Merge branch 'jmmut-feature/cplusplus' into develop

SConstruct

@@ -10,50 +10,90 @@ compiler = ARGUMENTS.get('compiler', 'gcc')
 #Paths
 system_include = '/usr/include'
 system_libpath = '/usr/lib'
-third_party_path = '#/third_party'
+third_party_path = os.getcwd() + '/third_party'
 
 build_tools = ['default']
-if compiler == 'icc':
+if compiler == 'intel':
     build_tools += ['intelc']
 
 
-#Build environment
-hpg_env = Environment(TOOLS = build_tools,
+#Build C environment
+hpg_c_env = Environment(TOOLS = build_tools,
 		  CFLAGS = ' -Wall -std=c99 -D_XOPEN_SOURCE=700 -D_BSD_SOURCE -D_GNU_SOURCE -D_REENTRANT ',
-		  CPPPATH = ['.', '#', system_include, '%s/libxml2' % system_include, '%s' % third_party_path, '%s/htslib' % third_party_path], 
+		  CPPPATH = ['.', '#', system_include, '%s/libxml2' % system_include, '%s' % third_party_path], 
 		  LIBPATH = [system_libpath],
 		  LINKFLAGS = [],
 		  LIBS = ['xml2', 'm', 'z', 'curl'])
 
 
 if os.environ.has_key('CPATH'):
     for dir in os.getenv('CPATH').split(':'):
-        hpg_env.Append(CPPPATH=[dir])
+        hpg_c_env.Append(CPPPATH=[dir])
 
 if os.environ.has_key('LIBRARY_PATH'):
     for dir in os.getenv('LIBRARY_PATH').split(':'):
-        hpg_env.Append(LIBPATH=[dir])
+        hpg_c_env.Append(LIBPATH=[dir])
 
-if compiler == 'icc':
-	hpg_env['CFLAGS'] += ' -msse4.2 -openmp '
-	hpg_env['LIBS'] += ['irc']
-	hpg_env['LINKFLAGS'] += ['-openmp']
+if compiler == 'intel':
+	hpg_c_env['CFLAGS'] += ' -msse4.2 -openmp '
+	hpg_c_env['LIBS'] += ['irc']
+	hpg_c_env['LINKFLAGS'] += ['-openmp']
 else:
-	hpg_env['CFLAGS'] += ' -fopenmp '
-	hpg_env['LINKFLAGS'] += ['-fopenmp']
+	hpg_c_env['CFLAGS'] += ' -fopenmp '
+	hpg_c_env['LINKFLAGS'] += ['-fopenmp']
 
-hpg_env['objects'] = []
-hpg_env.Decider('MD5-timestamp')
+if debug == 1:
+    hpg_c_env['CFLAGS'] += ' -O0 -g'
+else:
+    hpg_c_env['CFLAGS'] += ' -O2 '
 
+hpg_c_env['objects'] = []
+hpg_c_env.Decider('MD5-timestamp')
 
-# Third party
-third_party_env = Environment(TOOLS = hpg_env['TOOLS'])
-SConscript('third_party/SConscript', exports = ['third_party_env', 'debug', 'compiler'])
 
-hpg_env['CPPPATH'] += third_party_env['CPPPATH']
+
+
+#Build C++ environment
+hpg_cpp_env = Environment(TOOLS = build_tools,
+		  CFLAGS = ' -Wall -std=c++11 -D_XOPEN_SOURCE=700 -D_BSD_SOURCE -D_GNU_SOURCE -D_REENTRANT ',
+		  CPPPATH = ['.', '#', system_include, '%s/libxml2' % system_include, '%s' % third_party_path], 
+		  LIBPATH = [system_libpath],
+		  LINKFLAGS = [],
+		  LIBS = ['xml2', 'm', 'z', 'curl'])
+
+
+if os.environ.has_key('CPATH'):
+    for dir in os.getenv('CPATH').split(':'):
+        hpg_cpp_env.Append(CPPPATH=[dir])
+
+if os.environ.has_key('LIBRARY_PATH'):
+    for dir in os.getenv('LIBRARY_PATH').split(':'):
+        hpg_cpp_env.Append(LIBPATH=[dir])
+
+if compiler == 'intel':
+	hpg_cpp_env['CFLAGS'] += ' -msse4.2 -openmp '
+	hpg_cpp_env['LIBS'] += ['irc']
+	hpg_cpp_env['LINKFLAGS'] += ['-openmp']
+else:
+	hpg_cpp_env['CFLAGS'] += ' -fopenmp '
+	hpg_cpp_env['LINKFLAGS'] += ['-fopenmp']
+
+if debug == 1:
+    hpg_cpp_env['CFLAGS'] += ' -O0 -g'
+else:
+    hpg_cpp_env['CFLAGS'] += ' -O2 '
+
+hpg_cpp_env['objects'] = []
+hpg_cpp_env.Decider('MD5-timestamp')
+
+
+
+
+# Third party
+SConscript('third_party/SConscript', exports = ['hpg_c_env', 'hpg_cpp_env', 'debug', 'compiler'])
 
