Merge branch 'develop' into gha_update_pyver

AMICI-dev · Nov 16, 2023 · 730b490 · 730b490
2 parents b60e833 + 32730f0
commit 730b490
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Showing 21 changed files with 181 additions and 121 deletions.
diff --git a/.github/actions/install-apt-dependencies/action.yml b/.github/actions/install-apt-dependencies/action.yml
@@ -0,0 +1,16 @@
+name: Install apt dependencies
+description: Install apt dependencies for the AMICI Python package
+runs:
+  using: "composite"
+  steps:
+    - run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+              g++ \
+              libatlas-base-dev \
+              libboost-chrono-dev \
+              libboost-math-dev \
+              libboost-serialization-dev \
+              libhdf5-serial-dev \
+              swig
+      shell: bash
diff --git a/.github/actions/setup-doxygen/action.yml b/.github/actions/setup-doxygen/action.yml
@@ -0,0 +1,20 @@
+name: Set up doxygen
+description: |
+  Download, build, and install doxygen.
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install apt dependencies for doxygen
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+              bison \
+              ragel \
+              graphviz \
+              texlive-latex-extra
+      shell: bash
+
+    - name: Download and build doxygen
+      run: sudo scripts/downloadAndBuildDoxygen.sh
+      shell: bash
diff --git a/.github/actions/setup-sonar-tools/action.yml b/.github/actions/setup-sonar-tools/action.yml
@@ -0,0 +1,26 @@
+name: Set up Sonar tools
+description: Download and install sonar-scanner and build-wrapper
+runs:
+  using: "composite"
+  steps:
+    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
+      shell: bash
+    - run: echo "${HOME}/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
+      shell: bash
+
+    - name: Install sonarcloud tools
+      run: |
+        sudo apt-get install nodejs curl unzip \
+        && curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
+          https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
+        && unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
+        && curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
+          https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
+        && unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
+      shell: bash
diff --git a/.github/actions/setup-swig/action.yml b/.github/actions/setup-swig/action.yml
@@ -0,0 +1,20 @@
+name: Set up SWIG
+description: |
+  Download and build SWIG and set the SWIG environment variable to the path of
+  the SWIG executable.
+
+inputs:
+  swig_version:
+    description: 'Swig version to build'
+    required: false
+    default: '4.1.1'
+
+runs:
+  using: "composite"
+  steps:
+    - name: Download and build SWIG
+      run: scripts/downloadAndBuildSwig.sh
+      shell: bash
+
+    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-${{ inputs.swig_version }}/install/bin/swig" >> $GITHUB_ENV
+      shell: bash
diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -21,12 +21,10 @@ jobs:
       with:
         fetch-depth: 20
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+    - name: Set up SWIG
+      uses: ./.github/actions/setup-swig
 
-    - name: Build swig4
-      run: |
-        sudo scripts/downloadAndBuildSwig.sh
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: Create AMICI sdist
       run: |

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -24,12 +24,10 @@ jobs:
       with:
         fetch-depth: 20
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+    - name: Set up SWIG
+      uses: ./.github/actions/setup-swig
 
-    - name: Build swig4
-      run: |
-        sudo scripts/downloadAndBuildSwig.sh
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: sdist
       run: |

diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
@@ -37,11 +37,8 @@ jobs:
       with:
         fetch-depth: 20
 
-    # install dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig libatlas-base-dev
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
 

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -16,7 +16,6 @@ on:
 jobs:
   doxygen:
     name: Test Doxygen
-
     runs-on: ubuntu-22.04
 
     strategy:
@@ -32,26 +31,14 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-          bison \
-          ragel \
-          graphviz \
-          texlive-latex-extra
-
-    - name: Build doxygen
-      run: |
-        sudo scripts/downloadAndBuildDoxygen.sh
+    - name: Set up doxygen
+      uses: ./.github/actions/setup-doxygen
 
