Merge branch 'develop' into joss-submission

README.md

@@ -6,6 +6,4 @@ The main documentation is rendered on the [preCICE website](https://precice.org/
 
 Please report any [issues](https://github.com/precice/micro-manager/issues) and give us feedback through [one of our community channels](https://precice.org/community-channels.html).
 
-The concept and initial design of the Micro Manager has been discussed in
-
-Desai, Ishaan, & Bringedal, Carina & Uekermann, Benjamin. A flexible software approach to simulate two-scale coupled problems. ECCOMAS Congress 2022. [10.23967/eccomas.2022.037](https://doi.org/10.23967/eccomas.2022.037).
+The concept and initial design of the Micro Manager has been discussed in *Desai, Ishaan, & Bringedal, Carina & Uekermann, Benjamin. A flexible software approach to simulate two-scale coupled problems. ECCOMAS Congress 2022. [10.23967/eccomas.2022.037](https://doi.org/10.23967/eccomas.2022.037)*.

micro_manager/config.py

@@ -12,7 +12,7 @@ class Config:
     the config class in https://github.com/precice/fenics-adapter/tree/develop/fenicsadapter
     """
 
-    def __init__(self, config_filename):
+    def __init__(self, logger, config_filename):
         """
         Constructor of the Config class.
 
@@ -21,6 +21,8 @@ def __init__(self, config_filename):
         config_filename : string
             Name of the JSON configuration file
         """
+        self._logger = logger
+
         self._micro_file_name = None
 
         self._config_file_name = None
@@ -77,7 +79,7 @@ def read_json(self, config_filename):
                 else:
                     raise Exception("Write data dictionary as a value other than 'scalar' or 'vector'")
         except BaseException:
-            print("No write data names provided. Micro manager will only read data from preCICE.")
+            self._logger.info("No write data names provided. Micro manager will only read data from preCICE.")
 
         try:
             self._read_data_names = data["coupling_params"]["read_data_names"]
@@ -90,22 +92,22 @@ def read_json(self, config_filename):
                 else:
                     raise Exception("Read data dictionary as a value other than 'scalar' or 'vector'")
         except BaseException:
-            print("No read data names provided. Micro manager will only write data to preCICE.")
+            self._logger.info("No read data names provided. Micro manager will only write data to preCICE.")
 
         self._macro_domain_bounds = data["simulation_params"]["macro_domain_bounds"]
 
         try:
             self._ranks_per_axis = data["simulation_params"]["decomposition"]
         except BaseException:
-            print("Domain decomposition is not specified, so the Micro Manager will expect to be run in serial.")
+            self._logger.info("Domain decomposition is not specified, so the Micro Manager will expect to be run in serial.")
 
         try:
             if data["simulation_params"]["adaptivity"]:
                 self._adaptivity = True
             else:
                 self._adaptivity = False
         except BaseException:
-            print("Micro Manager will not adaptively run micro simulations, but instead will run all micro simulations in all time steps.")
+            self._logger.info("Micro Manager will not adaptively run micro simulations, but instead will run all micro simulations in all time steps.")
 
         if self._adaptivity:
             if data["simulation_params"]["adaptivity"]["type"] == "local":
@@ -126,7 +128,7 @@ def read_json(self, config_filename):
             if "similarity_measure" in data["simulation_params"]["adaptivity"]:
                 self._adaptivity_similarity_measure = data["simulation_params"]["adaptivity"]["similarity_measure"]
             else:
-                print("No similarity measure provided, using L1 norm as default")
+                self._logger.info("No similarity measure provided, using L1 norm as default")
                 self._adaptivity_similarity_measure = "L1"
 
             adaptivity_every_implicit_iteration = data["simulation_params"]["adaptivity"]["every_implicit_iteration"]
@@ -137,7 +139,7 @@ def read_json(self, config_filename):
                 self._adaptivity_every_implicit_iteration = False
 
             if not self._adaptivity_every_implicit_iteration:
-                print("Micro Manager will compute adaptivity once at the start of every time window")
+                self._logger.info("Micro Manager will compute adaptivity once at the start of every time window")
 
             self._write_data_names["active_state"] = False
             self._write_data_names["active_steps"] = False
@@ -153,20 +155,20 @@ def read_json(self, config_filename):
                 else:
                     raise Exception("Diagnostics data dictionary as a value other than 'scalar' or 'vector'")
         except BaseException:
-            print("No diagnostics data is defined. Micro Manager will not output any diagnostics data.")
+            self._logger.info("No diagnostics data is defined. Micro Manager will not output any diagnostics data.")
 
