Merge branch 'main' into contributor-agreement

Author: Zeitsperre

.github/workflows/testing.yml

@@ -18,6 +18,7 @@ jobs:
       - name: Harden Runner
         uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
         with:
+          disable-sudo: false
           egress-policy: block
           allowed-endpoints: >
             azure.archive.ubuntu.com:80
@@ -30,6 +31,8 @@ jobs:
 
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        with:
+            persist-credentials: false
 
       - name: Install linters
         run: |
@@ -47,16 +50,17 @@ jobs:
   build-netcdf:
     name: Build (${{ matrix.build_type }}; ${{ matrix.os }}; NetCDF=True)
     needs: lint
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ ubuntu-latest, macos-latest ]
-        build_type: [ Debug, Release ]
+        os: [ "ubuntu-latest", "macos-latest" ]
+        build_type: [ "Debug", "Release" ]
     steps:
       - name: Harden Runner
         uses: step-security/harden-runner@17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6 # v2.8.1
         with:
-          disable-sudo: true
+          disable-sudo: false
           egress-policy: block
           allowed-endpoints: >
             azure.archive.ubuntu.com:80
@@ -68,29 +72,45 @@ jobs:
 
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        with:
+          persist-credentials: false
+
+      - name: Install NetCDF (Ubuntu/apt)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libnetcdf-dev
+      - name: Install NetCDF4 (macOS/homebrew)
+        if: (matrix.os == 'macos-latest') && (!matrix.conda)
+        uses: tecolicom/actions-use-homebrew-tools@b9c066b79607fa3d71e0be05d7003bb75fd9ff34 # v1.3.0
+        with:
+          tools: netcdf
+          cache: "yes"
 
       - name: Fetch NetCDF CMake script
         run: |
           wget https://raw.githubusercontent.com/Kitware/VTK/master/CMake/FindNetCDF.cmake -P cmake
 
       - name: Build
         id: build
-        continue-on-error: true
         run: |
-          cmake .
-          cmake --build . --config ${{ matrix.build_type }} -j 3
+          mkdir build
+          cd build
+          cmake ..
+          cmake --build . --config ${{ matrix.build_type }} -j 3 --verbose
 
       - name: Run tests
         if: steps.build.outcome == 'success'
         run: |
-          ./Raven
-          ./Raven -v
+          ./build/Raven
+          ./build/Raven -v
 
   build:
     name: Build (${{ matrix.build_type }}; ${{ matrix.os }}; NetCDF=False)
     needs: lint
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
         build_type: [ Debug, Release ]
@@ -113,19 +133,28 @@ jobs:
 
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        with:
+          persist-credentials: false
 
       - name: Install dependencies (Windows)
         if: matrix.os == 'windows-latest'
         uses: lukka/get-cmake@2bcb1a4c14ab154443cc740dced0f9b6a8fb2b59 # v3.29.6
 
       - name: Build
         id: build
-        continue-on-error: true
         run: |
-          cmake .
-          cmake --build . --config ${{ matrix.build_type }} -j 3
+          mkdir build
+          cd build
+          cmake ..
+          cmake --build . --config ${{ matrix.build_type }} -j 3 --verbose
 
-      - name: Run tests
+      - name: Run tests (Windows)
+        if: ${{ matrix.os == 'windows-latest' && steps.build.outcome == 'success' }}
+        run: |
+          ./build/${{ matrix.build_type }}/Raven.exe
+          ./build/${{ matrix.build_type }}/Raven.exe -v
+      - name: Run tests (Ubuntu/macOS)
+        if: ${{ matrix.os != 'windows-latest' && steps.build.outcome == 'success' }}
         run: |
-          ./Raven
-          ./Raven -v
+          ./build/Raven
+          ./build/Raven -v

.gitignore

@@ -41,3 +41,6 @@ Makefile
 # Runtime artifacts
 Raven
 Raven_errors.txt
+
+# JetBrains
+.idea

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     - id: check-json
     - id: pretty-format-json
@@ -26,7 +26,7 @@ repos:
 #      - id: include-what-you-use
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.28.6
+    rev: 0.30.0
     hooks:
       - id: check-github-workflows
   - repo: meta

CMakeLists.txt

@@ -1,11 +1,18 @@
 cmake_minimum_required(VERSION 3.20)
 # made with help from Zhu Liang-Jun of IGSNRR in Beijing
-# modified for GitHub by Trevor James Smith of Ouranos in Montreal
+# modified for GitHub and C++11 by Trevor James Smith of Ouranos in Montreal
+# modified for lpsolve support by Maxim Krassovski of DFO
+
+# Set the C++ standard to C++11
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+SET(CMAKE_CXX_EXTENSIONS OFF)
 
