Index: /issm/trunk-jpl/src/wrappers/python/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/python/Makefile.am	(revision 27623)
+++ /issm/trunk-jpl/src/wrappers/python/Makefile.am	(revision 27624)
@@ -1,3 +1,3 @@
-AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@
+AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ @PROJINCL@
 AUTOMAKE_OPTIONS = subdir-objects
 
@@ -8,10 +8,5 @@
 
 #python io{{{
-if !WINDOWS
 lib_LTLIBRARIES = libISSMPython.la
-else
-noinst_LTLIBRARIES = libISSMPython.la
-lib_LTLIBRARIES =
-endif
 
 io_sources = \
@@ -20,29 +15,15 @@
 	./io/WritePythonData.cpp
 
-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)
+ALLCXXFLAGS= -fPIC -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS)
 
 libISSMPython_la_SOURCES = $(io_sources)
-libISSMPython_la_CXXFLAGS = ${ALL_CXXFLAGS}
+libISSMPython_la_CXXFLAGS= $(ALLCXXFLAGS)
 #}}}
 #api io{{{
-if !WINDOWS
 lib_LTLIBRARIES += libISSMApi.la
-else
-noinst_LTLIBRARIES += libISSMApi.la
-endif
-
-if !MSYS2
-api_sources= ./io/ApiPrintf.cpp
+api_sources		 = ./io/ApiPrintf.cpp
 
 libISSMApi_la_SOURCES = $(api_sources)
-libISSMApi_la_CXXFLAGS= ${ALLCXXFLAGS}
-endif
+libISSMApi_la_CXXFLAGS= $(ALLCXXFLAGS)
 #}}}
 #Wrappers {{{
@@ -64,6 +45,6 @@
 	MeshProfileIntersection_python.la \
 	NodeConnectivity_python.la \
-	ProcessRifts_python.la \
-	Triangle_python.la
+	Triangle_python.la \
+	ProcessRifts_python.la
 
 if CHACO
@@ -71,25 +52,12 @@
 endif
 #}}}
-# Dependencies {{{
-deps = $(MATHLIB) ${PYTHONLIB}
+#Flags and libraries {{{
+deps = $(MATHLIB) $(PYTHONLIB)
 
-# Triangle
-CXXFLAGS_FOR_TRI = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER
+#Triangle library
+AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER -D_WRAPPERS_
 
-# Python
-CXXFLAGS_FOR_PY = -D_HAVE_PYTHON_MODULES_
-
-if PYTHON3
-CXXFLAGS_FOR_PY += -DNPY_NO_DEPRECATED_API
-endif
-
-LDFLAGS_FOR_PY = -module $(PYTHONLINK) -shrext ${EXEEXT} -no-undefined
-
-AM_CXXFLAGS = ${CXXFLAGS_FOR_TRI} ${CXXFLAGS_FOR_PY}
-AM_LDFLAGS = ${LDFLAGS_FOR_PY}
-
-if !MSYS2
-AM_LDFLAGS += --export-dynamic -rdynamic
-endif
+#Python part
+AM_LDFLAGS = -module $(PYTHONLINK) -shrext ${EXEEXT} --export-dynamic -rdynamic -no-undefined
 
 if !VERSION
@@ -112,14 +80,12 @@
 endif
 
-AM_CXXFLAGS += -fPIC -D_WRAPPERS_
+AM_LDFLAGS 	+= --no-warnings
+AM_CXXFLAGS += -D_HAVE_PYTHON_MODULES_ -fPIC
 
-# Warning suppression
-AM_LDFLAGS 	+= --no-warnings
+if PYTHON3
+AM_CXXFLAGS += -DNPY_NO_DEPRECATED_API
+endif
 
-deps += ./libISSMPython.la ../../c/libISSMModules.la ../../c/libISSMCore.la
-
-if !MSYS2
-deps += ./libISSMApi.la
-endif
+deps += ./libISSMPython.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
 
 if ADOLC
@@ -131,87 +97,94 @@
 endif
 
-# Optimization flags
+#Optimization flags:
 AM_CXXFLAGS += $(CXXOPTFLAGS)
 #}}}
 # Module sources and dependencies {{{
-if !WINDOWS
-libISSMPython_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(MATHLIB)
-endif
-
-if VERSION
-libISSMPython_la_LDFLAGS =
-libISSMApi_la_LDFLAGS =
-else
-libISSMPython_la_LDFLAGS = -avoid-version
-libISSMApi_la_LDFLAGS = -avoid-version
-endif
+libISSMPython_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(MATHLIB)
 
 if STANDALONE_LIBRARIES
 libISSMPython_la_LDFLAGS = -static
 libISSMApi_la_LDFLAGS = -static
-deps += $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(MKLLIB) $(MPILIB) $(NEOPZLIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS)
+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
 
