Merge branch 'master' of https://github.com/libigl/libigl

Former-commit-id: 35cc355e6af66a44678b893a76bcfbd1208a3e0a

.gitignore

@@ -1,4 +1,5 @@
 # use glob syntax.
+scripts/change_name.sh
 syntax: glob
 *.o
 *.a

README.md

@@ -35,7 +35,7 @@ listed below.
 - TetGen  libigltetgen extra only
 - Embree  libiglembree extra only
 - tinyxml2  libiglxml extra only
- 
+
 ## Header only ##
 libigl is designed to work "out-of-the-box" as a headers only library. To
 include libigl in your project. You need only include the libigl/include/
@@ -72,31 +72,34 @@ Then run this example with:
 libigl is developed most often on Mac OS X, though has current users in Linux and Windows.
 
 ### Linux/Mac OS X/Cygwin ###
-  
+
 libigl may also be compiled to a static library. This is advantageous when
 building a project with libigl, since the header only directive can slow down
 compile times.
 
 To build the entire libigl library producing lib/libigl.a, issue:
-  
+
+    cd build
     make lib
-  
+
 You may need to edit Makefile.conf accordingly. Best to give yourself an
 `IGL_USERNAME` and add a custom install suite for yourself. Then you can enable
 appropriate extras.
-  
+
 #### Extras ####
 Once you've set up an `IGL_USERNAME` and enabled extras within Makefile.conf.
 You can build the extra libraries (into lib/ligiglpng.a, lib/libiglmatlab.a,
 lib/libigltetgen.a, lib/libiglmosek.a, etc.) by issuing:
-  
+
+    cd build
     make extras
-  
+
 #### Examples ####
 You can make a slew of examples by issuing:
-  
+
+    cd build
     make examples
-  
+
 #### External ####
 Finally there are a number of external libraries that we include in
 ./external/ because they are either difficult to obtain or they have been
@@ -190,6 +193,57 @@ To get started, we advise that you take a look at a few examples:
 
     ./examples/ReAntTweakBar/
 
+## Extras ##
+Libigl compartmentalizes dependences via its organization into a _main_ libigl
+library and "extras." 
+
+
+### bbw ###
+This library extra contains functions for computing Bounded Biharmonic Weights, can
+be used with and without the [mosek](#mosek) extra via the `IGL_NO_MOSEK`
+macro.
+
+### boost ###
+This library extra utilizes the graph functions in the boost library for find
+connected components and performing breadth-first traversals.
+
+### cgal ###
+This library extra utilizes CGAL's efficient and exact intersection and
+proximity queries.
+
+### embree ###
+This library extra utilizes embree's efficient ray tracing queries.
+
+### matlab ###
+This library extra provides support for reading and writing `.mat` workspace
+files, interfacing with Matlab at run time and compiling mex functions.
+
+### mosek ###
+This library extra utilizes mosek's efficient interior-point solver for
+quadratic programs.
+
+### png ###
+This library extra uses `libpng` and `YImage` to read and write `.png` files.
+
+### svd3x3 ###
+This library extra implements "as-rigid-as-possible" (ARAP) deformation
+techniques using the fast singular value decomposition routines
+written specifically for 3x3 matrices to use `SSE` intrinsics. This extra can
+still be compiled without sse support and support should be determined
+automatically at compile time via the `__SSE__` macro.
+
+### tetgen ###
+This library extra provides a simplified wrapper to the tetgen 3d tetrahedral meshing
+library.
+
+### viewer ###
+This library extra utilizes glfw and glew to open an opengl context and launch
+a simple mesh viewer.
+
+### xml ###
+This library extra utilizes tinyxml2 to read and write serialized classes
+containing Eigen matrices and other standard simple data-structures.
+
 ## Development ##
 Further documentation for developers is listed in tutorial.html,
 style_guidelines.html

Makefile → build/Makefile

@@ -16,76 +16,64 @@ CFLAGS += $(OPTFLAGS)
 #CFLAGS += -DIGL_NO_OPENGL -DIGL_NO_ANTTWEAKBAR
 # We use well-supported features of c++11
 
-EXTRA_DIRS=
+EXTRAS=
 ifeq ($(IGL_WITH_BBW),1)
-	EXTRA_DIRS+=include/igl/bbw
 	EXTRAS += bbw
 endif
 ifeq ($(IGL_WITH_BOOST),1)
-	EXTRA_DIRS+=include/igl/boost
 	EXTRAS += boost
 endif
 ifeq ($(IGL_WITH_CGAL),1)
-	EXTRA_DIRS+=include/igl/cgal
 	EXTRAS += cgal
 endif
 ifeq ($(IGL_WITH_EMBREE),1)
-	EXTRA_DIRS+=include/igl/embree
 	EXTRAS += embree
 endif
 ifeq ($(IGL_WITH_MATLAB),1)
-	EXTRA_DIRS+=include/igl/matlab
 	EXTRAS += matlab
 endif
 ifeq ($(IGL_WITH_MOSEK),1)
-	EXTRA_DIRS+=include/igl/mosek
 	EXTRAS += mosek
 endif
 ifeq ($(IGL_WITH_PNG),1)
-	EXTRA_DIRS+=include/igl/png
 	EXTRAS += png
 endif
 ifeq ($(IGL_WITH_SVD3X3),1)
-	EXTRA_DIRS+=include/igl/svd3x3
 	EXTRAS += svd3x3
 endif
 ifeq ($(IGL_WITH_TETGEN),1)
 	# append tetgen extra dir
-	EXTRA_DIRS+=include/igl/tetgen
 	EXTRAS += tetgen
 endif
 ifeq ($(IGL_WITH_VIEWER),1)
-	EXTRA_DIRS+=include/igl/viewer
 	EXTRAS += viewer
 endif
 ifeq ($(IGL_WITH_XML),1)
-	EXTRA_DIRS+=include/igl/xml
 	EXTRAS += xml
 endif
 
 .PHONY: examples
 .PHONY: extras
 debug: lib extras
-lib: lib/libigl.a
+lib: ../lib/libigl.a
 examples: lib extras
-	make -C examples
+	make -C ../examples
 extras:
-	for p in  $(EXTRA_DIRS); \
+	for p in  $(EXTRAS); \
 	do \
-	echo "cd $$p" ; \
-	$(MAKE) -C $$p $(DEBUG); \
+	$(MAKE) -f Makefile_$$p $(DEBUG); \
 	done
 
 
 #############################################################################
 # SOURCE 
 #############################################################################
-CPP_FILES=$(wildcard include/igl/*.cpp)
-H_FILES=$(wildcard include/igl/*.h)
+CPP_FILES=$(wildcard ../include/igl/*.cpp)
+H_FILES=$(wildcard ../include/igl/*.h)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-Iinclude/
+INC+=-I../include/
 
 #############################################################################
 # DEPENDENCIES
@@ -100,7 +88,7 @@ INC+=$(EIGEN3_INC)
 
 # AntTweakBar dependency
 #ANTTWEAKBAR_INC=-I$(DEFAULT_PREFIX)/include
-ANTTWEAKBAR_INC=-Iexternal/AntTweakBar/include
+ANTTWEAKBAR_INC=-I../external/AntTweakBar/include
 INC+=$(ANTTWEAKBAR_INC)
 
