MAC_BUILD = '-shared -macAccelerate --with-fftw3=/usr/local --with-netcdf=/usr/local -noarpack'
 DEFAULT_MAC_BUILD = '-shared -macAccelerate -noarpack'
 DEFAULT_MAC_CCOMPILER = 'clang'
 DEFAULT_MAC_CXXCOMPILER = 'clang++'
 CPPTRAJ_CXX = ' '
 IS_OSX = sys.platform.startswith('darwin')
 
 if IS_OSX:
+    # Hack to fix conda
     import distutils.sysconfig as sc
     compiler = sc.get_config_var('CC') or ''
     if compiler == 'gcc':
+        # This must be a conda install that uses a a pure compiler name (rather
+        # than an absolute path).
         DEFAULT_MAC_CCOMPILER = "/usr/bin/gcc"
         DEFAULT_MAC_CXXCOMPILER = "/usr/bin/g++"
 
+
 def add_cpptraj_cxx_to_config(fn, cpptraj_cxx=CPPTRAJ_CXX):
     with open(fn, 'r') as fconfig:
         lines = fconfig.readlines()
+
     with open('tmp.h', 'w') as fh:
         for idx, line in enumerate(lines):
             if line.startswith('CXX='):
+                print('line', line)
                 lines[idx] = ' '.join((line.strip(), cpptraj_cxx, '\n'))
         fh.write(''.join(lines))
     subprocess.check_call('mv tmp.h {}'.format(fn), shell=True)
 
+
 def is_clang(cc):
+    # both cpptraj and pytraj give priority for CXX and CC environments
+    # check them first.
     out = subprocess.check_output([cc, '--version']).decode()
     return 'clang' in out
 
+
 def ensure_gnu():
+    # both cpptraj and pytraj give priority for CXX and CC environments
+    # check them first.
     cc = os.getenv('CC', '')
     gcc_exe = cc if cc else 'gcc'
+
     if is_clang(gcc_exe):
         print('{} --version'.format(gcc_exe))
-        print('{} here is actually clang compiler. Please export correct PATH for the real g++\n'.format(gcc_exe))
+        print(
+            '{} here is actually clang compiler. Please export correct PATH for the real g++\n'.
+            format(gcc_exe))
         print('Or export CXX and CC environments')
         print('e.g: ')
         print('    export CC=/usr/local/bin/gcc-5')
         print('    export CXX=/usr/local/bin/g++-5')
         sys.exit(1)
 
+
 def get_compiler_and_build_flag():
     args = parse_args()
+
     openmp_flag = '-openmp' if args.openmp else ''
-    if openmp_flag and not IS_OSX:
-        assert get_openmp_flag(), 'your system must support openmp'
+    if openmp_flag:
+        # we turn off OSX openmp anyway, so do not need to check
+        if not IS_OSX:
+            assert get_openmp_flag(), 'your system must support openmp'
+
     install_type = args.install_type
     debug = '-debug' if args.debug else ''
-    has_numpy = check_numpy()
-    compiler, build_flag_ = determine_compiler_and_build_flag(has_numpy)
-    amberhome = os.environ.get('AMBERHOME', '')
-    amberlib = '-amberlib' if amberhome and args.amberlib else ''
-    build_flag = construct_build_flag(build_flag_, amberlib, openmp_flag, debug)
-    if install_type == 'github':
-        print('install libcpptraj from github')
-        subprocess.check_call('git clone https://github.com/Amber-MD/cpptraj'.split())
-    else:
-        print('install libcpptraj from current ./cpptraj folder')
-    return compiler, build_flag
 
-def check_numpy():
     try:
         import numpy as np
-        return True
+        has_numpy = True
     except ImportError:
-        return False
+        has_numpy = False
 
-def determine_compiler_and_build_flag(has_numpy):
+    # better name for COMPILER?
+    # cpptraj: ./configure gnu
+    # e.g: COMPILER=gnu python ./scripts/install_libcpptraj.py
     os_dependent_default_compiler = 'clang' if IS_OSX else 'gnu'
-    compiler_env = os.environ.get('COMPILER', '')
+    compiler_env = os.environ.get('COMPILER',
+                                  '')  # intel | pgi | clang | cray?
     if compiler_env:
         print('libcpptraj: Using COMPILER env = ', compiler_env)
         compiler = compiler_env
@@ -87,64 +99,127 @@ def determine_compiler_and_build_flag(has_numpy):
             compiler = ''
     if compiler == 'gnu':
         ensure_gnu()
+    amberhome = os.environ.get('AMBERHOME', '')
+    amberlib = '-amberlib' if amberhome and args.amberlib else ''
+
     prefix = sys.prefix
     if has_numpy and find_lib('openblas'):
-        build_flag_ = '--with-blas={prefix} -openblas -noarpack'.format(prefix=prefix)
+        # likely having openblas?
+        build_flag_ = ('--with-blas={prefix} '
+                       '-openblas -noarpack'.format(prefix=prefix))
     elif has_numpy:
-        build_flag_ = handle_numpy_without_openblas()
+        print('has_numpy but can not find openblas')
+        print('try blas and lapack')
+        try:
+            blas_prefix = np.__config__.blas_opt_info['library_dirs'][0].strip(
+                'lib')
+            lapack_prefix = np.__config__.lapack_opt_info['library_dirs'][
+                0].strip('lib')
+            build_flag_ = (
+                '-noarpack --with-blas={blas_prefix} --with-lapack={lapack_prefix}'
+                .format(blas_prefix=blas_prefix, lapack_prefix=lapack_prefix))
+        except (KeyError, IndexError):
+            build_flag_ = '-noarpack'
     else:
+        # user gets lucky?
         build_flag_ = '-noarpack'
-    zip_stuff = ' --with-bzlib={prefix} --with-zlib={prefix} '.format(prefix=prefix)
-    build_flag_ += zip_stuff
-    return compiler, build_flag_
 
