Update GitHub Actions where needed

.github/workflows/brief.yml

@@ -27,20 +27,20 @@ jobs:
     runs-on: ${{ matrix.platform }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: seanmiddleditch/gha-setup-ninja@master
 
       - name: Add msbuild to PATH (Windows)
         if: matrix.platform == 'windows-latest'
-        uses: ilammy/msvc-dev-cmd@v1.6.0
+        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@v2
+        uses: actions/cache@v4
         with:
           path: |
             ./dependencies
@@ -114,7 +114,7 @@ jobs:
           echo "COMPILER_LAUNCHER=ccache" >> "${GITHUB_ENV}"
       - name: cache ccache files
         if: matrix.platform != 'windows-latest'
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{runner.workspace}}/.ccache
           key:
@@ -185,13 +185,13 @@ jobs:
         package_option: ["-DWITH_STABLE_PACKAGES=ON"]
         cpp_standard: [98, 20]
         language_bindings:
-          ["-DWITH_JAVA=True -DWITH_PYTHON=True -DWITH_CSHARP=True"]
-        container: ["quay.io/pypa/manylinux2010_x86_64"]
+          ["-DWITH_JAVA=True -DWITH_PYTHON=True"]
+        container: ["quay.io/pypa/manylinux_2_28_x86_64"]
     runs-on: ${{ matrix.platform }}
     container: ${{ matrix.container}}
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - name: install Swig 4 from source
         run: |
           yum install -y pcre-devel
@@ -213,7 +213,7 @@ jobs:
           ctest --version
       - name: Install dependencies, configure, build
         run: |
-          yum install -y libxml2-devel check-devel java-devel mono-devel
+          yum install -y libxml2-devel check-devel java-devel
           cd ..
           mkdir build
           cd build

.github/workflows/doxygen.yml

@@ -9,10 +9,11 @@ on:
 
 jobs:
   build:
+    if: github.repository_owner == 'sbmlteam'
     runs-on: ubuntu-latest
     steps:
     - name: Checkout code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - uses: seanmiddleditch/gha-setup-ninja@master
 
@@ -52,7 +53,7 @@ jobs:
         cmake --build . --config Release --target api_docs_cpp
 
     - name: Deploy
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./docs/formatted/cpp-api

.github/workflows/extensive.yml

@@ -80,20 +80,20 @@ jobs:
     runs-on: ${{ matrix.platform }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: seanmiddleditch/gha-setup-ninja@master
 
       - name: Add msbuild to PATH (Windows)
         if: matrix.platform == 'windows-latest'
-        uses: ilammy/msvc-dev-cmd@v1.6.0
+        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@v2
+        uses: actions/cache@v4
         with:
           path: |
             ./dependencies
@@ -178,7 +178,7 @@ jobs:
           echo "COMPILER_LAUNCHER=ccache" >> "${GITHUB_ENV}"
       - name: cache ccache files
         if: matrix.platform != 'windows-latest'
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{runner.workspace}}/.ccache
           key:

.github/workflows/matlab.yml

@@ -12,12 +12,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - uses: seanmiddleditch/gha-setup-ninja@master
 
     - name: Set up MATLAB
-      uses: matlab-actions/setup-matlab@v1
+      uses: matlab-actions/setup-matlab@v2
       # with:
       #   release: ${{ env.MATLAB_VERSION }}
 
@@ -58,6 +58,6 @@ jobs:
         cmake --build . --config Debug --target matlab_binding_OutputSBML
 
     - name: Run Test
-      uses: matlab-actions/run-command@v1
+      uses: matlab-actions/run-command@v2
       with:
         command: cd('../build/src/bindings/matlab/test'); runTests

.github/workflows/octave.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Checkout submodules
       run: git submodule update --init --recursive
@@ -65,7 +65,7 @@ jobs:
       run: LD_LIBRARY_PATH=../../../../.. octave --eval "runTests()"
 
     - name: Upload
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v4
       with:
         path: ${{runner.workspace}}/build/octave_${{ matrix.os }}.tar.gz
         name: octave_${{ matrix.os }}.tar.gz

.github/workflows/store-artefact.yml

@@ -32,20 +32,20 @@ jobs:
     runs-on: ${{ matrix.platform }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: seanmiddleditch/gha-setup-ninja@master
 
