Installing headers in subdirectories and converted include directives to match the subdirectory structure (also see email to frankcvs)

.settings/org.eclipse.cdt.core.prefs

@@ -0,0 +1,4 @@
+#Wed Aug 18 18:00:45 EDT 2010
+eclipse.preferences.version=1
+environment/project/cdt.managedbuild.toolchain.gnu.macosx.base.1359703544/append=true
+environment/project/cdt.managedbuild.toolchain.gnu.macosx.base.1359703544/appendContributed=true

CppUnitLite/Makefile.am

@@ -7,6 +7,7 @@ headers = TestHarness.h
 sources = Failure.cpp SimpleString.cpp Test.cpp TestRegistry.cpp TestResult.cpp
 headers += $(sources:.cpp=.h)
 
-noinst_HEADERS = $(headers)
+CppUnitLitedir = $(pkgincludedir)/CppUnitLite
+CppUnitLite_HEADERS = $(headers)
 noinst_LIBRARIES = libCppUnitLite.a
 libCppUnitLite_a_SOURCES = $(sources)

Makefile.am

@@ -6,7 +6,9 @@
 ACLOCAL_AMFLAGS = -I m4
 
 # make automake install some standard but missing files
-AUTOMAKE_OPTIONS = foreign
+# also use nostdinc to turn off -I. and -I.., we do not need them because 
+# header files are qualified so they can be included in external projects.
+AUTOMAKE_OPTIONS = foreign nostdinc
 
 # All the sub-directories that need to be built
 SUBDIRS = CppUnitLite colamd spqr_mini base geometry inference linear nonlinear slam . tests wrap  
@@ -31,7 +33,12 @@ libgtsam_la_SOURCES =
 libgtsam_la_LIBADD = $(SUBLIBS)
 libgtsam_la_LDFLAGS = -version-info 0:0:0
 
-# Add these files to make dure they're in the distribution
+# Store the absolute path to the directory above gtsam for the include path,
+# saves us from having an extra 'gtsam' subdirectory.
+BORG_SRCROOT := $(shell cd $(top_srcdir)/.. && pwd)
+AM_MAKEFLAGS = "BORG_SRCROOT=$(BORG_SRCROOT)"
+
+# Add these files to make sure they're in the distribution
 noinst_HEADERS = gtsam.h
 EXTRA_DIST = autogen.sh configure.ac THANKS 
 

base/DSF.h

@@ -16,7 +16,7 @@
 #include <set>
 #include <map>
 #include <boost/foreach.hpp>
-#include "BTree.h"
+#include <gtsam/base/BTree.h>
 
 namespace gtsam {
 

base/DSFVector.cpp

@@ -7,7 +7,7 @@
  *               As a result, the size of the forest is prefixed.
  */
 
-#include "DSFVector.h"
+#include <gtsam/base/DSFVector.h>
 
 using namespace std;
 

base/FixedVector.h

@@ -6,9 +6,9 @@
 
 #pragma once
 
-#include <Testable.h>
+#include <gtsam/base/Testable.h>
 #include <stdarg.h>
-#include <Vector.h>
+#include <gtsam/base/Vector.h>
 
 namespace gtsam {
 

base/Lie-inl.h

@@ -7,7 +7,7 @@
 
 #pragma once
 
-#include "Lie.h"
+#include <gtsam/base/Lie.h>
 
 #define INSTANTIATE_LIE(T) \
   template T between(const T&, const T&); \

base/Lie.h

@@ -8,7 +8,7 @@
 #pragma once
 
 #include <string>
-#include "Matrix.h"
+#include <gtsam/base/Matrix.h>
 
 namespace gtsam {
 

base/Makefile.am

@@ -3,6 +3,10 @@
 # provides some base Math and data structures, as well as test-related utilities
 #----------------------------------------------------------------------------------------------------
 
+# use nostdinc to turn off -I. and -I.., we do not need them because 
+# header files are qualified so they can be included in external projects.
+AUTOMAKE_OPTIONS = nostdinc
+
 headers =
 sources = 
 check_PROGRAMS = 
@@ -38,11 +42,12 @@ noinst_PROGRAMS = tests/timeMatrix
 # The headers are installed in $(includedir)/gtsam: 
 #----------------------------------------------------------------------------------------------------
 headers += $(sources:.cpp=.h)
-pkginclude_HEADERS = $(headers)
+basedir = $(pkgincludedir)/base
+base_HEADERS = $(headers)
 noinst_LTLIBRARIES = libbase.la
 libbase_la_SOURCES = $(sources)
 
-AM_CPPFLAGS = -I$(boost) -I$(top_srcdir)
+AM_CPPFLAGS = -I$(boost) -I$(BORG_SRCROOT)
 
 if USE_BLAS
 AM_CPPFLAGS += -DGT_USE_CBLAS

base/Matrix.cpp

@@ -38,9 +38,9 @@ extern "C" {
 #include <suitesparse/ldl.h>
 #endif
 
-#include "Matrix.h"
-#include "Vector.h"
-#include "svdcmp.h"
+#include <gtsam/base/Matrix.h>
+#include <gtsam/base/Vector.h>
+#include <gtsam/base/svdcmp.h>
 
 using namespace std;
 namespace ublas = boost::numeric::ublas;

base/Matrix.h

@@ -14,7 +14,7 @@
 #include <boost/format.hpp>
 #include <boost/numeric/ublas/matrix.hpp>
 #include <boost/tuple/tuple.hpp>
-#include "Vector.h"
+#include <gtsam/base/Vector.h>
 
