Merge pull request #254 from xylar/build_with_cmake

Several small fixes to support conda-forge

When I tried to build the `mpas_tools` package on conda-forge, I ran into 3 issues:
* compilers (g++ for linux and clang for OSX) don't work well with our simple make file
* in clang, there is a conflict between `std::merge` and the local definition of `merge` in the cell culler (and probably the same issue in g++ but not a fatal error).
* The test for the python interface to the mesh conversion tools needs to use the 'Agg' backend for matplotlib because CI doesn't have a display.

This merge adds support for a cmake build of `mesh_conversion_tools` and fixes the other two issues above in the hopes of making another minor release that will work without patching on conda-forge.

Author: xylar

conda_package/docs/conf.py

@@ -63,9 +63,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.0.1'
+version = u'0.0.2'
 # The full version, including alpha/beta/rc tags.
-release = u'0.0.1'
+release = u'0.0.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

conda_package/mpas_tools/tests/test_conversion.py

@@ -2,6 +2,8 @@
 
 from mpas_tools.conversion import convert, cull, mask
 from mpas_tools.io import write_netcdf
+import matplotlib
+matplotlib.use('Agg')
 from geometric_features import read_feature_collection
 import xarray
 

conda_package/recipe/build.sh

@@ -10,14 +10,10 @@ ${PYTHON} -m pip install . --no-deps -vv
 
 cd mesh_tools/mesh_conversion_tools
 
-export CXX=${GXX}
-export CFLAGS="-O3 -std=c++0x -fopenmp -lstdc++"
-
+# build and install JIGSAW
+mkdir build
+cd build
+cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_BUILD_TYPE=Release ..
 make
-
-install -d ${PREFIX}/bin/
-for exec in MpasMeshConverter.x MpasCellCuller.x MpasMaskCreator.x
-do
-  install -m 755 ${exec} ${PREFIX}/bin/
-done
+make install
 

conda_package/recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "mpas_tools" %}
-{% set version = "0.0.1" %}
+{% set version = "0.0.2" %}
 
 package:
   name: '{{ name|lower }}'
@@ -17,6 +17,7 @@ build:
 requirements:
   build:
     - {{ compiler('cxx') }}
+    - cmake
   host:
     - python
     - hdf5

conda_package/setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import setup, find_packages
 
-version = '0.0.1'
+version = '0.0.2'
 
 setup(name='mpas_tools',
       version=version,

mesh_tools/mesh_conversion_tools/CMakeLists.txt

@@ -0,0 +1,19 @@
+cmake_minimum_required (VERSION 3.0.2)
+project (mesh_conversion_tools)
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
+
+include_directories (netcdf-cxx-4.2 .)
+
+set(SOURCES netcdf_utils.cpp netcdf-cxx-4.2/ncvalues.cpp netcdf-cxx-4.2/netcdf.cpp)
+
+add_executable (MpasMeshConverter.x mpas_mesh_converter.cpp ${SOURCES})
+target_link_libraries (MpasMeshConverter.x netcdf)
+
+add_executable (MpasCellCuller.x mpas_cell_culler.cpp ${SOURCES})
+target_link_libraries (MpasCellCuller.x netcdf)
+
+add_executable (MpasMaskCreator.x mpas_mask_creator.cpp jsoncpp.cpp ${SOURCES})
+target_link_libraries (MpasMaskCreator.x netcdf)
+
+install (TARGETS MpasMeshConverter.x MpasCellCuller.x MpasMaskCreator.x DESTINATION bin)

mesh_tools/mesh_conversion_tools/mpas_cell_culler.cpp

@@ -16,7 +16,7 @@
 
 using namespace std;
 
-enum { merge, invert, preserve };
+enum { mergeOp, invertOp, preserveOp };
 
 int nCells, nVertices, nEdges, vertexDegree, maxEdges;
 bool spherical, periodic;
@@ -155,13 +155,13 @@ int main ( int argc, char *argv[] ) {
 		for ( int i = 3; i < argc; i+=2 ) {
 			foundOperation = false;
 			if (strcmp(argv[i], "-m") == 0 ) {
-				mask_ops.push_back(static_cast<int>(merge));
+				mask_ops.push_back(static_cast<int>(mergeOp));
 				foundOperation = true;
 			} else if ( strcmp(argv[i], "-i") == 0 ){
-				mask_ops.push_back(static_cast<int>(invert));
+				mask_ops.push_back(static_cast<int>(invertOp));
 				foundOperation = true;
 			} else if ( strcmp(argv[i], "-p") == 0 ){
-				mask_ops.push_back(static_cast<int>(preserve));
+				mask_ops.push_back(static_cast<int>(preserveOp));
 				foundOperation = true;
 			} else if ( strcmp(argv[i], "-c") == 0 ){
 				outputMap = true;
@@ -471,8 +471,8 @@ int mergeCellMasks(const string masksFilename, const int maskOp){/*{{{*/
 		}
 	}
 