 ## OpenGL dependency
@@ -112,34 +100,34 @@ INC+=$(ANTTWEAKBAR_INC)
 obj: 
 	mkdir -p obj
 
-lib/libigl.a: obj $(OBJ_FILES)
+../lib/libigl.a: obj $(OBJ_FILES)
 	mkdir -p lib
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: include/igl/%.cpp include/igl/%.h
+obj/%.o: ../include/igl/%.cpp ../include/igl/%.h
 	$(GG) $(CFLAGS) $(AFLAGS) -c -o $@ $< $(INC)
 
-lib/igl.framework/:
-	mkdir -p $@
-	cp lib/*.a $@
-	mv $@/libigl.a $@/igl
-	mkdir -p $@/Libraries
-	mv $@/*.a $@/Libraries
-	mkdir -p $@/Headers
-	cp $(H_FILES) $@/Headers
-	for p in $(EXTRAS); \
-	do \
-	mkdir $@/Headers/$$p; \
-	cp include/igl/$$p/*.h $@/Headers/$$p; \
-	done
+#lib/igl.framework/:
+#	mkdir -p $@
+#	cp lib/*.a $@
+#	mv $@/libigl.a $@/igl
+#	mkdir -p $@/Libraries
+#	mv $@/*.a $@/Libraries
+#	mkdir -p $@/Headers
+#	cp $(H_FILES) $@/Headers
+#	for p in $(EXTRAS); \
+#	do \
+#	mkdir $@/Headers/$$p; \
+#	cp include/igl/$$p/*.h $@/Headers/$$p; \
+#	done
 
 
 clean:
-	rm -rf lib/igl.framework/
+	rm -rf ../lib/igl.framework/
 	rm -f obj/*.o
-	rm -f lib/libigl.a
-	make -C examples clean
+	rm -f ../lib/libigl.a
+	make -C ../examples clean
 	for p in  $(EXTRA_DIRS); \
 	do \
 	echo "cd $$p" ; \

Makefile.conf → build/Makefile.conf

@@ -10,6 +10,7 @@ GG=g++
 #GG=g++-mp-4.3       15.5s
 #GG=g++-mp-4.7       19.9s
 
+CFLAGS += -DIGL_STATIC_LIBRARY
 CFLAGS += -Wall
 CFLAGS += -std=c++11
 

include/igl/bbw/Makefile → build/Makefile_bbw

@@ -1,22 +1,21 @@
-include ../../../Makefile.conf
-
 .PHONY: all
 all: libiglbbw
 debug: libiglbbw
 
-include ../../../Makefile.conf
+include Makefile.conf
 all: OPTFLAGS += -O3 -DNDEBUG $(OPENMP)
 debug: OPTFLAGS += -g -Wall
 CFLAGS += $(OPTFLAGS)
 
 .PHONY: libiglbbw
-libiglbbw: obj ../../../lib/libiglbbw.a
+libiglbbw: obj ../lib/libiglbbw.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/bbw/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
@@ -47,13 +46,13 @@ endif
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglbbw.a: $(OBJ_FILES)
+../lib/libiglbbw.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	$(GG) $(AFLAGS) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglbbw.a
+	rm -f ../lib/libiglbbw.a

include/igl/boost/Makefile → build/Makefile_boost

@@ -1,21 +1,22 @@
-include ../../../Makefile.conf
+include Makefile.conf
 
 .PHONY: all
 all: libiglboost
 debug: libiglboost
 
-include ../../../Makefile.conf
+include Makefile.conf
 all: CFLAGS += -O3 -DNDEBUG
 debug: CFLAGS += -g -Wall 
 
 .PHONY: libiglboost
-libiglboost: obj ../../../lib/libiglboost.a
+libiglboost: obj ../lib/libiglboost.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/boost/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
@@ -31,13 +32,13 @@ INC+=$(BOOST_INC)
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglboost.a: $(OBJ_FILES)
+../lib/libiglboost.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	g++ $(AFLAGS) $(OPENMP) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglboost.a
+	rm -f ../lib/libiglboost.a

include/igl/cgal/Makefile → build/Makefile_cgal

@@ -3,18 +3,19 @@
 all: libiglcgal
 debug: libiglcgal
 
-include ../../../Makefile.conf
+include Makefile.conf
 all: CFLAGS += -O3 -DNDEBUG 
 debug: CFLAGS += -g -Wall -Werror
 
 .PHONY: libcgal
-libiglcgal: obj ../../../lib/libiglcgal.a
+libiglcgal: obj ../lib/libiglcgal.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/cgal/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
@@ -32,13 +33,13 @@ INC+=$(CGAL_INC)
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglcgal.a: $(OBJ_FILES)
+../lib/libiglcgal.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	g++ $(AFLAGS) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglcgal.a
+	rm -f ../lib/libiglcgal.a

include/igl/embree/Makefile → build/Makefile_embree

@@ -1,21 +1,22 @@
-include ../../../Makefile.conf
+include Makefile.conf
 
 .PHONY: all
 all: libiglembree
 debug: libiglembree
 
-include ../../../Makefile.conf
+include Makefile.conf
 all: CFLAGS += -O3 -DNDEBUG -std=c++11
 debug: CFLAGS += -g -Wall -std=c++11
 
 .PHONY: libiglembree
-libiglembree: obj ../../../lib/libiglembree.a
+libiglembree: obj ../lib/libiglembree.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/embree/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
@@ -24,9 +25,9 @@ EIGEN3_INC=-I$(DEFAULT_PREFIX)/include/eigen3 -I$(DEFAULT_PREFIX)/include/eigen3
 INC+=$(EIGEN3_INC)
 
 # embree dependency
-#EMBREE=../../../external/embree
+#EMBREE=../external/embree
 #EMBREE_INC=-I$(EMBREE)/common -I$(EMBREE)/rtcore/
-EMBREE=../../../external/embree/
+EMBREE=../external/embree/
 EMBREE_INC=-I$(EMBREE)/ -I$(EMBREE)/embree
 #EMBREE_LIB=-L$(EMBREE)/bin -lrtcore -lsys
 INC+=$(EMBREE_INC)
@@ -34,13 +35,13 @@ INC+=$(EMBREE_INC)
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglembree.a: $(OBJ_FILES)
+../lib/libiglembree.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	g++ $(AFLAGS) $(OPENMP) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglembree.a
+	rm -f ../lib/libiglembree.a

include/igl/matlab/Makefile → build/Makefile_matlab

@@ -1,4 +1,4 @@
-include ../../../Makefile.conf
+include Makefile.conf
 all: CFLAGS += -O3 -DNDEBUG
 debug: CFLAGS += -g -Wall -Werror
 
@@ -7,13 +7,14 @@ all: libiglmatlab
 debug: libiglmatlab
 
 .PHONY: libmatlab
-libiglmatlab: obj ../../../lib/libiglmatlab.a
+libiglmatlab: obj ../lib/libiglmatlab.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/matlab/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
@@ -33,13 +34,13 @@ INC+=$(MATLAB_INC)
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglmatlab.a: $(OBJ_FILES)
+../lib/libiglmatlab.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	g++ $(AFLAGS) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglmatlab.a
+	rm -f ../lib/libiglmatlab.a

include/igl/mosek/Makefile → build/Makefile_mosek

@@ -1,22 +1,23 @@
-include ../../../Makefile.conf
+include Makefile.conf
 
 .PHONY: all
 all: libiglmosek
 debug: libiglmosek
 
-include ../../../Makefile.conf
+include Makefile.conf
 all: OPTFLAGS += -O3 -DNDEBUG $(OPENMP)
 debug: OPTFLAGS += -g -Wall
 CFLAGS += $(OPTFLAGS)
 
