GHA: split into smaller jobs

.github/actions/setup-amici-cpp/action.yml

@@ -0,0 +1,44 @@
+name: Set up AMICI C++
+description: |
+  Build the AMICI C++ interface and set things for for coverage analysis.
+  (Currently ubuntu-only).
+
+runs:
+  using: "composite"
+  steps:
+    # BioNetGen Path
+    - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+      shell: bash
+
+    # use all available cores
+    - run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
+      shell: bash
+
+    # enable coverage
+    - run: echo "ENABLE_GCOV_COVERAGE=TRUE" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Set up Sonar tools
+      uses: ./.github/actions/setup-sonar-tools
+
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
+    - name: Install additional apt dependencies
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+            cmake \
+            python3-venv \
+            lcov
+      shell: bash
+
+    - name: Build AMICI dependencies
+      run: scripts/buildDependencies.sh
+      shell: bash
+
+    - name: Build AMICI
+      run: scripts/buildAmici.sh
+      shell: bash
+      env:
+        CI_SONARCLOUD: "TRUE"

.github/workflows/test_python_cplusplus.yml

@@ -9,19 +9,12 @@ on:
 
 jobs:
   build:
-    name: Tests Ubuntu
-
-    # TODO: prepare image with more deps preinstalled
+    name: C++ tests Ubuntu
     runs-on: ubuntu-22.04
 
-    env:
-      AMICI_PARALLEL_COMPILE: ""
-      ENABLE_GCOV_COVERAGE: "TRUE"
-      CI_SONARCLOUD: "TRUE"
-
     strategy:
       matrix:
-        python-version: [ 3.9 ]
+        python-version: [ "3.9" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -33,89 +26,13 @@ jobs:
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
-
-    - 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
-      run: |
-        sudo apt-get update \
-          && sudo apt-get install -y \
-            cmake \
-            python3-venv \
-            lcov
 
-    - name: Build AMICI dependencies
-      run: scripts/buildDependencies.sh
-
-    - name: Build AMICI
-      run: CI_SONARCLOUD=TRUE scripts/buildAmici.sh
+    - name: Set up AMICI C++ libraries
+      uses: ./.github/actions/setup-amici-cpp
 
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
 
-    - name: Install python package
-      run: scripts/installAmiciSource.sh
-
-    - name: Python tests
-      run: |
-        source build/venv/bin/activate \
-        && pytest \
-          --ignore-glob=*petab* \
-          --ignore-glob=*test_splines.py \
-          --cov=amici \
-          --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
-          --cov-append \
-          --durations=10 \
-          ${AMICI_DIR}/python/tests
-
-
-    - name: Python tests splines
-      if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}}
-      run: |
-        source build/venv/bin/activate \
-        && pytest \
-          --cov=amici \
-          --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
-          --cov-append \
-          --durations=10 \
-          ${AMICI_DIR}/python/tests/test_splines.py
-
-    - name: Install notebook dependencies
-      run: |
-        source build/venv/bin/activate \
-        && pip install jax[cpu]
-
-    - name: example notebooks
-      run: scripts/runNotebook.sh python/examples/example_*/
-
-    - name: doc notebooks
-      run: scripts/runNotebook.sh documentation/GettingStarted.ipynb
-
-    - name: Codecov Python
-      uses: codecov/[email protected]
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        file: build/coverage_py.xml
-        flags: python
-        fail_ci_if_error: true
-        verbose: true
-
-    - name: lcov
-      run: |
-        lcov --compat-libtool --no-external \
-        -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \
-        -b ${AMICI_DIR} -c -o coverage_cpp.info \
-        && lcov --compat-libtool --no-external \
-        -d ${AMICI_DIR}/python/sdist/build/temp_amici/CMakeFiles/amici.dir/src \
-        -b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \
-        && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
-
     - name: Codecov CPP
       uses: codecov/[email protected]
       with: