Author: Alastair McKinstry <mckinstry@debian.org>
Description: Python3 changes
Last-Updated: 2021-01-28
Forwarded: no

Index: adios-1.13.1/wrappers/numpy/setup3.py
===================================================================
--- /dev/null
+++ adios-1.13.1/wrappers/numpy/setup3.py
@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+# Author:  Jong Choi
+# Contact: choij@ornl.gov
+
+from distutils.extension import Extension
+import numpy as np
+
+# Use mpi4py dist utils: https://bitbucket.org/mpi4py/mpi4py
+#from mpidistutils import setup
+from distutils.core import setup
+from distutils.spawn import find_executable
+from distutils.core import Command
+
+import subprocess
+import sys
+
+m1 = Extension('adios3', 
+               sources=['adios3.cpp'], 
+               define_macros=[('_NOMPI', None)],
+               include_dirs = [np.get_include(), '../../src/public'],
+               library_dirs = ['../../debian/tmp/usr/lib'],
+               libraries = [],
+               extra_objects = [],
+               extra_compile_args = ['-Wno-uninitialized',
+                                     '-Wno-unused-function'])
+
+cmd = find_executable("adios_config")
+if cmd == None:
+    sys.stderr.write(
+        "adios_config is not installed nor found. "
+        "Please install Adios or check PATH.\n")
+    sys.exit(-1)
+
+p = subprocess.Popen(["adios_config", "-c", "-s"], stdout=subprocess.PIPE)
+pp = p.communicate()[0].decode(encoding='UTF-8').strip()
+for path in str(pp).split(" "):
+    if path.startswith('-I'):
+        m1.include_dirs.append(path.replace('-I', '', 1))
+
+p = subprocess.Popen(["adios_config", "-l", "-s"], stdout=subprocess.PIPE)
+pp = p.communicate()[0].decode(encoding='UTF-8').strip()
+for path in str(pp).split(" "):
+    if path.startswith('-L'):
+        m1.library_dirs.append(path.replace('-L', '', 1))
+    if path.startswith('-l'):
+        m1.libraries.append(path.replace('-l', '', 1))
+
+class adios_test(Command):
+    user_options = []
+    def initialize_options(self):
+        pass
+
+    def finalize_options(self):
+        pass
+
+    def run(self):
+        ##import subprocess
+        ##import sys
+        ##errno = subprocess.call([sys.executable, 'tests/test_adios.py', 'tests/config.xml'])
+        ##raise SystemExit(errno)
+        import os
+        import sys
+        import unittest
+        setup_file = sys.modules['__main__'].__file__
+        setup_dir = os.path.abspath(os.path.dirname(setup_file))
+        test_loader = unittest.defaultTestLoader
+        test_runner = unittest.TextTestRunner()
+        test_suite = test_loader.discover(os.path.join(setup_dir, 'test'))
+        test_runner.run(test_suite)
+
+setup(name = 'adios',
+      version = '1.9.0',
+      description = 'Python Module for Adios',
+      author = 'Jong Choi',
+      author_email = 'yyalli@gmail.com',
+      url = 'http://www.olcf.ornl.gov/center-projects/adios/',
+      cmdclass={'test': adios_test},
+      ext_modules = [m1])
Index: adios-1.13.1/wrappers/numpy/setup3_mpi.py
===================================================================
--- /dev/null
+++ adios-1.13.1/wrappers/numpy/setup3_mpi.py
@@ -0,0 +1,134 @@
+#!/usr/bin/env python3
+# Author:  Jong Choi
+# Contact: choij@ornl.gov
+
+
+import os
+import sys
+import getopt
+import numpy as np
+
+## Credit: http://svn.apache.org/repos/asf/subversion/tags/0.20.1/subversion/bindings/swig/python/setup.py
+def _do_usage():
+  print ("Usage: setup.py [OPTIONS] build")
+  print ("       setup.py install [--prefix PREFIX]")
+  print ("       setup.py install_lib [--install-dir DIR]")
+  print ("")
+  print ("Options:")
+  print ("   -I dir      " + \
+        "search DIR for includes (multiple instances allowed)")
+  print ("   -L dir      " + \
+        "search DIR for libraries (multiple instances allowed)")
+  print ("   -C option   " + \
+        "pass OPTION to the compiler at compile time (multiple instances " + \
+        "allowed)")
+  print ("   -R option   " + \
+        "pass OPTION to the compiler at link time (multiple instances " + \
+        "allowed)")
+  sys.exit(0)
+
+# Default option values
+include_dirs = ['../../src/public', np.get_include()]
+library_dirs = ['../../debian/tmp/usr/lib']
+extra_compile_args = []
+extra_link_args = []
+
+# No args?  Give usage.
+if len(sys.argv) < 2:
+  _do_usage()
+
+# Parse the command-line arguments, keeping what we want and letting
+# distutils have the rest.  Distutils parameters should come after
+# the target as in 'python setup.py build --prefix=/usr/local' and
+# parameters for us should appear before the target as in
+# 'python setup.py -I/usr/include build'.
+options, leftovers = getopt.getopt(sys.argv[1:], "I:L:C:R:h",
+                                   ["help"])
+for option in options:
+  if option[0] == '-I':
+    include_dirs.append(option[1])
+  if option[0] == '-L':
+    library_dirs.append(option[1])
+  if option[0] == '-C':
+    extra_compile_args.append(option[1])
+  if option[0] == '-R':
+    extra_link_args.append(option[1])
+  if option[0] == '-h':
+    _do_usage()
+
+  if option[0] == '--help':
+    _do_usage()
+
+  # All long options just get passed through
+  if option[0][:2] == '--':
+    leftovers.append(option[0])
+    leftovers.append(option[1])
+sys.argv[1:] = leftovers
+
+from distutils.extension import Extension
+
+# Use mpi4py dist utils: https://bitbucket.org/mpi4py/mpi4py
+from conf.mpidistutils import setup
+#from distutils.core import setup
+from distutils.spawn import find_executable
+from distutils.core import Command
+
+import subprocess
+
+extra_compile_args.insert(0, '-Wno-uninitialized')
+extra_compile_args.insert(0, '-Wno-unused-function')
+
+m1 = Extension('adios3_mpi', 
+               sources=['adios3_mpi.cpp'], 
+               define_macros=[],
+               include_dirs = include_dirs,
+               library_dirs = library_dirs,
+               libraries = [],
+               extra_objects = [],
+               extra_compile_args = extra_compile_args,
+               extra_link_args = extra_link_args)
+
+cmd = find_executable("adios_config")
+if cmd == None:
+    sys.stderr.write(
+        "adios_config is not installed nor found. "
+        "Please install Adios or check PATH.\n")
+    sys.exit(-1)
+
+p = subprocess.Popen(["adios_config", "-c"], stdout=subprocess.PIPE)
+pp = p.communicate()[0].decode(encoding='UTF-8').strip()
+for path in str(pp).split(" "):
+    if path.startswith('-I'):
+        m1.include_dirs.append(path.replace('-I', '', 1))
+
+p = subprocess.Popen(["adios_config", "-l"], stdout=subprocess.PIPE)
+pp = p.communicate()[0].decode(encoding='UTF-8').strip()
+for path in str(pp).split(" "):
+    if path.startswith('-L'):
+        m1.library_dirs.append(path.replace('-L', '', 1))
+    if path.startswith('-l'):
+        m1.libraries.append(path.replace('-l', '', 1))
+
+class adios_test(Command):
+    user_options = []
+    def initialize_options(self):
+        pass
+
+    def finalize_options(self):
+        pass
+
+    def run(self):
+        import subprocess
+        import sys
+        errno = subprocess.call([sys.executable, 'tests/test_adios_mpi.py', 'tests/config_mpi.xml'])
+        raise SystemExit(errno)
+    
+setup(name = 'adios3_mpi',
+      version = '1.9.0',
+      description = 'Python Module for Adios MPI',
+      author = 'Jong Choi',
+      author_email = 'yyalli@gmail.com',
+      url = 'http://www.olcf.ornl.gov/center-projects/adios/',
+      cmdclass={'test': adios_test},
+      executables = [],
+      ext_modules = [m1])
Index: adios-1.13.1/wrappers/numpy/setup_mpi.py
===================================================================
--- adios-1.13.1.orig/wrappers/numpy/setup_mpi.py
+++ adios-1.13.1/wrappers/numpy/setup_mpi.py
@@ -6,6 +6,7 @@
 import os
 import sys
 import argparse
+import numpy as np
 
