RangeShifter 3.0 merge (develop into main)

.gitignore

@@ -15,6 +15,7 @@ build-Release/
 *.workspace
 *.mk
 *.tags
+/build/
 
 # Hidden source
 /RangeShiftR/src/.*

RandomCheck.h → Allele.h

@@ -1,40 +1,36 @@
+#ifndef ALLELEH
+#define ALLELEH
+
 /*----------------------------------------------------------------------------
- *	
- *	Copyright (C) 2020 Greta Bocedi, Stephen C.F. Palmer, Justin M.J. Travis, Anne-Kathleen Malchow, Damaris Zurell 
- *	
+ *
+ *	Copyright (C) 2026 Greta Bocedi, Stephen C.F. Palmer, Justin M.J. Travis, Anne-Kathleen Malchow, Roslyn Henry, Théo Pannetier, Jette Wolff, Damaris Zurell
+ *
  *	This file is part of RangeShifter.
- *	
+ *
  *	RangeShifter is free software: you can redistribute it and/or modify
  *	it under the terms of the GNU General Public License as published by
  *	the Free Software Foundation, either version 3 of the License, or
  *	(at your option) any later version.
- *	
+ *
  *	RangeShifter is distributed in the hope that it will be useful,
  *	but WITHOUT ANY WARRANTY; without even the implied warranty of
  *	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  *	GNU General Public License for more details.
- *	
+ *
  *	You should have received a copy of the GNU General Public License
  *	along with RangeShifter. If not, see <https://www.gnu.org/licenses/>.
- *	
+ *
+ * File Created by Roslyn Henry March 2023. Code adapted from NEMO (https://nemo2.sourceforge.io/)
  --------------------------------------------------------------------------*/
-
-
-//---------------------------------------------------------------------------
-
-#ifndef RandomCheckH
-#define RandomCheckH
-
-#include <fstream>
-using namespace std;
-
-#include "Parameters.h"
-#include "RSrandom.h"
-
-void randomCheck(void);
 
-extern paramSim *paramsSim;
-extern RSrandom *pRandom;
 
-//---------------------------------------------------------------------------
+class Allele {
+	const float value;
+	const float dominance;
+public:
+	Allele(float alleleValue, float alleleDominance) : value(alleleValue), dominance(alleleDominance) { }
+	~Allele() {}
+	float getAlleleValue() const { return value; };
+	float getDominanceCoef() const { return dominance; };
+};
 #endif

CMakeLists.txt

@@ -1,30 +1,35 @@
 # Config file for compilation with CMake
 
-if (NOT batchmode) # that is, RScore as a standalone
+if(NOT batchmode) # that is, RScore as a standalone
 	cmake_minimum_required(VERSION 3.10)
 	# set the project name and version
-	project(RScore VERSION 2.1.0)
+	project(RScore VERSION 3.0.0)
 	# specify the C++ standard
-	set(CMAKE_CXX_STANDARD 17)
+	set(CMAKE_CXX_STANDARD 20)
 	set(CMAKE_CXX_STANDARD_REQUIRED True)
-	add_executable(RScore Main.cpp 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 Utils.cpp)
+
+	add_executable(RScore Main.cpp Species.cpp Cell.cpp Community.cpp FractalGenerator.cpp GeneticFitnessTrait.cpp Individual.cpp Landscape.cpp Management.cpp Model.cpp NeutralStatsManager.cpp Parameters.cpp Patch.cpp Population.cpp DispersalTrait.cpp RSrandom.cpp NeutralTrait.cpp SpeciesTrait.cpp SubCommunity.cpp Utils.cpp "unit_tests/testIndividual.cpp" "unit_tests/testNeutralStats.cpp" "unit_tests/testPopulation.cpp")
+
+	# turn on unit tests
+	add_compile_definitions("UNIT_TESTS")
 else() # that is, RScore compiled as library within RangeShifter_batch
-	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 Utils.cpp)
+
+	add_library(RScore Species.cpp Cell.cpp Community.cpp FractalGenerator.cpp GeneticFitnessTrait.cpp Individual.cpp Landscape.cpp Management.cpp Model.cpp NeutralStatsManager.cpp Parameters.cpp Patch.cpp Population.cpp DispersalTrait.cpp RSrandom.cpp NeutralTrait.cpp SpeciesTrait.cpp SubCommunity.cpp Utils.cpp)
 endif()
 
