From f44ff52a81650cf5f2a6b1e11f0194e468756672 Mon Sep 17 00:00:00 2001
From: DannyArends
Date: Wed, 28 Feb 2018 15:46:43 +0100
Subject: OS detection, and version script generator selection via VGEN

---
 Makefile | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

(limited to 'Makefile')

diff --git a/Makefile b/Makefile
index f8bacbf..23b834f 100644
--- a/Makefile
+++ b/Makefile
@@ -41,7 +41,19 @@
 GEMMA_VERSION = $(shell cat ./VERSION)
 
 # Set this variable to either LNX or MAC
-SYS                    = LNX # LNX|MAC (Linux is the default)
+ifeq ($(OS),Windows_NT)
+  SYS = WIN
+  VGEN = scripts/gen_version_info.cmd
+else
+  UNAME_S := $(shell uname -s)
+  ifeq ($(UNAME_S),Darwin)
+    SYS = MAC
+  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
@@ -149,7 +161,7 @@ OBJS = $(SOURCES:.cpp=.o)
 all: $(OUTPUT)
 
 ./src/version.h:
-	./scripts/gen_version_info.sh > src/version.h
+	$(VGEN) > src/version.h
 
 $(OUTPUT): $(OBJS)
 	$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
-- 
cgit v1.2.3


From 2fc39eb39792384f797bc29002a0a6b3ef2d50d3 Mon Sep 17 00:00:00 2001
From: DannyArends
Date: Wed, 28 Feb 2018 16:07:43 +0100
Subject: Windows compilation paths, and restructuring the -isystem

---
 Makefile | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)

(limited to 'Makefile')

diff --git a/Makefile b/Makefile
index 23b834f..a1b9b76 100644
--- a/Makefile
+++ b/Makefile
@@ -65,8 +65,20 @@ OPENBLAS_LEGACY        =                  # Using older OpenBlas
 FORCE_STATIC           =                  # Static linking of libraries
 GCC_FLAGS              = -Wall -O3 -std=gnu++11 # extra flags -Wl,--allow-multiple-definition
 TRAVIS_CI              =                  # used by TRAVIS for testing
-EIGEN_INCLUDE_PATH     = /usr/include/eigen3
-OPENBLAS_INCLUDE_PATH  = /usr/local/opt/openblas/include
+
+GSL_INCLUDE_PATH =
+ifeq ($(SYS), WIN)
+  GSL_INCLUDE_PATH = -Ic:/GnuWin32/include
+  EIGEN_INCLUDE_PATH = -I../eigen-git-mirror
+  OPENBLAS_INCLUDE_PATH = -I../OpenBLAS-v0.2.19-Win64-int32/include
+else
+  OPENBLAS_INCLUDE_PATH = -isystem//usr/local/opt/openblas/include
+  ifeq ($(SYS), MAC)
+  EIGEN_INCLUDE_PATH = -isystem//usr/local/include/eigen3
+  else
+  EIGEN_INCLUDE_PATH = -isystem//usr/include/eigen3
+  endif
+endif
 
 # --------------------------------------------------------------------
 # Edit below this line with caution
@@ -85,13 +97,13 @@ endif
 
 ifeq ($(CPP), clang++)
   # macOS Homebrew settings (as used on Travis-CI)
-  GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ -isystem/$(OPENBLAS_INCLUDE_PATH) -isystem//usr/local/include/eigen3 -Wl,-L/usr/local/opt/openblas/lib
+  GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ $(OPENBLAS_INCLUDE_PATH) $(EIGEN_INCLUDE_PATH) -Wl,-L/usr/local/opt/openblas/lib
 endif
 
 ifdef WITH_OPENBLAS
   OPENBLAS=1
   # WITH_LAPACK =  # OPENBLAS usually includes LAPACK
-  CPPFLAGS += -DOPENBLAS -isystem/$(OPENBLAS_INCLUDE_PATH)
+  CPPFLAGS += -DOPENBLAS $(OPENBLAS_INCLUDE_PATH)
   ifdef OPENBLAS_LEGACY
     # Legacy version (mostly for Travis-CI)
     CPPFLAGS += -DOPENBLAS_LEGACY
@@ -99,10 +111,14 @@ ifdef WITH_OPENBLAS
 endif
 