 ## Credit: http://svn.apache.org/repos/asf/subversion/tags/0.20.1/subversion/bindings/swig/python/setup.py
 # def _do_usage():
@@ -27,7 +28,7 @@ import argparse
 #   sys.exit(0)
 
 # Default option values
-include_dirs = ['../../src/public']
+include_dirs = ['../../src/public', np.get_include()]
 library_dirs = ['../../debian/tmp/usr/lib']
 extra_compile_args = []
 extra_link_args = []
@@ -66,7 +67,6 @@ extra_link_args = []
 # sys.argv[1:] = leftovers
 
 from distutils.extension import Extension
-import numpy as np
 
 # Use mpi4py dist utils: https://bitbucket.org/mpi4py/mpi4py
 from conf.mpidistutils import setup
@@ -77,7 +77,6 @@ from distutils.core import Command
 import subprocess
 from subprocess import check_output
 
-include_dirs.insert(0, np.get_include())
 extra_compile_args.insert(0, '-Wno-uninitialized')
 extra_compile_args.insert(0, '-Wno-unused-function')
 
Index: adios-1.13.1/wrappers/numpy/Makefile
===================================================================
--- adios-1.13.1.orig/wrappers/numpy/Makefile
+++ adios-1.13.1/wrappers/numpy/Makefile
@@ -1,17 +1,24 @@
 MPI=n
 CYTHON=n
+CYTHON3=n
 
-OBJ = adios.so
+OBJ = adios.so adios3.so
 
 ifeq ($(CYTHON), y)
 	OBJ := adios.cpp $(OBJ)
 endif
+ifeq ($(CYTHON3), y)
+	OBJ :=  adios3.cpp $(OBJ)
+endif
 
 ifeq ($(MPI),y)
-	OBJ += adios_mpi.so
+	OBJ += adios_mpi.so adios3_mpi.so
 	ifeq ($(CYTHON), y)
 		OBJ := adios_mpi.cpp $(OBJ)
 	endif
+	ifeq ($(CYTHON3), y)
+		OBJ := adios3_mpi.cpp $(OBJ)
+	endif
 endif
 
 
@@ -24,19 +31,31 @@ default:
 	@echo "> make MPI=y python"
 	@echo ""
 
-python: $(OBJ)
+python3: $(OBJ)
 
 adios.cpp:  adios.pyx
-	cython --cplus adios.pyx
+	cython3 --cplus adios.pyx
+
+adios3.cpp:  adios.pyx
+	cython3 --cplus -3 -o adios3.cpp adios.pyx 
 
-adios.so:  
-	python setup.py build_ext -lrt
+adios.so:  adios.cpp
+	python3 setup.py build_ext -lrt
+
+adios3.so: adios3.cpp 
+	python3 setup3.py build_ext -lrt
 
 adios_mpi.cpp:  adios_mpi.pyx
-	cython --cplus adios_mpi.pyx
+	cython3 --cplus adios_mpi.pyx
+
+adios3_mpi.cpp:  adios_mpi.pyx
+	cython3 --cplus -3 -o adios3_mpi.cpp adios_mpi.pyx
+
+adios_mpi.so:  adios_mpi.cpp
+	python3 setup_mpi.py build
 
-adios_mpi.so:  
-	python setup_mpi.py build
+adios3_mpi.so:  adios3_mpi.cpp
+	python3 setup3_mpi.py build
 
 clean:
 	rm -rf build
Index: adios-1.13.1/utils/gpp/type_mapper.py
===================================================================
--- adios-1.13.1.orig/utils/gpp/type_mapper.py
+++ adios-1.13.1/utils/gpp/type_mapper.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 c_types = {
     'string' : 'string',
Index: adios-1.13.1/utils/skel/bin/skel
===================================================================
--- adios-1.13.1.orig/utils/skel/bin/skel
+++ adios-1.13.1/utils/skel/bin/skel
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 import sys
 import os.path
Index: adios-1.13.1/utils/skel/bin/skel_cat.py
===================================================================
--- adios-1.13.1.orig/utils/skel/bin/skel_cat.py
+++ adios-1.13.1/utils/skel/bin/skel_cat.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 import argparse
 import os
Index: adios-1.13.1/utils/skel/bin/skel_extract.py
===================================================================
--- adios-1.13.1.orig/utils/skel/bin/skel_extract.py
+++ adios-1.13.1/utils/skel/bin/skel_extract.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 from __future__ import absolute_import, division, print_function, unicode_literals
 import argparse
Index: adios-1.13.1/utils/skel/etc/templates/create_suite.tmpl
===================================================================
--- adios-1.13.1.orig/utils/skel/etc/templates/create_suite.tmpl
+++ adios-1.13.1/utils/skel/etc/templates/create_suite.tmpl
@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/bin/bash
 