-if !WINDOWS
-libISSMApi_la_LIBADD = $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(MATHLIB)
-endif
+libISSMApi_la_LIBADD = $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(MATHLIB)
 
 BamgConvertMesh_python_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp
-BamgConvertMesh_python_la_LIBADD = ${deps}
+BamgConvertMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+BamgConvertMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 BamgMesher_python_la_SOURCES = ../BamgMesher/BamgMesher.cpp
-BamgMesher_python_la_LIBADD = ${deps}
+BamgMesher_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+BamgMesher_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 BamgTriangulate_python_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp
-BamgTriangulate_python_la_LIBADD = ${deps}
+BamgTriangulate_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+BamgTriangulate_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 if CHACO
 Chaco_python_la_SOURCES = ../Chaco/Chaco.cpp
-Chaco_python_la_LIBADD = ${deps} $(CHACOLIB)
+Chaco_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+Chaco_python_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 endif
 
 ContourToMesh_python_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp
-ContourToMesh_python_la_LIBADD = ${deps}
+ContourToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+ContourToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
 
 ContourToNodes_python_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp
-ContourToNodes_python_la_LIBADD = ${deps}
+ContourToNodes_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+ContourToNodes_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 ElementConnectivity_python_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp
-ElementConnectivity_python_la_LIBADD = ${deps}
+ElementConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+ElementConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 ExpToLevelSet_python_la_SOURCES = ../ExpToLevelSet/ExpToLevelSet.cpp
-ExpToLevelSet_python_la_LIBADD = ${deps}
+ExpToLevelSet_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+ExpToLevelSet_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(NEOPZLIB)
+
+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_LIBADD = ${deps}
-
-InterpFromMesh2d_python_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp
-InterpFromMesh2d_python_la_LIBADD = ${deps}
+InterpFromGridToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+InterpFromGridToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
 
 InterpFromMeshToGrid_python_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp
-InterpFromMeshToGrid_python_la_LIBADD = ${deps}
+InterpFromMeshToGrid_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+InterpFromMeshToGrid_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
 
 InterpFromMeshToMesh2d_python_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp
-InterpFromMeshToMesh2d_python_la_LIBADD = ${deps}
+InterpFromMeshToMesh2d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+InterpFromMeshToMesh2d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB)
 
 InterpFromMeshToMesh3d_python_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp
-InterpFromMeshToMesh3d_python_la_LIBADD = ${deps}
+InterpFromMeshToMesh3d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+InterpFromMeshToMesh3d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB)
 
 IssmConfig_python_la_SOURCES = ../IssmConfig/IssmConfig.cpp
-IssmConfig_python_la_LIBADD = ${deps}
+IssmConfig_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+IssmConfig_python_la_LIBADD = ${deps} $(DAKOTALIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB)
 
 MeshPartition_python_la_SOURCES = ../MeshPartition/MeshPartition.cpp
-MeshPartition_python_la_LIBADD = ${deps}
+MeshPartition_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+MeshPartition_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(METISLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 MeshProfileIntersection_python_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp
-MeshProfileIntersection_python_la_LIBADD = ${deps}
+MeshProfileIntersection_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+MeshProfileIntersection_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 NodeConnectivity_python_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp
-NodeConnectivity_python_la_LIBADD = ${deps}
+NodeConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+NodeConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 Triangle_python_la_SOURCES = ../Triangle/Triangle.cpp
-Triangle_python_la_LIBADD = ${deps} $(TRIANGLELIB)
+Triangle_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+Triangle_python_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 ProcessRifts_python_la_SOURCES = ../ProcessRifts/ProcessRifts.cpp
-ProcessRifts_python_la_LIBADD = ${deps}
+ProcessRifts_python_la_CXXFLAGS = ${AM_CXXFLAGS}
+ProcessRifts_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 #}}}