Index: /issm/trunk-jpl/src/wrappers/matlab/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 27618)
+++ /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 27619)
@@ -1,3 +1,3 @@
-AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ @PROJINCL@
+AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @BOOSTINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ @PROJINCL@
 AUTOMAKE_OPTIONS = subdir-objects
 
@@ -68,8 +68,8 @@
 	NodeConnectivity_matlab.la \
 	PointCloudFindNeighbors_matlab.la \
+	ProcessRifts_matlab.la \
 	PropagateFlagsFromConnectivity_matlab.la \
-	Triangle_matlab.la \
-	ProcessRifts_matlab.la \
-	Scotch_matlab.la
+	Scotch_matlab.la \
+	Triangle_matlab.la
 
 if CHACO
@@ -93,5 +93,5 @@
 CXXFLAGS_FOR_TRI = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER
 
-#Matlab part
+# MATLAB
 CXXFLAGS_FOR_MEX = -D_HAVE_MATLAB_MODULES_ $(MEXOPTFLAGS) $(MEXCXXFLAGS)
 CPPFLAGS_FOR_MEX = $(MATLABINCL)
@@ -148,5 +148,5 @@
 deps += ${LIBADD_FOR_MEX}
 
-#Optimization flags:
+# Optimization flags
 AM_CXXFLAGS += $(CXXOPTFLAGS)
 #}}}
Index: /issm/trunk-jpl/src/wrappers/python/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/python/Makefile.am	(revision 27618)
+++ /issm/trunk-jpl/src/wrappers/python/Makefile.am	(revision 27619)
@@ -1,3 +1,3 @@
-AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ @PROJINCL@
+AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ @PROJINCL@
 AUTOMAKE_OPTIONS = subdir-objects
 
@@ -8,5 +8,10 @@
 
 #python io{{{
+if !WINDOWS
 lib_LTLIBRARIES = libISSMPython.la
+else
+noinst_LTLIBRARIES = libISSMPython.la
+lib_LTLIBRARIES =
+endif
 
 io_sources = \
@@ -15,5 +20,12 @@
 	./io/WritePythonData.cpp
 
-ALLCXXFLAGS= -fPIC -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS)
+ALL_CXXFLAGS= -fPIC -D_WRAPPERS_
+
+if MSYS2
+ALL_CXXFLAGS += -D_DO_NOT_LOAD_GLOBALS_ # Cannot have undefined symbols under MSYS2
+ALL_CXXFLAGS += -D_USE_MATH_DEFINES # Need to open fence to math.h definitions when --std=c++ is used (which is the default)
+endif
+
+ALL_CXXFLAGS += $(CXXOPTFLAGS) $(CXXFLAGS)
 
 libISSMPython_la_SOURCES = $(io_sources)
@@ -21,9 +33,16 @@
 #}}}
 #api io{{{
+if !WINDOWS
 lib_LTLIBRARIES += libISSMApi.la
-api_sources		 = ./io/ApiPrintf.cpp
+else
+noinst_LTLIBRARIES += libISSMApi.la
+endif
+
+if !MSYS2
+api_sources= ./io/ApiPrintf.cpp
 
 libISSMApi_la_SOURCES = $(api_sources)
 libISSMApi_la_CXXFLAGS= $(ALLCXXFLAGS)
+endif
 #}}}
 #Wrappers {{{
@@ -45,6 +64,6 @@
 	MeshProfileIntersection_python.la \
 	NodeConnectivity_python.la \
-	Triangle_python.la \
-	ProcessRifts_python.la
+	ProcessRifts_python.la \
+	Triangle_python.la
 
 if CHACO
@@ -52,12 +71,21 @@
 endif
 #}}}
-#Flags and libraries {{{
+# Dependencies {{{
 deps = $(MATHLIB) ${PYTHONLIB}
 
-#Triangle library
+# Triangle
 AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER -D_WRAPPERS_
 
-#Python part
-AM_LDFLAGS = -module $(PYTHONLINK) -shrext ${EXEEXT} --export-dynamic -rdynamic -no-undefined
+# Python
+AM_LDFLAGS = -module $(PYTHONLINK) -shrext ${EXEEXT} -no-undefined
+AM_CXXFLAGS += -D_HAVE_PYTHON_MODULES_
+
+if PYTHON3
+AM_CXXFLAGS += -DNPY_NO_DEPRECATED_API
+endif
+
+if !MSYS2
+AM_LDFLAGS += --export-dynamic -rdynamic
+endif
 
 if !VERSION
@@ -80,12 +108,14 @@
 endif
 
+AM_CXXFLAGS += -fPIC -D_WRAPPERS_
+
+# Warning suppression
 AM_LDFLAGS 	+= --no-warnings
-AM_CXXFLAGS += -D_HAVE_PYTHON_MODULES_ -fPIC
-
-if PYTHON3
-AM_CXXFLAGS += -DNPY_NO_DEPRECATED_API
-endif
-
-deps += ./libISSMPython.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
+
+deps += ./libISSMPython.la ../../c/libISSMModules.la ../../c/libISSMCore.la
+
+if !MSYS2
+deps += ./libISSMApi.la
+endif
 
