Run github tests on old stella releases

.github/workflows/old_stella_releases.yml

@@ -0,0 +1,185 @@
+# Run these tests automatically on Github on every push and pull request.
+# Use the macOS operating system, which has 4 cores.
+name: Check old stella releases
+on: [push]
+
+# We always run in a bash shell
+defaults:
+  run:
+    shell: bash
+
+# First build stella, and then perform python tests
+jobs:
+
+#-----------------------------------------------------------------------
+#                             Python tests                              
+#-----------------------------------------------------------------------
+
+  # Perform python tests one by one
+  stella_v0.5: 
+    runs-on: ubuntu-22.04
+    env:
+      OMPI_MCA_rmaps_base_oversubscribe: yes
+      MPIRUN: mpiexec -np
+      STELLA_SYSTEM: gnu_ubuntu
+
+    # Run the same set-up multiple times
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "1 - Does stella run "
+          #- name: "2 - Geometry"
+          #- name: "3 - Gyrokinetic equation"
+          #- name: "4 - Flux tube"
+          #- name: "5 - Diagnostics"
+          #- name: "6 - Full Flux Surface"
+          #- name: "7 - Electromagnetic effects"
+
+    steps:
+
+      # Check-out repository under $GITHUB_WORKSPACE
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      # Install dependencies
+      - name: Install dependencies and python virtual environment
+        run: |
+          sudo apt update
+          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
+          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev
+          pip3 install --user -r AUTOMATIC_TESTS/requirements.txt
+          sed -i 's/nproc = 16/nproc = 4/g' AUTOMATIC_TESTS/config.ini 
+
+      # Coppy stella executable from AUTOMATIC_TESTS/numerical_tests/stella_releases
+      - name: Download stella 
+        run: |
+          cp AUTOMATIC_TESTS/numerical_tests/stella_releases/stella_v0.7 stella
+    
+      # Perform python tests  
+      - name: Numerical python tests
+        run: |
+          # Make stella executable
+          chmod +x stella
+          
+          # Run one of the python tests
+          if ${{ contains(matrix.config.name, '1 -') }}; then make numerical-tests-1; fi
+          if ${{ contains(matrix.config.name, '2 -') }}; then make numerical-tests-2; fi
+          if ${{ contains(matrix.config.name, '3 -') }}; then make numerical-tests-3; fi
+          if ${{ contains(matrix.config.name, '4 -') }}; then make numerical-tests-4; fi
+          if ${{ contains(matrix.config.name, '5 -') }}; then make numerical-tests-5; fi
+          if ${{ contains(matrix.config.name, '6 -') }}; then make numerical-tests-6; fi
+          if ${{ contains(matrix.config.name, '7 -') }}; then make numerical-tests-7; fi
+          
+  # Perform python tests one by one
+  stella_v0.6: 
+    runs-on: ubuntu-22.04
+    env:
+      OMPI_MCA_rmaps_base_oversubscribe: yes
+      MPIRUN: mpiexec -np
+      STELLA_SYSTEM: gnu_ubuntu
+
+    # Run the same set-up multiple times
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "1 - Does stella run "
+          #- name: "2 - Geometry"
+          #- name: "3 - Gyrokinetic equation"
+          #- name: "4 - Flux tube"
+          #- name: "5 - Diagnostics"
+          #- name: "6 - Full Flux Surface"
+          #- name: "7 - Electromagnetic effects"
+
+    steps:
+
+      # Check-out repository under $GITHUB_WORKSPACE
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      # Install dependencies
+      - name: Install dependencies and python virtual environment
