Merge pull request #17 from RangeShifter/cmake

Use Cmake

.gitignore

@@ -0,0 +1,87 @@
+.gitignore
+#README.md
+
+# CodeLite
+/.build-debug/
+/Debug/
+/Release/
+/RNG_test/
+.codelite/
+compile_commands.json
+Makefile
+.build-release/
+build-Release/
+*.project
+*.workspace
+*.mk
+*.tags
+
+# Hidden source
+/RangeShiftR/src/.*
+
+# Windows files
+/RangeShiftR/src/*.dll
+
+# History files
+.Rhistory
+.Rapp.history
+
+# RStudio files
+.Rproj.user/
+/RangeShiftR/.Rproj.user/
+#/RangeShiftR/RangeShiftR.Rproj
+/RangeShiftR/Read-and-delete-me
+/RangeShiftR/.Rhistory
+#/RangeShiftR/.Rbuildignore
+
+# Session Data files
+.RData
+tags
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+*.tar.gz
+/RangeShiftR/src/*.o
+/RangeShiftR/src/RangeShiftR.so
+
+
+# Windows files
+/RangeShiftR/src/*.dll
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# Output from Rcpp compile.attributes()
+#/RangeShiftR/R/RcppExports.R
+#/RangeShiftR/src/RcppExports.cpp
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+#/RangeShiftR/man/
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# compilation files
+*.o
+
+# Visual Studio
+.vs/
+out/

CMakeLists.txt

@@ -0,0 +1,11 @@
+# Config file for compilation with CMake
+# Only relevant for Batch mode, but this file needs to live in the RScore folder
+
+add_library(RScore Species.cpp Cell.cpp Community.cpp FractalGenerator.cpp Genome.cpp Individual.cpp Landscape.cpp Model.cpp Parameters.cpp Patch.cpp Population.cpp RandomCheck.cpp RSrandom.cpp SubCommunity.cpp)
+
+# pass config definitions to compiler
+if(CMAKE_SYSTEM_NAME STREQUAL "Linux" OR CMAKE_SYSTEM_NAME STREQUAL "Darwin")
+	target_compile_definitions(RScore PRIVATE "RSDEBUG" "RSWIN64" "LINUX_CLUSTER")
+else() # Windows
+	target_compile_definitions(RScore PRIVATE "RSDEBUG" "RSWIN64")
+endif()

Community.cpp

@@ -1700,8 +1700,8 @@ Rcpp::IntegerMatrix Community::addYearToPopList(int rep, int yr) {  // TODO: def
 					} else {
 						pSubComm = (SubCommunity*)subcomm;
 						pop = pSubComm->getPopStats();
-						//pop_map_year(ppLand.dimY-1-y,x) = pop.nInds; // use indices like this because matrix gets transposed upon casting it into a raster on R-level
-						pop_map_year(ppLand.dimY-1-y,x) = pop.nAdults;
+						pop_map_year(ppLand.dimY-1-y,x) = pop.nInds; // use indices like this because matrix gets transposed upon casting it into a raster on R-level
+						//pop_map_year(ppLand.dimY-1-y,x) = pop.nAdults;
 					}
 				}
 			}

Community.h

@@ -52,9 +52,9 @@ Last updated: 25 June 2021 by Anne-Kathleen Malchow
 #include <vector>
 #include <algorithm>
 using namespace std;
-//#if RS_RCPP && !R_CMD
+#if RS_RCPP
 #include "../Version.h"
-//#endif
+#endif
 
 //#if !RS_RCPP && R_CMD
 //#include "../../Batch/Version.h"