 if ADOLC
@@ -97,94 +127,87 @@
 endif
 
-#Optimization flags:
+# Optimization flags
 AM_CXXFLAGS += $(CXXOPTFLAGS)
 #}}}
 # Module sources and dependencies {{{
-libISSMPython_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(MATHLIB)
+if !WINDOWS
+libISSMPython_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB)
+endif
+
+if VERSION
+libISSMPython_la_LDFLAGS =
+libISSMApi_la_LDFLAGS =
+else
+libISSMPython_la_LDFLAGS = -avoid-version
+libISSMApi_la_LDFLAGS = -avoid-version
+endif
 
 if STANDALONE_LIBRARIES
 libISSMPython_la_LDFLAGS = -static
 libISSMApi_la_LDFLAGS = -static
-deps += $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(CHACOLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS)
-endif
-
-libISSMApi_la_LIBADD = $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(MATHLIB)
+deps += $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(NEOPZLIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(OSLIBS)
+endif
+
+if !WINDOWS
+libISSMApi_la_LIBADD = $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB)
+endif
 
 BamgConvertMesh_python_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp
-BamgConvertMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgConvertMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+BamgConvertMesh_python_la_LIBADD = ${deps}
 
 BamgMesher_python_la_SOURCES = ../BamgMesher/BamgMesher.cpp
-BamgMesher_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgMesher_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+BamgMesher_python_la_LIBADD = ${deps}
 
 BamgTriangulate_python_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp
-BamgTriangulate_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgTriangulate_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+BamgTriangulate_python_la_LIBADD = ${deps}
 
 if CHACO
 Chaco_python_la_SOURCES = ../Chaco/Chaco.cpp
-Chaco_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-Chaco_python_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+Chaco_python_la_LIBADD = ${deps} $(CHACOLIB)
 endif
 
 ContourToMesh_python_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp
-ContourToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ContourToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
+ContourToMesh_python_la_LIBADD = ${deps}
 
 ContourToNodes_python_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp
-ContourToNodes_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ContourToNodes_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+ContourToNodes_python_la_LIBADD = ${deps}
 
 ElementConnectivity_python_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp
-ElementConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ElementConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+ElementConnectivity_python_la_LIBADD = ${deps}
 
 ExpToLevelSet_python_la_SOURCES = ../ExpToLevelSet/ExpToLevelSet.cpp
-ExpToLevelSet_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ExpToLevelSet_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(NEOPZLIB)
+ExpToLevelSet_python_la_LIBADD = ${deps}
+
+InterpFromGridToMesh_python_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp
+InterpFromGridToMesh_python_la_LIBADD = ${deps}
 
 InterpFromMesh2d_python_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp
-InterpFromMesh2d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMesh2d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
-
-InterpFromGridToMesh_python_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp
-InterpFromGridToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromGridToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
+InterpFromMesh2d_python_la_LIBADD = ${deps}
 
 InterpFromMeshToGrid_python_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp
-InterpFromMeshToGrid_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToGrid_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
+InterpFromMeshToGrid_python_la_LIBADD = ${deps}
 
 InterpFromMeshToMesh2d_python_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp
-InterpFromMeshToMesh2d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToMesh2d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB)
+InterpFromMeshToMesh2d_python_la_LIBADD = ${deps}
 
 InterpFromMeshToMesh3d_python_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp
-InterpFromMeshToMesh3d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToMesh3d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB)
+InterpFromMeshToMesh3d_python_la_LIBADD = ${deps}
 
 IssmConfig_python_la_SOURCES = ../IssmConfig/IssmConfig.cpp
-IssmConfig_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-IssmConfig_python_la_LIBADD = ${deps} $(DAKOTALIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB)
+IssmConfig_python_la_LIBADD = ${deps}
 
 MeshPartition_python_la_SOURCES = ../MeshPartition/MeshPartition.cpp
-MeshPartition_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-MeshPartition_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(METISLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+MeshPartition_python_la_LIBADD = ${deps}
 
 MeshProfileIntersection_python_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp
-MeshProfileIntersection_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-MeshProfileIntersection_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+MeshProfileIntersection_python_la_LIBADD = ${deps}
 
 NodeConnectivity_python_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp
-NodeConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-NodeConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+NodeConnectivity_python_la_LIBADD = ${deps}
 
 Triangle_python_la_SOURCES = ../Triangle/Triangle.cpp
-Triangle_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-Triangle_python_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+Triangle_python_la_LIBADD = ${deps} $(TRIANGLELIB)
 
 ProcessRifts_python_la_SOURCES = ../ProcessRifts/ProcessRifts.cpp
-ProcessRifts_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ProcessRifts_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
-#}}}
+ProcessRifts_python_la_LIBADD = ${deps}
+#}}}