 /**
  * Vector is a *global* typedef

base/SPQRUtil.cpp

@@ -7,7 +7,7 @@
  */
 
 #include <map>
-#include "SPQRUtil.h"
+#include <gtsam/base/SPQRUtil.h>
 
 using namespace std;
 

base/SPQRUtil.h

@@ -8,10 +8,10 @@
 
 #pragma once
 
-#include "Matrix.h"
+#include <gtsam/base/Matrix.h>
 
 #ifdef GT_USE_LAPACK
-#include <spqr_mini/spqr_subset.hpp>
+#include <gtsam/spqr_mini/spqr_subset.hpp>
 
 namespace gtsam {
 

base/TestableAssertions.h

@@ -8,7 +8,7 @@
 
 #include <vector>
 #include <boost/foreach.hpp>
-#include "Testable.h"
+#include <gtsam/base/Testable.h>
 
 namespace gtsam {
 

base/Vector.cpp

@@ -25,7 +25,7 @@
 #include <boost/random/normal_distribution.hpp>
 #include <boost/random/variate_generator.hpp>
 
-#include "Vector.h"
+#include <gtsam/base/Vector.h>
 
 using namespace std;
 namespace ublas = boost::numeric::ublas;

base/numericalDerivative.h

@@ -11,8 +11,8 @@
 #include <boost/function.hpp>
 #include <boost/bind.hpp>
 
-#include "Lie.h"
-#include "Matrix.h"
+#include <gtsam/base/Lie.h>
+#include <gtsam/base/Matrix.h>
 
 //#define LINEARIZE_AT_IDENTITY
 

base/svdcmp.cpp

@@ -8,7 +8,7 @@
 #include <math.h>    /* for 'fabs' */
 #include <iostream>
 #include <vector>
-#include "Matrix.h"
+#include <gtsam/base/Matrix.h>
 
 using namespace std;
 

base/tests/testBTree.cpp

@@ -11,8 +11,8 @@
 #include <boost/assign/std/list.hpp> // for +=
 using namespace boost::assign;
 
-#include <CppUnitLite/TestHarness.h>
-#include "BTree.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/base/BTree.h>
 
 using namespace std;
 using namespace gtsam;

base/tests/testDSF.cpp

@@ -10,9 +10,9 @@
 #include <boost/assign/std/list.hpp>
 #include <boost/assign/std/set.hpp>
 using namespace boost::assign;
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 
-#include "DSF.h"
+#include <gtsam/base/DSF.h>
 
 using namespace std;
 using namespace gtsam;

base/tests/testDSFVector.cpp

@@ -10,9 +10,9 @@
 #include <boost/assign/std/list.hpp>
 #include <boost/assign/std/set.hpp>
 using namespace boost::assign;
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 
-#include "DSFVector.h"
+#include <gtsam/base/DSFVector.h>
 
 using namespace std;
 using namespace gtsam;

base/tests/testFixedVector.cpp

@@ -3,9 +3,9 @@
  * @author Alex Cunningham
  */
 
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 
-#include <FixedVector.h>
+#include <gtsam/base/FixedVector.h>
 
 using namespace gtsam;
 

base/tests/testMatrix.cpp

@@ -6,12 +6,12 @@
  **/
 
 #include <iostream>
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 #include <boost/tuple/tuple.hpp>
 #include <boost/foreach.hpp>
 #include <boost/numeric/ublas/matrix_proxy.hpp>
 #include <boost/numeric/ublas/io.hpp>
-#include "Matrix.h"
+#include <gtsam/base/Matrix.h>
 
 using namespace std;
 using namespace gtsam;

base/tests/testSPQRUtil.cpp

@@ -5,8 +5,8 @@
  **/
 
 #include <iostream>
-#include <CppUnitLite/TestHarness.h>
-#include "SPQRUtil.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/base/SPQRUtil.h>
 
 using namespace std;
 using namespace gtsam;

base/tests/testVector.cpp

@@ -5,9 +5,9 @@
  **/
 
 #include <iostream>
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 #include <boost/tuple/tuple.hpp>
-#include "Vector.h"
+#include <gtsam/base/Vector.h>
 
 using namespace std;
 using namespace gtsam;

base/tests/timeMatrix.cpp

@@ -7,7 +7,7 @@
 #include <iostream>
 #include <boost/numeric/ublas/matrix_proxy.hpp>
 #include <boost/timer.hpp>
-#include "Matrix.h"
+#include <gtsam/base/Matrix.h>
 
 using namespace std;
 using namespace gtsam;

colamd/Makefile.am

@@ -9,7 +9,8 @@ noinst_LTLIBRARIES = libcolamd.la
 
 # We normally would not install these headers
 # but they are included in the templated class FactorGraph-inl.h so we need them
-pkginclude_HEADERS = colamd.h ccolamd.h UFconfig.h 
+colamddir = $(pkgincludedir)/colamd
+colamd_HEADERS = colamd.h ccolamd.h UFconfig.h 
 