-def handle_numpy_without_openblas():
-    import numpy as np
-    try:
-        blas_prefix = np.__config__.blas_opt_info['library_dirs'][0].strip('lib')
-        lapack_prefix = np.__config__.lapack_opt_info['library_dirs'][0].strip('lib')
-        return '-noarpack --with-blas={blas_prefix} --with-lapack={lapack_prefix}'.format(blas_prefix=blas_prefix, lapack_prefix=lapack_prefix)
-    except (KeyError, IndexError):
-        return '-noarpack'
+    zip_stuff = ' --with-bzlib={prefix} --with-zlib={prefix} '.format(
+        prefix=prefix)
+    build_flag_ += zip_stuff
 
-def construct_build_flag(build_flag_, amberlib, openmp_flag, debug):
     if IS_OSX:
         build_flag = ' '.join((DEFAULT_MAC_BUILD, amberlib))
     else:
         build_flag = '--requires-flink ' + ' '.join(('-shared', build_flag_, amberlib, openmp_flag))
+        # FIXME: remove --requires-flink if https://github.com/Amber-MD/cpptraj/issues/585 is resolved
+
     build_flag = ' '.join((build_flag, debug, '-nosanderlib'))
-    return build_flag
+
+    if install_type == 'github':
+        print('install libcpptraj from github')
+        subprocess.check_call(
+            'git clone https://github.com/Amber-MD/cpptraj'.split())
+    else:
+        print('install libcpptraj from current ./cpptraj folder')
+    return compiler, build_flag
+
 
 def install_libcpptraj(compiler='', build_flag='', n_cpus=4):
+    '''
+
+    Parameters
+    ----------
+    compiler : str, {'clang', 'gnu'}
+    build_flag : str
+    '''
     cwd = os.getcwd()
     try:
         os.chdir('./cpptraj')
     except OSError:
         raise OSError('please try python scripts/install_cpptraj.py github')
     os.environ['CPPTRAJHOME'] = os.getcwd()
+
     try:
         os.mkdir('./lib')
     except OSError:
         pass
-    cm = 'bash configure {build_flag} {compiler}'.format(build_flag=build_flag, compiler=compiler)
+
+    cm = 'bash configure {build_flag} {compiler}'.format(
+        build_flag=build_flag,
+        compiler=compiler)
+
     print('configure command: ', cm)
     subprocess.check_call(cm, shell=True)
+
     if IS_OSX:
         add_cpptraj_cxx_to_config('config.h', CPPTRAJ_CXX)
+
     subprocess.check_call('make libcpptraj -j{}'.format(n_cpus).split())
     os.chdir(cwd)
 
+
 def parse_args():
     import argparse
     parser = argparse.ArgumentParser(description='install options')
     parser.add_argument('-openmp', action='store_true', help='use openmp')
-    parser.add_argument('-amberlib', action='store_true', help='use use amberlib if $AMBERHOME is set')
+    parser.add_argument(
+        '-amberlib',
+        action='store_true',
+        help='use use amberlib if $AMBERHOME is set')
     parser.add_argument('-debug', action='store_true', help='debug')
     parser.add_argument('-j', default=4, help='n_cpus')
-    parser.add_argument('install_type', default='', nargs='?', help='install_type in amber')
-    return parser.parse_args()
+    parser.add_argument(
+        'install_type', default='', nargs='?', help='install_type in amber')
+    args = parser.parse_args()
+    return args
+
+
+def _install_libcpptraj_win_msys2():
+    PREFIX = '/usr/local/'
+    PREFIX2 = '/mingw64/'
+    # assume you do all the setup
+    command = """
+    sh configure --with-netcdf={PREFIX} \
+                 --with-blas={PREFIX2} \
+                 --with-arpack={PREFIX2} \
+                 --with-readline={PREFIX2} \
+                 -openblas \
+                 -shared \
+                 -windows \
+                 gnu
+    """.format(
+        PREFIX=PREFIX, PREFIX2=PREFIX2).strip()
+    subprocess.check_call(command, shell=True)
+    subprocess.check_call('make libcpptraj -j2', shell=True)
+    # will create libcpptraj.dll.a
+    # shutil.copy('lib/libcpptraj.so', 'lib/cpptraj.lib')
+
 
 if __name__ == '__main__':
-    args = parse_args()
-    compiler, build_flag = get_compiler_and_build_flag()
-    install_libcpptraj(compiler, build_flag, args.j)
+    if sys.platform.startswith('win'):
+        install_libcpptraj()
+    else:
+        args = parse_args()
+        compiler, build_flag = get_compiler_and_build_flag()
+        install_libcpptraj(compiler, build_flag, args.j)