 #for test in $test_plan.get_tests():
 <%= '#####Start Test#####' %>
Index: adios-1.13.1/utils/skel/lib/skel_bpls.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_bpls.py
+++ adios-1.13.1/utils/skel/lib/skel_bpls.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+F#!/usr/bin/python3
 
 import re
 
Index: adios-1.13.1/utils/skel/lib/skel_bpy.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_bpy.py
+++ adios-1.13.1/utils/skel/lib/skel_bpy.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 import yaml
 
Index: adios-1.13.1/utils/skel/lib/skel_install.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_install.py
+++ adios-1.13.1/utils/skel/lib/skel_install.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 from __future__ import absolute_import, division, print_function, unicode_literals
 import skel_settings
 
Index: adios-1.13.1/utils/skel/lib/skel_makefile.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_makefile.py
+++ adios-1.13.1/utils/skel/lib/skel_makefile.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 # from __future__ import absolute_import, division, print_function, unicode_literals
 from __future__ import print_function, unicode_literals
Index: adios-1.13.1/utils/skel/lib/skel_params.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_params.py
+++ adios-1.13.1/utils/skel/lib/skel_params.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 from __future__ import absolute_import, division, print_function, unicode_literals
 import sys
 import os
Index: adios-1.13.1/utils/skel/lib/skel_replay.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_replay.py
+++ adios-1.13.1/utils/skel/lib/skel_replay.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 import argparse
 import os
Index: adios-1.13.1/utils/skel/lib/skel_settings.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_settings.py
+++ adios-1.13.1/utils/skel/lib/skel_settings.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 from __future__ import absolute_import, division, print_function
 import sys
 import os.path
Index: adios-1.13.1/utils/skel/lib/skel_source.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_source.py
+++ adios-1.13.1/utils/skel/lib/skel_source.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 from __future__ import absolute_import, division, print_function, unicode_literals
 import sys
 import os
Index: adios-1.13.1/utils/skel/lib/skel_submit.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_submit.py
+++ adios-1.13.1/utils/skel/lib/skel_submit.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 from __future__ import absolute_import, division, print_function, unicode_literals
 import argparse
 import os
Index: adios-1.13.1/utils/skel/lib/skel_suite.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_suite.py
+++ adios-1.13.1/utils/skel/lib/skel_suite.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 import argparse
 import os
Index: adios-1.13.1/utils/skel/lib/skel_template.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_template.py
+++ adios-1.13.1/utils/skel/lib/skel_template.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 import argparse
 import os
Index: adios-1.13.1/utils/skel/lib/skel_test_plan.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_test_plan.py
+++ adios-1.13.1/utils/skel/lib/skel_test_plan.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 import yaml
 
Index: adios-1.13.1/utils/skel/lib/skel_xml.py
===================================================================
--- adios-1.13.1.orig/utils/skel/lib/skel_xml.py
+++ adios-1.13.1/utils/skel/lib/skel_xml.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 
 from __future__ import absolute_import, division, print_function, unicode_literals
 import argparse
Index: adios-1.13.1/wrappers/numpy/setup.py
===================================================================
--- adios-1.13.1.orig/wrappers/numpy/setup.py
+++ adios-1.13.1/wrappers/numpy/setup.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
 # Author:  Jong Choi
 # Contact: choij@ornl.gov
 
@@ -16,7 +16,7 @@ import sys
 from subprocess import check_output
 
 m1 = Extension('adios.adios',
-               sources=['adios.cpp'],
+               sources=['adios3.cpp'],
                define_macros=[('_NOMPI', None)],
                include_dirs = [np.get_include(), '../../src/public'],
                library_dirs = ['../../debian/tmp/usr/lib'],