+        run: |
+          sudo apt update
+          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
+          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev
+          pip3 install --user -r AUTOMATIC_TESTS/requirements.txt
+          sed -i 's/nproc = 16/nproc = 4/g' AUTOMATIC_TESTS/config.ini 
+
+      # Coppy stella executable from AUTOMATIC_TESTS/numerical_tests/stella_releases
+      - name: Download stella 
+        run: |
+          cp AUTOMATIC_TESTS/numerical_tests/stella_releases/stella_v0.6 stella
+    
+      # Perform python tests  
+      - name: Numerical python tests
+        run: |
+          # Make stella executable
+          chmod +x stella
+          
+          # Run one of the python tests
+          if ${{ contains(matrix.config.name, '1 -') }}; then make numerical-tests-1; fi
+          if ${{ contains(matrix.config.name, '2 -') }}; then make numerical-tests-2; fi
+          if ${{ contains(matrix.config.name, '3 -') }}; then make numerical-tests-3; fi
+          if ${{ contains(matrix.config.name, '4 -') }}; then make numerical-tests-4; fi
+          if ${{ contains(matrix.config.name, '5 -') }}; then make numerical-tests-5; fi
+          if ${{ contains(matrix.config.name, '6 -') }}; then make numerical-tests-6; fi
+          if ${{ contains(matrix.config.name, '7 -') }}; then make numerical-tests-7; fi
+
+
+  # Perform python tests one by one
+  stella_v0.7: 
+    runs-on: ubuntu-22.04
+    env:
+      OMPI_MCA_rmaps_base_oversubscribe: yes
+      MPIRUN: mpiexec -np
+      STELLA_SYSTEM: gnu_ubuntu
+
+    # Run the same set-up multiple times
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "1 - Does stella run "
+          #- name: "2 - Geometry"
+          #- name: "3 - Gyrokinetic equation"
+          #- name: "4 - Flux tube"
+          #- name: "5 - Diagnostics"
+          #- name: "6 - Full Flux Surface"
+          #- name: "7 - Electromagnetic effects"
+
+    steps:
+
+      # Check-out repository under $GITHUB_WORKSPACE
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      # Install dependencies
+      - name: Install dependencies and python virtual environment
+        run: |
+          sudo apt update
+          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
+          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev
+          pip3 install --user -r AUTOMATIC_TESTS/requirements.txt
+          sed -i 's/nproc = 16/nproc = 4/g' AUTOMATIC_TESTS/config.ini 
+
+      # Coppy stella executable from AUTOMATIC_TESTS/numerical_tests/stella_releases
+      - name: Download stella 
+        run: |
+          cp AUTOMATIC_TESTS/numerical_tests/stella_releases/stella_v0.7 stella
+    
+      # Perform python tests  
+      - name: Numerical python tests
+        run: |
+          # Make stella executable
+          chmod +x stella
+          
+          # Run one of the python tests
+          if ${{ contains(matrix.config.name, '1 -') }}; then make numerical-tests-1; fi
+          if ${{ contains(matrix.config.name, '2 -') }}; then make numerical-tests-2; fi
+          if ${{ contains(matrix.config.name, '3 -') }}; then make numerical-tests-3; fi
+          if ${{ contains(matrix.config.name, '4 -') }}; then make numerical-tests-4; fi
+          if ${{ contains(matrix.config.name, '5 -') }}; then make numerical-tests-5; fi
+          if ${{ contains(matrix.config.name, '6 -') }}; then make numerical-tests-6; fi
+          if ${{ contains(matrix.config.name, '7 -') }}; then make numerical-tests-7; fi

