Set default logger to stdout and add output directory setting option for file loggers

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## latest
 
+- Set default logger to stdout and add output directory setting option for file loggers https://github.com/precice/micro-manager/pull/139
 - Remove the `adaptivity_data` data structure and handle all adaptivity data internally https://github.com/precice/micro-manager/pull/137
 - Improve logging by wrapping Python logger in a class https://github.com/precice/micro-manager/pull/133
 - Refactor large parts of solve and adaptivity to group datasets and simplify handling https://github.com/precice/micro-manager/pull/135

micro_manager/adaptivity/adaptivity.py

@@ -5,6 +5,7 @@
 from math import exp
 from typing import Callable
 from warnings import warn
+import subprocess
 from micro_manager.tools.logging_wrapper import Logger
 
 import numpy as np
@@ -37,9 +38,17 @@ def __init__(self, configurator, rank) -> None:
             configurator.get_adaptivity_similarity_measure()
         )
 
-        self._metrics_logger = Logger(
-            "Adaptivity", "adaptivity-metrics.csv", rank, csv_logger=True
-        )
+        output_dir = configurator.get_output_dir()
+
+        if output_dir is not None:
+            subprocess.run(["mkdir", "-p", output_dir])  # Create output directory
+            self._metrics_logger = Logger(
+                __name__, output_dir + "/adaptivity-metrics.csv", rank, csv_logger=True
+            )
+        else:
+            self._metrics_logger = Logger(
+                __name__, "adaptivity-metrics.csv", rank=rank, csv_logger=True
+            )
 
         self._metrics_logger.log_info_one_rank(
             "Time Window,Avg Active Sims,Avg Inactive Sims,Max Active,Max Inactive"

micro_manager/config.py

@@ -58,6 +58,8 @@ def __init__(self, config_file_name):
         self._postprocessing_file_name = None
         self._initialize_once = False
 
+        self._output_dir = None
+
     def set_logger(self, logger):
         """
         Set the logger for the Config class.
@@ -91,6 +93,13 @@ def _read_json(self, config_file_name):
             .replace(".py", "")
         )
 
+        try:
+            self._output_dir = self._data["output_dir"]
+        except BaseException:
+            self._logger.log_info_one_rank(
+                "No output directory provided. Output (including logging) will be saved in the current working directory."
+            )
+
         try:
             self._write_data_names = self._data["coupling_params"]["write_data_names"]
             assert isinstance(
@@ -640,3 +649,14 @@ def create_single_sim_object(self):
             True if initialization is done only once, False otherwise.
         """
         return self._initialize_once
+
+    def get_output_dir(self):
+        """
+        Get the name of the output directory.
+
+        Returns
+        -------
+        output_dir : string
+            Name of the output folder.
+        """
+        return self._output_dir

micro_manager/micro_manager.py

@@ -57,9 +57,7 @@ def __init__(self, config_file: str) -> None:
         """
         super().__init__(config_file)
 
-        self._logger = Logger(
-            "MicroManagerCoupling", "micro-manager-coupling.log", self._rank
-        )
+        self._logger = Logger(__name__, None, self._rank)
 
         self._config.set_logger(self._logger)
         self._config.read_json_micro_manager()

micro_manager/tools/logging_wrapper.py

@@ -3,14 +3,17 @@
 Provides a logging wrapper for the Micro Manager classes.
 """
 import logging
+import sys
 
 
 class Logger:
     """
     Provides a logging wrapper for the Micro Manager classes.
     """
 
-    def __init__(self, name, log_file, rank=0, level=logging.INFO, csv_logger=False):
+    def __init__(
+        self, name, log_file=None, rank=0, level=logging.INFO, csv_logger=False
+    ):
         """
         Set up a logger.
 