 ifdef DEBUG
-  CPPFLAGS += -g $(GCC_FLAGS) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+  CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) $(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
 else
   # release mode
-  CPPFLAGS += -DNDEBUG $(GCC_FLAGS) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+  CPPFLAGS += -DNDEBUG $(GCC_FLAGS) $(GSL_INCLUDE_PATH) $(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+endif
+
+ifeq ($(SYS), WIN)
+  CPPFLAGS += -Duint="unsigned int" -D__CRT__NO_INLINE -D__STRING="__STRINGIFY"
 endif
 
 ifdef SHOW_COMPILER_WARNINGS
-- 
cgit v1.2.3


From 9b6cc6e0955d9b6acc88ee8801729ae6fcc60d8b Mon Sep 17 00:00:00 2001
From: DannyArends
Date: Wed, 28 Feb 2018 23:37:52 +0100
Subject: Makefile changes, to compile under windows

---
 Makefile | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'Makefile')

diff --git a/Makefile b/Makefile
index a1b9b76..235d1b6 100644
--- a/Makefile
+++ b/Makefile
@@ -68,9 +68,9 @@ TRAVIS_CI              =                  # used by TRAVIS for testing
 
 GSL_INCLUDE_PATH =
 ifeq ($(SYS), WIN)
-  GSL_INCLUDE_PATH = -Ic:/GnuWin32/include
-  EIGEN_INCLUDE_PATH = -I../eigen-git-mirror
-  OPENBLAS_INCLUDE_PATH = -I../OpenBLAS-v0.2.19-Win64-int32/include
+  GSL_INCLUDE_PATH = -isystemc:/MinGW/include -LC:/MinGW/lib
+  EIGEN_INCLUDE_PATH = -isystem../eigen-git-mirror
+  OPENBLAS_INCLUDE_PATH = -isystem../OpenBLAS-v0.2.19-Win64-int32/include -L../OpenBLAS-v0.2.19-Win64-int32/lib
 else
   OPENBLAS_INCLUDE_PATH = -isystem//usr/local/opt/openblas/include
   ifeq ($(SYS), MAC)
@@ -118,7 +118,7 @@ else
 endif
 
 ifeq ($(SYS), WIN)
-  CPPFLAGS += -Duint="unsigned int" -D__CRT__NO_INLINE -D__STRING="__STRINGIFY"
+  CPPFLAGS += -Duint="unsigned int" -D__CRT__NO_INLINE -D__STRING="__STRINGIFY" -DWINDOWS -DWITH_GSLCBLAS=1
 endif
 
 ifdef SHOW_COMPILER_WARNINGS
-- 
cgit v1.2.3


From 64799368da26440c014ecfcf435f7ca3a44d8d15 Mon Sep 17 00:00:00 2001
From: DannyArends
Date: Thu, 1 Mar 2018 15:55:10 +0100
Subject: Trying to fix the -isystem/ failure of travis

---
 Makefile | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

(limited to 'Makefile')

diff --git a/Makefile b/Makefile
index 235d1b6..e7fe655 100644
--- a/Makefile
+++ b/Makefile
@@ -68,15 +68,15 @@ TRAVIS_CI              =                  # used by TRAVIS for testing
 
 GSL_INCLUDE_PATH =
 ifeq ($(SYS), WIN)
-  GSL_INCLUDE_PATH = -isystemc:/MinGW/include -LC:/MinGW/lib
-  EIGEN_INCLUDE_PATH = -isystem../eigen-git-mirror
-  OPENBLAS_INCLUDE_PATH = -isystem../OpenBLAS-v0.2.19-Win64-int32/include -L../OpenBLAS-v0.2.19-Win64-int32/lib
+  GSL_INCLUDE_PATH = -isystem/c:/MinGW/include -LC:/MinGW/lib
+  EIGEN_INCLUDE_PATH = ../eigen-git-mirror
+  OPENBLAS_INCLUDE_PATH = ../OpenBLAS-v0.2.19-Win64-int32/include -L../OpenBLAS-v0.2.19-Win64-int32/lib
 else
-  OPENBLAS_INCLUDE_PATH = -isystem//usr/local/opt/openblas/include
+  OPENBLAS_INCLUDE_PATH = /usr/local/opt/openblas/include
   ifeq ($(SYS), MAC)
-  EIGEN_INCLUDE_PATH = -isystem//usr/local/include/eigen3
+  EIGEN_INCLUDE_PATH = /usr/local/include/eigen3
   else
-  EIGEN_INCLUDE_PATH = -isystem//usr/include/eigen3
+  EIGEN_INCLUDE_PATH = /usr/include/eigen3
   endif
 endif
 