Model.cpp

@@ -152,17 +152,10 @@ DEBUGLOG << endl << "RunModel(): generating new landscape ..." << endl;
 DEBUGLOG << "RunModel(): finished resetting landscape" << endl << endl;
 #endif
 		pLandscape->generatePatches();
-//#if VCL
 		if (v.viewLand || sim.saveMaps) {
 			pLandscape->setLandMap();
 			pLandscape->drawLandscape(rep,0,ppLand.landNum);
 		}
-//#endif
-//#if BATCH
-//		if (sim.saveMaps) {
-//			pLandscape->drawLandscape(rep,0,ppLand.landNum);
-//		}
-//#endif
 #if RSDEBUG
 DEBUGLOG << endl << "RunModel(): finished generating patches" << endl;
 #endif
@@ -313,12 +306,8 @@ DEBUGLOG << "RunModel(): completed updating carrying capacity" << endl;
 DEBUGLOG << "RunModel(): completed initialisation, rep=" << rep
 	<< " pSpecies=" << pSpecies << endl;
 #endif
-#if BATCH
-#if RS_RCPP && !R_CMD
+#if BATCH && RS_RCPP && !R_CMD
 	Rcpp::Rcout << "RunModel(): completed initialisation " << endl;
-#else
-	cout << "RunModel(): completed initialisation " << endl;
-#endif
 #endif
 
 	// open a new individuals file for each replicate
@@ -926,7 +915,7 @@ return errorfolder;
 //For outputs and population visualisations pre-reproduction
 void PreReproductionOutput(Landscape *pLand,Community *pComm,int rep,int yr,int gen)
 {
-#if RSDEBUG || VCL
+#if RSDEBUG
 landParams ppLand = pLand->getLandParams();
 #endif
 simParams sim = paramsSim->getSim();
@@ -1341,22 +1330,6 @@ if (dem.stageStruct){
 			outPar << endl;
 		}
 	}
-#if VCL
-	else {
-
-	// NOTE: TO PREVENT COMPILING FOR BATCH MODE, THIS CODE NEEDS TO BE INCLUDED IN COMPILER
-	// CONDITIONAL BLOCK  AS SHOWN
-
-//	outPar << "Row count: " << frmSpecies->transMatrix->RowCount << endl;
-//	outPar << "Col count: " << frmSpecies->transMatrix->ColCount << endl;
-		for (int i = 1; i < frmSpecies->transMatrix->RowCount; i++) {
-			for (int j = 1; j < frmSpecies->transMatrix->ColCount; j++) {
-				outPar << frmSpecies->transMatrix->Cells[j][i].ToDouble() << "\t";
-			}
-			outPar << endl;
-		}
-	}
-#endif
 	outPar << endl;
 #endif
 */

Model.h

@@ -49,9 +49,9 @@ Last updated: 26 October 2021 by Steve Palmer
 #include <sys/types.h>
 #include <sys/stat.h>
 
-//#if RS_RCPP && !R_CMD
+#if RS_RCPP
 #include "../Version.h"
-//#endif
+#endif
 
 //#if !RS_RCPP && R_CMD
 //#include "../../Batch/Version.h"
@@ -75,12 +75,12 @@ extern ofstream DEBUGLOG;
 #if RS_RCPP && !R_CMD
 Rcpp::List RunModel(
 	Landscape*,	// pointer to Landscape
-	int					// sequential simulation number (always 0 for VCL version)
+	int					// sequential simulation number
 );
 #else
 int RunModel(
 	Landscape*,	// pointer to Landscape
-	int					// sequential simulation number (always 0 for VCL version)
+	int					// sequential simulation number
 );
 #endif // RS_RCPP && !R_CMD
 bool CheckDirectory(void);
@@ -125,11 +125,11 @@ extern Community *pComm;
 const bool batchMode = true;
 extern string landFile;
 extern vector <string> hfnames;
-extern string habmapname;		// see FormLand.cpp (VCL) OR Main.cpp (batch)
-extern string patchmapname;	// see FormLand.cpp (VCL) OR Main.cpp (batch)
-extern string distnmapname;	// see FormLand.cpp (VCL) OR Main.cpp (batch)
-extern string costmapname;	// see FormMove.cpp (VCL) OR Main.cpp (batch)
-extern string genfilename;	// see FormGenetics.cpp (VCL) OR Main.cpp (batch)
+extern string habmapname;		// see Main.cpp (batch)
+extern string patchmapname;	// see Main.cpp (batch)
+extern string distnmapname;	// see Main.cpp (batch)
+extern string costmapname;	// see Main.cpp (batch)
+extern string genfilename;	// see Main.cpp (batch)
 extern RSrandom *pRandom;
 
 // these functions to have different version for GUI and batch applications ...

