Lots of updates to code locations, get Tester working with tutorial

CMakeLists.txt

@@ -160,7 +160,6 @@ OPTION(NEKTAR_BUILD_PYTHON     "Build Nektar++ Python bindings" OFF)
 OPTION(NEKTAR_BUILD_PACKAGES   "Build Nektar++ binary packages" OFF)
 MARK_AS_ADVANCED(NEKTAR_BUILD_PACKAGES)
 
-
 OPTION(NEKTAR_TEST_ALL "Include full set of regression tests to this build." OFF)
 OPTION(NEKTAR_TEST_USE_HOSTFILE "Use a hostfile to explicitly specify number of
 slots." OFF)
@@ -250,6 +249,7 @@ INCLUDE (ThirdPartyOCE)
 INCLUDE (ThirdPartyTriangle)
 INCLUDE (ThirdPartyTetGen)
 INCLUDE (ThirdPartyCCM)
+INCLUDE (ThirdPartyPython)
 INCLUDE (FindCFI)
 
 INCLUDE (Doxygen)

cmake/NektarCommon.cmake

@@ -249,3 +249,43 @@ MACRO(ADD_NEKTAR_TEST name)
             COMMAND Tester ${CMAKE_CURRENT_SOURCE_DIR}/Tests/${name}.tst)
     ENDIF()
 ENDMACRO(ADD_NEKTAR_TEST)
+
+#
+# ADD_NEKPY_LIBRARY(name SOURCES src1 src2 ...)
+#
+# Adds a new NekPy library with the given sources.
+#
+MACRO(ADD_NEKPY_LIBRARY name)
+    CMAKE_PARSE_ARGUMENTS(NEKPY "" "" "SOURCES" ${ARGN})
+    SET(NEKPY_NAME ${name})
+
+    # Create library.
+    ADD_LIBRARY(_${name} SHARED ${NEKPY_SOURCES})
+
+    # Python requires a .so extension, even on OS X.
+    SET_TARGET_PROPERTIES(_${name} PROPERTIES PREFIX "")
+    SET_TARGET_PROPERTIES(_${name} PROPERTIES SUFFIX ".so")
+
+    ADD_DEPENDENCIES(_${name} boost-numpy)
+
+    # Add target link libraries.
+    TARGET_LINK_LIBRARIES(_${name}
+        ${Boost_SYSTEM_LIBRARY}
+        ${Boost_PYTHON_LIBRARY}
+        ${BOOST_NUMPY_LIB}
+        ${PYTHON_LIBRARIES}
+        ${name})
+
+    # Install __init__.py files.
+    CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/cmake/python/init.py.in
+        ${CMAKE_BINARY_DIR}/NekPy/${name}/__init__.py)
+    SET_TARGET_PROPERTIES(_${name} PROPERTIES
+        LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/NekPy/${name})
+ENDMACRO()
+
+MACRO(ADD_NEKPY_EXECUTABLE name source)
+    # Copy the files into binary directory.
+    INSTALL(FILES ${source} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
+    FILE(COPY ${source} DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    ADD_CUSTOM_TARGET(${name} SOURCES ${source})
+ENDMACRO()
\ No newline at end of file

