Swell logger extends logging.Logger

src/swell/deployment/create_experiment.py

@@ -21,7 +21,7 @@
 from swell.swell_path import get_swell_path
 from swell.utilities.dictionary import add_comments_to_dictionary, dict_get
 from swell.utilities.jinja2 import template_string_jinja2
-from swell.utilities.logger import Logger
+from swell.utilities.logger import Logger, get_logger
 from swell.utilities.slurm import prepare_scheduling_dict
 
 
@@ -36,7 +36,7 @@ def clone_config(
     advanced: bool
 ) -> str:
     # Create a logger
-    logger = Logger('SwellCloneExperiment')
+    logger = get_logger('SwellCloneExperiment')
 
     # Check that configuration exists and is a YAML file
     if not os.path.isfile(configuration):
@@ -76,7 +76,7 @@ def prepare_config(
 
     # Create a logger
     # ---------------
-    logger = Logger('SwellPrepSuiteConfig')
+    logger = get_logger('SwellPrepSuiteConfig')
 
     # Assert valid method
     # -------------------
@@ -167,7 +167,7 @@ def create_experiment_directory(
 
     # Create a logger
     # ---------------
-    logger = Logger('SwellCreateExperiment')
+    logger = get_logger('SwellCreateExperiment')
 
     # Call the experiment config and suite generation
     # ------------------------------------------------
@@ -277,7 +277,7 @@ def copy_platform_files(
             src_path_file = os.path.join(platform_path, os.path.split(s)[0], src_file)
             dst_path_file = os.path.join(exp_suite_path, '{}'.format(src_file))
             if os.path.exists(src_path_file):
-                logger.trace('Copying {} to {}'.format(src_path_file, dst_path_file))
+                logger.debug('Copying {} to {}'.format(src_path_file, dst_path_file))
                 shutil.copy(src_path_file, dst_path_file)
 
 

src/swell/deployment/launch_experiment.py

@@ -11,7 +11,7 @@
 import os
 
 # local imports
-from swell.utilities.logger import Logger
+from swell.utilities.logger import get_logger
 from swell.utilities.shell_commands import run_subprocess
 
 # --------------------------------------------------------------------------------------------------
@@ -27,7 +27,7 @@ def __init__(
         log_path: str
     ) -> None:
 
-        self.logger = Logger('DeployWorkflow')
+        self.logger = get_logger('DeployWorkflow')
         self.suite_path = suite_path
         self.experiment_name = experiment_name
         self.no_detach = no_detach
@@ -88,7 +88,8 @@ def cylc_run_experiment(self) -> None:  # NB: Could be a factory based on workfl
             self.logger.info(' ', False)
 
             # Launch the job monitor
-            self.logger.input('Launching the TUI, press \'q\' at any time to exit the TUI')
+            self.logger.critical('Launching the TUI, press \'q\' at any time to exit the TUI')
+            input()
             self.logger.info(' ', False)
             self.logger.info('TUI can be relaunched with:')
             self.logger.info(' ', False)

src/swell/tasks/base/task_base.py

@@ -24,7 +24,7 @@
 from swell.utilities.config import Config
 from swell.utilities.data_assimilation_window_params import DataAssimilationWindowParams
 from swell.utilities.datetime_util import Datetime
-from swell.utilities.logger import Logger
+from swell.utilities.logger import get_logger
 from swell.utilities.render_jedi_interface_files import JediConfigRendering
 from swell.utilities.geos import Geos
 
@@ -46,7 +46,7 @@ def __init__(
 
         # Create message logger
         # ---------------------
-        self.logger = Logger(task_name)
+        self.logger = get_logger(task_name)
 
         # Write out the initialization info
         # ---------------------------------

src/swell/test/code_tests/code_tests.py

@@ -11,7 +11,7 @@
 import os
 import unittest
 
-from swell.utilities.logger import Logger
+from swell.utilities.logger import get_logger
 from swell.test.code_tests.slurm_test import SLURMConfigTest
 from swell.test.code_tests.test_pinned_versions import PinnedVersionsTest
 from swell.test.code_tests.unused_variables_test import UnusedVariablesTest
@@ -24,12 +24,12 @@
 def code_tests() -> None:
 
     # Create a logger
-    logger = Logger('TestSuite')
-    logger.test('Running Swell Test Suite')
+    logger = get_logger('TestSuite')
+    logger.info('Running Swell Test Suite')
 
-    # Default log_info testing to false
-    os.environ.setdefault("LOG_INFO", "0")
-    # Set to 1 when errors are being debugged
+    # Default log_level minimum to warning
+    os.environ.setdefault("LOGLEVEL", "WARNING")
+    # Set to INFO or DEBUG when errors are being debugged
 
     # Create a test suite
     test_suite = unittest.TestSuite()

src/swell/test/code_tests/missing_obs_test.py

@@ -1,7 +1,7 @@
 from swell.utilities.datetime_util import Datetime
 from swell.utilities.run_jedi_executables import check_obs
 from swell.utilities.render_jedi_interface_files import JediConfigRendering
-from swell.utilities.logger import Logger
+from swell.utilities.logger import get_logger
 from datetime import datetime as dt
 
 '''
@@ -14,7 +14,7 @@
 # Set fields
 path_to_observing_sys_yamls = 'missing_obs_test/experiment/run/20211212T000000Z/' + \
                               'geos_atmosphere/observing_system_records'
-logger = Logger('Missing Obs Test')
+logger = get_logger('Missing Obs Test')
 cycle_time_str = '20211212T000000Z'
 cycle_time = dt.strptime(cycle_time_str, '%Y%m%dT%H%M%SZ')
 experiment_root = 'missing_obs_test'

src/swell/test/code_tests/slurm_test.py

@@ -7,10 +7,10 @@
 
 # --------------------------------------------------------------------------------------------------
 
-import logging
 import unittest
 
 from swell.utilities.slurm import prepare_scheduling_dict
+from swell.utilities.logger import get_logger
 from unittest.mock import patch, Mock
 
