Homogenizing exchange-flux custom_data naming under R_EX_*

.github/workflows/build_binaries.yml

@@ -12,18 +12,18 @@ jobs:
     strategy:
       matrix:
         projects: [
-          {short_name: "physiboss-tutorial", project: "physiboss-tutorial", name: "PhysiBoSS tutorial", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"},
-          {short_name: "physiboss-tutorial-invasion", project: "physiboss-tutorial-invasion", name: "PhysiBoSS Cancer Invasion", binary: "invasion_model", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"},
-          {short_name: "physiboss-cell-lines", project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"},
-          {short_name: "template_BM", project: "template_BM", name: "PhysiBoSS Template", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"},
+          {short_name: "physiboss-tutorial", project: "physiboss-tutorial", name: "PhysiBoSS tutorial", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-12"},
+          {short_name: "physiboss-tutorial-invasion", project: "physiboss-tutorial-invasion", name: "PhysiBoSS Cancer Invasion", binary: "invasion_model", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-12"},
+          {short_name: "physiboss-cell-lines", project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-12"},
+          {short_name: "template_BM", project: "template_BM", name: "PhysiBoSS Template", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-12"},
           {short_name: "template", project: "template", name: "PhysiCell Template", binary: "project", extra_run: ""},
           {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
           {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
           {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
           {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
         ]
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     steps:
     - uses: actions/checkout@v4
@@ -127,17 +127,17 @@ jobs:
           {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
        ]
 
-    runs-on: macos-13
+    runs-on: macos-15-intel
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Install dependencies
       run : |
-        if ! brew list gcc@13 &>/dev/null; then
-          brew install gcc@13
+        if ! brew list gcc@14 &>/dev/null; then
+          brew install gcc@14
         else
-          echo "gcc@13 is already installed."
+          echo "gcc@14 is already installed."
         fi
 
     - name: Build ${{ matrix.projects.name }} project
@@ -146,15 +146,15 @@ jobs:
         make ${{ matrix.projects.project }}
         make clean
         ${{ matrix.projects.extra_run }}
-        make PHYSICELL_CPP=g++-13 static
-        cp ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos13
+        make PHYSICELL_CPP=g++-14 static
+        cp ${{ matrix.projects.binary }} ${{ matrix.projects.short_name }}_macos_intel
 
     - name: Caching produced project binary 
       uses: actions/cache@v4
       with:
         path: |
-          ${{ github.workspace }}/${{ matrix.projects.binary }}_macos13
-        key: ${{ runner.os }}-macos13-${{ github.run_id }}
+          ${{ github.workspace }}/${{ matrix.projects.short_name }}_macos_intel
+        key: ${{ runner.os }}-macos-intel-${{ github.run_id }}
 
     - name: Look at the generated binary
       run: |
@@ -184,10 +184,10 @@ jobs:
 
     - name: Install dependencies
       run : |
-        if ! brew list gcc@13 &>/dev/null; then
-          brew install gcc@13
+        if ! brew list gcc@14 &>/dev/null; then
+          brew install gcc@14
         else
-          echo "gcc@13 is already installed."
+          echo "gcc@14 is already installed."
         fi
 
     - name: Build ${{ matrix.projects.name }} project
@@ -196,15 +196,15 @@ jobs:
         make ${{ matrix.projects.project }}
         make clean
         ${{ matrix.projects.extra_run }}
-        make PHYSICELL_CPP=g++-13 static
-        cp ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macosm1
+        make PHYSICELL_CPP=g++-14 static
+        cp ${{ matrix.projects.binary }} ${{ matrix.projects.short_name }}_macos_arm
 
     - name: Caching produced project binary 
       uses: actions/cache@v4
       with:
         path: |
-          ${{ github.workspace }}/${{ matrix.projects.binary }}_macosm1
-        key: ${{ runner.os }}-macosm1-${{ github.run_id }}
+          ${{ github.workspace }}/${{ matrix.projects.short_name }}_macos_arm
+        key: ${{ runner.os }}-macos-arm-${{ github.run_id }}
 
     - name: Look at the generated binary
       run: |
@@ -227,7 +227,7 @@ jobs:
           {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
         ]
 
-    runs-on: macos-13
+    runs-on: macos-15-intel
     needs: [macos_step0a, macos_step0b]
 
     steps:
@@ -237,20 +237,19 @@ jobs:
       uses: actions/cache@v4
       with:
         path: |
-          ${{ github.workspace }}/${{ matrix.projects.binary }}_macosm1
-        key: ${{ runner.os }}-macosm1-${{ github.run_id }}
+          ${{ github.workspace }}/${{ matrix.projects.short_name }}_macos_arm
+        key: ${{ runner.os }}-macos-arm-${{ github.run_id }}
 
     - name: Caching produced project binary 
       uses: actions/cache@v4
       with:
         path: |
-          ${{ github.workspace }}/${{ matrix.projects.binary }}_macos13
-        key: ${{ runner.os }}-macos13-${{ github.run_id }}
+          ${{ github.workspace }}/${{ matrix.projects.short_name }}_macos_intel
+        key: ${{ runner.os }}-macos-intel-${{ github.run_id }}
 
     - name: Creating universal binary
       run: | 
-        lipo -create -output ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos13 ${{ matrix.projects.binary }}_macosm1
-
+        lipo -create -output ${{ matrix.projects.binary }} ${{ matrix.projects.short_name }}_macos_arm ${{ matrix.projects.short_name }}_macos_intel
     - name: Checking universal binary
       run: |
         lipo -archs ${{ matrix.projects.binary }}

