Merge remote-tracking branch 'origin/development' into sk/test-rate-r…

…ule-converter-rigorously

.github/workflows/brief.yml

@@ -1,7 +1,19 @@
 name: CMake (rapid build on push)
 
+<<<<<<< HEAD
 on: 
 
+=======
+on:
+  push:
+    paths:
+        - "src/**"
+        - "CMakeModules/**"
+        - "CMakeLists.txt"
+        - "VERSION.txt"
+        - "!.github/**"
+        - ".github/workflows/brief.yml"
+>>>>>>> origin/development
 env:
   BUILD_TYPE: Release
 
@@ -81,7 +93,7 @@ jobs:
         shell: bash
         run: |
           sudo apt-get update
-          sudo apt-get install -y check ccache
+          sudo apt-get install -y check ccache r-base mono-devel
           echo PYTHON_LINKING_OPTION="-DWITH_PYTHON=ON -DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
           echo R_BINDINGS="-DWITH_R=True" >> "${GITHUB_ENV}"
           git clone https://github.com/libexpat/libexpat

.github/workflows/matlab.yml

@@ -1,15 +1,26 @@
 name: Matlab (ubuntu) build and test
 
+<<<<<<< HEAD
 on: []
+=======
+on:
+  push:
+    paths:
+        - "src/**"
+        - "CMakeModules/**"
+        - "CMakeLists.txt"
+        - "VERSION.txt"
+        - "!.github/**"
+        - ".github/workflows/matlab.yml"
+>>>>>>> origin/development
 
 env:
-  MATLAB_VERSION: R2021a
-  CC: gcc-9
-  CXX: g++-9
+  CC: gcc-10
+  CXX: g++-10
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
@@ -18,8 +29,6 @@ jobs:
 
     - name: Set up MATLAB
       uses: matlab-actions/setup-matlab@v2
-      # with:
-      #   release: ${{ env.MATLAB_VERSION }}
 
     - name: Install Ubuntu dependencies
       shell: bash

.github/workflows/octave.yml

@@ -1,6 +1,18 @@
 name: Octave
 
+<<<<<<< HEAD
 on: 
+=======
+on:
+  push:
+    paths:
+        - "src/**"
+        - "CMakeModules/**"
+        - "CMakeLists.txt"
+        - "VERSION.txt"
+        - "!.github/**"
+        - ".github/workflows/octave.yml"
+>>>>>>> origin/development
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
@@ -11,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-22.04]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -21,13 +33,11 @@ jobs:
       run: git submodule update --init --recursive
 
     - name: update 
-      if: matrix.os == 'ubuntu-latest'
       shell: bash
       run: |
            sudo apt-get update
 
     - name: add linux dependencies
-      if: matrix.os == 'ubuntu-latest'
       shell: bash
       run: |
            sudo apt-get install swig liboctave-dev

.github/workflows/store-artefact.yml

@@ -1,9 +1,9 @@
-name: Nightly build (binaries)
+name: Weekly build (binaries)
 
 on:
   workflow_dispatch:
   schedule:
-    - cron: "0 5 * * *"
+    - cron: "0 5 * * 0"
 
 env:
   BUILD_TYPE: Release
@@ -39,25 +39,11 @@ jobs:
         if: matrix.platform == 'windows-latest'
         uses: ilammy/msvc-dev-cmd@v1
 
