Fix tests and add CHANGELOG entry

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## latest
 
+- Improve logging by wrapping Python logger in a class https://github.com/precice/micro-manager/pull/133
 - Add information about adaptivity tuning parameters https://github.com/precice/micro-manager/pull/131
 - Put computation of counting active steps inside the adaptivity variant `if` condition https://github.com/precice/micro-manager/pull/130
 

micro_manager/micro_manager.py

@@ -665,7 +665,7 @@ def _solve_micro_simulations(self, micro_sims_input: list, dt: float) -> list:
                             self._mesh_vertex_coords[count], micro_sims_input[count]
                         )
                     )
-                    self._logger.error(error_message)
+                    self._logger.log_error_any_rank(error_message)
                     self._has_sim_crashed[count] = True
 
         # If interpolate is off, terminate after crash
@@ -782,7 +782,7 @@ def _solve_micro_simulations_with_adaptivity(
                             self._mesh_vertex_coords[active_id]
                         )
                     )
-                    self._logger.error(error_message)
+                    self._logger.log_error_any_rank(error_message)
                     self._has_sim_crashed[active_id] = True
 
         # If interpolate is off, terminate after crash

micro_manager/tools/logging_wrapper.py

@@ -30,7 +30,9 @@ def __init__(self, name, log_file, rank=0, level=logging.INFO):
         handler.setLevel(level)
 
         formatter = logging.Formatter(
-            "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+            "["
+            + str(self._rank)
+            + "] %(asctime)s - %(name)s - %(levelname)s - %(message)s"
         )
         handler.setFormatter(formatter)
 
@@ -81,4 +83,4 @@ def log_error_any_rank(self, message):
         message : string
             Message to log.
         """
-        self._logger.error("[" + str(self._rank) + "] " + message)
+        self._logger.error(message)

tests/unit/test_adaptivity_parallel.py

@@ -31,7 +31,7 @@ def test_update_inactive_sims_global_adaptivity(self):
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
         adaptivity_controller = GlobalAdaptivityCalculator(
-            configurator, MagicMock(), 5, global_ids, rank=self._rank, comm=self._comm
+            configurator, 5, global_ids, rank=self._rank, comm=self._comm
         )
 
         # Force the activation of sim #0 and #4
@@ -105,7 +105,7 @@ def test_update_all_active_sims_global_adaptivity(self):
         configurator.get_adaptivity_coarsening_const = MagicMock(return_value=0.2)
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L2rel")
         adaptivity_controller = GlobalAdaptivityCalculator(
-            configurator, MagicMock(), 5, global_ids, rank=self._rank, comm=self._comm
+            configurator, 5, global_ids, rank=self._rank, comm=self._comm
         )
 
         adaptivity_controller._adaptivity_data_names = {
@@ -173,7 +173,7 @@ def test_communicate_micro_output(self):
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
         adaptivity_controller = GlobalAdaptivityCalculator(
-            configurator, MagicMock(), 5, global_ids, rank=self._rank, comm=self._comm
+            configurator, 5, global_ids, rank=self._rank, comm=self._comm
         )
 
         adaptivity_controller.communicate_micro_output(

tests/unit/test_adaptivity_serial.py

@@ -68,7 +68,7 @@ def test_get_similarity_dists(self):
         """
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
-        adaptivity_controller = AdaptivityCalculator(configurator, logger=MagicMock())
+        adaptivity_controller = AdaptivityCalculator(configurator)
         adaptivity_controller._hist_param = 0.5
         adaptivity_controller._adaptivity_data_names = [
             "micro-scalar-data",
@@ -102,7 +102,7 @@ def test_update_active_sims(self):
         """
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
-        adaptivity_controller = AdaptivityCalculator(configurator, logger=MagicMock())
+        adaptivity_controller = AdaptivityCalculator(configurator)
         adaptivity_controller._refine_const = self._refine_const
         adaptivity_controller._coarse_const = self._coarse_const
         adaptivity_controller._adaptivity_data_names = [
@@ -127,8 +127,7 @@ def test_adaptivity_norms(self):
         """
         Test functionality for calculating similarity criteria between pairs of simulations using different norms in class AdaptivityCalculator.
         """
-        logger = MagicMock()
-        calc = AdaptivityCalculator(Config(logger, "micro-manager-config.json"), logger)
+        calc = AdaptivityCalculator(Config("micro-manager-config.json"))
 
         fake_data = np.array([[1], [2], [3]])
         self.assertTrue(
@@ -209,7 +208,7 @@ def test_associate_active_to_inactive(self):
         """
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
-        adaptivity_controller = AdaptivityCalculator(configurator, logger=MagicMock())
+        adaptivity_controller = AdaptivityCalculator(configurator)
         adaptivity_controller._refine_const = self._refine_const
         adaptivity_controller._coarse_const = self._coarse_const
         adaptivity_controller._adaptivity_data_names = [
@@ -236,9 +235,7 @@ def test_update_inactive_sims_local_adaptivity(self):
         """
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
-        adaptivity_controller = LocalAdaptivityCalculator(
-            configurator, logger=MagicMock()
-        )
+        adaptivity_controller = LocalAdaptivityCalculator(configurator)
         adaptivity_controller._refine_const = self._refine_const
         adaptivity_controller._coarse_const = self._coarse_const
         adaptivity_controller._adaptivity_data_names = [

tests/unit/test_micro_manager.py

@@ -119,7 +119,7 @@ def test_config(self):
         """
         Test if the functions in the Config class work.
         """
-        config = micro_manager.Config(MagicMock(), "micro-manager-config.json")
+        config = micro_manager.Config("micro-manager-config.json")
         config.read_json_micro_manager()
         self.assertEqual(config._config_file_name.split("/")[-1], "dummy-config.xml")
         self.assertEqual(config._micro_file_name, "test_micro_manager")

tests/unit/test_snapshot_computation.py

@@ -136,7 +136,7 @@ def test_config(self):
         """
         Test if the functions in the SnapshotConfig class work.
         """
-        config = Config(MagicMock(), "snapshot-config.json")
+        config = Config("snapshot-config.json")
         config.read_json_snapshot()
 
         self.assertEqual(