 # optional cmake command line arguments (e.g, "cmake -D COMPILE_LIB=ON" .)
 option(COMPILE_LIB "If ON, will create a dynamic lib file (default: OFF)" OFF)
 option(COMPILE_EXE "If ON, will create a executable file (default: ON)" ON)
 option(PYTHON, "If ON, will create a share library for python (default: OFF)" OFF)
+option(LPSOLVE, "If ON, will link to lp_solve optimization library (default: OFF)" OFF)
 
 # Setup Project
 PROJECT(Raven CXX)
@@ -14,15 +21,22 @@ PROJECT(Raven CXX)
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
 
 # Find NetCDF
-find_package(NetCDF)
+find_package(NetCDF) #may also be 'netCDF'
+if (NOT NetCDF_FOUND)
+  message(STATUS "NetCDF not found, trying netCDF")
+  find_package(netCDF)
+endif()
+
+# Find HDF5
+find_package(HDF5)
 
 # find header & source
 file(GLOB HEADER "src/*.h")
 file(GLOB SOURCE "src/*.cpp")
 
 # Create library with Python bindings
 # To work, install pybind11, making sure it comes with cmake files (conda install -c conda-forge pybind11)
-if (PYTHON)
+if(PYTHON)
   SET(PYBIND11_NEWPYTHON ON)
   find_package(Python COMPONENTS REQUIRED Interpreter Development)
   find_package(pybind11 CONFIG REQUIRED)
@@ -43,15 +57,33 @@ if(COMPILE_EXE)
     ${SOURCE}
     ${HEADER}
   )
-  target_compile_definitions(Raven PUBLIC STANDALONE)
   set_target_properties(Raven PROPERTIES LINKER_LANGUAGE CXX)
+
+  # Remove deprecation warnings for GCC
+  IF(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+    target_compile_options(Raven PRIVATE "-Wno-deprecated")
+    message(STATUS "Modified compile flags with '-Wno-deprecated'")
+  ENDIF()
+
+  if(LPSOLVE)
+    target_link_directories(Raven PRIVATE lib/lp_solve)  # where liblpsolve55.so is located
+    target_link_libraries(Raven lpsolve55)
+    add_definitions(-D_LPSOLVE_)
+  endif()
 endif()
 
-IF(NETCDF_FOUND)
+if(NETCDF_FOUND)
   add_definitions(-Dnetcdf)
   include_directories(${NetCDF_INCLUDE_DIRS})
   target_link_libraries(Raven NetCDF::NetCDF)
-ENDIF()
+elseif(netCDF_FOUND)
+  add_definitions(-Dnetcdf)
+  include_directories(${NetCDF_INCLUDE_DIRS})
+  target_link_libraries(Raven netcdf)
+endif()
+
+source_group("Header Files" FILES ${HEADER})
+source_group("Source Files" FILES ${SOURCE})
 
 source_group("Header Files" FILES ${HEADER})
 source_group("Source Files" FILES ${SOURCE})

README.md

@@ -2,9 +2,9 @@
 
 The code repository for the Raven Hydrological Modelling Framework developed at the University of Waterloo.
 
-Release versions, tutorials, documentation, and more distributed at [the Raven website](http://raven.uwaterloo.ca/Main.html).
+Release versions, tutorials, documentation, and more distributed at [the Raven website](https://raven.uwaterloo.ca/Main.html).
 
-Intended for use with Visual Studio Community Edition 2021, but also provided with Windows/linux/unix/MacOS g++ makefile and CMake configuration file.
+Intended for use with Visual Studio Community Edition 2022, but also provided with Windows/linux/unix/MacOS g++ makefile and CMake configuration file.
 