 .PHONY: libiglmosek
-libiglmosek: obj ../../../lib/libiglmosek.a
+libiglmosek: obj ../lib/libiglmosek.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/mosek/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
@@ -40,13 +41,13 @@ INC+=$(MOSEK_INC)
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglmosek.a: $(OBJ_FILES)
+../lib/libiglmosek.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	g++ $(AFLAGS) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglmosek.a
+	rm -f ../lib/libiglmosek.a

include/igl/png/Makefile → build/Makefile_png

@@ -1,4 +1,4 @@
-include ../../../Makefile.conf
+include Makefile.conf
 all: CFLAGS += -O3 -DNDEBUG 
 debug: CFLAGS += -g -Wall -Werror
 
@@ -7,18 +7,19 @@ all: libiglpng
 debug: libiglpng
 
 .PHONY: libpng
-libiglpng: obj ../../../lib/libiglpng.a
+libiglpng: obj ../lib/libiglpng.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/png/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
 # YIMG dependency
-YIMG=../../../external/yimg
+YIMG=../external/yimg
 YIMG_INC=-I$(YIMG)
 INC+=$(YIMG_INC)
 YIMG_STATIC_LIB=$(YIMG)/libyimg.a
@@ -29,13 +30,13 @@ INC+=-I/opt/local/include/
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglpng.a: $(OBJ_FILES)
+../lib/libiglpng.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	g++ $(AFLAGS) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglpng.a
+	rm -f ../lib/libiglpng.a

include/igl/svd3x3/Makefile → build/Makefile_svd3x3

@@ -1,28 +1,29 @@
-include ../../../Makefile.conf
+include Makefile.conf
 
 .PHONY: all
 all: libiglsvd3x3
 debug: libiglsvd3x3
 
-include ../../../Makefile.conf
+include Makefile.conf
 all: OPTFLAGS += -O3 -DNDEBUG $(OPENMP)
 debug: OPTFLAGS += -g -Wall
 CFLAGS += $(OPTFLAGS) -std=c++11
 
 .PHONY: libiglsvd3x3
-libiglsvd3x3: obj ../../../lib/libiglsvd3x3.a
+libiglsvd3x3: obj ../lib/libiglsvd3x3.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/svd3x3/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
 # SVD 
 SINGULAR_VALUE_DECOMPOSITION_INC=\
-	-I../../../external/Singular_Value_Decomposition/
+	-I../external/Singular_Value_Decomposition/
 # Eigen dependency
 EIGEN3_INC=-I$(DEFAULT_PREFIX)/include/eigen3 -I$(DEFAULT_PREFIX)/include/eigen3/unsupported
 INC+=$(EIGEN3_INC) $(SINGULAR_VALUE_DECOMPOSITION_INC)
@@ -39,13 +40,13 @@ INC+=$(MATLAB_INC)
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglsvd3x3.a: $(OBJ_FILES)
+../lib/libiglsvd3x3.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	$(GG) $(AFLAGS) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglsvd3x3.a
+	rm -f ../lib/libiglsvd3x3.a

include/igl/tetgen/Makefile → build/Makefile_tetgen

@@ -3,18 +3,19 @@
 all: libigltetgen
 debug: libigltetgen
 
-include ../../../Makefile.conf
+include Makefile.conf
 all: CFLAGS += -O3 -DNDEBUG 
 debug: CFLAGS += -g -Wall -Werror
 
 .PHONY: libtetgen
-libigltetgen: obj ../../../lib/libigltetgen.a
+libigltetgen: obj ../lib/libigltetgen.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/tetgen/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
@@ -23,7 +24,7 @@ EIGEN3_INC=-I$(DEFAULT_PREFIX)/include/eigen3 -I$(DEFAULT_PREFIX)/include/eigen3
 INC+=$(EIGEN3_INC)
 
 # Tetgen dependency
-TETGEN=../../../external/tetgen
+TETGEN=../external/tetgen
 TETGEN_INC=-I$(TETGEN)
 INC+=$(TETGEN_INC)
 TETGEN_STATIC_LIB=$(TETGEN)/libtet.a
@@ -31,13 +32,13 @@ TETGEN_STATIC_LIB=$(TETGEN)/libtet.a
 obj: 
 	mkdir -p obj
 
-../../../lib/libigltetgen.a: $(OBJ_FILES)
+../lib/libigltetgen.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	g++ $(AFLAGS) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libigltetgen.a
+	rm -f ../lib/libigltetgen.a

include/igl/viewer/Makefile → build/Makefile_viewer

@@ -1,4 +1,4 @@
-include ../../../Makefile.conf
+include Makefile.conf
 all: CFLAGS += -O3 -DNDEBUG -fopenmp
 debug: CFLAGS += -g -Wall -Werror -fopenmp
 
@@ -7,13 +7,14 @@ all: libiglviewer
 debug: libiglviewer
 
 .PHONY: libviewer
-libiglviewer: obj ../../../lib/libiglviewer.a
+libiglviewer: obj ../lib/libiglviewer.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/viewer/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
@@ -23,12 +24,12 @@ INC+=$(EIGEN3_INC)
 
 # GLFW dependency
 ifndef GLFW
-	GLFW=../../../external/glfw/
+	GLFW=../external/glfw/
 endif
 GLFW_INC=-I$(GLFW)/include
 INC+=$(GLFW_INC)
 ifndef ANTTWEAKBAR
-	ANTTWEAKBAR=../../../external/AntTweakBar/
+	ANTTWEAKBAR=../external/AntTweakBar/
 endif
 # Viewer also uses source files from AntTweakBar for font rendering
 ANTTWEAKBAR_INC=-I$(ANTTWEAKBAR)/include -I$(ANTTWEAKBAR)/src
@@ -37,13 +38,13 @@ INC+=$(ANTTWEAKBAR_INC)
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglviewer.a: $(OBJ_FILES)
+../lib/libiglviewer.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	g++ $(AFLAGS) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglmatlab.a
+	rm -f ../lib/libiglmatlab.a

include/igl/xml/Makefile → build/Makefile_xml

@@ -1,4 +1,4 @@
-include ../../../Makefile.conf
+include Makefile.conf
 
 .PHONY: all
 all: 
@@ -6,18 +6,19 @@ debug:
 #all: libiglxml
 #debug: libiglxml
 
-include ../../../Makefile.conf
+include Makefile.conf
 all: CFLAGS += -O3 -DNDEBUG
 debug: CFLAGS += -g -Wall
 
 .PHONY: libiglxml
-libiglxml: obj ../../../lib/libiglxml.a
+libiglxml: obj ../lib/libiglxml.a
 
-CPP_FILES=$(wildcard *.cpp)
+SRC_DIR=../include/igl/xml/
+CPP_FILES=$(wildcard $(SRC_DIR)*.cpp)
 OBJ_FILES=$(addprefix obj/,$(notdir $(CPP_FILES:.cpp=.o)))
 
 # include igl headers
-INC+=-I../../../include/
+INC+=-I../include/
 
 # EXPECTS THAT CFLAGS IS ALREADY SET APPROPRIATELY 
 
@@ -26,17 +27,17 @@ EIGEN3_INC=-I$(DEFAULT_PREFIX)/include/eigen3 -I$(DEFAULT_PREFIX)/include/eigen3
 INC+=$(EIGEN3_INC)
 