cmake/ThirdPartyPython.cmake

+########################################################################
+#
+# ThirdParty configuration for Nektar++
+#
+# Python interfaces
+#
+########################################################################
+
+IF (NEKTAR_BUILD_PYTHON)
+    # Find Python
+    FIND_PACKAGE(PythonInterp  REQUIRED)
+    FIND_PACKAGE(PythonLibsNew REQUIRED)
+    INCLUDE_DIRECTORIES(SYSTEM ${PYTHON_INCLUDE_DIRS})
+
+    # Include headers from root directory for config file.
+
+    # Try to find Boost.NumPy
+    FIND_LIBRARY(BOOST_NUMPY_LIB boost_numpy PATHS ${Boost_LIBRARY_DIRS})
+
+    # If we can't find it, pull it from git and compile it
+    IF (NOT BOOST_NUMPY_LIB)
+        INCLUDE(ExternalProject)
+        EXTERNALPROJECT_ADD(
+            boost-numpy
+            PREFIX ${TPSRC}
+            GIT_REPOSITORY http://github.com/ndarray/Boost.NumPy.git
+            STAMP_DIR ${TPBUILD}/stamp
+            DOWNLOAD_DIR ${TPSRC}
+            SOURCE_DIR ${TPSRC}/boost-numpy
+            BINARY_DIR ${TPBUILD}/boost-numpy
+            TMP_DIR ${TPBUILD}/boost-numpy-tmp
+            INSTALL_DIR ${TPDIST}
+            CONFIGURE_COMMAND ${CMAKE_COMMAND}
+                -G ${CMAKE_GENERATOR} -DCMAKE_INSTALL_PREFIX:PATH=${TPDIST} -DBUILD_EXAMPLES=OFF -DBUILD_TESTS=OFF -DLIBRARY_TYPE=STATIC
+                ${TPSRC}/boost-numpy
+            )
+
+        SET(BOOST_NUMPY_LIB ${TPDIST}/lib64/${CMAKE_STATIC_LIBRARY_PREFIX}boost_numpy${CMAKE_STATIC_LIBRARY_SUFFIX})
+        INCLUDE_DIRECTORIES(SYSTEM ${TPDIST}/include)
+        CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/cmake/python/setup.py.in ${CMAKE_BINARY_DIR}/setup.py)
+
+        ADD_CUSTOM_TARGET(nekpy-install-user
+            DEPENDS _MultiRegions
+            COMMAND python setup.py install --user
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
+
+        FILE(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/NekPy)
+        FILE(WRITE ${CMAKE_BINARY_DIR}/NekPy/__init__.py "# placeholder")
+    ELSE()
+        ADD_CUSTOM_TARGET(boost-numpy ALL)
+        ADD_DEFINITIONS(-DBOOST_HAS_NUMPY)
+    ENDIF()
+ENDIF()

cmake/python/init.py.in

+from ._${NEKPY_NAME} import *

cmake/python/setup.py.in

+from distutils.core import setup
+
+libs = ['LibUtilities', 'StdRegions', 'SpatialDomains', 'LocalRegions', 'MultiRegions']
+
+setup(name='NekPy',
+      version='${NEKTAR_VERSION}',
+      package_dir={ '': '${CMAKE_BINARY_DIR}' },
+      packages=[ 'NekPy' ] + [ 'NekPy.%s' % l for l in libs ],
+      package_data={ 'NekPy.%s' % l : ['_%s.so' % l] for l in libs }
+)

library/CMakeLists.txt

@@ -28,6 +28,5 @@ IF (NEKTAR_UTILITY_FIELDCONVERT OR NEKTAR_UTILITY_NEKMESH OR NEKTAR_BUILD_SOLVER
 ENDIF()
 
 IF (NEKTAR_BUILD_PYTHON)
-    SUBDIRS(Python)
     INCLUDE_DIRECTORIES(Python)
 ENDIF()

library/LibUtilities/CMakeLists.txt

@@ -431,6 +431,10 @@ IF( NEKTAR_USE_PETSC )
     ADD_DEPENDENCIES(LibUtilities petsc-3.7.2)
 ENDIF( NEKTAR_USE_PETSC )
 
+IF (NEKTAR_BUILD_PYTHON)
+    SUBDIRS(Python)
+ENDIF()
+
 # HDF5
 IF( NEKTAR_USE_HDF5 )
     TARGET_LINK_LIBRARIES(LibUtilities LINK_PUBLIC ${HDF5_LIBRARIES})

library/Python/LibUtilities/CMakeLists.txt → library/LibUtilities/Python/CMakeLists.txt