-      ### configure the operating system ###
-      - name: Cache Windows dependencies and SWIG
-        # On Windows, the dependencies live inside the source folder, ie `.`.
-        # For the CI, we put SWIG there too, for simplicity.
-        if: matrix.platform == 'windows-latest'
-        id: cache-win-dependencies-static
-        uses: actions/cache@v4
-        with:
-          path: |
-            ./dependencies
-            ./swig
-          key: ${{ runner.os }}-dependencies-static-2
-
       - name: Download pre-built Windows dependencies and SWIG
         # Windows dependencies have to be in a subfolder called `dependencies`, directly under the git repository root.
         # also gets SWIG, completing the set of dependencies needed for windows
         if:
-          matrix.platform == 'windows-latest' &&
-          steps.cache-win-dependencies-static.outputs.cache-hit != 'true'
+          matrix.platform == 'windows-latest'
         shell: bash
         run: |
           curl -L https://github.com/sbmlteam/libSBML-dependencies/releases/download/latest/libSBML-dependencies-1.0.1-x64-Release-static.zip > dependencies.zip
@@ -92,7 +78,7 @@ jobs:
         shell: bash
         run: |
           sudo apt-get update
-          sudo apt-get install -y check ccache
+          sudo apt-get install -y check mono-devel
           echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
           echo CSHARP_OPTION="-DWITH_CSHARP=True" >> "${GITHUB_ENV}"
           git clone https://github.com/libexpat/libexpat
@@ -106,7 +92,7 @@ jobs:
         if: matrix.platform == 'macos-latest'
         shell: bash
         run: |
-          brew install check swig ccache
+          brew install check swig
           echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
           echo CSHARP_OPTION="-DWITH_CSHARP=OFF" >> "${GITHUB_ENV}"
 
@@ -117,31 +103,6 @@ jobs:
           echo R_PLATFORM_SPECIFIC_OPTIONS="-DWITH_CREATE_R_SOURCE=ON
           -DWITH_SKIP_R_BINARY=ON" >> "${GITHUB_ENV}"
 
-      ### setup ccache, not on Windows ###
-      - name: Prepare ccache timestamp
-        if: matrix.platform != 'windows-latest'
-        id: ccache_cache_timestamp
-        shell: cmake -P {0}
-        run: |
-          string(TIMESTAMP current_date "%Y-%m-%d-%H;%M;%S" UTC)
-          message("::set-output name=timestamp::${current_date}")
-      - name: Set ccache cache directory
-        if: matrix.platform != 'windows-latest'
-        shell: bash
-        run: |
-          echo "CCACHE_DIR=${{runner.workspace}}/.ccache" >> "${GITHUB_ENV}"
-          echo "COMPILER_LAUNCHER=ccache" >> "${GITHUB_ENV}"
-      - name: cache ccache files
-        if: matrix.platform != 'windows-latest'
-        uses: actions/cache@v4
-        with:
-          path: ${{runner.workspace}}/.ccache
-          key:
-            ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp}}
-          restore-keys: |
-            ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp }}
-            ${{ runner.os }}-
-
       ### build the project ###
       - name: Create Build Environment
         run: cmake -E make_directory ${{runner.workspace}}/build
@@ -231,7 +192,7 @@ jobs:
             Windows (zip, libSBML ${{env.LIBSBML_VERSION}},
             ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
           path: ${{runner.workspace}}/install/*
-          retention-days: 1
+          retention-days: 7
           if-no-files-found: error
 
       - name: Upload MacOS binary archive
@@ -244,19 +205,19 @@ jobs:
           path: |
             ${{runner.workspace}}/install/*
             ${{runner.workspace}}/build/r-binaries/*
-          retention-days: 1
+          retention-days: 7
           if-no-files-found: error
 
       - name: Upload Ubuntu binary archive
         if: matrix.platform == 'ubuntu-latest'
         uses: actions/upload-artifact@v4
         with:
           name:
-            Ubuntu nightly (zip, libSBML ${{env.LIBSBML_VERSION}},
+            Ubuntu (zip, libSBML ${{env.LIBSBML_VERSION}},
             ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
           path: |
             ${{runner.workspace}}/install/*
-          retention-days: 1
+          retention-days: 7
           if-no-files-found: error
   manylinuxbuild:
     if: github.repository_owner == 'sbmlteam'
@@ -359,7 +320,8 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name:
-            Manylinux nightly (zip, libSBML ${{env.LIBSBML_VERSION}},
+            Manylinux (zip, libSBML ${{env.LIBSBML_VERSION}},
             ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
           path:
             install/
+          retention-days: 7