     - name: Run doxygen
-      run: |
-        scripts/run-doxygen.sh
+      run: scripts/run-doxygen.sh
 
   sphinx:
     name: Test Sphinx
-
     runs-on: ubuntu-22.04
 
     strategy:
@@ -68,11 +55,9 @@ jobs:
       - run: git fetch --prune --unshallow
 
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-      - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.1.1/install/bin/swig" >> $GITHUB_ENV
 
-      - name: Build doxygen
-        run: |
-          sudo scripts/downloadAndBuildDoxygen.sh
+      - name: Set up doxygen
+        uses: ./.github/actions/setup-doxygen
 
       # install amici dependencies
       - name: apt
@@ -85,10 +70,7 @@ jobs:
               pandoc \
               python3-venv \
 
-      - name: Build swig
-        run: |
-          sudo scripts/downloadAndBuildSwig.sh
+      - uses: ./.github/actions/setup-swig
 
       - name: sphinx
-        run: |
-          scripts/run-sphinx.sh
+        run: scripts/run-sphinx.sh
diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -22,17 +22,14 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    # install amici dependencies
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     - name: apt
       run: |
         sudo apt-get update \
           && sudo apt-get install -y \
-            cmake \
-            g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libhdf5-serial-dev \
-            swig
+            cmake
 
     - name: Build suitesparse
       run: |
@@ -70,16 +67,8 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    # install amici dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-            g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libhdf5-serial-dev \
-            swig
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     - name: Create AMICI sdist
       run: |

diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
@@ -35,11 +35,9 @@ jobs:
       with:
         fetch-depth: 20
 
-    # install dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig libatlas-base-dev
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     - run: pip3 install petab shyaml build
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -34,14 +34,14 @@ jobs:
         with:
           fetch-depth: 20
 
+      - name: Install apt dependencies
+        uses: ./.github/actions/install-apt-dependencies
+
       # install dependencies
       - name: apt
         run: |
           sudo apt-get update \
-            && sudo apt-get install -y \
-            swig \
-            libatlas-base-dev \
-            python3-venv
+            && sudo apt-get install -y python3-venv
 
       - name: Build BNGL
         run: |

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -35,23 +35,11 @@ jobs:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
     - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
-    # sonar cloud
-    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
-    - run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
-    - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
-    - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
-    - run: echo "${HOME}/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
-
-    # TODO: add to ci image
-    - name: Install sonarcloud tools
-      run: |
-        sudo apt-get install nodejs curl unzip \
-        && curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
-          https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
-        && unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
-        && curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
-          https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
-        && unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
+    - name: Set up Sonar tools
+      uses: ./.github/actions/setup-sonar-tools
+
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     # install amici dependencies
     - name: apt
@@ -60,12 +48,7 @@ jobs:
           && sudo apt-get install -y \
             cmake \
             g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libboost-chrono-dev \
-            libhdf5-serial-dev \
             python3-venv \
-            swig \
             lcov \
             libboost-math-dev
 

diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
@@ -41,15 +41,8 @@ jobs:
       with:
         fetch-depth: 20
 
-    # install dependencies
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-          swig \
-          libatlas-base-dev \
-          libhdf5-serial-dev \
-          libboost-math-dev
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
 
     # install AMICI
     - name: Build BNGL

diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -40,10 +40,10 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - name: apt
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig4.0 libatlas-base-dev
+
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/installAmiciSource.sh
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/run-SBMLTestsuite.sh ${{ matrix.cases }}
 

diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
@@ -34,20 +34,17 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     # install amici dependencies
     - name: apt
       run: |
         sudo apt-get update \
           && sudo apt-get install -y \
             cmake \
-            g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libhdf5-serial-dev \
             python3-venv \
-            swig \
-            valgrind \
-            libboost-math-dev
+            valgrind
 
     - name: Build AMICI
       run: |
@@ -78,20 +75,17 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
     # install amici dependencies
     - name: apt
       run: |
         sudo apt-get update \
           && sudo apt-get install -y \
             cmake \
-            g++ \
-            libatlas-base-dev \
-            libboost-serialization-dev \
-            libhdf5-serial-dev \
             python3-venv \
-            swig \
-            valgrind \
-            libboost-math-dev
+            valgrind
 
     - name: Build AMICI
       run: |