-SET(LIBUTILITIES_SOURCES
+ADD_NEKPY_LIBRARY(LibUtilities SOURCES
     LibUtilities.cpp
     BasicUtils/SessionReader.cpp
     BasicUtils/SharedArray.cpp
@@ -7,5 +7,3 @@ SET(LIBUTILITIES_SOURCES
     Foundations/Points.cpp
     LinearAlgebra/NekMatrix.cpp
     )
-
-ADD_NEKPY_LIBRARY(LibUtilities LIBUTILITIES_SOURCES)

library/LocalRegions/CMakeLists.txt

@@ -49,5 +49,9 @@ ADD_NEKTAR_LIBRARY(LocalRegions
     SUMMARY "Nektar++ LocalRegions library"
     DESCRIPTION "This library provides physical space expansions on the various supported regions.")
 
+IF (NEKTAR_BUILD_PYTHON)
+    SUBDIRS(Python)
+ENDIF()
+
 INSTALL(DIRECTORY ./ DESTINATION ${NEKTAR_INCLUDE_DIR}/LocalRegions
     COMPONENT dev FILES_MATCHING PATTERN "*.h" PATTERN "*.hpp")

library/Python/LocalRegions/CMakeLists.txt → library/LocalRegions/Python/CMakeLists.txt

-SET(LOCALREGIONS_SOURCES
+ADD_NEKPY_LIBRARY(LocalRegions SOURCES
     LocalRegions.cpp
     Expansion.cpp
     QuadExp.cpp
     SegExp.cpp
     TriExp.cpp
     )
-
-ADD_NEKPY_LIBRARY(LocalRegions LOCALREGIONS_SOURCES)

library/MultiRegions/CMakeLists.txt

@@ -150,6 +150,10 @@ IF( NEKTAR_USE_PETSC )
     ADD_DEPENDENCIES(MultiRegions petsc-3.7.2)
 ENDIF( NEKTAR_USE_PETSC )
 
+IF (NEKTAR_BUILD_PYTHON)
+    SUBDIRS(Python)
+ENDIF()
+
 INSTALL(DIRECTORY ./ DESTINATION ${NEKTAR_INCLUDE_DIR}/MultiRegions COMPONENT dev FILES_MATCHING PATTERN "*.h" PATTERN "*.hpp")
 
 

library/Python/MultiRegions/CMakeLists.txt → library/MultiRegions/Python/CMakeLists.txt

-SET(MULTIREGIONS_SOURCES
+ADD_NEKPY_LIBRARY(MultiRegions SOURCES
     MultiRegions.cpp
     ExpList.cpp
     ExpList2D.cpp
     )
-
-ADD_NEKPY_LIBRARY(MultiRegions MULTIREGIONS_SOURCES)

library/SpatialDomains/CMakeLists.txt

@@ -78,5 +78,9 @@ IF( NEKTAR_USE_SCOTCH )
     ADD_DEPENDENCIES(SpatialDomains scotch-6.0.0)
 ENDIF ()
 
+IF (NEKTAR_BUILD_PYTHON)
+    SUBDIRS(Python)
+ENDIF()
+
 INSTALL(DIRECTORY ./ DESTINATION ${NEKTAR_INCLUDE_DIR}/SpatialDomains
     COMPONENT dev FILES_MATCHING PATTERN "*.h" PATTERN "*.hpp")

library/Python/SpatialDomains/CMakeLists.txt → library/SpatialDomains/Python/CMakeLists.txt

-SET(SPATIALDOMAINS_SOURCES
+ADD_NEKPY_LIBRARY(SpatialDomains SOURCES
     SpatialDomains.cpp
     Geometry.cpp
     Geometry1D.cpp
@@ -7,6 +7,4 @@ SET(SPATIALDOMAINS_SOURCES
     SegGeom.cpp
     QuadGeom.cpp
     TriGeom.cpp
-    )
-
-ADD_NEKPY_LIBRARY(SpatialDomains SPATIALDOMAINS_SOURCES)
+    )
\ No newline at end of file

library/StdRegions/CMakeLists.txt

@@ -55,5 +55,9 @@ ADD_NEKTAR_LIBRARY(StdRegions
     SUMMARY "Nektar++ StdRegions library"
     DESCRIPTION "This library provides construction of the reference expansions for the various 1D, 2D and 3D regions.")
 
+IF (NEKTAR_BUILD_PYTHON)
+    SUBDIRS(Python)
+ENDIF()
+
 INSTALL(DIRECTORY ./ DESTINATION ${NEKTAR_INCLUDE_DIR}/StdRegions COMPONENT dev FILES_MATCHING PATTERN "*.h" PATTERN "*.hpp")
 

library/Python/StdRegions/CMakeLists.txt → library/StdRegions/Python/CMakeLists.txt

-SET(STDREGIONS_SOURCES
+ADD_NEKPY_LIBRARY(StdRegions SOURCES
     StdRegions.cpp
     StdExpansion.cpp
     StdSegExp.cpp
     StdTriExp.cpp
     StdQuadExp.cpp
     )
-
-ADD_NEKPY_LIBRARY(StdRegions STDREGIONS_SOURCES)

tests/TestData.cpp

@@ -83,6 +83,11 @@ namespace Nektar
         return m_processes;
     }
 
+    bool TestData::IsPythonTest() const
+    {
+        return m_pythonTest;
+    }
+
     std::string TestData::GetMetricType(unsigned int pId) const
     {
         ASSERTL0(pId < m_metrics.size(), "Metric ID out of range.");
@@ -147,10 +152,16 @@ namespace Nektar
             tmp = testElement->FirstChildElement("executable");
             ASSERTL0(tmp, "Cannot find 'executable' for test.");
             m_executable = fs::path(tmp->GetText());
+
+            // Test to see if this test requires Python
+            std::string needsPython;
+            tmp->QueryStringAttribute("python", &needsPython);
+            m_pythonTest = needsPython == "true";
+
 #if defined(RELWITHDEBINFO)
-            m_executable += "-rg";
+            m_executable += m_pythonTest ? "" : "-rg";
 #elif !defined(NDEBUG)
-            m_executable += "-g";
+            m_executable += m_pythonTest ? "" : "-g";
 #endif
         }
 

tests/TestData.h

@@ -65,6 +65,7 @@ namespace Nektar
         const fs::path&    GetExecutable() const;
         const std::string& GetParameters() const;
         const unsigned int& GetNProcesses() const;
+        bool IsPythonTest() const;
 
         std::string GetMetricType(unsigned int pId) const;
         unsigned int GetNumMetrics() const;
@@ -85,6 +86,7 @@ namespace Nektar
         TiXmlDocument*                  m_doc;
         std::vector<TiXmlElement*>      m_metrics;
         std::vector<DependentFile>      m_files;
+        bool                            m_pythonTest;
 
         void Parse(TiXmlDocument* pDoc);
     };

tests/Tester.cpp.in

@@ -198,13 +198,15 @@ int main(int argc, char *argv[])
             fs::copy_file(source, dest);
         }
 
+        // If we're Python, copy script too.
+
         // Construct test command to run. If in debug mode, append "-g"
         // Output from stdout and stderr are directed to the files output.out
         // and output.err, respectively.
 
 #ifdef NEKTAR_TEST_FORCEMPIEXEC
 #else
-	    if (file.GetNProcesses() > 1)
+        if (file.GetNProcesses() > 1)
 #endif
         {
             command += "@MPIEXEC@ @MPIEXEC_NUMPROC_FLAG@ "
@@ -220,9 +222,16 @@ int main(int argc, char *argv[])
         fs::path execPath = startDir / file.GetExecutable();
         if (!fs::exists(execPath))
         {
+            ASSERTL0(!file.IsPythonTest(), "Python script not found.");
             execPath = file.GetExecutable();
         }
 
+        if (file.IsPythonTest())
+        {
+            command += "PYTHONPATH=\"@BUILD_PATH\" ";
+            command += "python ";
+        }
+
         command += PortablePath(execPath);
         command += " ";
         command += file.GetParameters();