AUTOMATIC_TESTS/numerical_tests/stella_releases/README.md

@@ -0,0 +1,6 @@
+
+
+The stella releases are found at:
+https://github.com/stellaGK/stella/releases
+
+Note that for stella_v0.7 we commented line 224 in run_parameters.f90 (error = .true.), in order to allow stella to run when the variables `fapar` and `fbpar` are set in the input file. Since these variables are needed for stella_v0.6.

AUTOMATIC_TESTS/numerical_tests/stella_releases/stella_v0.5

@@ -0,0 +1 @@
+/home/cookie/Documents/GitHub/stella-v0.5/stella

AUTOMATIC_TESTS/numerical_tests/stella_releases/stella_v0.6

@@ -0,0 +1 @@
+/home/cookie/Documents/GitHub/stella-v0.6/stella

AUTOMATIC_TESTS/numerical_tests/stella_releases/stella_v0.7

@@ -0,0 +1 @@
+/home/cookie/Documents/GitHub/stella-v0.7/stella

AUTOMATIC_TESTS/numerical_tests/test_1_whether_stella_runs/test_whether_stella_runs.py

@@ -75,6 +75,11 @@ def test_whether_correct_quantities_are_present_in_netcdf_file(error=False):
     # Find the netcdf output file which was generated during our local stella run
     local_netcdf_file = local_stella_run_directory / input_filename.replace('.in', '.out.nc')
 
+    # Different stella versions have different variables
+    stella_v8 = True
+    stella_v7 = False
+    stella_v6 = False
+
     # Open the netcdf file
     with xr.open_dataset(local_netcdf_file) as local_netcdf:
 
@@ -99,22 +104,35 @@ def test_whether_correct_quantities_are_present_in_netcdf_file(error=False):
 
         # Check whether all the diagnostics data is present in the netcdf file
         dist_extensions = ['_vs_vpamus', '_vs_zvpas', '_vs_zmus', '_vs_zvpamus']
-        expected_keys = ['t', 'omega', 'phi2', 'apar2', 'bpar2', 'omega']; new_keys = True
+        expected_keys = ['t', 'omega', 'phi2', 'apar2', 'bpar2', 'omega']; 
         expected_keys += [i+j for i in ['pflux', 'qflux', 'vflux'] for j in ['_vs_s', '_vs_kxkyzs']]
         expected_keys += [i+j for i in ['g2', 'h2', 'f2', 'g2nozonal', 'h2nozonal', 'f2nozonal'] for j in dist_extensions]
         expected_keys += ['g2_vs_zkykxs', 'h2_vs_zkykxs', 'f2_vs_zkykxs']
         for key in expected_keys:
             if (key not in local_netcdf): 
-                print(f'ERROR: The quantity {key} could not be found in the netcdf file.'); new_keys = False
+                print(f'ERROR: The quantity {key} could not be found in the netcdf file.')
+                stella_v8 = False; stella_v7 = True
 
         # Try old stella names
-        if new_keys==False:
+        if stella_v7==True:
             print('--------------------------------------------------')
-            print(' The new stella keys werent found, try old keys.')
+            print(' The new stella keys werent found, try older keys.')
             print('--------------------------------------------------')
-            expected_keys = ['t', 'omega', 'phi2', 'apar2', 'bpar2', 'pflx', 'vflx', 'phi_vs_t', 'phi2_vs_kxky', \
+            expected_keys = ['t', 'omega', 'phi2', 'apar2', 'bpar2', 'qflx', 'pflx', 'vflx', 'phi_vs_t', 'phi2_vs_kxky', \
                'pflx_vs_kxky', 'vflx_vs_kxky', 'qflx_vs_kxky', 'pflux_x', 'vflux_x', 'qflux_x', \
-               'dens_x', 'upar_x', 'temp_x', 'pflx_kxky', 'vflx_kxky', 'qflx_kxky', 'gvmus', 'gzvs']  
+               'dens_x', 'upar_x', 'temp_x', 'pflx_kxky', 'vflx_kxky', 'qflx_kxky', 'gvmus', 'gzvs'] 
+            for key in expected_keys:
+               if (key not in local_netcdf): 
+                   print(f'ERROR: The quantity {key} could not be found in the netcdf file.'); 
+                   stella_v7 = False; stella_v6 = True
+
+        # Try old stella names
+        if stella_v6==True:
+            print('--------------------------------------------------')
+            print(' The new stella keys werent found, try older keys.')
+            print('--------------------------------------------------')
+            expected_keys = ['t', 'omega', 'phi2', 'phi_vs_t', 'phi2_vs_kxky', 'pflux_x', 'vflux_x', 'qflux_x', \
+               'dens_x', 'upar_x', 'temp_x', 'pflx_kxky', 'vflx_kxky', 'qflx_kxky', 'gvmus', 'gzvs'] 
             for key in expected_keys:
                if (key not in local_netcdf): 
                    print(f'ERROR: The quantity {key} could not be found in the netcdf file.'); error = True