-# pass config definitions to compiler
-target_compile_definitions(RScore PRIVATE RSWIN64)
+if(OMP)
+	find_package(OpenMP COMPONENTS CXX)
+	if(OpenMP_CXX_FOUND)
+		target_link_libraries(RScore PUBLIC OpenMP::OpenMP_CXX)
+	endif()
+endif()
 
 # enable LINUX_CLUSTER macro on Linux + macOS
 if(CMAKE_SYSTEM_NAME STREQUAL "Linux" OR CMAKE_SYSTEM_NAME STREQUAL "Darwin")
 	add_compile_definitions("LINUX_CLUSTER")
 endif()
 
-# Debug Mode by default, unless "release" is passed
-if(NOT DEFINED release)
-	add_compile_definitions(RSDEBUG)
-endif()
 
 if(NOT batchmode)
 	target_include_directories(RScore PUBLIC "${PROJECT_BINARY_DIR}")
-endif() 
+endif()

CONTRIBUTING.md

@@ -17,7 +17,7 @@ RangeShifter is distributed with three user interfaces, each living in their own
 
 All three share the same source code for the core simulation (i.e., the actual model), which lives in this repo (RScore). Each of the interfaces keeps a copy of this core code in a subfolder called RScore, kept in sync with the RScore repo via a git subtree (see Git subtree usage section). 
 
-⚠️ If you wish to propose a change to one of the interfaces, please do so in the corresponding repo: [RangeShifter batch mode](https://github.com/RangeShifter/RangeShifter_batch_dev), [RangeShiftR package](https://github.com/RangeShifter/RangeShiftR-package-dev).
+⚠ If you wish to propose a change to one of the interfaces, please do so in the corresponding repo: [RangeShifter batch mode](https://github.com/RangeShifter/RangeShifter_batch_dev), [RangeShiftR package](https://github.com/RangeShifter/RangeShiftR-package-dev).
 
 *The RangeShifter GUI is currently being rewritten, and is not open source yet.
 
@@ -26,7 +26,7 @@ All three share the same source code for the core simulation (i.e., the actual m
 #### Maintainers
 
 - [@JetteReeg](https://github.com/JetteReeg): RScore repo and lead in R package
-- [@TheoPannetier](https://github.com/TheoPannetier): RScore repo and lead in batch mode
+
 
 Maintainers are responsible for coordinating development efforts and ensuring that RangeShifter keeps building continuously.
 
@@ -61,12 +61,17 @@ In the meantime, we encourage contributors to work in small and frequent commits
 
 Any changes regarding the RangeShifter core code should be done in this repository and can afterwards be synced with all interfaces using the git subtree feature (see [Git subtree](https://github.com/RangeShifter/RScore/tree/main?tab=readme-ov-file#usage-git-subtree) section in the README). 
 
+
 #### Bugs
 
-To report a bug, please [open an issue](https://github.com/RangeShifter/RangeShiftR-package-dev/issues/new), using the Bug Report template. 
-Please do check if a related issue has already open on one of the other interfaces ([here](https://github.com/RangeShifter/RangeShifter_batch-dev/issues) for the batch interface or [here](https://github.com/RangeShifter/RangeShiftR-package-dev) for the R package interface).
+To report a bug, please [open an issue](https://github.com/RangeShifter/RangeShiftR-package/issues/new), using the Bug Report template. 
+Please do check if a related issue has already open on one of the other interfaces ([here](https://github.com/RangeShifter/RangeShifter_batch/issues) for the batch interface or [here](https://github.com/RangeShifter/RangeShiftR-package) for the R package interface).
+
 To propose a bug fix (thank you!!), please create and work on your own branch or fork, from either `main` or `develop` (preferred), and open a pull request when your fix is ready to be merged into the original branch.
 
+As a prerequisite for merging, please ensure that your version passes status check (that is, RScore can still build, and all unit tests are still satisfied). 
+This can be seen in the Actions panel for every commit and at the bottom of the pull request.
+
 Maintainers will review the pull request, possibly request changes, and eventually integrate the bug fix into RScore, and update the subtrees to bring the fix to all interfaces.
 
 #### New features