 
 # our src
 
-SConscript('c/SConscript', exports = ['hpg_env', 'third_party_env', 'debug', 'compiler'])
-SConscript('cpp/SConscript', exports = ['hpg_env', 'third_party_env', 'debug', 'compiler'])
+SConscript('c/SConscript', exports = ['hpg_c_env', 'debug', 'compiler'])
+SConscript('cpp/SConscript', exports = ['hpg_cpp_env', 'debug', 'compiler'])

c/SConscript

@@ -1,16 +1,17 @@
+import os
 
-Import('hpg_env', 'third_party_env', 'compiler', 'debug')
+Import('hpg_c_env', 'compiler', 'debug')
 
-env = hpg_env.Clone()
+env = hpg_c_env.Clone()
 
-#commons_path =     '#/c/common-libs'
-#bioinfo_path =     '#/c/bioinfo-libs'
-c_src_path =        '#/c/src'
-aligners_path =     '#/c/src/aligners'
-bioformats_path =   '#/c/src/bioformats'
-commons_path =      '#/c/src/commons'
-containers_path =   '#/c/src/containers'
-math_path =         '#/c/src/math'
+#commons_path =     os.getcwd() + '/common-libs'
+#bioinfo_path =     os.getcwd() + '/bioinfo-libs'
+c_src_path =        os.getcwd() + '/src'
+aligners_path =     os.getcwd() + '/src/aligners'
+bioformats_path =   os.getcwd() + '/src/bioformats'
+commons_path =      os.getcwd() + '/src/commons'
+containers_path =   os.getcwd() + '/src/containers'
+math_path =         os.getcwd() + '/src/math'
 
 VariantDir('build', 'src', duplicate=0)
 
@@ -25,4 +26,4 @@ SConscript('src/containers/SConscript', exports = ['env', 'debug', 'compiler'])
 SConscript('src/math/SConscript', exports = ['env', 'debug', 'compiler'])
 
 
-env.Library('build/hpg', third_party_env['objects'] + env['objects'])
+env.Library('build/hpg', env['objects'])

c/src/aligners/SConscript

@@ -6,11 +6,6 @@ Import('env', 'compiler', 'debug')
 aligners_env = env.Clone()
 aligners_env['objects'] = []
 
-if debug == 1:
-    aligners_env['CFLAGS'] += ' -O0 -g'
-else:
-    aligners_env['CFLAGS'] += ' -O3 '
-
 
 # Targets
 aligners = ['bwt', 'sw']

c/src/bioformats/SConscript

@@ -6,11 +6,6 @@ Import('env', 'compiler', 'debug')
 formats_env = env.Clone()
 formats_env['objects'] = []
 
-if debug == 1:
-    formats_env['CFLAGS'] += ' -O0 -g'
-else:
-    formats_env['CFLAGS'] += ' -O3 '
-
 
 # Targets
 formats = ['family', 'fastq', 'bam', 'gff', 'bed', 'ped', 'features', 'vcf', 'db']

c/src/commons/SConscript

@@ -9,11 +9,6 @@ commonsenv = env.Clone()
 commonsenv['objects'] = []
 commonsenv.Decider('MD5-timestamp')
 
-if debug == 1:
-    commonsenv['CFLAGS'] += ' -O0 -g'
-else:
-    commonsenv['CFLAGS'] += ' -O3 '
-
 
 # Targets
 commons_obj = commonsenv.Object(Glob('./*.c'))

c/src/containers/SConscript

@@ -10,11 +10,6 @@ containersenv = env.Clone()
 containersenv['objects'] = []
 containersenv.Decider('MD5-timestamp')
 
-if debug == 1:
-    containersenv['CFLAGS'] += ' -O0 -g'
-else:
-    containersenv['CFLAGS'] += ' -O3 '
-
 
 # Targets
 containers_obj = containersenv.Object(Glob('./*.c'))

c/src/math/SConscript

@@ -20,11 +20,6 @@ if os.environ.has_key('CPATH'):
 
 math_env.Decider('MD5-timestamp')
 
-if debug == 1:
-    math_env['CFLAGS'] += ' -O0 -g'
-else:
-    math_env['CFLAGS'] += ' -O3 -g'
-
 