 # --------------------------------------------------------------------------------------------------
@@ -24,7 +24,7 @@ class SLURMConfigTest(unittest.TestCase):
     @patch("platform.platform")
     def test_slurm_config(self, platform_mocked: Mock, mock_global_defaults: Mock) -> None:
 
-        logger = logging.getLogger()
+        logger = get_logger()
 
         # Fake user-specified global values (for consistent unit tests)
         mock_global_defaults.return_value = {"qos": "dastest"}

src/swell/test/code_tests/test_generate_observing_system.py

@@ -2,7 +2,7 @@
 import unittest
 import subprocess
 from datetime import datetime as dt
-from swell.utilities.logger import Logger
+from swell.utilities.logger import get_logger
 from swell.utilities.get_channels import get_channels
 from swell.test.code_tests.testing_utilities import suppress_stdout
 from swell.utilities.observing_system_records import ObservingSystemRecords
@@ -27,7 +27,7 @@ class GenerateObservingSystemTest(unittest.TestCase):
 
     @classmethod
     def setUpClass(cls):
-        cls.logger = Logger("GenerateObservingSystemTest")
+        cls.logger = get_logger("GenerateObservingSystemTest")
         cls.observing_system_records_path = "./output/"
         cls.dt_cycle_time = dt.strptime("20211212T000000Z", "%Y%m%dT%H%M%SZ")
         cls.path_to_gsi_records = os.path.join("GEOS_mksi/", "sidb")
@@ -48,10 +48,15 @@ def test_geos_mksi_broken(self):
         abort_message = "\nHERE IS THE TRACEBACK: \n----------------------\n\n" + \
                         "Missing active channels for cris-fsr_npp, " + \
                         "Confirm that you are using the right version of GEOSmksi"
+
         with self.assertRaises(SystemExit) as abort, suppress_stdout():
+            # Suppress logging output for test
+            log_level = self.logger.level
+            self.logger.setLevel(60)
             get_channels(self.observing_system_records_path, observations[0],
                          self.dt_cycle_time, self.logger)
             self.assertEqual(abort.exception, abort_message)
+            self.logger.setLevel(log_level)
 
     def test_geos_mksi_develop(self):
 

src/swell/test/code_tests/test_pinned_versions.py

@@ -1,15 +1,15 @@
 import os
 import unittest
 import subprocess
-from swell.utilities.logger import Logger
+from swell.utilities.logger import get_logger
 from swell.test.code_tests.testing_utilities import suppress_stdout
 from swell.utilities.pinned_versions.check_hashes import check_hashes
 
 
 class PinnedVersionsTest(unittest.TestCase):
 
     def test_wrong_hash(self) -> None:
-        logger = Logger("PinnedVersionsTest")
+        logger = get_logger("PinnedVersionsTest")
         jedi_bundle_dir = "jedi_bundle/"
         if not os.path.exists(jedi_bundle_dir):
             os.makedirs(jedi_bundle_dir)
@@ -25,5 +25,9 @@ def test_wrong_hash(self) -> None:
         abort_message = "Wrong commit hashes found for these repositories in jedi_bundle: [oops]"
         # Run check hash (expect abort)
         with self.assertRaises(SystemExit) as abort, suppress_stdout():
+            # Suppress logging output for test
+            log_level = logger.level
+            logger.setLevel(60)
             check_hashes(jedi_bundle_dir, logger)
             self.assertEqual(abort.exception, abort_message)
+            logger.setLevel(log_level)

src/swell/test/platform_tests/check_hashes_discover.py

@@ -1,6 +1,6 @@
-from swell.utilities.logger import Logger
+from swell.utilities.logger import get_logger
 import swell.utilities.pinned_versions.check_hashes import check_hashes
 
-logger = Logger("CheckHashesTest")
+logger = get_logger("CheckHashesTest")
 bundle = "/discover/nobackup/projects/gmao/advda/jedi_bundles/current_pinned_jedi_bundle/source/"
 check_hashes(bundle, logger)

src/swell/test/test_driver.py

@@ -7,6 +7,7 @@
 # --------------------------------------------------------------------------------------------------
 
 import importlib
+import os
 
 # --------------------------------------------------------------------------------------------------
 
@@ -20,6 +21,9 @@ def test_wrapper(test: str) -> None:
     # Test script
     test_script_file = 'swell.test.'+test+'.'+test
 
+    # Suppress warning from NUMEXPR
+    os.environ['NUMEXPR_MAX_THREADS'] = str(8)
+
     # Import the correct method
     test_method = getattr(importlib.import_module(test_script_file), test)
 

src/swell/utilities/build.py

@@ -11,7 +11,7 @@
 import shutil
 from typing import Tuple
 
-from swell.utilities.logger import Logger
+from swell.utilities.logger import get_logger
 from jedi_bundle.utils.yaml import load_yaml
 from jedi_bundle.config.config import check_platform
 from jedi_bundle.bin.jedi_bundle import get_default_config
@@ -93,7 +93,7 @@ def set_jedi_bundle_config(
 
     # Add pinned_versions to jedi_bundle_config if applicable
     if use_pinned:
-        logger = Logger("LoadPinnedVersions")
+        logger = get_logger("LoadPinnedVersions")
         pinned_config_file = get_pinned_vers_path()
         pinned_versions_dict = load_yaml(logger, pinned_config_file)
         jedi_bundle_config['pinned_versions'] = pinned_versions_dict