Parameters.h

@@ -60,9 +60,9 @@ Last updated: 25 June 2021 by Steve Palmer
 #include <stdlib.h>
 #include <vector>
 using namespace std;
-//#if RS_RCPP && !R_CMD
+#if RS_RCPP
 #include "../Version.h"
-//#endif
+#endif
 
 //#if !RS_RCPP && R_CMD
 //#include "../../Batch/Version.h"

Patch.h

@@ -68,9 +68,9 @@ Last updated: 25 June 2021 by Steve Palmer
 #include <vector>
 using namespace std;
 
-//#if RS_RCPP && !R_CMD
+#if RS_RCPP
 #include "../Version.h"
-//#endif
+#endif
 
 //#if !RS_RCPP && R_CMD
 //#include "../../Batch/Version.h"

Population.cpp

@@ -433,12 +433,6 @@ void Population::reproduction(const float localK,const float envval,const int re
 int ninds = (int)inds.size();
 #if RSDEBUG
 //DEBUGLOG << "Population::reproduction(): this=" << this
-//#if BUTTERFLYDISP
-//	<< " option=" << option
-//#endif // BUTTERFLYDISP 
-//#if RS_CONTAIN
-//	<< " hab=" << hab
-//#endif // RS_CONTAIN 
 //	<< " ninds=" << ninds
 //	<< endl;
 #endif // RSDEBUG 
@@ -464,12 +458,8 @@ if (dem.repType == 0) nsexes = 1; else nsexes = 2;
 
 #if RSDEBUG
 //DEBUGLOG << "Population::reproduction(): this=" << this
-//#if RS_CONTAIN
-//	<< " hab=" << hab
-//#else
 //	<< " pSpecies=" << pSpecies
 //	<< " localK=" << localK << " envval=" << envval << " resol=" << resol
-//#endif // RS_CONTAIN 
 //	<< " sstruct.nStages=" << sstruct.nStages << " nsexes=" << nsexes << " ninds=" << ninds
 //	<< endl;
 #endif

RSrandom.h

@@ -40,9 +40,9 @@ Last updated: 12 January 2021 by Steve Palmer
 #include <fstream>
 //#include <iostream>
 
-//#if RS_RCPP && !R_CMD
+#if RS_RCPP
 #include "../Version.h"
-//#endif
+#endif
 
 //#if !RS_RCPP && R_CMD
 //#include "../../Batch/Version.h"

RandomCheck.h

@@ -28,9 +28,9 @@
 #include <fstream>
 using namespace std;
 
-//#if RS_RCPP && !R_CMD
+#if RS_RCPP
 #include "../Version.h"
-//#endif
+#endif
 
 //#if !RS_RCPP && R_CMD
 //#include "../../Batch/Version.h"

Species.h

@@ -45,9 +45,9 @@ Last updated: 28 July 2021 by Greta Bocedi
 #ifndef SpeciesH
 #define SpeciesH
 
-//#if RS_RCPP && !R_CMD
+#if RS_RCPP
 #include "../Version.h"
-//#endif
+#endif
 
 //#if !RS_RCPP && R_CMD
 //#include "../../Batch/Version.h"

SubCommunity.h

@@ -50,9 +50,9 @@ Last updated: 26 October 2021 by Steve Palmer
 #include <algorithm>
 using namespace std;
 
-//#if RS_RCPP && !R_CMD
+#if RS_RCPP
 #include "../Version.h"
-//#endif
+#endif
 
 //#if !RS_RCPP && R_CMD
 //#include "../../Batch/Version.h"