 Note unconventional two-space tabbing conventions.
 If you would like to work with the active development of Raven's core, please do so on a branch and coordinate commits to the trunk with the Raven development team.
@@ -32,3 +32,4 @@ So that the ```cmake``` command to build Raven as solely a dynamic library becom
 ```bash
 cmake -DCOMPILE_LIB=ON -DCOMPILE_EXE=OFF ../
 ```
+Raven can alternately be bullt in unix/MacOS using the makefile provided with the source code (g++ must be installed on the machine). Lastly, it may be compiled within Visual Studio Community Edition 2022.

src/Advection.cpp

@@ -25,7 +25,9 @@ CmvAdvection::CmvAdvection(string constit_name,
   _constit_ind=pTransModel->GetConstituentIndex(constit_name);
 
   int nAdvConnections    =pTransModel->GetNumAdvConnections();
+  int nWaterStores       =pTransModel->GetNumWaterCompartments();
   CHydroProcessABC::DynamicSpecifyConnections(3*nAdvConnections+1);//+2 once GW added
+  //CHydroProcessABC::DynamicSpecifyConnections(nAdvConnections+nWaterStores+1);//+2 once GW added
 
   for (int q=0;q<nAdvConnections;q++) //for regular advection
   {
@@ -42,18 +44,29 @@ CmvAdvection::CmvAdvection(string constit_name,
     iFrom[2*nAdvConnections+q]=pModel->GetStateVarIndex(CONSTITUENT_SRC,_constit_ind);
     iTo  [2*nAdvConnections+q]=iTo[q];
   }
+  //for Dirichlet source corrections
+  //for (int ii = 0; ii < nWaterStores; ii++) {
+  //  iFrom[nAdvConnections+ii]=pModel->GetStateVarIndex(CONSTITUENT_SRC,_constit_ind);
+  //  iTo  [nAdvConnections+ii]=pTransModel->GetStorWaterIndex(ii);
+  // }
+
   //advection into surface water
   int iSW=pModel->GetStateVarIndex(SURFACE_WATER);
   int   m=pTransModel->GetLayerIndex(_constit_ind,iSW);
   iFrom[3*nAdvConnections]=pModel->GetStateVarIndex(CONSTITUENT,m);
   iTo  [3*nAdvConnections]=pModel->GetStateVarIndex(CONSTITUENT_SW,0);
 
+  //iFrom[nAdvConnections+nWaterStores]=pModel->GetStateVarIndex(CONSTITUENT,m);
+  //iTo  [nAdvConnections+nWaterStores]=pModel->GetStateVarIndex(CONSTITUENT_SW,0);
+
   //advection into groundwater
   //int iGW=pModel->GetStateVarIndex(GROUNDWATER);
   //int   m=pTransModel->GetLayerIndex(constit_ind,iGW);
   //iFrom[3*nAdvConnections+1]=pModel->GetStateVarIndex(CONSTITUENT,m);
   //iTo  [3*nAdvConnections+1]=pModel->GetStateVarIndex(CONSTITUENT_GW,0);
 
+  //iFrom[nAdvConnections+nWaterStores+1]=pModel->GetStateVarIndex(CONSTITUENT,m);
+  //iTo  [nAdvConnections+nWaterStores+1]=pModel->GetStateVarIndex(CONSTITUENT_SW,0);
 }
 
 //////////////////////////////////////////////////////////////////
@@ -223,6 +236,8 @@ void   CmvAdvection::GetRatesOfChange(const double      *state_vars,
       mass          =sv[iFrom[q]];
       dirichlet_mass=Cs*sv[iFromWater]; //Cs*V
       rates[nAdvConnections+q]+=(dirichlet_mass-mass)/Options.timestep; //From CONSTITUENT_SRC
+      //iiFromWater=pTransModel->GetWaterStorIndexFromSVIndex(iFromWater);
+      //rates[nAdvConnections+iiFromWater]+=(dirichlet_mass-mass)/Options.timestep; //From CONSTITUENT_SRC //JRC: Reduced memory edit (or _aStorIndex[iFromWater])
       sv[iFrom[q]]=dirichlet_mass;      //override previous mass/enthalpy
     }
 
@@ -237,6 +252,8 @@ void   CmvAdvection::GetRatesOfChange(const double      *state_vars,
       mass          =sv[iTo[q]];
       dirichlet_mass=Cs*sv[iToWater]; //C*V
       rates[2*nAdvConnections+q]+=(dirichlet_mass-mass)/Options.timestep; //From CONSTITUENT_SRC
+      //iiToWater=pTransModel->GetWaterStorIndexFromSVIndex(iToWater);
+      //rates[nAdvConnections+iiToWater]+=(dirichlet_mass-mass)/Options.timestep; //From CONSTITUENT_SRC //JRC: Reduced memory edit (or _aStorIndex[iFromWater] of size _nWaterStores)
       sv[iTo[q]]=dirichlet_mass;      //override previous mass/enthalpy
     }