Remove run_micro_manager.py from examples and tests

precice · May 17, 2024 · 08d70c0 · 08d70c0
1 parent 00069e0
commit 08d70c0
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Showing 7 changed files with 11 additions and 55 deletions.
diff --git a/.github/workflows/run-adaptivity-test.yml b/.github/workflows/run-adaptivity-test.yml
@@ -35,14 +35,14 @@ jobs:
         working-directory: micro-manager/tests/integration/test_unit_cube
         run: |
           export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
-          python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-local-adaptivity.json
+          python3 unit_cube.py & micro-manager-precice micro-manager-config-local-adaptivity.json
 
       - name: Run integration test with global adaptivity
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
         run: |
           export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
-          python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-global-adaptivity.json
+          python3 unit_cube.py & micro-manager-precice micro-manager-config-global-adaptivity.json
 
   adaptivity_unit_tests_serial:
     name: Run adaptivity unit tests in serial

diff --git a/.github/workflows/run-domain-decomposition-tests.yml b/.github/workflows/run-domain-decomposition-tests.yml
@@ -41,12 +41,12 @@ jobs:
       - name: Run integration test (variant 1)
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
-        run: mpiexec -n 2 --allow-run-as-root python3 run_micro_manager.py --config micro-manager-config-parallel-1.json & python3 unit_cube.py
+        run: mpiexec -n 2 --allow-run-as-root micro-manager-precice micro-manager-config-parallel-1.json & python3 unit_cube.py
 
       - name: Run integration test (variant 2)
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
-        run: mpiexec -n 6 --oversubscribe --allow-run-as-root python3 run_micro_manager.py --config micro-manager-config-parallel-2.json & python3 unit_cube.py
+        run: mpiexec -n 6 --oversubscribe --allow-run-as-root micro-manager-precice micro-manager-config-parallel-2.json & python3 unit_cube.py
 
   domain_decomposition_unit_tests:
     name: Run domain decomposition unit tests

diff --git a/.github/workflows/run-macro-micro-dummy.yml b/.github/workflows/run-macro-micro-dummy.yml
@@ -35,12 +35,12 @@ jobs:
       - name: Run python macro-micro dummy
         timeout-minutes: 3
         working-directory: micro-manager/examples
-        run: python3 python-dummy/run_micro_manager.py --config micro-manager-config.json & python3 macro_dummy.py
+        run: python3 micro-manager-precice micro-manager-config.json & python3 macro_dummy.py
 
       - name: Run adaptive python macro-micro dummy
         timeout-minutes: 3
         working-directory: micro-manager/examples
-        run: python3 python-dummy/run_micro_manager.py --config micro-manager-adaptivity-config.json & python3 macro_dummy.py
+        run: python3 micro-manager-precice micro-manager-adaptivity-config.json & python3 macro_dummy.py
 
       - name: Run c++ macro-micro dummy
         timeout-minutes: 3
@@ -50,9 +50,9 @@ jobs:
           pip install pybind11
           c++ -O3 -Wall -shared -std=c++11 -fPIC $(python3 -m pybind11 --includes) micro_cpp_dummy.cpp -o micro_dummy$(python3-config --extension-suffix)
           cd ../
-          python3 cpp-dummy/run_micro_manager.py --config micro-manager-config.json & python3 macro_dummy.py
+          python3 micro-manager-precice micro-manager-config.json & python3 macro_dummy.py
 
       - name: Run adaptive c++ macro-micro dummy
         timeout-minutes: 3
         working-directory: micro-manager/examples
-        run: python3 cpp-dummy/run_micro_manager.py --config micro-manager-adaptivity-config.json & python3 macro_dummy.py
+        run: python3 micro-manager-precice micro-manager-adaptivity-config.json & python3 macro_dummy.py
diff --git a/examples/cpp-dummy/run_micro_manager.py b/examples/cpp-dummy/run_micro_manager.py
diff --git a/examples/python-dummy/run_micro_manager.py b/examples/python-dummy/run_micro_manager.py
diff --git a/tests/integration/test_unit_cube/run_micro_manager.py b/tests/integration/test_unit_cube/run_micro_manager.py
diff --git a/tests/unit/test_micro_simulation_crash_handling.py b/tests/unit/test_micro_simulation_crash_handling.py
@@ -39,6 +39,8 @@ def test_crash_handling(self):
         expected_crash_scalar_data = 55 / 49
 
         manager = micro_manager.MicroManager("micro-manager-config_crash.json")
+        manager.initialize()
+
         manager._number_of_nearest_neighbors = 3  # reduce number of neighbors to 3
         manager._local_number_of_sims = 4
         manager._has_sim_crashed = [False] * 4
@@ -84,6 +86,7 @@ def test_crash_handling_with_adaptivity(self):
         expected_crash_scalar_data = 55 / 49
 
         manager = micro_manager.MicroManager("micro-manager-config_crash.json")
+        manager.initialize()
 
         manager._number_of_nearest_neighbors = 3  # reduce number of neighbors to 3
         manager._local_number_of_sims = 5