 # These are the sources for the library:
 libcolamd_la_SOURCES = colamd.c colamd_global.c ccolamd.c ccolamd_global.c

geometry/Cal3_S2.cpp

@@ -7,7 +7,7 @@
 #include <fstream>
 #include <iostream>
 
-#include "Cal3_S2.h"
+#include <gtsam/geometry/Cal3_S2.h>
 
 namespace gtsam {
 using namespace std;

geometry/Cal3_S2.h

@@ -6,8 +6,8 @@
 
 #pragma once
 
-#include "Matrix.h"
-#include "Point2.h"
+#include <gtsam/base/Matrix.h>
+#include <gtsam/geometry/Point2.h>
 #include <math.h>
 
 namespace gtsam {

geometry/CalibratedCamera.cpp

@@ -5,8 +5,8 @@
  *      Author: dellaert
  */
 
-#include "Point2.h"
-#include "CalibratedCamera.h"
+#include <gtsam/geometry/Point2.h>
+#include <gtsam/geometry/CalibratedCamera.h>
 
 namespace gtsam {
 

geometry/CalibratedCamera.h

@@ -8,8 +8,8 @@
 #ifndef CalibratedCAMERA_H_
 #define CalibratedCAMERA_H_
 
-#include "Pose2.h"
-#include "Pose3.h"
+#include <gtsam/geometry/Pose2.h>
+#include <gtsam/geometry/Pose3.h>
 
 namespace gtsam {
 

geometry/Makefile.am

@@ -2,6 +2,10 @@
 # GTSAM geometry
 #----------------------------------------------------------------------------------------------------
 
+# use nostdinc to turn off -I. and -I.., we do not need them because 
+# header files are qualified so they can be included in external projects.
+AUTOMAKE_OPTIONS = nostdinc
+
 headers =
 sources = 
 check_PROGRAMS = 
@@ -33,10 +37,11 @@ noinst_PROGRAMS = timeRot3 timeCalibratedCamera
 # The headers are installed in $(includedir)/gtsam: 
 #----------------------------------------------------------------------------------------------------
 headers += $(sources:.cpp=.h)
-pkginclude_HEADERS = $(headers)
+geometrydir = $(pkgincludedir)/geometry
+geometry_HEADERS = $(headers)
 noinst_LTLIBRARIES = libgeometry.la
 libgeometry_la_SOURCES = $(sources)
-AM_CPPFLAGS = -I$(boost) -I$(top_srcdir) -I$(top_srcdir)/base
+AM_CPPFLAGS = -I$(boost) -I$(BORG_SRCROOT)
 
 #----------------------------------------------------------------------------------------------------
 # rules to build local programs

geometry/Point2.cpp

@@ -4,8 +4,8 @@
  * @author  Frank Dellaert
  */
 
-#include "Point2.h"
-#include "Lie-inl.h"
+#include <gtsam/geometry/Point2.h>
+#include <gtsam/base/Lie-inl.h>
 
 using namespace std;
 

geometry/Point2.h

@@ -7,10 +7,10 @@
 #pragma once
 
 #include <boost/serialization/nvp.hpp>
-#include "Vector.h"
-#include "Matrix.h"
-#include "Testable.h"
-#include "Lie.h"
+#include <gtsam/base/Vector.h>
+#include <gtsam/base/Matrix.h>
+#include <gtsam/base/Testable.h>
+#include <gtsam/base/Lie.h>
 
 namespace gtsam {
 

geometry/Point3.cpp

@@ -3,8 +3,8 @@
  * @brief 3D Point
  */
 
-#include "Point3.h"
-#include "Lie-inl.h"
+#include <gtsam/geometry/Point3.h>
+#include <gtsam/base/Lie-inl.h>
 
 
 namespace gtsam {

geometry/Point3.h

@@ -12,9 +12,9 @@
 
 #include <boost/serialization/nvp.hpp>
 
-#include "Matrix.h"
-#include "Testable.h"
-#include "Lie.h"
+#include <gtsam/base/Matrix.h>
+#include <gtsam/base/Testable.h>
+#include <gtsam/base/Lie.h>
 
 namespace gtsam {
 

geometry/Pose2.cpp

@@ -3,8 +3,8 @@
  * @brief 2D Pose
  */
 
-#include "Pose2.h"
-#include "Lie-inl.h"
+#include <gtsam/geometry/Pose2.h>
+#include <gtsam/base/Lie-inl.h>
 
 using namespace std;
 

geometry/Pose2.h

@@ -10,11 +10,11 @@
 #pragma once
 
 #include <boost/optional.hpp>
-#include "Matrix.h"
-#include "Testable.h"
-#include "Lie.h"
-#include "Point2.h"
-#include "Rot2.h"
+#include <gtsam/base/Matrix.h>
+#include <gtsam/base/Testable.h>
+#include <gtsam/base/Lie.h>
+#include <gtsam/geometry/Point2.h>
+#include <gtsam/geometry/Rot2.h>
 