 # Targets
 algebra_obj = math_env.Object(Glob('algebra/*.c'))

third_party/SConscript

@@ -1,66 +1,55 @@
 
+import os 
 
-Import('third_party_env', 'compiler', 'debug')
-
-# initialize environment
-third_party_libs = []
-third_party_env['objects'] = []
-third_party_env['CPPPATH'] = ['#/third_party/']
-third_party_env.Decider('MD5-timestamp')
-
-if compiler == 'icc':
-	third_party_env['CFLAGS'] = ' -msse4.2 -openmp '
-	third_party_env['LIBS'] = ['irc']
-	third_party_env['LINKFLAGS'] = ['-openmp']
-else:
-	third_party_env['CFLAGS'] = ' -fopenmp '
-	third_party_env['LINKFLAGS'] = ['-fopenmp']
-
-if debug == 1:
-    third_party_env['CFLAGS'] = ' -O0 -g'
-else:
-    third_party_env['CFLAGS'] = ' -O2 '
+Import('hpg_c_env', 'hpg_cpp_env', 'compiler', 'debug')
 
+third_party_c_objs = []
+third_party_cpp_objs = []
+hpg_c_env['CPPPATH'] += [os.getcwd()]
+hpg_cpp_env['CPPPATH'] += [os.getcwd()]
 
 # Compile argtable/ objects
-argtableenv = third_party_env.Clone()
+argtableenv = hpg_c_env.Clone()
 argtableenv['CFLAGS'] += ' -DHAVE_CONFIG_H -fPIC -DPIC'
 
-third_party_libs += argtableenv.Object(Glob('argtable/*.c'))
+third_party_c_objs += argtableenv.Object(Glob('argtable/*.c'))
 
 # Compile config/ objects
-configenv = third_party_env.Clone()
+configenv = hpg_c_env.Clone()
 configenv['CFLAGS'] += ' -DHAVE_CONFIG_H -D_REENTRANT -Wall -Wshadow -Wextra -Wdeclaration-after-statement -Wno-unused-parameter'
 
-third_party_libs += configenv.Object(Glob('config/*.c'))
+third_party_c_objs += configenv.Object(Glob('config/*.c'))
 
 
 # Compile jansson/ objects
-janssonenv = third_party_env.Clone()
+janssonenv = hpg_c_env.Clone()
 janssonenv['CFLAGS'] +=  ' -DHAVE_CONFIG_H -Wall -Wextra -Wdeclaration-after-statement -fPIC -DPIC'
-janssonenv['CPPPATH'] += ['#/third_party/jansson/']
+janssonenv['CPPPATH'] += [os.getcwd() + '/jansson']
+hpg_c_env['CPPPATH'] += [os.getcwd() + '/jansson/']
 
-third_party_libs += janssonenv.Object(Glob('jansson/*.c'))
+third_party_c_objs += janssonenv.Object(Glob('jansson/*.c'))
 
 # Compile sqlite/ objects
-sqliteenv = third_party_env.Clone()
+sqliteenv = hpg_c_env.Clone()
 sqliteenv['CFLAGS'] += ' -DHAVE_CONFIG_H -fPIC -DPIC'
 
-third_party_libs += sqliteenv.Object(Glob('sqlite/*.c'))
+third_party_c_objs += sqliteenv.Object(Glob('sqlite/*.c'))
+third_party_cpp_objs += sqliteenv.Object(Glob('sqlite/*.c'))
 
 
 # Compile cprops/ objects but ONLY those used for our libraries
-cpropsenv = third_party_env.Clone()
+cpropsenv = hpg_c_env.Clone()
 cpropsenv['CFLAGS'] += ' -D_REENTRANT -D_GNU_SOURCE -DHAVE_CONFIG_H '
 
-third_party_libs += cpropsenv.Object(['cprops/avl.c', 'cprops/collection.c', 'cprops/hashlist.c', 'cprops/hashtable.c', 'cprops/heap.c', 'cprops/linked_list.c', 'cprops/log.c', 'cprops/mempool.c', 'cprops/rb.c', 'cprops/util.c', 'cprops/vector.c', 'cprops/trie.c', 'cprops/mtab.c'])
+third_party_c_objs += cpropsenv.Object(['cprops/avl.c', 'cprops/collection.c', 'cprops/hashlist.c', 'cprops/hashtable.c', 'cprops/heap.c', 'cprops/linked_list.c', 'cprops/log.c', 'cprops/mempool.c', 'cprops/rb.c', 'cprops/util.c', 'cprops/vector.c', 'cprops/trie.c', 'cprops/mtab.c'])
 
 
 # we don't compile samtools and hts ourselves, delegate in their makefiles
 # that generate samtools/libbam.a and htslib/libhts.a
 from subprocess import call
 call("make")
-
+hpg_c_env['CPPPATH'] += [os.getcwd() + '/htslib/']
 
 # return all objects
-third_party_env['objects'] += third_party_libs
+hpg_c_env['objects'] += third_party_c_objs
+hpg_cpp_env['objects'] += third_party_cpp_objs