Makefile

# Profile?
# Set this variable to true if you wish to profile the codes.
WANT_PROFILING=false

# Which profiling tool to use?
# Assuming you have TAU installed and setup properly, 
# you can instrument codes with it to get detailed multi-threaded profiling.
# Otherwise, gprof is able to give you some information without threading info.
# Choose one of: gprof, TAU
PROFILER_OF_CHOICE=gprof

# Perform extra sanity checking?
# Set this variable to true 
# if you wish the codes to perform extra sanity checking 
# (to the possible detriment of performance).
WANT_EXTRA_SANITY_CHECKING=false

# Compile with debugging symbols?
# Set this variable to true 
# if you wish the codes to be built with debugging symbols 
# (increases code size and does not always produce accurate stepping in a debugger 
# when optimization is turned on).
WANT_DEBUGGING=false

# Compile with tracing logic turned on?
# Set this variable to true if you want to use instrumentation provided 
# in the sources for debugging purposes 
# and are willing to accept the overhead such instrumentation introduces.
WITH_INTERNAL_TRACING=false

# Compile with performance metrics turned on?
# Set this variable to true if you want to use instrumentation provided 
# in the sources for performance measurement purposes 
# and are willing to accept the overhead such instrumentation introduces.
WITH_INTERNAL_METRICS=false

# Use Cython?
# Set this variable to true if you wish to build the Python wrapper 
# with Cython rather than the directly using the Python C API.
# (Do not set this to true if you do not have Cython installed.)
USE_CYTHON=false


### NOTE: No user-servicable parts below this line! ###


CXXFLAGS=
CXX_WARNING_FLAGS=-Wall
CXX_OPTIMIZATION_FLAGS=-O3
CXX_SHARED_LIB_FLAGS=-fPIC
CXXFLAGS+= $(CXX_WARNING_FLAGS) $(CXX_OPTIMIZATION_FLAGS) $(CXX_SHARED_LIB_FLAGS)

LIBS=

ifeq ($(WANT_DEBUGGING), true)
CXX_DEBUG_FLAGS=-g
CXXFLAGS+= $(CXX_DEBUG_FLAGS)
else
CXX_DEBUG_FLAGS=
endif

ifeq ($(WANT_EXTRA_SANITY_CHECKING), true)
DEFINE_KHMER_EXTRA_SANITY_CHECKS=-DKHMER_EXTRA_SANITY_CHECKS
CXXFLAGS+= $(DEFINE_KHMER_EXTRA_SANITY_CHECKS)
else
DEFINE_KHMER_EXTRA_SANITY_CHECKS=
endif

ifeq ($(WANT_PROFILING), true)
ifeq ($(PROFILER_OF_CHOICE), TAU)
CXX=tau_cxx.sh
endif
ifeq ($(PROFILER_OF_CHOICE), gprof)
PROFILING_LIBS=-pg
CXXFLAGS+= -pg
LIBS+= $(PROFILING_LIBS)
endif
endif

ifeq ($(WITH_INTERNAL_TRACING), true)
CXXFLAGS+= -DWITH_INTERNAL_TRACING
endif

ifeq ($(WITH_INTERNAL_METRICS), true)
CXXFLAGS+= -DWITH_INTERNAL_METRICS
endif

ifeq ($(USE_CYTHON), true)
CYTHON_ENABLED_BOOL=True
else
CYTHON_ENABLED_BOOL=False
endif

# Place POSIX threads last in linking order, if needed.
ifneq ($(shell uname), Linux)
LIBS+= -pthread
endif

all: lib_files python_files

clean:
	cd lib && make clean
	cd python && make clean
	cd tests && rm -rf khmertest_*

doc: FORCE
	cd doc && make html

lib_files:
	cd lib && \
	make CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS)" LIBS="$(LIBS)"

python_files: lib_files
	cd python && \
	make 	DEFINE_KHMER_EXTRA_SANITY_CHECKS="$(DEFINE_KHMER_EXTRA_SANITY_CHECKS)" \
		CXX_DEBUG_FLAGS="$(CXX_DEBUG_FLAGS)" \
		CYTHON_ENABLED_BOOL="$(CYTHON_ENABLED_BOOL)"
#	python setup.py build_ext -i

test: all
	nosetests -v -x

FORCE: