Introducing premake

1 files changed, 0 insertions, 276 deletions

diff --git a/Makefile b/Makefile
deleted file mode 100644
index 1009a6e..0000000
--- a/Makefile
+++ /dev/null
@@ -1,276 +0,0 @@
-# Generic Makefile for GEMMA
-#
-# Supported platforms
-#
-#       Unix / Linux               LNX (default)
-#       Mac                        OSX
-#       GNU Guix                   GUIX (set to profile)
-#
-# Compilation options
-#       static compilation         FORCE_STATIC
-#
-# Examples:
-#
-#    Make GEMMA on Linux without OPENBLAS support:
-#
-#      make WITH_OPENBLAS=
-#
-#    Disable debug info and checks (release mode is slightly faster)
-#
-#      make debug
-#
-#    Force static compilation
-#
-#      make static
-#
-#    Static build may require some extra flags
-#
-#      make WITH_GFORTRAN=1 EXTRA_FLAGS=-L/gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib static
-#
-#    Run tests with
-#
-#      make check
-#
-#    Run quick (development) tests with
-#
-#      make fast-check
-#
-#    Run full (lengthy) tests with
-#
-#      make check-all
-#
-#    To compile with CLANG
-#
-#      make CXX=clang++
-#
-#    See also the INSTALL.md document in the source tree at
-#
-#      https://github.com/genetics-statistics/GEMMA/blob/master/INSTALL.md
-
-GEMMA_VERSION = $(shell cat ./VERSION)
-
-# Set this variable to either LNX or OSX
-ifeq ($(OS),Windows_NT)
-  SYS = WIN
-  VGEN = scripts/gen_version_info.cmd
-else
-  UNAME_S := $(shell uname -s)
-  ifeq ($(UNAME_S),Darwin)
-    SYS = OSX
-  else
-    SYS = LNX # default to linux
-  endif
-  VGEN = scripts/gen_version_info.sh
-endif
-
-# Leave blank after "=" to disable; put "= 1" to enable
-DIST_NAME              = gemma-$(GEMMA_VERSION)
-DEBUG                  = 1                # DEBUG mode, set DEBUG=0 for a release
-PROFILING              =                  # Add profiling info
-SHOW_COMPILER_WARNINGS =
-WITH_OPENBLAS          = 1                # Without OpenBlas uses LAPACK
-WITH_ATLAS             =                  # In place of OpenBlas(?)
-WITH_LAPACK            =                  # Force linking LAPACK (if OpenBlas lacks it)
-WITH_GSLCBLAS          =                  # Force linking gslcblas (if OpenBlas lacks it)
-WITH_GFORTRAN          =                  # Add -lgfortran (if OpenBlas does not pull it in)
-OPENBLAS_LEGACY        =                  # Using older OpenBlas
-FORCE_STATIC           =                  # Static linking of libraries
-GCC_FLAGS              = -DHAVE_INLINE -pthread -Wall -std=gnu++11 # extra flags -Wl,--allow-multiple-definition
-EXTRA_FLAGS            =
-
-GSL_INCLUDE_PATH =
-ifeq ($(SYS), WIN)
-  GSL_INCLUDE_PATH = -isystemc:/MinGW/include -LC:/MinGW/lib
-  OPENBLAS_INCLUDE_PATH = ../OpenBLAS-v0.2.19-Win64-int32/include -L../OpenBLAS-v0.2.19-Win64-int32/lib
-else
-  OPENBLAS_INCLUDE_PATH = /usr/local/opt/openblas/include
-  ifndef GUIX
-    ifdef GUIX_ENVIRONMENT
-      GUIX=$(GUIX_ENVIRONMENT)
-    endif
-  endif
-  ifdef GUIX
-    # Effectively disable paths for GNU Guix
-    OPENBLAS_INCLUDE_PATH = .