 #AntTweakbar dependency
-ANTTWEAKBAR_INC=-I../../../external/AntTweakBar/include
+ANTTWEAKBAR_INC=-I../external/AntTweakBar/include
 
 # xml dependency
 # TODO: linux, 32 bit etc
-TINYXML2=../../../external/tinyxml2
+TINYXML2=../external/tinyxml2
 TINYXML2_INC=-I$(TINYXML2)
 #TINYXML2_LIB=-L$(TINYXML2) -ltinyxml2
 INC+=$(TINYXML2_INC) $(ANTTWEAKBAR_INC)
 
 # AntTweakBar dependency
-ANTTWEAKBAR_INC=-I../../../external/AntTweakBar/include
+ANTTWEAKBAR_INC=-I../external/AntTweakBar/include
 INC+=$(ANTTWEAKBAR_INC)
 
 #CFLAGS+=-std=c++11
@@ -44,13 +45,13 @@ INC+=$(ANTTWEAKBAR_INC)
 obj: 
 	mkdir -p obj
 
-../../../lib/libiglxml.a: $(OBJ_FILES)
+../lib/libiglxml.a: $(OBJ_FILES)
 	rm -f $@
 	ar cqs $@ $(OBJ_FILES)
 
-obj/%.o: %.cpp %.h
+obj/%.o: $(SRC_DIR)/%.cpp $(SRC_DIR)/%.h
 	g++ $(AFLAGS) $(CFLAGS) -c -o $@ $< $(INC)
 
 clean:
 	rm -f obj/*.o
-	rm -f ../../../lib/libiglxml.a
+	rm -f ../lib/libiglxml.a

examples/MatlabWorkspace/Makefile

@@ -1,7 +1,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 IGL=../../
 IGL_LIB=-L$(IGL)/lib -ligl

examples/MatlabWorkspace/example.cpp

@@ -3,13 +3,13 @@
 #include <igl/readDMAT.h>
 #include <cstdio>
 
-#ifndef IGL_HEADER_ONLY
+#ifdef IGL_STATIC_LIBRARY
 #  define IGL_HEADER_ONLY
 #  define IGL_HEADER_ONLY_WAS_NOT_DEFINED
 #endif
 #include <igl/matlab/MatlabWorkspace.h>
 #include <igl/on_boundary.h>
-#ifdef IGL_HEADER_ONLY_WAS_NOT_DEFINED
+#ifndef IGL_STATIC_LIBRARY_WAS_NOT_DEFINED
 #  undef IGL_HEADER_ONLY
 #endif
 

examples/ReAntTweakBar/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 

examples/affine/Makefile

@@ -4,14 +4,14 @@
 all: example
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 .PHONY: example
 
 igl_lib=../../
 eigen=$(DEFAULT_PREFIX)/include/eigen3
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include -I$(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/ambient-occlusion-mex/mexFunction.cpp

@@ -1,6 +1,6 @@
 #include "parse_rhs.h"
 
-#include <igl/matlab/mexStream.h>
+#include <igl/matlab/MexStream.h>
 #include <igl/embree/ambient_occlusion.h>
 
 #include <igl/read_triangle_mesh.h>
@@ -16,7 +16,7 @@ void mexFunction(int nlhs, mxArray *plhs[],
 {
   // This is useful for debugging whether Matlab is caching the mex binary
   //mexPrintf("%s %s\n",__TIME__,__DATE__);
-  igl::mexStream mout;
+  igl::MexStream mout;
   std::streambuf *outbuf = std::cout.rdbuf(&mout);
 
   using namespace std;

examples/ambient-occlusion/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 

examples/ambient-occlusion/example.cpp

@@ -357,7 +357,7 @@ int main(int argc, char * argv[])
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   if(vV.size() > 0)

examples/arap/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 

examples/arap/example.cpp

@@ -432,8 +432,8 @@ void display()
   const double floor_offset =
     -2./bbd*(V.col(1).maxCoeff()-mid(1));
   glTranslated(0,floor_offset,0);
-  const float GREY[4] = {0.5,0.5,0.6,1.0};
-  const float DARK_GREY[4] = {0.2,0.2,0.3,1.0};
+  //const float GREY[4] = {0.5,0.5,0.6,1.0};
+  //const float DARK_GREY[4] = {0.2,0.2,0.3,1.0};
 
   //draw_floor(GREY,DARK_GREY);
   draw_floor();

examples/basic_topology/Makefile

@@ -2,12 +2,12 @@
 all: example1
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 igl_lib=../../
 eigen_lib=$(DEFAULT_PREFIX)/include/eigen3/
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include -I$(eigen_lib)
 lib=-L$(igl_lib)/lib -ligl
 

examples/basic_topology/example1.cpp

@@ -11,7 +11,7 @@
 #include <igl/read_triangle_mesh.h>
 #include <igl/write_triangle_mesh.h>
 #include <igl/triangle_triangle_adjacency.h>
-#include <igl/edgetopology.h>
+#include <igl/edge_topology.h>
 
 using namespace std;
 
@@ -44,7 +44,7 @@ int main (int argc, const char * argv[])
     Eigen::MatrixXi FE;
     Eigen::MatrixXi EF;
 
-    igl::edgetopology(V,F,EV,FE, EF);
+    igl::edge_topology(V,F,EV,FE, EF);
     cout << EV << endl << FE << endl << EF << endl;
     cout << "-------------" << endl;
 

examples/bbw/Makefile

@@ -1,4 +1,4 @@
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 CXX=g++
 

examples/beach-balls/Makefile

@@ -2,13 +2,13 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: obj example
 
 .PHONY: example
 
-CFLAGS=-g -std=c++11
+CFLAGS+=-g -std=c++11
 
 LIBIGL=../../
 LIBIGL_INC=-I$(LIBIGL)/include

examples/camera/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: obj example
 

examples/cat/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,7 +11,7 @@ all: example
 igl_lib=../../
 eigen=$(DEFAULT_PREFIX)/include/eigen3/
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include -I$(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/colored-mesh/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 

examples/colored-mesh/example.cpp

@@ -530,7 +530,7 @@ int main(int argc, char * argv[])
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   if(vV.size() > 0)

examples/dmat/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,7 +11,7 @@ all: example
 igl_lib=../../
 eigen=$(DEFAULT_PREFIX)/include/eigen3
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include -I$(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/eigen-gotchas/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,7 +11,7 @@ all: example
 igl_lib=../../
 eigen=-I$(DEFAULT_PREFIX)/include/eigen3 -I$(DEFAULT_PREFIX)/include/eigen3/unsupported
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include $(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/embree/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 

examples/example_fun/Makefile

@@ -3,11 +3,11 @@
 all: example_static example_header_only
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 igl_lib=../../
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include
 
 STATIC_LIB=-ligl -L../../lib

examples/example_fun/example.cpp

@@ -8,7 +8,7 @@ int main(int argc, char * argv[])
   example_fun(d);
   int i = 4;
   example_fun(i);
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
   const char * s = "string";
   example_fun(s);
 #endif

examples/file_contents_as_string/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -10,7 +10,7 @@ all: example
 
 igl_lib=../../
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include
 lib=-L$(igl_lib)/lib -ligl
 

examples/flare-eyes/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: obj example
 

examples/flare-eyes/example.cpp

@@ -662,7 +662,7 @@ int main(int argc, char * argv[])
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   if(vV.size() > 0)

examples/get_seconds/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -10,7 +10,7 @@ all: example
 
 igl_lib=../../
 
-CFLAGS=-g -Wall
+CFLAGS+=-g -Wall
 inc=-I$(igl_lib)/include
 lib=-L$(igl_lib)/lib -ligl
 

examples/glslversion/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -10,7 +10,7 @@ all: example
 
 igl_lib=../../
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include
 lib=$(OPENGL_LIB) $(GLUT_LIB) -L$(igl_lib)/lib -ligl
 

examples/glut_speed_test/Makefile

@@ -4,13 +4,13 @@
 all: example
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 .PHONY: example
 
 igl_lib=../../
 
-CFLAGS=-g -Wall 
+CFLAGS+=-g -Wall 
 inc=-I$(igl_lib)/include
 lib=$(OPENGL_LIB) $(GLUT_LIB) -L$(igl_lib)/lib -ligl
 

examples/harwell_boeing/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,7 +11,7 @@ all: example
 igl_lib=../../
 eigen=-I$(DEFAULT_PREFIX)/include/eigen3 -I$(DEFAULT_PREFIX)/include/eigen3/unsupported
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include $(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/intersections/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 

examples/intersections/example.cpp

@@ -24,7 +24,7 @@
 #include <igl/pathinfo.h>
 #include <igl/Camera.h>
 #include <igl/get_seconds.h>
-#include <igl/cgal/selfintersect.h>
+#include <igl/cgal/remesh_self_intersections.h>
 #include <igl/cgal/intersect_other.h>
 
 #ifdef __APPLE__
@@ -477,9 +477,10 @@ void color_selfintersections(
   using namespace Eigen;
   MatrixXd SV;
   MatrixXi SF,IF;
-  SelfintersectParam params;
+  VectorXi J,IM;
+  RemeshSelfIntersectionsParam params;
   params.detect_only = true;
-  selfintersect(V,F,params,SV,SF,IF);
+  remesh_self_intersections(V,F,params,SV,SF,IF,J,IM);
   C.resize(F.rows(),3);
   C.col(0).setConstant(0.4);
   C.col(1).setConstant(0.8);
@@ -606,7 +607,7 @@ int main(int argc, char * argv[])
     //  }
     //  //if(F.size() > T.size() || F.size() == 0)
     //  {
-    //    boundary_faces(T,F);
+    //    boundary_facets(T,F);
     //  }
     }
     if(vV.size() > 0)
@@ -622,13 +623,13 @@ int main(int argc, char * argv[])
     return true;
   };
 
-  if(!read_triangle_mesh(filename,V,F,N))
+  if(!read(filename,V,F,N))
   {
     return 1;
   }
   if(has_other)
   {
-    if(!read_triangle_mesh(argv[2],U,G,W))
+    if(!read(argv[2],U,G,W))
     {
       return 1;
     }

examples/is_dir/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -10,7 +10,7 @@ all: example
 
 igl_lib=../../
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include
 lib=-L$(igl_lib)/lib -ligl
 

examples/marching_cubes/Makefile

@@ -6,12 +6,12 @@ all: example
 .PHONY: example
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 igl_lib=../../
 eigen=-I$(DEFAULT_PREFIX)/include/eigen3
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include $(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/meshio/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,7 +11,7 @@ all: example
 igl_lib=../../
 eigen=-I$(DEFAULT_PREFIX)/include/eigen3
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include $(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/mode/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,7 +11,7 @@ all: example
 igl_lib=../../
 eigen=$(DEFAULT_PREFIX)/include/eigen3/
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include -I$(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/multi-viewport/Makefile

@@ -8,7 +8,7 @@ all: example
 .PHONY:  example
 
 LIBIGL=/usr/local/igl/libigl/
-include $(LIBIGL)/Makefile.conf
+include $(LIBIGL)/build/Makefile.conf
 LIBIGL_INC=-I$(LIBIGL)/include
 LIBIGL_LIB=-L$(LIBIGL)/lib -ligl -liglembree
 

examples/patches/Makefile

@@ -2,13 +2,13 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: obj example
 
 .PHONY: example
 
-CFLAGS=-g -std=c++11
+CFLAGS+=-g -std=c++11
 
 LIBIGL=../../
 LIBIGL_INC=-I$(LIBIGL)/include

examples/patches/example.cpp

@@ -25,7 +25,7 @@
 #include <igl/boost/components.h>
 #include <igl/boost/bfs_orient.h>
 #include <igl/orient_outward.h>
-#include <igl/embree/orient_outward_ao.h>
+#include <igl/embree/reorient_facets_raycast.h>
 #include <igl/unique_simplices.h>
 #include <igl/C_STR.h>
 #include <igl/write_triangle_mesh.h>
@@ -567,9 +567,11 @@ void init_patches()
   switch(orient_method)
   {
     case ORIENT_METHOD_AO:
+    {
       cout<<"orient_outward_ao()"<<endl;
-      orient_outward_ao(V,F,CC,100, F.rows() * 100,F,I);
+      reorient_facets_raycast(V,F,F,I);
       break;
+    }
     case ORIENT_METHOD_OUTWARD:
     default:
       cout<<"orient_outward()"<<endl;
@@ -757,7 +759,7 @@ int main(int argc, char * argv[])
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   if(vV.size() > 0)

examples/patches/temp.rbr

@@ -1,7 +1,7 @@
-camera_rotation: TW_TYPE_QUAT4D 0.221720768269005 -0.655276665457443 -0.211493904735977 0.690451099560792
+camera_rotation: TW_TYPE_QUAT4D 0.152085375459856 -0.590495112202136 -0.114509193857288 0.784266029838584
 center_type: CenterType orbit
-wireframe_visible: TW_TYPE_BOOLCPP 0
+wireframe_visible: TW_TYPE_BOOLCPP 1
 fill_visible: TW_TYPE_BOOLCPP 1
-rotation_type: RotationType igl_trackball
+rotation_type: RotationType two-axis-valuator-fixed-up
 orient_method: OrientMethod ambient-occlusion
 

examples/path_tests/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -10,7 +10,7 @@ all: example
 
 igl_lib=../../
 
-CFLAGS=-g -Wall
+CFLAGS+=-g -Wall
 inc=-I$(igl_lib)/include
 lib=-L$(igl_lib)/lib -ligl
 

examples/pathinfo/Makefile

@@ -4,13 +4,13 @@
 all: example
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 .PHONY: example
 
 igl_lib=../../
 
-CFLAGS=-g -Wall 
+CFLAGS+=-g -Wall 
 inc=-I$(igl_lib)/include
 lib=-L$(igl_lib)/lib -ligl
 

examples/principal_curvature/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: curvature
 
@@ -11,14 +11,13 @@ all: curvature
 igl_lib=../../
 eigen=-I$(DEFAULT_PREFIX)/include/eigen3
 
