ci_pipeline.yml now more similar to upstream

.github/workflows/ci_pipeline.yml

@@ -42,7 +42,7 @@ jobs:
 
     strategy:
       matrix:
-        python: ['3.7', '3.8', '3.9', '3.10']
+        python: ['3.8', '3.9', '3.10']
         env: ['base', 'fenics', 'mpi4py', 'petsc']
 
     defaults:
@@ -127,6 +127,52 @@ jobs:
             data_libpressio
             coverage_libpressio_3.10.dat
          
+  user_monodomain_tests_linux:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: "pySDC/projects/Monodomain/etc/environment-monodomain.yml"
+          create-args: >-
+              python=3.10
+
+      - name: Compile C++ ionic models
+        env:
+          IONIC_MODELS_PATH: "pySDC/projects/Monodomain/problem_classes/ionicmodels/cpp"
+        run: |
+          c++ -O3 -Wall -shared -std=c++11 -fPIC -fvisibility=hidden $(python3 -m pybind11 --includes) ${IONIC_MODELS_PATH}/bindings_definitions.cpp -o ${IONIC_MODELS_PATH}/ionicmodels$(python3-config --extension-suffix)
+      
+      - name: Run pytest for CPU stuff
+        run: |
+          echo "print('Loading sitecustomize.py...')
+          import coverage
+          coverage.process_startup() " > sitecustomize.py
+          coverage run -m pytest --continue-on-collection-errors -v --durations=0 pySDC/tests -m monodomain
+
+      - name: Make coverage report
+        run: |
+          mv data data_monodomain
+          coverage combine
+          mv .coverage coverage_monodomain_3.10.dat
+
+      - name: Uploading artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: cpu-test-artifacts
+          path: |
+            data_monodomain
+            coverage_monodomain_3.10.dat
+
+
 #  user_cpu_tests_macos:
 #    runs-on: macos-12
 #
@@ -170,6 +216,7 @@ jobs:
       - lint
       - user_cpu_tests_linux
       - user_libpressio_tests
+      - user_monodomain_tests_linux
 #       - wait_for_gitlab
 
     defaults:
@@ -194,7 +241,7 @@ jobs:
         run: |
           ls -artl cpu-test-artifacts
           cp cpu-test-artifacts/data_3.10/* data/.
-          python -m coverage combine cpu-test-artifacts/coverage_*.dat
+          python -m coverage combine cpu-test-artifacts/coverage_*_3.10.dat
           python -m coverage xml
           python -m coverage html
 
@@ -310,4 +357,3 @@ jobs:
 #          rm -rf data
 #          unzip artifacts.zip
 #
-