@@ -19,7 +22,7 @@ def __init__(self, name, log_file, rank=0, level=logging.INFO, csv_logger=False)
         name : string
             Name of the logger.
         log_file : string
-            Name of the log file.
+            Name of the log file (default is None).
         rank : int, optional
             Rank of the logger (default is 0).
         level : int, optional
@@ -30,16 +33,21 @@ def __init__(self, name, log_file, rank=0, level=logging.INFO, csv_logger=False)
 
         self._rank = rank
 
-        handler = logging.FileHandler(log_file)
+        if log_file is None:
+            handler = logging.StreamHandler(sys.stdout)
+        else:
+            handler = logging.FileHandler(log_file)
+
         handler.setLevel(level)
 
         if csv_logger:
             formatter = logging.Formatter("%(message)s")
         else:
             formatter = logging.Formatter(
-                "["
+                "("
                 + str(self._rank)
-                + "] %(asctime)s - %(name)s - %(levelname)s - %(message)s"
+                + ") %(asctime)s - %(name)s - %(levelname)s - %(message)s",
+                datefmt="%m/%d/%Y %I:%M:%S %p",
             )
 
         handler.setFormatter(formatter)

tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json

@@ -1,5 +1,6 @@
 {
     "micro_file_name": "micro_dummy",
+    "output_dir": "adaptivity_output",
     "coupling_params": {
         "precice_config_file_name": "precice-config.xml",
         "macro_mesh_name": "macro-cube-mesh",

tests/unit/test_adaptivity_parallel.py

@@ -30,6 +30,8 @@ def test_update_inactive_sims_global_adaptivity(self):
 
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
+        configurator.get_output_dir = MagicMock(return_value="output_dir")
+
         adaptivity_controller = GlobalAdaptivityCalculator(
             configurator, 5, global_ids, rank=self._rank, comm=self._comm
         )
@@ -108,6 +110,7 @@ def test_update_all_active_sims_global_adaptivity(self):
         configurator.get_adaptivity_refining_const = MagicMock(return_value=0.05)
         configurator.get_adaptivity_coarsening_const = MagicMock(return_value=0.2)
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L2rel")
+        configurator.get_output_dir = MagicMock(return_value="output_dir")
 
         adaptivity_controller = GlobalAdaptivityCalculator(
             configurator, 5, global_ids, rank=self._rank, comm=self._comm
@@ -175,6 +178,8 @@ def test_communicate_micro_output(self):
 
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
+        configurator.get_output_dir = MagicMock(return_value="output_dir")
+
         adaptivity_controller = GlobalAdaptivityCalculator(
             configurator, 5, global_ids, rank=self._rank, comm=self._comm
         )

tests/unit/test_adaptivity_serial.py

@@ -68,6 +68,8 @@ def test_get_similarity_dists(self):
         """
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
+        configurator.get_output_dir = MagicMock(return_value="output_dir")
+
         adaptivity_controller = AdaptivityCalculator(configurator, 0)
         adaptivity_controller._hist_param = 0.5
         adaptivity_controller._adaptivity_data_names = [
@@ -102,6 +104,8 @@ def test_update_active_sims(self):
         """
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
+        configurator.get_output_dir = MagicMock(return_value="output_dir")
+
         adaptivity_controller = AdaptivityCalculator(configurator, 0)
         adaptivity_controller._refine_const = self._refine_const
         adaptivity_controller._coarse_const = self._coarse_const
@@ -208,6 +212,8 @@ def test_associate_active_to_inactive(self):
         """
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
+        configurator.get_output_dir = MagicMock(return_value="output_dir")
+
         adaptivity_controller = AdaptivityCalculator(configurator, 0)
         adaptivity_controller._refine_const = self._refine_const
         adaptivity_controller._coarse_const = self._coarse_const
@@ -235,6 +241,8 @@ def test_update_inactive_sims_local_adaptivity(self):
         """
         configurator = MagicMock()
         configurator.get_adaptivity_similarity_measure = MagicMock(return_value="L1")
+        configurator.get_output_dir = MagicMock(return_value="output_dir")
+
         adaptivity_controller = LocalAdaptivityCalculator(
             configurator, 0, MagicMock(), 5
         )