-CFLAGS=-g -O3
 inc=-I$(igl_lib)/include $(eigen)
 
 curvature: curvature.o
-	g++ $(CFLAGS) -o curvature curvature.o $(lib)
+	g++ $(CFLAGS) $(OPENMP) -o curvature curvature.o $(lib)
 
 curvature.o: curvature.cpp
-	g++ $(CFLAGS) -c curvature.cpp -o curvature.o $(inc)
+	g++ $(CFLAGS) $(OPENMP) -c curvature.cpp -o curvature.o $(inc)
 clean:
 	rm -f curvature.o
 	rm -f curvature

examples/principal_curvature/curvature.cpp

@@ -1,5 +1,5 @@
 
-#define IGL_HEADER_ONLY
+#undef IGL_STATIC_LIBRARY
 #include <igl/principal_curvature.h>
 #include <igl/read_triangle_mesh.h>
 #include <iostream>
@@ -44,7 +44,7 @@ void app_init(int argc, char* argv[], CurvatureCalculator& c, Eigen::MatrixXd& V
     }
     char* tmp;
     const char* meshName;
-    char * scaleFile;
+    //char * scaleFile;
     for (argc--, argv++; argc--; argv++)
     {
         if( (*argv)[0] == '-')

examples/quicklook-mesh/src/render_to_buffer.cpp

@@ -18,7 +18,7 @@ extern "C" {
 #include <igl/polygon_mesh_to_triangle_mesh.h>
 #include <igl/readOFF.h>
 #include <igl/readMESH.h>
-#include <igl/boundary_faces.h>
+#include <igl/boundary_facets.h>
 #include <igl/barycenter.h>
 #include <igl/doublearea.h>
 #include <igl/EPS.h>
@@ -395,7 +395,7 @@ bool render_to_buffer(
     }
     //if(F.size() > T.size() || F.size() == 0)
     {
-      boundary_faces(T,F);
+      boundary_facets(T,F);
     }
   }
   if(vV.size() > 0)

examples/randomly-sample-mesh/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: obj example
 

examples/randomly-sample-mesh/example.cpp

@@ -546,7 +546,7 @@ int main(int argc, char * argv[])
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   if(vV.size() > 0)

examples/render_to_png/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 # YIMG dependency
 YIMG=../../external/yimg

examples/rotate-widget/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: obj example
 

examples/rotate-widget/example.cpp

@@ -574,7 +574,7 @@ int main(int argc, char * argv[])
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   if(vV.size() > 0)

examples/scene-rotation/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: obj example
 

examples/scene-rotation/example.cpp

@@ -629,7 +629,7 @@ int main(int argc, char * argv[])
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   if(vV.size() > 0)

examples/scene-rotation/trackball.h

@@ -83,4 +83,4 @@ axis_to_quat(float a[3], float phi, float q[4]);
 void quat_to_axis(float q[4], float axis[3], float &phi);
 void add_quats_no_renorm(float q1[4], float q2[4], float dest[4]);
 void quat_rotate_point(float q[4], const float p1[3], float p2[3]);
-////Olga////
+////Olga////

examples/shadow-mapping/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: obj example
 

examples/shadow-mapping/example.cpp

@@ -19,7 +19,6 @@
 #include <igl/trackball.h>
 #include <igl/snap_to_canonical_view_quat.h>
 #include <igl/REDRUM.h>
-#include <igl/Camera.h>
 #include <igl/ReAntTweakBar.h>
 #include <igl/get_seconds.h>
 #include <igl/jet.h>
@@ -57,6 +56,14 @@
 #include <iostream>
 
 
+struct Camera
+{
+  Eigen::Vector3d pan;
+  Eigen::Quaterniond rotation;
+  double zoom;
+  double angle;
+  Camera():pan(0,0,0),rotation(1,0,0,0),zoom(1),angle(25){}
+};
 
 // Initialize shadow textures. Should be called on reshape()
 //
@@ -154,7 +161,7 @@ std::vector<Mesh> meshes;
 
 struct State
 {
-  igl::Camera camera;
+  ::Camera camera;
   State():
     camera()
   {
@@ -175,7 +182,7 @@ std::stack<State> redo_stack;
 
 bool is_rotating = false;
 int down_x,down_y;
-igl::Camera down_camera;
+::Camera down_camera;
 
 bool is_animating = false;
 double animation_start_time = 0;
@@ -276,7 +283,7 @@ void push_lightview_camera(const Eigen::Vector4f & light_pos)
     0,1,0);
 }
 
-void push_camera(const igl::Camera & camera)
+void push_camera(const ::Camera & camera)
 {
   using namespace igl;
   glMatrixMode(GL_MODELVIEW);
@@ -284,7 +291,7 @@ void push_camera(const igl::Camera & camera)
   // scale, pan
   glScaled(camera.zoom, camera.zoom, camera.zoom);
   double mat[4*4];
-  quat_to_mat(camera.rotation,mat);
+  quat_to_mat(camera.rotation.coeffs().data(),mat);
   glMultMatrixd(mat);
 }
 
@@ -454,7 +461,7 @@ void display()
     q.coeffs() =
       animation_to_quat.coeffs()*t + animation_from_quat.coeffs()*(1.-t);
     q.normalize();
-    copy(q.coeffs().data(),q.coeffs().data()+4,s.camera.rotation);
+    s.camera.rotation = q;
   }
   update_meshes();
 
@@ -577,7 +584,7 @@ void mouse_drag(int mouse_x, int mouse_y)
       case ROTATION_TYPE_IGL_TRACKBALL:
       {
         // Rotate according to trackball
-        igl::trackball<double>(
+        igl::trackball(
           width,
           height,
           2.0,
@@ -591,8 +598,7 @@ void mouse_drag(int mouse_x, int mouse_y)
       }
       case ROTATION_TYPE_TWO_AXIS_VALUATOR_FIXED_UP:
       {
-        Quaterniond down_q;
-        copy(down_camera.rotation,down_camera.rotation+4,down_q.coeffs().data());
+        Quaterniond down_q = down_camera.rotation;
         Vector3d axis(0,1,0);
         const double speed = 2.0;
         Quaterniond q;
@@ -615,7 +621,7 @@ void mouse_drag(int mouse_x, int mouse_y)
             q.normalize();
           }
         }
-        copy(q.coeffs().data(),q.coeffs().data()+4,s.camera.rotation);
+        s.camera.rotation = q;
         break;
       }
       default:
@@ -688,7 +694,7 @@ void key(unsigned char key, int mouse_x, int mouse_y)
       }else
       {
         push_undo();
-        igl::snap_to_canonical_view_quat<double>(
+        igl::snap_to_canonical_view_quat(
           s.camera.rotation,
           1.0,
           s.camera.rotation);
@@ -712,7 +718,7 @@ void TW_CALL set_rotation_type(const void * value, void * clientData)
     old_rotation_type != ROTATION_TYPE_TWO_AXIS_VALUATOR_FIXED_UP)
   {
     push_undo();
-    copy(s.camera.rotation,s.camera.rotation+4,animation_from_quat.coeffs().data());
+    animation_from_quat = s.camera.rotation;
     const Vector3d up = animation_from_quat.matrix() * Vector3d(0,1,0);
     Vector3d proj_up(0,up(1),up(2));
     if(proj_up.norm() == 0)
@@ -825,7 +831,7 @@ int main(int argc, char * argv[])
   rebar.TwNewBar("bar");
   TwDefine("bar label='Shadow Mapping' size='200 550' text=light alpha='200' color='68 68 68'");
   rebar.TwAddVarRW("camera_zoom", TW_TYPE_DOUBLE,&s.camera.zoom,"");
-  rebar.TwAddVarRW("camera_rotation", TW_TYPE_QUAT4D,s.camera.rotation,"");
+  rebar.TwAddVarRW("camera_rotation", TW_TYPE_QUAT4D,s.camera.rotation.coeffs().data(),"");
   TwType RotationTypeTW = ReTwDefineEnumFromString("RotationType","igl_trackball,two_axis_fixed_up");
   rebar.TwAddVarCB( "rotation_type", RotationTypeTW,
     set_rotation_type,get_rotation_type,NULL,"keyIncr=] keyDecr=[");
@@ -834,7 +840,7 @@ int main(int argc, char * argv[])
   rebar.load(REBAR_NAME);
 
   animation_from_quat = Quaterniond(1,0,0,0);
-  copy(s.camera.rotation,s.camera.rotation+4,animation_to_quat.coeffs().data());
+  animation_from_quat = s.camera.rotation;
   animation_start_time = get_seconds();
 