-    # RPATH = -Xlinker --rpath=$(GUIX)/lib
-    ifdef FORCE_STATIC
-      LIBS = -L$(GUIX)/lib
-    endif
-    GUIX_PROFILE =$(realpath $(GUIX))
-  endif
-endif
-
-# --------------------------------------------------------------------
-# Edit below this line with caution
-# --------------------------------------------------------------------
-
-BIN_DIR  = ./bin
-SRC_DIR  = ./src
-TEST_SRC_DIR  = ./test/src
-
-ifdef CXX # CXX defined in environment
-  CPP = $(CXX)
-  CC = $(CXX)
-else
-  CPP = g++
-endif
-
-ifeq ($(CPP), clang++)
-  GCC_FLAGS=-std=c++11 -isystem$(OPENBLAS_INCLUDE_PATH)
-  ifdef GUIX
-    CPPFLAGS += -I$(GUIX)/include/c++ -I$(GUIX)/include/c++/x86_64-unknown-linux-gnu
-  endif
-endif
-
-ifdef WITH_OPENBLAS
-  OPENBLAS=1
-  # WITH_LAPACK =  # OPENBLAS usually includes LAPACK
-  CPPFLAGS += -DOPENBLAS -isystem$(OPENBLAS_INCLUDE_PATH)
-  ifdef OPENBLAS_LEGACY
-    # Legacy version (mostly for Travis-CI)
-    CPPFLAGS += -DOPENBLAS_LEGACY
-  endif
-else
-  ifdef WITH_ATLAS
-    CPPFLAGS += -DUSE_BLAS=atlas
-  endif
-endif
-
-ifneq ($(CXX), clang++)
-  # Clang does not like these switches
-  debug check fast-check: CPPFLAGS += -Og -Wfatal-errors
-endif
-
-debug check fast-check: CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -Isrc
-
-profile: CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -Isrc
-
-release: CPPFLAGS += -DNDEBUG -g -O3 $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -Isrc
-
-static: CPPFLAGS += -DNDEBUG -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -Isrc
-
-
-ifeq ($(SYS), WIN)
-  CPPFLAGS += -Duint="unsigned int" -D__CRT__NO_INLINE -D__STRING="__STRINGIFY" -DWINDOWS -DWITH_GSLCBLAS=1
-endif
-
-ifdef SHOW_COMPILER_WARNINGS
-  CPPFLAGS += -Wall
-endif
-
-static: CPPFLAGS += -static
-
-LIBS += -lgsl -lz
-ifdef WITH_OPENBLAS
-  LIBS += -lopenblas
-  ifeq ($(SYS), OSX)
-    ifdef WITH_OPENBLAS
-      LIBS += -Wl,-L/usr/local/opt/openblas/lib
-    endif
-  endif
-else
-  LIBS += -latlas -lcblas -llapack -lblas
-endif
-ifdef WITH_GSLCBLAS
-  LIBS += -lgslcblas
-endif
-ifdef WITH_GFORTRAN
-  LIBS += -lgfortran -lquadmath
-endif
-ifdef EXTRA_FLAGS
-  LIBS += $(EXTRA_FLAGS)
-endif
-
-profile: LIBS += -Wl,--no-as-needed -lprofiler -Wl,--as-needed
-
-.PHONY: all test
-
-OUTPUT = $(BIN_DIR)/gemma
-
-# Detailed libary paths, D for dynamic and S for static
-
-ifdef WITH_LAPACK
-  LIBS += -llapack
-endif
-LIBS_OSX_D_LAPACK = -framework Accelerate
-
-ifdef WITH_LAPACK
-  ifeq ($(SYS), OSX)
-    LIBS += $(LIBS_OSX_D_LAPACK)
-    ifdef WITH_OPENBLAS
-      LIBS += -Wl,-L/usr/local/opt/openblas/lib
-    endif
-  endif
-endif
-
-HDR          = $(sort $(wildcard src/*.h)) ./src/version.h
-SOURCES      = $(sort $(wildcard src/*.cpp))
-
-# all
-OBJS = $(SOURCES:.cpp=.o)
-
-all: release
-
-release: $(OUTPUT)
-
-static: $(OUTPUT)
-
-debug profile: $(OUTPUT)
-
-./src/version.h: ./VERSION
-	$(shell bash $(VGEN) $(GUIX_PROFILE) > src/version.h)
-
-$(OUTPUT): $(OBJS)
-	$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
-
-$(OBJS): $(HDR)
-
-.SUFFIXES : .cpp .c .o $(SUFFIXES)
-
-./bin/unittests-gemma: $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(OBJS)
-	$(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o  $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma
-
-unittests: all ./bin/unittests-gemma
-	./bin/unittests-gemma
-
-fast-check: all unittests
-	rm -vf output/*
-	ruby -Eutf-8 -Itest ./test/dev_tests.rb | tee ./dev_test.log
-
-# Note the following tests are not robust for different architectures
-old-check: all unittests
-	rm -vf test/output/*
-	cd test && ./dev_test_suite.sh | tee ../test.log
-	grep -q 'success rate: 100%' test.log
-
-# Note the following tests are not robust for different architectures
-slow-check: all
-	rm -vf test/output/*
-	cd test && ./test_suite.sh | tee ../test.log
-	grep -q 'success rate: 100%' test.log
-
-# Note the following tests are not robust for different architectures
-lengthy-check: all
-	rm -vf test/output/*
-	cd test && ./lengthy_test_suite.sh | tee ../lengthy_test.log
-	grep -q 'success rate: 100%' lengthy_test.log
-
-check: fast-check
-
-clean:
-	rm -vf $(SRC_DIR)/*.o
-	rm -vf $(SRC_DIR)/*~
-	rm -vf $(TEST_SRC_DIR)/*.o
-	rm -vf $(OUTPUT)
-	rm -vf ./bin/unittests-gemma
-
-DIST_COMMON = *.md LICENSE VERSION Makefile
-DIST_SUBDIRS = src doc example bin
-
-tar: version all
-	@echo "Creating $(DIST_NAME)"
-	mkdir -p ./$(DIST_NAME)
-	cp $(DIST_COMMON) ./$(DIST_NAME)/
-	cp -r $(DIST_SUBDIRS) ./$(DIST_NAME)/
-	tar cvzf $(DIST_NAME).tar.gz ./$(DIST_NAME)/
-	rm -r ./$(DIST_NAME)