-	if ( maskOp == invert || maskOp == merge ) {
-		if ( maskOp == invert ) {
+	if ( maskOp == invertOp || maskOp == mergeOp ) {
+		if ( maskOp == invertOp ) {
 			for (i = 0; i < nCells; i++){
 				flattenedMask[i] = (flattenedMask[i] + 1) % 2;
 			}
@@ -481,7 +481,7 @@ int mergeCellMasks(const string masksFilename, const int maskOp){/*{{{*/
 		for ( i = 0; i < nCells; i++ ){
 			cullCell[i] = max(cullCell[i], flattenedMask[i]);
 		}
-	} else if ( maskOp == preserve ) {
+	} else if ( maskOp == preserveOp ) {
 		for ( i = 0; i < nCells; i++ ) {
 			if ( flattenedMask[i] && cullCell[i] ) {
 				cullCell[i] = 0;
@@ -614,21 +614,21 @@ int outputGridDimensions( const string outputFilename ){/*{{{*/
 	int nCellsNew, nEdgesNew, nVerticesNew;
 	// Return this code to the OS in case of failure.
 	static const int NC_ERR = 2;
-	
+
 	// set error behaviour (matches fortran behaviour)
 	NcError err(NcError::verbose_nonfatal);
-	
+
 	// open the scvtmesh file
 	NcFile grid(outputFilename.c_str(), NcFile::Replace, NULL, 0, NcFile::Offset64Bits);
 
 	/*
 	for(vec_int_itr = edgesOnCell.begin(); vec_int_itr != edgesOnCell.end(); ++vec_int_itr){
-		maxEdges = std::max(maxEdges, (int)(*vec_int_itr).size());	
+		maxEdges = std::max(maxEdges, (int)(*vec_int_itr).size());
 	}*/
-	
+
 	// check to see if the file was opened
 	if(!grid.is_valid()) return NC_ERR;
-	
+
 	// define dimensions
 	NcDim *nCellsDim;
 	NcDim *nEdgesDim;
@@ -652,7 +652,7 @@ int outputGridDimensions( const string outputFilename ){/*{{{*/
 	for(int iEdge = 0; iEdge < nEdges; iEdge++){
 		nEdgesNew += (edgeMap.at(iEdge) != -1);
 	}
-	
+
 	// write dimensions
 	if (!(nCellsDim =		grid.add_dim(	"nCells",		nCellsNew)		)) return NC_ERR;
 	if (!(nEdgesDim =		grid.add_dim(	"nEdges",		nEdgesNew)		)) return NC_ERR;
@@ -662,7 +662,7 @@ int outputGridDimensions( const string outputFilename ){/*{{{*/
 	if (!(timeDim = 		grid.add_dim(   "Time")							)) return NC_ERR;
 
 	grid.close();
-	
+
 	// file closed when file obj goes out of scope
 	return 0;
 }/*}}}*/
@@ -675,10 +675,10 @@ int outputGridAttributes( const string inputFilename, const string outputFilenam
 	 * **********************************************************************/
 	// Return this code to the OS in case of failure.
 	static const int NC_ERR = 2;
-	
+
 	// set error behaviour (matches fortran behaviour)
 	NcError err(NcError::verbose_nonfatal);
-	
+
 	// open the scvtmesh file
 	NcFile grid(outputFilename.c_str(), NcFile::Write);
 
@@ -689,7 +689,7 @@ int outputGridAttributes( const string inputFilename, const string outputFilenam
 	string history_str = "";
 	string id_str = "";
 	string parent_str = "";
-	
+
 	// write attributes
 	if(!spherical){
 		if (!(sphereAtt = grid.add_att(   "on_a_sphere", "NO\0"))) return NC_ERR;
@@ -734,7 +734,7 @@ int outputGridAttributes( const string inputFilename, const string outputFilenam
 	if (!(id = grid.add_att(   "file_id", id_str.c_str() ))) return NC_ERR;
 
 	grid.close();
-	
+
 	// file closed when file obj goes out of scope
 	return 0;
 }/*}}}*/
@@ -749,16 +749,16 @@ int mapAndOutputGridCoordinates( const string inputFilename, const string output
 	 * **********************************************************************/
 	// Return this code to the OS in case of failure.
 	static const int NC_ERR = 2;
-	
+
 	// set error behaviour (matches fortran behaviour)
 	NcError err(NcError::verbose_nonfatal);
-	
+
 	// open the scvtmesh file
 	NcFile grid(outputFilename.c_str(), NcFile::Write);
-	
+
 	// check to see if the file was opened
 	if(!grid.is_valid()) return NC_ERR;
-	
+
 	// fetch dimensions
 	NcDim *nCellsDim = grid.get_dim( "nCells" );
 	NcDim *nEdgesDim = grid.get_dim( "nEdges" );
@@ -774,7 +774,7 @@ int mapAndOutputGridCoordinates( const string inputFilename, const string output
 	NcVar *idx2cellVar, *idx2edgeVar, *idx2vertexVar;
 
 	int i, idx_map;
-	
+
 	double *xOld, *yOld, *zOld, *latOld, *lonOld;
 	double *xNew, *yNew, *zNew, *latNew, *lonNew;
 	int *idxToNew;
@@ -833,7 +833,7 @@ int mapAndOutputGridCoordinates( const string inputFilename, const string output
 	delete[] latNew;
 	delete[] lonNew;
 	delete[] idxToNew;
-	
+
 	//Build and write edge coordinate arrays
 	xOld = new double[nEdges];
 	yOld = new double[nEdges];
@@ -964,16 +964,16 @@ int mapAndOutputCellFields( const string inputFilename, const string outputFilen
 	 * ***************************************************************/
 	// Return this code to the OS in case of failure.
 	static const int NC_ERR = 2;
-	
+
 	// set error behaviour (matches fortran behaviour)
 	NcError err(NcError::verbose_nonfatal);
-	
+
 	// open the scvtmesh file
 	NcFile grid(outputFilename.c_str(), NcFile::Write);
-	
+
 	// check to see if the file was opened
 	if(!grid.is_valid()) return NC_ERR;
-	
+
 	// fetch dimensions
 	NcDim *nCellsDim = grid.get_dim( "nCells" );
 	NcDim *nEdgesDim = grid.get_dim( "nEdges" );
@@ -993,7 +993,7 @@ int mapAndOutputCellFields( const string inputFilename, const string outputFilen
 	double *areaCellNew;
 	int *tmp_arr_old, *nEdgesOnCellOld, *nEdgesOnCellNew;
 	int *tmp_arr_new;
-	
+
 	tmp_arr_old = new int[nCells*maxEdges];
 	nEdgesOnCellOld = new int[nCells];
 	nEdgesOnCellNew = new int[nCellsNew];
@@ -1106,7 +1106,7 @@ int mapAndOutputCellFields( const string inputFilename, const string outputFilen
 	delete[] tmp_arr_new;
 
 	// Map areaCell
-	areaCellNew = new double[nCellsNew]; 
+	areaCellNew = new double[nCellsNew];
 
 	for(int iCell = 0; iCell < nCells; iCell++){
 		if(cellMap.at(iCell) != -1){
@@ -1154,16 +1154,16 @@ int mapAndOutputEdgeFields( const string inputFilename, const string outputFilen
 	 * ***************************************************************/
 	// Return this code to the OS in case of failure.
 	static const int NC_ERR = 2;
-	
+
 	// set error behaviour (matches fortran behaviour)
 	NcError err(NcError::verbose_nonfatal);
-	
+
 	// open the scvtmesh file
 	NcFile grid(outputFilename.c_str(), NcFile::Write);
-	
+
 	// check to see if the file was opened
 	if(!grid.is_valid()) return NC_ERR;
-	
+
 	// fetch dimensions
 	NcDim *nEdgesDim = grid.get_dim( "nEdges" );
 	NcDim *maxEdges2Dim = grid.get_dim( "maxEdges2" );
@@ -1265,7 +1265,7 @@ int mapAndOutputEdgeFields( const string inputFilename, const string outputFilen
 #endif
 		}
 	}
-	
+
 	if (!(voeVar = grid.add_var("verticesOnEdge", ncInt, nEdgesDim, twoDim))) return NC_ERR;
 	if (!voeVar->put(verticesOnEdgeNew,nEdgesNew,2)) return NC_ERR;
 	if (!(coeVar = grid.add_var("cellsOnEdge", ncInt, nEdgesDim, twoDim))) return NC_ERR;
@@ -1394,16 +1394,16 @@ int mapAndOutputVertexFields( const string inputFilename, const string outputFil
 	 * ***************************************************************/
 	// Return this code to the OS in case of failure.
 	static const int NC_ERR = 2;
-	
+
 	// set error behaviour (matches fortran behaviour)
 	NcError err(NcError::verbose_nonfatal);
-	
+
 	// open the scvtmesh file
 	NcFile grid(outputFilename.c_str(), NcFile::Write);
-	
+
 	// check to see if the file was opened
 	if(!grid.is_valid()) return NC_ERR;
-	
+
 	// fetch dimensions
 	NcDim *nVerticesDim = grid.get_dim( "nVertices" );
 	NcDim *vertexDegreeDim = grid.get_dim( "vertexDegree" );