   // Init antweakbar

examples/skeleton/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: obj example
 

examples/skeleton/example.cpp

@@ -632,7 +632,7 @@ int main(int argc, char * argv[])
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   if(vV.size() > 0)

examples/slice/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,8 +11,8 @@ all: example
 igl_lib=../../
 eigen=-I$(DEFAULT_PREFIX)/include/eigen3 -I$(DEFAULT_PREFIX)/include/eigen3/unsupported
 
-#CFLAGS=-g
-CFLAGS=-Os -DNDEBUG
+#CFLAGS+=-g
+CFLAGS+=-Os -DNDEBUG
 inc=-I$(igl_lib)/include $(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/sort/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,7 +11,7 @@ all: example
 igl_lib=../../
 eigen=$(DEFAULT_PREFIX)/include/eigen3/
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include -I$(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/sortrows/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,7 +11,7 @@ all: example
 igl_lib=../../
 eigen=$(DEFAULT_PREFIX)/include/eigen3/
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include -I$(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/stdin_to_temp/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -10,7 +10,7 @@ all: example
 
 igl_lib=../../
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include
 lib=-L$(igl_lib)/lib -ligl
 

examples/svd/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -10,7 +10,7 @@ all: example
 
 igl_lib=../../
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include
 lib=-L$(igl_lib)/lib -ligl -framework Accelerate
 

examples/textured-mesh/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -23,7 +23,7 @@ EMBREE_LIB=-L$(EMBREE)/build -lembree -lsys
 
 # YIMAGE Library
 YIMG=$(LIBIGL)/external/yimg/
-YIMG_LIB=-L$(YIMG) -lyimg -lz -L/usr/X11/lib -lpng -bind_at_load
+YIMG_LIB=-L$(YIMG) -lyimg -lz -L/opt/local/lib -lpng -bind_at_load
 YIMG_INC=-I/usr/X11/include -I$(YIMG) 
 
 ANTTWEAKBAR_INC=-I$(LIBIGL)/external/AntTweakBar/include

examples/trackball/Makefile

@@ -4,13 +4,13 @@
 all: example
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 .PHONY: example
 
 igl_lib=../../
 
-CFLAGS=-g -Wall 
+CFLAGS+=-g -Wall 
 #deps=-MMD -MF depends.txt
 EIGEN3_INC=-I$(DEFAULT_PREFIX)/include/eigen3 -I$(DEFAULT_PREFIX)/include/eigen3/unsupported
 inc=-I$(igl_lib)/include $(EIGEN3_INC)

examples/transparency/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 

examples/transpose_blocks/Makefile

@@ -2,7 +2,7 @@
 .PHONY: all
 
 # Shared flags etc.
-include ../../Makefile.conf
+include ../../build/Makefile.conf
 
 all: example
 
@@ -11,7 +11,7 @@ all: example
 igl_lib=../../
 eigen=$(DEFAULT_PREFIX)/include/eigen3
 
-CFLAGS=-g
+CFLAGS+=-g
 inc=-I$(igl_lib)/include -I$(eigen)
 lib=-L$(igl_lib)/lib -ligl
 

examples/upright/Makefile

@@ -8,7 +8,7 @@ all: upright
 .PHONY: upright
 
 LIBIGL=/usr/local/igl/libigl/
-include $(LIBIGL)/Makefile.conf
+include $(LIBIGL)/build/Makefile.conf
 LIBIGL_INC=-I$(LIBIGL)/include
 LIBIGL_LIB=-L$(LIBIGL)/lib -ligl
 

examples/upright/example.cpp

@@ -339,7 +339,7 @@ bool save()
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   cout<<GREENGIN("Current baked model written to "+out_filename+".")<<endl;
@@ -502,7 +502,7 @@ int main(int argc, char * argv[])
   //  }
   //  //if(F.size() > T.size() || F.size() == 0)
   //  {
-  //    boundary_faces(T,F);
+  //    boundary_facets(T,F);
   //  }
   }
   if(vV.size() > 0)

include/igl/EPS.cpp

@@ -25,6 +25,6 @@ template <> IGL_INLINE double igl::EPS_SQ()
   return igl::DOUBLE_EPS_SQ;
 }
 
-#ifndef IGL_HEADER_ONLY
+#ifdef IGL_STATIC_LIBRARY
 // Explicit template specialization
 #endif

include/igl/EPS.h

@@ -25,7 +25,7 @@ namespace igl
   template <> IGL_INLINE double EPS_SQ<double>();
 }
 
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #  include "EPS.cpp"
 #endif
 

include/igl/ReAntTweakBar.h

@@ -275,7 +275,7 @@ namespace igl
 //TW_API int      TW_CALL TwRemoveVar(TwBar *bar, const char *name);
 //TW_API int      TW_CALL TwRemoveAllVars(TwBar *bar);
 
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #  include "ReAntTweakBar.cpp"
 #endif
 

include/igl/WindingNumberTree.h

@@ -140,7 +140,7 @@ inline igl::WindingNumberTree<Point>::WindingNumberTree(
   V(dummyV),
   SV(),
   F(),
-  //boundary(igl::boundary_faces<Eigen::MatrixXi,Eigen::MatrixXi>(F))
+  //boundary(igl::boundary_facets<Eigen::MatrixXi,Eigen::MatrixXi>(F))
   cap(),
   radius(std::numeric_limits<double>::infinity()),
   center(0,0,0)

include/igl/active_set.cpp

@@ -297,7 +297,7 @@ IGL_INLINE igl::SolverStatus igl::active_set(
     slice(A,known_i,1,Ak);
     Eigen::PlainObjectBase<DerivedB> Bk;
     slice(B,known_i,Bk);
-    MatrixXd Lambda_known_i = -(Ak*Z + 0.5*Bk);
+    MatrixXd Lambda_known_i = -(0.5*Ak*Z + 0.5*Bk);
     // reverse the lambda values for lx
     Lambda_known_i.block(nk,0,as_lx_count,1) = 
       (-1*Lambda_known_i.block(nk,0,as_lx_count,1)).eval();
@@ -347,7 +347,7 @@ IGL_INLINE igl::SolverStatus igl::active_set(
 }
 
