test scripts

tests/test_xppbe.py

@@ -3,7 +3,7 @@
 import pytest
 import csv
 import shutil
-from xppbe.Simulation import Simulation
+from xppbe import Simulation
 from xppbe import Allrun,Allclean
 
 def run_checkers(sim,sim_name,temp_dir):
@@ -40,6 +40,19 @@ def run_checkers(sim,sim_name,temp_dir):
     print('Checkers Passed!')
 
 
+def test_scripts():
+    with tempfile.TemporaryDirectory() as temp_dir:
+        sim_name = f'test_born_ion'
+        yaml_path = os.path.join(os.path.dirname(__file__),'simulations_yaml',sim_name+'.yaml')
+        sims_path = os.path.join(temp_dir,'sims')
+        os.mkdir(sims_path)
+        shutil.copy(yaml_path,os.path.join(sims_path,sim_name+'.yaml'))
+        Allrun(sims_path=sims_path, results_path=temp_dir)
+        sim = Simulation(yaml_path, results_path=temp_dir)
+        run_checkers(sim,sim_name,temp_dir)
+        Allclean(results_path=temp_dir)
+        assert len(os.listdir(os.path.join(temp_dir,'results'))) == 0
+
 
 @pytest.mark.parametrize(
  ('molecule'),

xppbe/Scripts

@@ -17,6 +17,24 @@ function Allrun() {
         exit 1
     fi
 
+    PYTHON_CODE="
+import os
+import sys
+from xppbe import Simulation
+
+yaml_path = os.path.abspath(sys.argv[1])
+
+results_path = '${results_path%/results}'
+plot_pbj = '--pbj' in sys.argv
+plot_mesh = '--mesh' in sys.argv
+
+sim = Simulation(yaml_path, results_path=results_path)
+sim.create_simulation()
+sim.adapt_model()
+sim.solve_model()
+sim.postprocessing(mesh=plot_mesh, pbj=plot_pbj)
+    "
+
     sims_count=0
     for script_path in "$sims_path"/*.yaml
     do
@@ -51,10 +69,10 @@ function Allrun() {
                 echo "Running step: $i" 
                 new_iters=$(echo "( $num_iters_per_step*$i)" | bc)
                 sed -i "s/^N_iters: [0-9]\+/N_iters: $new_iters/" $script_path
-                python "$main_dir/Simulation.py" "$script_path" "--results-path=${results_path%/results}"
+                python -c "$PYTHON_CODE" "$script_path"
             done
         fi
-        python "$main_dir/Simulation.py" "$script_path" "--results-path=${results_path%/results}" "$pbj_flag" "$mesh_flag"
+        python -c "$PYTHON_CODE" "$script_path" "$pbj_flag" "$mesh_flag"
 
         echo "Ending Simulation $sims_count : $script_name"
         echo ""

xppbe/Simulation.py

@@ -286,7 +286,6 @@ def get_simulation_paths(self,yaml_path, molecule_path=None, results_path=None):
 
 if __name__=='__main__':
 
-    os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
     yaml_path = os.path.abspath(sys.argv[1])
 
     results_path = os.path.dirname(__file__)