         try:
             self._micro_output_n = data["diagnostics"]["micro_output_n"]
         except BaseException:
-            print("Output interval of micro simulations not specified, if output is available then it will be called "
+            self._logger.info("Output interval of micro simulations not specified, if output is available then it will be called "
                   "in every time window.")
 
         try:
             if data["diagnostics"]["output_micro_sim_solve_time"]:
                 self._output_micro_sim_time = True
                 self._write_data_names["micro_sim_time"] = False
         except BaseException:
-            print("Micro manager will not output time required to solve each micro simulation in each time step.")
+            self._logger.info("Micro manager will not output time required to solve each micro simulation in each time step.")
 
     def get_config_file_name(self):
         """

micro_manager/micro_manager.py

@@ -62,7 +62,7 @@ def __init__(self, config_file: str) -> None:
         self._micro_sims_have_output = False
 
         self._logger.info("Provided configuration file: {}".format(config_file))
-        self._config = Config(config_file)
+        self._config = Config(self._logger, config_file)
 
         # Define the preCICE interface
         self._interface = precice.Interface(

tests/unit/test_adaptivity_serial.py

@@ -2,11 +2,9 @@
 from unittest.mock import MagicMock
 from micro_manager.adaptivity.adaptivity import AdaptivityCalculator
 from micro_manager.adaptivity.local_adaptivity import LocalAdaptivityCalculator
-from micro_manager.adaptivity.global_adaptivity import GlobalAdaptivityCalculator
 from micro_manager.config import Config
 import numpy as np
 from math import exp
-from mpi4py import MPI
 
 
 class TestLocalAdaptivity(TestCase):

tests/unit/test_domain_decomposition.py

@@ -7,7 +7,7 @@
 class TestDomainDecomposition(TestCase):
     def setUp(self) -> None:
         self._logger = MagicMock()
-        self._macro_bounds_3d = [-1, 1, -2, 2, -2, 8]
+        self._macro_bounds_3d = [-1, 1, -2, 2, -2, 8]  # Cuboid which is not symmetric around origin
 
     def test_rank5_outof_10_3d(self):
         """

tests/unit/test_micro_manager.py

@@ -1,5 +1,6 @@
 import numpy as np
 from unittest import TestCase
+from unittest.mock import MagicMock
 import micro_manager
 
 
@@ -35,6 +36,9 @@ def setUp(self):
         self.macro_bounds = [0.0, 25.0, 0.0, 25.0, 0.0, 25.0]
 
     def test_micromanager_constructor(self):
+        """
+        Test if the constructor of the MicroManager class passes correct values to member variables.
+        """
         manager = micro_manager.MicroManager('micro-manager-config.json')
 
         self.assertListEqual(manager._macro_bounds, self.macro_bounds)
@@ -43,6 +47,9 @@ def test_micromanager_constructor(self):
         self.assertEqual(manager._micro_n_out, 10)
 
     def test_initialize(self):
+        """
+        Test if the initialize function of the MicroManager class initializes member variables to correct values
+        """
         manager = micro_manager.MicroManager('micro-manager-config.json')
 
         manager.initialize()
@@ -57,6 +64,9 @@ def test_initialize(self):
         self.assertDictEqual(self.fake_write_data_names, manager._write_data_names)
 
     def test_read_write_data_from_precice(self):
+        """
+        Test if the internal functions _read_data_from_precice and _write_data_to_precice work as expected.
+        """
         manager = micro_manager.MicroManager('micro-manager-config.json')
 
         manager._write_data_to_precice(self.fake_write_data)
@@ -68,6 +78,9 @@ def test_read_write_data_from_precice(self):
                                  fake_data["macro-vector-data"].tolist())
 
     def test_solve_mico_sims(self):
+        """
+        Test if the internal function _solve_micro_simulations works as expected.
+        """
         manager = micro_manager.MicroManager('micro-manager-config.json')
         manager._local_number_of_sims = 4
         manager._micro_sims = [MicroSimulation() for _ in range(4)]
@@ -81,7 +94,10 @@ def test_solve_mico_sims(self):
                                  (fake_data["micro-vector-data"] + 1).tolist())
 
     def test_config(self):
-        config = micro_manager.Config('micro-manager-config.json')
+        """
+        Test if the functions in the Config class work.
+        """
+        config = micro_manager.Config(MagicMock(), 'micro-manager-config.json')
 
         self.assertEqual(config._config_file_name.split("/")[-1], "dummy-config.xml")
         self.assertEqual(config._micro_file_name, "test_micro_manager")