.github/workflows/build_binaries_cmake.yml

@@ -0,0 +1,77 @@
+# This starter workflow is for a CMake project running on multiple platforms. There is a different starter workflow if you just want a single platform.
+# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-single-platform.yml
+name: Build binaries CMake
+
+on:
+  push:
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      # Set fail-fast to false to ensure that feedback is delivered for all matrix combinations. Consider changing this to true when your workflow is stable.
+      fail-fast: false
+
+      # Set up a matrix to run the following 3 configurations:
+      # 1. <Windows, Release, latest MSVC compiler toolchain on the default runner image, default generator>
+      # 2. <Linux, Release, latest GCC compiler toolchain on the default runner image, default generator>
+      # 3. <Linux, Release, latest Clang compiler toolchain on the default runner image, default generator>
+      #
+      # To add more build types (Release, Debug, RelWithDebInfo, etc.) customize the build_type list.
+      matrix:
+        include:
+          - os: windows-latest
+            c_compiler: cl
+            cpp_compiler: cl
+            build_physiboss: "ON"
+          - os: ubuntu-latest
+            c_compiler: gcc
+            cpp_compiler: g++
+            build_physiboss: "ON"
+          - os: ubuntu-latest
+            c_compiler: clang
+            cpp_compiler: clang++
+            build_physiboss: "ON"
+          - os: macos-latest
+            c_compiler: gcc-15
+            cpp_compiler: g++-15
+            build_physiboss: "ON"
+          # - os: macos-latest
+          #   c_compiler: cc
+          #   cpp_compiler: c++
+          #   build_physiboss: "ON"
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set reusable strings
+      # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
+      id: strings
+      shell: bash
+      run: |
+        echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
+
+    - name: Install dependencies (Linux)
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libomp-dev
+
+    - name: Configure CMake
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: >
+        cmake -B ${{ steps.strings.outputs.build-output-dir }}
+        -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
+        -DCMAKE_C_COMPILER=${{ matrix.c_compiler }}
+        -DCMAKE_BUILD_TYPE=Release
+        -DPHYSICELL_BUILD_PHYSIBOSS=${{ matrix.build_physiboss }}
+        -S ${{ github.workspace }}
+
+    - name: Build
+      # Build your program with the given configuration. Note that --config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
+      run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config Release

.github/workflows/tests.yml

@@ -13,8 +13,8 @@ jobs:
       matrix:
         os: [
           {name: "Ubuntu", os: "ubuntu-latest", shell: "bash", compiler: "g++"},
-          {name: "MacOS 13", os: "macos-13", shell: "bash", compiler: "g++-12"},
-          {name: "MacOS 14 (M1)", os: "macos-14", shell: "bash", compiler: "g++-13"},
+          {name: "MacOS 15", os: "macos-15-intel", shell: "bash", compiler: "g++-14"},
+          {name: "MacOS 14 (M1)", os: "macos-14", shell: "bash", compiler: "g++-14"},
           {name: "Windows", os: "windows-latest", shell: "msys2", compiler: "g++"},
         ]
         projects: [
@@ -24,14 +24,15 @@ jobs:
           {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project", config: "config/Fibre_Degradation/mymodel_matrix_degradation.xml", max_time: 120, output_folder: ""},
           {project: "physiboss-tutorial", name: "PhysiBoSS Tutorial", binary: "project", config: "config/cell_cycle/PhysiCell_settings.xml", max_time: 300, output_folder: "output"},
           {project: "worm-sample", name: "PhysiCell worm", binary: "worm", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
-          {project: "virus-macrophage-sample", name: "Virus Macrophage", binary: "virus-sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
-          {project: "mechano-sample", name: "PhysiCell Mechano", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
+          {project: "virus-macrophage-sample", name: "Virus Macrophage", binary: "virus-sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
+          {project: "mechano-sample", name: "PhysiCell Mechano", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "cancer-biorobots-sample", name: "PhysiCell Cancer Biorobots", binary: "cancer_biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "biorobots-sample", name: "PhysiCell Biorobots", binary: "biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "celltypes3-sample", name: "PhysiCell Celltypes3", binary: "celltypes3", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "custom-division-sample", name: "PhysiCell custom division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "interaction-sample", name: "PhysiCell interactions", binary: "interaction_demo", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "pred-prey-farmer", name: "PhysiCell prey predator", binary: "pred_prey", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
+          {project: "dfba_unit_test", name: "PhysiCelldFBA Unit Test", binary: "dfba-unit-test", config: "config/Unit_test_mass_conversion.xml", max_time: 20, output_folder: ""},
           {project: "rules-sample", name: "PhysiCell rules sample", binary: "rules_sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "asymmetric-division-sample", name: "PhysiCell asymmetric division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "episode-sample", name: "PhysiCell Episode", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: ""},
@@ -48,11 +49,18 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
+    - if: matrix.os.name == 'Ubuntu'
+      run: sudo apt-get update && sudo apt-get install -y liblapack-dev libbz2-dev
+
+    - if: runner.os == 'macOS'
+      run: brew install lapack bzip2
+
+
     - if: matrix.os.name == 'Windows'
       uses: msys2/setup-msys2@v2
       with:
         update: true
-        install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates mingw-w64-x86_64-diffutils
+        install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates diffutils
 
     - name: Build ${{ matrix.projects.name }} project 
       run: |