 namespace gtsam {
 

geometry/Pose3.cpp

@@ -4,8 +4,8 @@
  */
 
 #include <iostream>
-#include "Pose3.h"
-#include "Lie-inl.h"
+#include <gtsam/geometry/Pose3.h>
+#include <gtsam/base/Lie-inl.h>
 
 using namespace std;
 using namespace boost::numeric::ublas;

geometry/Pose3.h

@@ -9,10 +9,10 @@
 
 #include <boost/numeric/ublas/vector_proxy.hpp>
 
-#include "Point3.h"
-#include "Rot3.h"
-#include "Testable.h"
-#include "Lie.h"
+#include <gtsam/geometry/Point3.h>
+#include <gtsam/geometry/Rot3.h>
+#include <gtsam/base/Testable.h>
+#include <gtsam/base/Lie.h>
 
 namespace gtsam {
 

geometry/Rot2.cpp

@@ -5,8 +5,8 @@
  *      Author: Frank Dellaert
  */
 
-#include "Rot2.h"
-#include "Lie-inl.h"
+#include <gtsam/geometry/Rot2.h>
+#include <gtsam/base/Lie-inl.h>
 
 using namespace std;
 

geometry/Rot2.h

@@ -9,10 +9,10 @@
 #define ROT2_H_
 
 #include <boost/optional.hpp>
-#include "Testable.h"
-#include "Point2.h"
-#include "Matrix.h"
-#include "Lie.h"
+#include <gtsam/base/Testable.h>
+#include <gtsam/geometry/Point2.h>
+#include <gtsam/base/Matrix.h>
+#include <gtsam/base/Lie.h>
 
 namespace gtsam {
 

geometry/Rot3.cpp

@@ -6,8 +6,8 @@
  * @author  Frank Dellaert
  */
 
-#include "Rot3.h"
-#include "Lie-inl.h"
+#include <gtsam/geometry/Rot3.h>
+#include <gtsam/base/Lie-inl.h>
 
 using namespace std;
 

geometry/Rot3.h

@@ -11,9 +11,9 @@
 #pragma once
 
 #include <boost/math/constants/constants.hpp>
-#include "Point3.h"
-#include "Testable.h"
-#include "Lie.h"
+#include <gtsam/geometry/Point3.h>
+#include <gtsam/base/Testable.h>
+#include <gtsam/base/Lie.h>
 
 namespace gtsam {
 

geometry/SimpleCamera.cpp

@@ -5,8 +5,8 @@
  *      Author: dellaert
  */
 
-#include "SimpleCamera.h"
-#include "CalibratedCamera.h"
+#include <gtsam/geometry/SimpleCamera.h>
+#include <gtsam/geometry/CalibratedCamera.h>
 
 using namespace std;
 

geometry/SimpleCamera.h

@@ -8,8 +8,8 @@
 #ifndef SIMPLECAMERA_H_
 #define SIMPLECAMERA_H_
 
-#include "CalibratedCamera.h"
-#include "Cal3_S2.h"
+#include <gtsam/geometry/CalibratedCamera.h>
+#include <gtsam/geometry/Cal3_S2.h>
 
 namespace gtsam {
 

geometry/StereoCamera.cpp

@@ -4,7 +4,7 @@
  * @author  Chris Beall
  */
 
-#include "StereoCamera.h"
+#include <gtsam/geometry/StereoCamera.h>
 
 using namespace std;
 using namespace gtsam;

geometry/StereoCamera.h

@@ -7,10 +7,10 @@
 #pragma once
 
 #include "boost/tuple/tuple.hpp"
-#include <Cal3_S2.h>
-#include <Pose3.h>
-#include <Lie.h>
-#include "StereoPoint2.h"
+#include <gtsam/geometry/Cal3_S2.h>
+#include <gtsam/geometry/Pose3.h>
+#include <gtsam/base/Lie.h>
+#include <gtsam/geometry/StereoPoint2.h>
 
 namespace gtsam {
 

geometry/StereoPoint2.cpp

@@ -5,5 +5,5 @@
  *      Author: dellaert
  */
 
-#include "StereoPoint2.h"
+#include <gtsam/geometry/StereoPoint2.h>
 

geometry/StereoPoint2.h

@@ -9,10 +9,10 @@
 #define STEREOPOINT2_H_
 
 #include <iostream>
-#include <Vector.h>
-#include <Testable.h>
-#include <Lie.h>
-#include <Point2.h>
+#include <gtsam/base/Vector.h>
+#include <gtsam/base/Testable.h>
+#include <gtsam/base/Lie.h>
+#include <gtsam/geometry/Point2.h>
 
 namespace gtsam {
 

geometry/Tensor1.h

@@ -6,7 +6,7 @@
  */
 
 #pragma once
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace tensors {
 

geometry/Tensor1Expression.h

@@ -10,7 +10,7 @@
 #include <math.h>
 #include <iostream>
 #include <stdexcept>
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace tensors {
 