 
-#ifndef IGL_HEADER_ONLY
+#ifdef IGL_STATIC_LIBRARY
 // Explicit template specialization
 template igl::SolverStatus igl::active_set<double, Eigen::Matrix<double, -1, 1, 0, -1, 1>, Eigen::Matrix<int, -1, 1, 0, -1, 1>, Eigen::Matrix<double, -1, 1, 0, -1, 1>, double, Eigen::Matrix<double, -1, 1, 0, -1, 1>, double, Eigen::Matrix<double, -1, 1, 0, -1, 1>, Eigen::Matrix<double, -1, 1, 0, -1, 1>, Eigen::Matrix<double, -1, 1, 0, -1, 1>, Eigen::Matrix<double, -1, 1, 0, -1, 1> >(Eigen::SparseMatrix<double, 0, int> const&, Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> > const&, Eigen::PlainObjectBase<Eigen::Matrix<int, -1, 1, 0, -1, 1> > const&, Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> > const&, Eigen::SparseMatrix<double, 0, int> const&, Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> > const&, Eigen::SparseMatrix<double, 0, int> const&, Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> > const&, Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> > const&, Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> > const&, igl::active_set_params const&, Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1, 0, -1, 1> >&);
 #endif

include/igl/active_set.h

@@ -20,7 +20,10 @@ namespace igl
   // using QR decomposition otherwise:
   //   http://www.okstate.edu/sas/v8/sashtml/ormp/chap5/sect32.htm
   //
-  // ACTIVE_SET Minimize quadratic energy Z'*A*Z + Z'*B + C with constraints
+  // ACTIVE_SET Minimize quadratic energy 
+  //
+  // 0.5*Z'*A*Z + Z'*B + C with constraints
+  //
   // that Z(known) = Y, optionally also subject to the constraints Aeq*Z = Beq,
   // and further optionally subject to the linear inequality constraints that
   // Aieq*Z <= Bieq and constant inequality constraints lx <= x <= ux
@@ -103,7 +106,7 @@ struct igl::active_set_params
     {};
 };
 
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #  include "active_set.cpp"
 #endif
 

include/igl/adjacency_list.cpp

@@ -158,7 +158,7 @@ IGL_INLINE void igl::adjacency_list(
   
 }
 
-#ifndef IGL_HEADER_ONLY
+#ifdef IGL_STATIC_LIBRARY
 // Explicit template specialization
 // generated by autoexplicit.sh
 template void igl::adjacency_list<Eigen::Matrix<int, -1, -1, 0, -1, -1>, int>(Eigen::PlainObjectBase<Eigen::Matrix<int, -1, -1, 0, -1, -1> > const&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, bool);

include/igl/adjacency_list.h

@@ -44,7 +44,7 @@ namespace igl
 
 }
 
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #  include "adjacency_list.cpp"
 #endif
 

include/igl/adjacency_matrix.cpp

@@ -63,7 +63,7 @@ IGL_INLINE void igl::adjacency_matrix(
   }
 }
 
-#ifndef IGL_HEADER_ONLY
+#ifdef IGL_STATIC_LIBRARY
 // Explicit template specialization
 template void igl::adjacency_matrix<int>(Eigen::Matrix<int, -1, -1, 0, -1, -1> const&, Eigen::SparseMatrix<int, 0, int>&);
 template void igl::adjacency_matrix<double>(Eigen::Matrix<int, -1, -1, 0, -1, -1> const&, Eigen::SparseMatrix<double, 0, int>&);

include/igl/adjacency_matrix.h

@@ -44,7 +44,7 @@ namespace igl
     Eigen::SparseMatrix<T>& A);
 }
 
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #  include "adjacency_matrix.cpp"
 #endif
 

include/igl/all_edges.h

@@ -27,7 +27,7 @@ namespace igl
     Eigen::MatrixXi & E);
 }
 
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #  include "all_edges.cpp"
 #endif
 

include/igl/all_pairs_distances.cpp

@@ -32,7 +32,7 @@ IGL_INLINE void igl::all_pairs_distances(
   }
 }
 
-#ifndef IGL_HEADER_ONLY
+#ifdef IGL_STATIC_LIBRARY
 // Explicit template specialization
 // generated by autoexplicit.sh
 template void igl::all_pairs_distances<Eigen::Matrix<double, -1, -1, 0, -1, -1> >(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, bool, Eigen::Matrix<double, -1, -1, 0, -1, -1>&);

include/igl/all_pairs_distances.h

@@ -34,7 +34,7 @@ namespace igl
     Mat & D);
 }
 
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #  include "all_pairs_distances.cpp"
 #endif
 

include/igl/angular_distance.h

@@ -23,7 +23,7 @@ namespace igl
     const Eigen::Quaterniond & B);
 }
 
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #include "angular_distance.cpp"
 #endif
 

include/igl/any_of.cpp

@@ -13,7 +13,7 @@ IGL_INLINE bool igl::any_of(const Mat & S)
   return std::any_of(S.data(),S.data()+S.size(),[](bool s){return s;});
 }
 
-#ifndef IGL_HEADER_ONLY
+#ifdef IGL_STATIC_LIBRARY
 // Explicit template specialization
 template bool igl::any_of<Eigen::Matrix<int, -1, 1, 0, -1, 1> >(Eigen::Matrix<int, -1, 1, 0, -1, 1> const&);
 #endif

include/igl/any_of.h

@@ -18,7 +18,7 @@ namespace igl
   template <typename Mat>
   IGL_INLINE bool any_of(const Mat & S);
 }
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #  include "any_of.cpp"
 #endif
 #endif

include/igl/arap_linear_block.cpp

@@ -7,7 +7,7 @@
 // obtain one at http://mozilla.org/MPL/2.0/.
 #include "arap_linear_block.h"
 #include "verbose.h"
-#include "cotangent.h"
+#include "cotmatrix_entries.h"
 #include <Eigen/Dense>
 
 template <typename MatV, typename MatF, typename Scalar>
@@ -81,7 +81,7 @@ IGL_INLINE void igl::arap_linear_block_spokes(
   }
   // gather cotangent weights
   Matrix<Scalar,Dynamic,Dynamic> C;
-  cotangent(V,F,C);
+  cotmatrix_entries(V,F,C);
   // should have weights for each edge
   assert(C.cols() == edges.rows());
   // loop over elements
@@ -149,7 +149,7 @@ IGL_INLINE void igl::arap_linear_block_spokes_and_rims(
   }
   // gather cotangent weights
   Matrix<Scalar,Dynamic,Dynamic> C;
-  cotangent(V,F,C);
+  cotmatrix_entries(V,F,C);
   // should have weights for each edge
   assert(C.cols() == edges.rows());
   // loop over elements
@@ -230,7 +230,7 @@ IGL_INLINE void igl::arap_linear_block_elements(
   }
   // gather cotangent weights
   Matrix<Scalar,Dynamic,Dynamic> C;
-  cotangent(V,F,C);
+  cotmatrix_entries(V,F,C);
   // should have weights for each edge
   assert(C.cols() == edges.rows());
   // loop over elements
@@ -251,7 +251,7 @@ IGL_INLINE void igl::arap_linear_block_elements(
 }
 
 
-#ifndef IGL_HEADER_ONLY
+#ifdef IGL_STATIC_LIBRARY
 // Explicit template specialization
 template IGL_INLINE void igl::arap_linear_block<Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<int, -1, -1, 0, -1, -1>, double>(Eigen::Matrix<double, -1, -1, 0, -1, -1> const&, Eigen::Matrix<int, -1, -1, 0, -1, -1> const&, int, igl::ARAPEnergyType, Eigen::SparseMatrix<double, 0, int>&);
 #endif

include/igl/arap_linear_block.h

@@ -71,7 +71,7 @@ namespace igl
     Eigen::SparseMatrix<Scalar> & Kd);
 }
 
-#ifdef IGL_HEADER_ONLY
+#ifndef IGL_STATIC_LIBRARY
 #  include "arap_linear_block.cpp"
 #endif