Merge commit 'ab4dc2cb0b2d165d439415271d01d798ae72afea' into new_gene…

…tics

src/RScore/.github/workflows/check.yml

@@ -0,0 +1,26 @@
+name: check
+on: push
+
+jobs:
+  check:
+    strategy:
+      matrix:
+        os: [windows-latest, ubuntu-latest, macos-latest]
+        include:
+          - os: windows-latest
+            path_to_exe: ./build/Debug/RScore.exe
+          - os: ubuntu-latest
+            path_to_exe: ./build/RScore
+          - os: macos-latest
+            path_to_exe: ./build/RScore
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: build
+        run: |
+          mkdir build && cd build
+          cmake ../ && cmake --build .
+          
+      - name: run
+        run: ${{ matrix.path_to_exe }}

src/RScore/Allele.h

@@ -11,6 +11,6 @@ class Allele {
 	~Allele() {}
 	float getAlleleValue() const { return value; };
 	float getDominanceCoef() const { return dominance; };
-	float getId() const { return id; }
+	int getId() const { return id; }
 };
 #endif

src/RScore/CMakeLists.txt

@@ -1,11 +1,30 @@
 # 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 GeneticLoad.cpp Individual.cpp Landscape.cpp Model.cpp NeutralStatsManager.cpp Parameters.cpp Patch.cpp Population.cpp QTLTrait.cpp RSrandom.cpp SNPTrait.cpp SubCommunity.cpp)
+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)
+	# specify the C++ standard
+	set(CMAKE_CXX_STANDARD 20)
+	set(CMAKE_CXX_STANDARD_REQUIRED True)
+	add_executable(RScore Main.cpp Species.cpp Cell.cpp Community.cpp FractalGenerator.cpp GeneticLoad.cpp Individual.cpp Landscape.cpp Model.cpp NeutralStatsManager.cpp Parameters.cpp Patch.cpp Population.cpp QTLTrait.cpp RSrandom.cpp SNPTrait.cpp SpeciesTrait.cpp SubCommunity.cpp Utils.cpp)
+else() # that is, RScore compiled as library within RangeShifter_batch
+	add_library(RScore Species.cpp Cell.cpp Community.cpp FractalGenerator.cpp GeneticLoad.cpp Individual.cpp Landscape.cpp Model.cpp NeutralStatsManager.cpp Parameters.cpp Patch.cpp Population.cpp QTLTrait.cpp RSrandom.cpp SNPTrait.cpp SpeciesTrait.cpp SubCommunity.cpp Utils.cpp)
+endif()
 
 # pass config definitions to compiler
+target_compile_definitions(RScore PRIVATE RSWIN64)
+
+# enable LINUX_CLUSTER macro on Linux + macOS
 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")
+	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() 

src/RScore/CONTRIBUTING.md

@@ -0,0 +1,81 @@
+# The RangeShifter platform - An eco-evolutionary modelling framework
+
+## How to contribute
+
+Thank you for your interest in contributing to the RangeShifter platform. 
+In this document we will give you guidance on how to contribute to the RangeShifter project regarding issues, bug fixing and adding new features.
+
+## Repo structure
+
+![Rangeshifter repo structure](RS_repos.png)
+
+RangeShifter is distributed with three user interfaces, each living in their own repo:
+
+- the RangeShifter GUI (clickable Windows interface)*
+- RangeShifter Batch Mode (command line interface)
+- the RangeShiftR package (R interface)
+
+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).
+
+*The RangeShifter GUI is currently being rewritten, and is not open source yet.
+
+## Roles
+
+#### 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.
+
+#### Developers
+
+Regular contributors and members of the [RangeShifter development team](https://github.com/orgs/RangeShifter/people), including maintainers.
+
+#### Contributors
+
+Anyone who whishes to make changes to RangeShifter's code, including regular developers.
+
+## Branching policy
+
+![](branches.png)
+
+*Check out the [Git cheatsheet](https://github.com/RangeShifter/RScore/git_cheatsheet.md) for a reminder on the main git commands*
+
+This policy applies to RScore and all three RangeShifter interfaces.
+RangeShifter uses the following branching structure:
+
+- `main` is the default branch, where stable releases live. Because it contains the version of RangeShifter that users normally interact with, it must be stable and build at all times.
+Only maintainers should make significant changes to `main`, normally by merging `develop` into `main` to make newly developed features available to users, and marking a release while doing so.
+- `develop` is the development branch containing new, in-development features. It is the reference branch for all developers. Contributors may make small changes directly to `develop` but should ensure that new changes do not break the build. If one happens to break `develop`, it should be their top priority to fix it as this will disrupt the work of all other contributors.
+Larger changes should instead be developed on feature branches.
+- Larger changes should be first developed on feature (e.g. `cmake`, `mutualism`, etc.) or contributor (e.g., `theo`) branches. Contributors are welcome to experiment and break such branches at any time, as this will not impact users or other contributors.
+
+When progress is deemed satisfactory, changes can be brought to `develop`. Please open a pull request on GitHub, and assign at least one maintainer as a reviewer. As a pre-requisite, RangeShifter must build on the branch before merging. Please enter a descriptive title and use the description field to describe what you have changed. 
+
+In the meantime, we encourage contributors to work in small and frequent commits, and to merge `develop` into their branch often to update their branch with newest changes.
+
+### Contributing to RangeShifter core code
+
+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 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.
+
+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
+
+Do you have an idea of a new feature in the RangeShifter platform that should be integrated and is of use for other RangeShifter users? 
+Please get in touch with the RangeShifter development team ([email protected]) to discuss a collaboration.
+
+⚠️ We advise to contact the developer team as early as possible if you plan on implementing a new feature. This could prevent simultaneous development of the same feature and coordinate potential joint development.
+
+Alternatively, proceed as with the bug fix above: create your own branch or fork _from `develop`_ and work from there, and submit a pull request when your new features are ready to join the core code. 
+We recommend that you update your branch regularly to new changes on `develop` (using `git merge develop`) to reduce the risk of merge conflicts or your version getting out-of-touch in the late stages of development.
+We also recommend that you work in small commits, as this makes the code easier to debug, and makes it easier for maintainers to understand your contributions when reviewing a pull request.

src/RScore/Cell.cpp

@@ -59,18 +59,12 @@ Cell::Cell(int xx, int yy, intptr patch, float hab)
 }
 
 Cell::~Cell() {
-#if RSDEBUG
-	//DEBUGLOG << "Cell::~Cell(): this = " << this << " smsData = " << smsData << endl;
-#endif
 	habIxx.clear();
 	habitats.clear();
 	if (smsData != 0) {
 		if (smsData->effcosts != 0) delete smsData->effcosts;
 		delete smsData;
 	}
-#if RSDEBUG
-	//DEBUGLOG << "Cell::~Cell(): deleted" << endl;
-#endif
 }
 
 void Cell::setHabIndex(short hx) {
@@ -118,12 +112,6 @@ void Cell::setPatch(intptr p) {
 }
 intptr Cell::getPatch(void)
 {
-#if RSDEBUG
-	//DebugGUI(("Cell::getPatch(): this=" + Int2Str((int)this)
-	//	+ " x=" + Int2Str(x) + " y=" + Int2Str(y)
-	//	+ " habIxx[0]=" + Int2Str(habIxx[0]) + " pPatch=" + Int2Str(pPatch)
-	//).c_str());
-#endif
 	return pPatch;
 }