geometry/Tensor2.h

@@ -6,7 +6,7 @@
  */
 
 #pragma once
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace tensors {
 

geometry/Tensor2Expression.h

@@ -9,7 +9,7 @@
 
 #include <stdexcept>
 #include <iostream>
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace tensors {
 

geometry/Tensor3.h

@@ -6,7 +6,7 @@
  */
 
 #pragma once
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace tensors {
 

geometry/Tensor3Expression.h

@@ -8,7 +8,7 @@
 #pragma once
 
 #include <iostream>
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace tensors {
 

geometry/Tensor4.h

@@ -6,7 +6,7 @@
  */
 
 #pragma once
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace tensors {
 

geometry/Tensor5.h

@@ -6,7 +6,7 @@
  */
 
 #pragma once
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace tensors {
 

geometry/Tensor5Expression.h

@@ -8,7 +8,7 @@
 #pragma once
 
 #include <iostream>
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace tensors {
 

geometry/projectiveGeometry.cpp

@@ -6,8 +6,8 @@
  */
 
 #include <boost/foreach.hpp>
-#include "tensorInterface.h"
-#include "projectiveGeometry.h"
+#include <gtsam/geometry/tensorInterface.h>
+#include <gtsam/geometry/projectiveGeometry.h>
 
 namespace gtsam {
 

geometry/projectiveGeometry.h

@@ -8,7 +8,7 @@
 #pragma once
 
 #include <list>
-#include "tensors.h"
+#include <gtsam/geometry/tensors.h>
 
 namespace gtsam {
 

geometry/tensorInterface.cpp

@@ -5,7 +5,7 @@
  * @author: Frank Dellaert
  */
 
-#include "tensorInterface.h"
+#include <gtsam/geometry/tensorInterface.h>
 
 using namespace std;
 using namespace tensors;

geometry/tensorInterface.h

@@ -7,8 +7,8 @@
 
 #pragma once
 
-#include "tensors.h"
-#include "Matrix.h"
+#include <gtsam/geometry/tensors.h>
+#include <gtsam/base/Matrix.h>
 
 namespace gtsam {
 

geometry/tensors.h

@@ -17,17 +17,17 @@ namespace tensors {
 } // namespace tensors
 
 // Expression templates
-#include "Tensor1Expression.h"
-#include "Tensor2Expression.h"
-#include "Tensor3Expression.h"
+#include <gtsam/geometry/Tensor1Expression.h>
+#include <gtsam/geometry/Tensor2Expression.h>
+#include <gtsam/geometry/Tensor3Expression.h>
 // Tensor4 not needed so far
-#include "Tensor5Expression.h"
+#include <gtsam/geometry/Tensor5Expression.h>
 
 // Actual tensor classes
-#include "Tensor1.h"
-#include "Tensor2.h"
-#include "Tensor3.h"
-#include "Tensor4.h"
-#include "Tensor5.h"
+#include <gtsam/geometry/Tensor1.h>
+#include <gtsam/geometry/Tensor2.h>
+#include <gtsam/geometry/Tensor3.h>
+#include <gtsam/geometry/Tensor4.h>
+#include <gtsam/geometry/Tensor5.h>
 
 

geometry/tests/testCal3_S2.cpp

@@ -3,9 +3,9 @@
  * @brief Unit tests for transform derivatives
  */
 
-#include <CppUnitLite/TestHarness.h>
-#include "numericalDerivative.h"
-#include "Cal3_S2.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam/geometry/Cal3_S2.h>
 
 using namespace gtsam;
 

geometry/tests/testCalibratedCamera.cpp

@@ -6,9 +6,9 @@
 
 #include <iostream>
 
-#include <CppUnitLite/TestHarness.h>
-#include "numericalDerivative.h"
-#include "CalibratedCamera.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam/geometry/CalibratedCamera.h>
 
 using namespace std;
 using namespace gtsam;

geometry/tests/testHomography2.cpp

@@ -10,13 +10,13 @@
 #include <boost/assign/std/list.hpp> // for operator +=
 using namespace boost::assign;
 
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 
-#include "Testable.h"
-#include "tensors.h"
-#include "tensorInterface.h"
-#include "projectiveGeometry.h"
-#include "Pose3.h"
+#include <gtsam/base/Testable.h>
+#include <gtsam/geometry/tensors.h>
+#include <gtsam/geometry/tensorInterface.h>
+#include <gtsam/geometry/projectiveGeometry.h>
+#include <gtsam/geometry/Pose3.h>
 
 using namespace std;
 using namespace gtsam;
@@ -139,7 +139,7 @@ namespace gtsam {
 	}
 }
 
