GHA: Test composite actions

AMICI-dev · Nov 15, 2023 · fef657e · fef657e
1 parent eccdc1f
commit fef657e
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Showing 9 changed files with 41 additions and 44 deletions.
diff --git a/.github/actions/install-apt-dependencies/action.yml b/.github/actions/install-apt-dependencies/action.yml
@@ -0,0 +1,15 @@
+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 \
+              libatlas-base-dev \
+              libboost-chrono-dev \
+              libboost-math-dev \
+              libboost-serialization-dev \
+              libhdf5-serial-dev \
+              swig
+      shell: bash
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_install.yml b/.github/workflows/test_install.yml
@@ -22,17 +22,15 @@ 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
+            g++
 
     - name: Build suitesparse
       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
@@ -53,19 +53,17 @@ jobs:
           https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
         && unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
 
+    - 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 \
-            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 +34,18 @@ 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: |