@@ -97,13 +97,13 @@ endif
 
 ifeq ($(CPP), clang++)
   # macOS Homebrew settings (as used on Travis-CI)
-  GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ $(OPENBLAS_INCLUDE_PATH) $(EIGEN_INCLUDE_PATH) -Wl,-L/usr/local/opt/openblas/lib
+  GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ -isystem/$(OPENBLAS_INCLUDE_PATH) -isystem/$(EIGEN_INCLUDE_PATH) -Wl,-L/usr/local/opt/openblas/lib
 endif
 
 ifdef WITH_OPENBLAS
   OPENBLAS=1
   # WITH_LAPACK =  # OPENBLAS usually includes LAPACK
-  CPPFLAGS += -DOPENBLAS $(OPENBLAS_INCLUDE_PATH)
+  CPPFLAGS += -DOPENBLAS -isystem/$(OPENBLAS_INCLUDE_PATH)
   ifdef OPENBLAS_LEGACY
     # Legacy version (mostly for Travis-CI)
     CPPFLAGS += -DOPENBLAS_LEGACY
@@ -111,10 +111,10 @@ ifdef WITH_OPENBLAS
 endif
 
 ifdef DEBUG
-  CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) $(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+  CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
 else
   # release mode
-  CPPFLAGS += -DNDEBUG $(GCC_FLAGS) $(GSL_INCLUDE_PATH) $(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+  CPPFLAGS += -DNDEBUG $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
 endif
 
 ifeq ($(SYS), WIN)
-- 
cgit v1.2.3


From dd3ca7014de2d8f1a2cec36cc22ff93b1e929cc4 Mon Sep 17 00:00:00 2001
From: DannyArends
Date: Thu, 1 Mar 2018 15:58:04 +0100
Subject: Early morning extra fwd slash failure, fixed in this commit

---
 Makefile | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'Makefile')

diff --git a/Makefile b/Makefile
index e7fe655..bdb58b2 100644
--- a/Makefile
+++ b/Makefile
@@ -68,7 +68,7 @@ TRAVIS_CI              =                  # used by TRAVIS for testing
 
 GSL_INCLUDE_PATH =
 ifeq ($(SYS), WIN)
-  GSL_INCLUDE_PATH = -isystem/c:/MinGW/include -LC:/MinGW/lib
+  GSL_INCLUDE_PATH = -isystemc:/MinGW/include -LC:/MinGW/lib
   EIGEN_INCLUDE_PATH = ../eigen-git-mirror
   OPENBLAS_INCLUDE_PATH = ../OpenBLAS-v0.2.19-Win64-int32/include -L../OpenBLAS-v0.2.19-Win64-int32/lib
 else
@@ -97,13 +97,13 @@ endif
 
 ifeq ($(CPP), clang++)
   # macOS Homebrew settings (as used on Travis-CI)
-  GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ -isystem/$(OPENBLAS_INCLUDE_PATH) -isystem/$(EIGEN_INCLUDE_PATH) -Wl,-L/usr/local/opt/openblas/lib
+  GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ -isystem$(OPENBLAS_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Wl,-L/usr/local/opt/openblas/lib
 endif
 
 ifdef WITH_OPENBLAS
   OPENBLAS=1
   # WITH_LAPACK =  # OPENBLAS usually includes LAPACK
-  CPPFLAGS += -DOPENBLAS -isystem/$(OPENBLAS_INCLUDE_PATH)
+  CPPFLAGS += -DOPENBLAS -isystem$(OPENBLAS_INCLUDE_PATH)
   ifdef OPENBLAS_LEGACY
     # Legacy version (mostly for Travis-CI)
     CPPFLAGS += -DOPENBLAS_LEGACY
@@ -111,10 +111,10 @@ ifdef WITH_OPENBLAS
 endif
 
 ifdef DEBUG
-  CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+  CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
 else
   # release mode
-  CPPFLAGS += -DNDEBUG $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
+  CPPFLAGS += -DNDEBUG $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
 endif
 
 ifeq ($(SYS), WIN)
-- 
cgit v1.2.3