-#include "numericalDerivative.h"
+#include <gtsam/base/numericalDerivative.h>
 
 /* ************************************************************************* */
 TEST( Homography2, patchH)

geometry/tests/testPoint2.cpp

@@ -4,8 +4,8 @@
  * @author Frank Dellaert
  **/
 
-#include <CppUnitLite/TestHarness.h>
-#include "Point2.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/geometry/Point2.h>
 
 using namespace std;
 using namespace gtsam;

geometry/tests/testPoint3.cpp

@@ -3,8 +3,8 @@
  * @brief  Unit tests for Point3 class
  */   
 
-#include <CppUnitLite/TestHarness.h>
-#include "Point3.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/geometry/Point3.h>
 
 using namespace gtsam;
 

geometry/tests/testPose2.cpp

@@ -4,12 +4,12 @@
  */
 
 #include <math.h>
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 #include <iostream>
-#include "numericalDerivative.h"
-#include "Pose2.h"
-#include "Point2.h"
-#include "Rot2.h"
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam/geometry/Pose2.h>
+#include <gtsam/geometry/Point2.h>
+#include <gtsam/geometry/Rot2.h>
 
 using namespace gtsam;
 using namespace std;

geometry/tests/testPose3.cpp

@@ -4,9 +4,9 @@
  */
 
 #include <math.h>
-#include <CppUnitLite/TestHarness.h>
-#include "numericalDerivative.h"
-#include "Pose3.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam/geometry/Pose3.h>
 
 using namespace std;
 using namespace gtsam;

geometry/tests/testRot2.cpp

@@ -4,9 +4,9 @@
  * @author  Frank Dellaert
  */
 
-#include <CppUnitLite/TestHarness.h>
-#include "numericalDerivative.h"
-#include "Rot2.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam/geometry/Rot2.h>
 
 using namespace gtsam;
 

geometry/tests/testRot3.cpp

@@ -4,11 +4,11 @@
  * @author  Alireza Fathi
  */
 
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 #include <boost/math/constants/constants.hpp>
-#include "numericalDerivative.h"
-#include "Point3.h"
-#include "Rot3.h"
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam/geometry/Point3.h>
+#include <gtsam/geometry/Rot3.h>
 
 using namespace gtsam;
 

geometry/tests/testSimpleCamera.cpp

@@ -7,9 +7,9 @@
 #include <math.h>
 #include <iostream>
 
-#include <CppUnitLite/TestHarness.h>
-#include "numericalDerivative.h"
-#include "SimpleCamera.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam/geometry/SimpleCamera.h>
 
 using namespace std;
 using namespace gtsam;

geometry/tests/testStereoCamera.cpp

@@ -5,9 +5,9 @@
  * @author  Chris Beall
  */
 
-#include <CppUnitLite/TestHarness.h>
-#include <numericalDerivative.h>
-#include "StereoCamera.h"
+#include <gtsam/CppUnitLite/TestHarness.h>
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam/geometry/StereoCamera.h>
 
 using namespace std;
 using namespace gtsam;

geometry/tests/testTensors.cpp

@@ -10,11 +10,11 @@
 #include <boost/assign/std/list.hpp> // for operator +=
 using namespace boost::assign;
 
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 
-#include "tensors.h"
-#include "tensorInterface.h"
-#include "projectiveGeometry.h"
+#include <gtsam/geometry/tensors.h>
+#include <gtsam/geometry/tensorInterface.h>
+#include <gtsam/geometry/projectiveGeometry.h>
 
 using namespace std;
 using namespace gtsam;

geometry/tests/testTrifocal.cpp

@@ -10,11 +10,11 @@
 #include <boost/assign/std/list.hpp> // for operator +=
 using namespace boost::assign;
 
-#include <CppUnitLite/TestHarness.h>
+#include <gtsam/CppUnitLite/TestHarness.h>
 
-#include "tensors.h"
-#include "tensorInterface.h"
-#include "projectiveGeometry.h"
+#include <gtsam/geometry/tensors.h>
+#include <gtsam/geometry/tensorInterface.h>
+#include <gtsam/geometry/projectiveGeometry.h>
 
 using namespace std;
 using namespace gtsam;

geometry/timeCalibratedCamera.cpp

@@ -7,7 +7,7 @@
 #include <time.h>
 #include <iostream>
 
-#include "CalibratedCamera.h"
+#include <gtsam/geometry/CalibratedCamera.h>
 
 using namespace std;
 using namespace gtsam;

geometry/timeRot3.cpp

@@ -7,7 +7,7 @@
 #include <time.h>
 #include <iostream>
 
-#include "Rot3.h"
+#include <gtsam/geometry/Rot3.h>
 
 using namespace std;
 using namespace gtsam;

inference/BayesNet-inl.h

@@ -14,8 +14,8 @@
 #include <boost/assign/std/vector.hpp> // for +=
 using namespace boost::assign;
 
-#include "Ordering.h"
-#include "BayesNet.h"
+#include <gtsam/inference/Ordering.h>
+#include <gtsam/inference/BayesNet.h>
 //#include "FactorGraph-inl.h"
 //#include "Conditional.h"
 

inference/BayesNet.h

@@ -13,8 +13,8 @@
 #include <boost/serialization/list.hpp>
 #include <boost/serialization/shared_ptr.hpp>
 
-#include "Testable.h"
-#include "Key.h"
+#include <gtsam/base/Testable.h>
+#include <gtsam/inference/Key.h>
 
 namespace gtsam {
 

inference/BayesTree-inl.h

@@ -15,11 +15,11 @@
 #include <fstream>
 using namespace boost::assign;
 