       - name: Add msbuild to PATH (Windows)
         if: matrix.platform == 'windows-latest'
-        uses: ilammy/msvc-dev-cmd@v1.6.0
+        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@v2
+        uses: actions/cache@v4
         with:
           path: |
             ./dependencies
@@ -133,12 +133,11 @@ jobs:
           echo "COMPILER_LAUNCHER=ccache" >> "${GITHUB_ENV}"
       - name: cache ccache files
         if: matrix.platform != 'windows-latest'
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{runner.workspace}}/.ccache
           key:
-            ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp
-            }}
+            ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp}}
           restore-keys: |
             ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp }}
             ${{ runner.os }}-
@@ -226,22 +225,22 @@ jobs:
       ### Upload installed versions ###
       - name: Upload Windows binary archive
         if: matrix.platform == 'windows-latest'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name:
             Windows (zip, libSBML ${{env.LIBSBML_VERSION}},
-            ${{env.ARTIFACT_NAME_SUFFIX}})
+            ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
           path: ${{runner.workspace}}/install/*
           retention-days: 1
           if-no-files-found: error
 
       - name: Upload MacOS binary archive
         if: matrix.platform == 'macos-latest'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name:
             MacOS (zip, libSBML ${{env.LIBSBML_VERSION}},
-            ${{env.ARTIFACT_NAME_SUFFIX}})
+            ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
           path: |
             ${{runner.workspace}}/install/*
             ${{runner.workspace}}/build/r-binaries/*
@@ -250,14 +249,13 @@ jobs:
 
       - name: Upload Ubuntu binary archive
         if: matrix.platform == 'ubuntu-latest'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name:
             Ubuntu nightly (zip, libSBML ${{env.LIBSBML_VERSION}},
-            ${{env.ARTIFACT_NAME_SUFFIX}})
+            ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
           path: |
             ${{runner.workspace}}/install/*
-#            ${{runner.workspace}}/build/r-binaries/*
           retention-days: 1
           if-no-files-found: error
   manylinuxbuild:
@@ -279,12 +277,12 @@ jobs:
         cpp_standard: [98]
         language_bindings:
           ["-DWITH_JAVA=True -DWITH_PYTHON=True -DWITH_CSHARP=True -DWITH_R=True"]
-        container: ["quay.io/pypa/manylinux2010_x86_64"]
+        container: ["quay.io/pypa/manylinux_2_28_x86_64"]
     runs-on: ${{ matrix.platform }}
     container: ${{ matrix.container}}
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - name: install Swig 4 from source
         run: |
           yum install -y pcre-devel
@@ -365,18 +363,10 @@ jobs:
         run: |
           echo "ARTIFACT_NAME_SUFFIX=all-packages" >> "${GITHUB_ENV}"
 
-      - name: Upload Manylinux2010 binary archive
-        uses: actions/upload-artifact@v1 # note v1 used here, because v2 incompatible
+      - name: Upload Manylinux binary archive
+        uses: actions/upload-artifact@v4
         with:
           name:
-            Manylinux2010 nightly (zip, libSBML ${{env.LIBSBML_VERSION}},
-            ${{env.ARTIFACT_NAME_SUFFIX}})
-          path: ../install # paths handled differently by v1 - note that "./install/*" does not work
-
-      # - name: Upload Manylinux2010 R binary archive
-        # uses: actions/upload-artifact@v1 # note v1 used here, because v2 incompatible
-        # with:
-          # name:
-            # Manylinux2010 R nightly (zip, libSBML ${{env.LIBSBML_VERSION}},
-            # ${{env.ARTIFACT_NAME_SUFFIX}})
-          # path: ../build/r-binaries # paths handled differently by v1 - note that v1 doesn't allow multiple paths
+            Manylinux nightly (zip, libSBML ${{env.LIBSBML_VERSION}},
+            ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
+          path: ../install

artefacts.md

@@ -18,6 +18,6 @@ The artefacts are built using [virtual machines provided by GitHub Actions](http
 - Precompiled version of libSBML, built using the [libxml2](http://xmlsoft.org/) parser. Contains interfaces to C, C++, C# (Mono), Python, and R.
 - Precompiled R package for libSBML. 
 
-## CentOS 6 ([ManyLinux2010](quay.io/pypa/manylinux2010_x86_64))
+## CentOS 6 ([ManyLinux2014](quay.io/pypa/manylinux2014_x86_64))
 - Precompiled version of libSBML, built using the [libxml2](http://xmlsoft.org/) parser. Contains interfaces to C, C++, C# (Mono), Python, and R.
 - Precompiled R package for libSBML (as a separate artefact).