-#include "Conditional.h"
-#include "BayesTree.h"
-#include "Ordering.h"
-#include "inference-inl.h"
-#include "Key.h"
+#include <gtsam/inference/Conditional.h>
+#include <gtsam/inference/BayesTree.h>
+#include <gtsam/inference/Ordering.h>
+#include <gtsam/inference/inference-inl.h>
+#include <gtsam/inference/Key.h>
 
 namespace gtsam {
 

inference/BayesTree.h

@@ -14,11 +14,11 @@
 #include <boost/serialization/list.hpp>
 #include <stdexcept>
 
-#include "Testable.h"
-#include "FactorGraph.h"
-#include "BayesNet.h"
-#include "Key.h"
-#include "IndexTable.h"
+#include <gtsam/base/Testable.h>
+#include <gtsam/inference/FactorGraph.h>
+#include <gtsam/inference/BayesNet.h>
+#include <gtsam/inference/Key.h>
+#include <gtsam/inference/IndexTable.h>
 
 namespace gtsam {
 

inference/BinaryConditional.h

@@ -15,9 +15,9 @@
 #include <boost/foreach.hpp> // TODO: make cpp file
 #include <boost/serialization/list.hpp>
 #include <boost/serialization/vector.hpp>
-#include "Conditional.h"
-#include "Key.h"
-#include "SymbolMap.h"
+#include <gtsam/inference/Conditional.h>
+#include <gtsam/inference/Key.h>
+#include <gtsam/inference/SymbolMap.h>
 
 namespace gtsam {
 

inference/ClusterTree-inl.h

@@ -10,7 +10,7 @@
 
 #include <boost/foreach.hpp>
 
-#include "ClusterTree.h"
+#include <gtsam/inference/ClusterTree.h>
 
 namespace gtsam {
 

inference/ClusterTree.h

@@ -9,7 +9,7 @@
 #pragma once
 
 #include <boost/shared_ptr.hpp>
-#include "Ordering.h"
+#include <gtsam/inference/Ordering.h>
 
 namespace gtsam {
 

inference/Conditional.h

@@ -12,8 +12,8 @@
 #include <boost/serialization/string.hpp>
 #include <boost/serialization/access.hpp>
 #include <boost/serialization/nvp.hpp>
-#include "Testable.h"
-#include "Key.h"
+#include <gtsam/base/Testable.h>
+#include <gtsam/inference/Key.h>
 
 namespace gtsam {
 

inference/EliminationTree-inl.h

@@ -11,7 +11,7 @@
 #include <stdexcept>
 #include <functional>
 #include <boost/foreach.hpp>
-#include "EliminationTree.h"
+#include <gtsam/inference/EliminationTree.h>
 
 namespace gtsam {
 

inference/EliminationTree.h

@@ -9,8 +9,8 @@
 #pragma once
 
 #include <set>
-#include "IndexTable.h"
-#include "ClusterTree.h"
+#include <gtsam/inference/IndexTable.h>
+#include <gtsam/inference/ClusterTree.h>
 
 namespace gtsam {
 

inference/Factor.h

@@ -12,9 +12,9 @@
 
 #include <list>
 #include <boost/utility.hpp> // for noncopyable
-#include "Testable.h"
-#include "Key.h"
-#include "SymbolMap.h"
+#include <gtsam/base/Testable.h>
+#include <gtsam/inference/Key.h>
+#include <gtsam/inference/SymbolMap.h>
 
 namespace gtsam {
 

inference/FactorGraph-inl.h

@@ -20,11 +20,11 @@
 #include <boost/tuple/tuple.hpp>
 #include <boost/format.hpp>
 #include <boost/graph/prim_minimum_spanning_tree.hpp>
-#include "ccolamd.h"
-#include "Ordering.h"
-#include "FactorGraph.h"
-#include "graph-inl.h"
-#include "DSF.h"
+#include <gtsam/colamd/ccolamd.h>
+#include <gtsam/inference/Ordering.h>
+#include <gtsam/inference/FactorGraph.h>
+#include <gtsam/inference/graph-inl.h>
+#include <gtsam/base/DSF.h>
 
 #define INSTANTIATE_FACTOR_GRAPH(F) \
   template class FactorGraph<F>; \

inference/FactorGraph.h

@@ -16,11 +16,11 @@
 #include <boost/serialization/vector.hpp>
 #include <boost/serialization/shared_ptr.hpp>
 
-#include "Testable.h"
-#include "BayesNet.h"
-#include "graph.h"
-#include "Key.h"
-#include "SymbolMap.h"
+#include <gtsam/base/Testable.h>
+#include <gtsam/inference/BayesNet.h>
+#include <gtsam/inference/graph.h>
+#include <gtsam/inference/Key.h>
+#include <gtsam/inference/SymbolMap.h>
 
 namespace gtsam {
 

inference/ISAM-inl.h

@@ -8,9 +8,9 @@
 #include <boost/assign/std/list.hpp> // for operator +=
 using namespace boost::assign;
 
-#include "Conditional.h"
-#include "ISAM.h"
-#include "BayesTree-inl.h"
+#include <gtsam/inference/Conditional.h>
+#include <gtsam/inference/ISAM.h>
+#include <gtsam/inference/BayesTree-inl.h>
 
 namespace gtsam {
 

inference/ISAM.h

@@ -15,10 +15,10 @@
 #include <boost/serialization/list.hpp>
 #include <stdexcept>
 
-#include "Testable.h"
-#include "FactorGraph.h"
-#include "BayesNet.h"
-#include "BayesTree.h"
+#include <gtsam/base/Testable.h>
+#include <gtsam/inference/FactorGraph.h>
+#include <gtsam/inference/BayesNet.h>
+#include <gtsam/inference/BayesTree.h>
 
 namespace gtsam {
 

inference/ISAM2-inl.h

@@ -10,13 +10,13 @@ using namespace boost::assign;
 
 #include <set>
 
-#include "NonlinearFactorGraph-inl.h"
-#include "GaussianFactor.h"
-#include "VectorConfig.h"
+#include <gtsam/nonlinear/NonlinearFactorGraph-inl.h>
+#include <gtsam/linear/GaussianFactor.h>
+#include <gtsam/linear/VectorConfig.h>
 
-#include "Conditional.h"
-#include "BayesTree-inl.h"
-#include "ISAM2.h"
+#include <gtsam/inference/Conditional.h>
+#include <gtsam/inference/BayesTree-inl.h>
+#include <gtsam/inference/ISAM2.h>
 
 namespace gtsam {
 

inference/ISAM2.h

@@ -15,13 +15,13 @@
 #include <boost/serialization/list.hpp>
 #include <stdexcept>
 
-#include "Testable.h"
-#include "FactorGraph.h"
-#include "NonlinearFactorGraph.h"
-#include "BayesNet.h"
-#include "BayesTree.h"
-#include "Key.h"
-#include "SymbolMap.h"
+#include <gtsam/base/Testable.h>
+#include <gtsam/inference/FactorGraph.h>
+#include <gtsam/nonlinear/NonlinearFactorGraph.h>
+#include <gtsam/inference/BayesNet.h>
+#include <gtsam/inference/BayesTree.h>
+#include <gtsam/inference/Key.h>
+#include <gtsam/inference/SymbolMap.h>
 
 namespace gtsam {
 

inference/IndexTable.h

@@ -9,7 +9,7 @@
 
 #include <map>
 #include <boost/foreach.hpp> // TODO should not be in header
-#include "Testable.h"
+#include <gtsam/base/Testable.h>
 
 namespace gtsam {
 

inference/JunctionTree-inl.h

@@ -10,9 +10,9 @@
 
 #include <boost/foreach.hpp>
 
-#include "SymbolicFactorGraph.h"
-#include "BayesTree-inl.h"
-#include "JunctionTree.h"
+#include <gtsam/inference/SymbolicFactorGraph.h>
+#include <gtsam/inference/BayesTree-inl.h>
+#include <gtsam/inference/JunctionTree.h>
 
 namespace gtsam {
 

inference/JunctionTree.h

@@ -10,9 +10,9 @@
 
 #include <set>
 #include <boost/shared_ptr.hpp>
-#include "BayesTree.h"
-#include "ClusterTree.h"
-#include "SymbolicConditional.h"
+#include <gtsam/inference/BayesTree.h>
+#include <gtsam/inference/ClusterTree.h>
+#include <gtsam/inference/SymbolicConditional.h>
 
 namespace gtsam {
 

inference/Key.h

@@ -16,7 +16,7 @@
 #include <boost/lexical_cast.hpp>
 #endif
 
-#include "Testable.h"
+#include <gtsam/base/Testable.h>
 
 #define ALPHA '\224'
 

inference/Makefile.am

@@ -2,6 +2,10 @@
 # GTSAM core functionality: base classes for inference, as well as symbolic and discrete
 #----------------------------------------------------------------------------------------------------
 
+# use nostdinc to turn off -I. and -I.., we do not need them because 
+# header files are qualified so they can be included in external projects.
+AUTOMAKE_OPTIONS = nostdinc
+
 headers =
 sources = 
 check_PROGRAMS = 
@@ -50,10 +54,11 @@ noinst_PROGRAMS = tests/timeSymbolMaps
 # The headers are installed in $(includedir)/gtsam: 
 #----------------------------------------------------------------------------------------------------
 headers += $(sources:.cpp=.h)
-pkginclude_HEADERS = $(headers)
+inferencedir = $(pkgincludedir)/inference
+inference_HEADERS = $(headers)
 noinst_LTLIBRARIES = libinference.la
 libinference_la_SOURCES = $(sources)
-AM_CPPFLAGS = -I$(boost) -I$(top_srcdir) -I$(top_srcdir)/colamd -I$(top_srcdir)/base 
+AM_CPPFLAGS = -I$(boost) -I$(BORG_SRCROOT)
 AM_CXXFLAGS =
 
 #----------------------------------------------------------------------------------------------------