Make loggers module-specific

Matplolib sometimes logs verbosely to info, so this stops using the root logger
pinellolab · Oct 20, 2021 · c2bdd96 · c2bdd96
1 parent 8196b6a
commit c2bdd96
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Showing 8 changed files with 69 additions and 51 deletions.
diff --git a/CRISPResso2/CRISPRessoAggregateCORE.py b/CRISPResso2/CRISPRessoAggregateCORE.py
@@ -21,16 +21,19 @@
 
 
 import logging
-logging.basicConfig(level=logging.INFO,
+logging.basicConfig(
                      format='%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
                      datefmt='%a, %d %b %Y %H:%M:%S',
                      stream=sys.stderr,
                      filemode="w"
                      )
-error   = logging.critical
-warn    = logging.warning
-debug   = logging.debug
-info    = logging.info
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+error   = logger.critical
+warn    = logger.warning
+debug   = logger.debug
+info    = logger.info
 
 _ROOT = os.path.abspath(os.path.dirname(__file__))
 
@@ -77,7 +80,7 @@ def main():
              warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
         log_filename=_jp('CRISPRessoAggregate_RUNNING_LOG.txt')
-        logging.getLogger().addHandler(logging.FileHandler(log_filename))
+        logger.addHandler(logging.FileHandler(log_filename))
 
         with open(log_filename, 'w+') as outfile:
               outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' % ' '.join(sys.argv))

diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py
@@ -16,16 +16,19 @@
 from CRISPResso2 import CRISPRessoReport
 
 import logging
-logging.basicConfig(level=logging.INFO,
+logging.basicConfig(
                      format='%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
                      datefmt='%a, %d %b %Y %H:%M:%S',
                      stream=sys.stderr,
                      filemode="w"
                      )
-error   = logging.critical
-warn    = logging.warning
-debug   = logging.debug
-info    = logging.info
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+error   = logger.critical
+warn    = logger.warning
+debug   = logger.debug
+info    = logger.info
 
 _ROOT = os.path.abspath(os.path.dirname(__file__))
 
@@ -134,7 +137,7 @@ def main():
                  warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
         log_filename=_jp('CRISPRessoBatch_RUNNING_LOG.txt')
-        logging.getLogger().addHandler(logging.FileHandler(log_filename))
+        logger.addHandler(logging.FileHandler(log_filename))
 
         with open(log_filename, 'w+') as outfile:
             outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' % ' '.join(sys.argv))

diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py
@@ -41,17 +41,21 @@
 #    sys.exit(1)
 
 import logging
-#from test._mock_backport import inplace
-logging.basicConfig(level=logging.INFO,
+
+logging.basicConfig(
                      format='%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
                      datefmt='%a, %d %b %Y %H:%M:%S',
                      stream=sys.stderr,
                      filemode="w"
                      )
-error   = logging.critical
-warn    = logging.warning
-debug   = logging.debug
-info    = logging.info
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+error   = logger.critical
+warn    = logger.warning
+debug   = logger.debug
+info    = logger.info
 
 ####Support functions###
 
@@ -855,7 +859,7 @@ def print_stacktrace_if_debug():
             warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
         finally:
-            logging.getLogger().addHandler(logging.FileHandler(log_filename))
+            logger.addHandler(logging.FileHandler(log_filename))
 
             with open(log_filename, 'w+') as outfile:
                 outfile.write('CRISPResso version %s\n[Command used]:\n%s\n\n[Execution log]:\n' %(CRISPRessoShared.__version__, crispresso_cmd_to_write))

diff --git a/CRISPResso2/CRISPRessoCompareCORE.py b/CRISPResso2/CRISPRessoCompareCORE.py
@@ -14,16 +14,18 @@
 from CRISPResso2 import CRISPRessoReport
 
 import logging
-logging.basicConfig(level=logging.INFO,
+logging.basicConfig(
                      format='%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
                      datefmt='%a, %d %b %Y %H:%M:%S',
                      stream=sys.stderr,
                      filemode="w"
                      )
-error = logging.critical
-warn  = logging.warning
-debug = logging.debug
-info  = logging.info
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+error   = logger.critical
+warn    = logger.warning
+debug   = logger.debug
+info    = logger.info
 
 
 def check_library(library_name):
@@ -141,7 +143,7 @@ def main():
                  warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
         log_filename=_jp('CRISPRessoCompare_RUNNING_LOG.txt')
-        logging.getLogger().addHandler(logging.FileHandler(log_filename))
+        logger.addHandler(logging.FileHandler(log_filename))
 
         with open(log_filename, 'w+') as outfile:
                   outfile.write('[Command used]:\nCRISPRessoCompare %s\n\n[Execution log]:\n' % ' '.join(sys.argv))

diff --git a/CRISPResso2/CRISPRessoMetaCORE.py b/CRISPResso2/CRISPRessoMetaCORE.py
@@ -19,16 +19,19 @@
 
 
 import logging
-logging.basicConfig(level=logging.INFO,
+logging.basicConfig(
                      format='%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
                      datefmt='%a, %d %b %Y %H:%M:%S',
                      stream=sys.stderr,
                      filemode="w"
                      )
-error   = logging.critical
-warn    = logging.warning
-debug   = logging.debug
-info    = logging.info
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+error   = logger.critical
+warn    = logger.warning
+debug   = logger.debug
+info    = logger.info
 
 _ROOT = os.path.abspath(os.path.dirname(__file__))
 
@@ -228,7 +231,7 @@ def main():
             warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
         log_filename=_jp('CRISPRessoMeta_RUNNING_LOG.txt')
-        logging.getLogger().addHandler(logging.FileHandler(log_filename))
+        logger.addHandler(logging.FileHandler(log_filename))
 
         with open(log_filename, 'w+') as outfile:
             outfile.write('[Command used]:\n%s\n\n[Execution log]:\n' % ' '.join(sys.argv))

diff --git a/CRISPResso2/CRISPRessoPooledCORE.py b/CRISPResso2/CRISPRessoPooledCORE.py
@@ -24,18 +24,18 @@
 import traceback
 
 import logging
-logging.basicConfig(level=logging.INFO,
+logging.basicConfig(
                      format='%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
                      datefmt='%a, %d %b %Y %H:%M:%S',
                      stream=sys.stderr,
                      filemode="w"
                      )
-error   = logging.critical
-warn    = logging.warning
-debug   = logging.debug
-info    = logging.info
-
-
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+error   = logger.critical
+warn    = logger.warning
+debug   = logger.debug
+info    = logger.info
 
 _ROOT = os.path.abspath(os.path.dirname(__file__))
 
@@ -396,7 +396,7 @@ def main():
             warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
         log_filename=_jp('CRISPRessoPooled_RUNNING_LOG.txt')
-        logging.getLogger().addHandler(logging.FileHandler(log_filename))
+        logger.addHandler(logging.FileHandler(log_filename))
 
         crispresso2_info_file = os.path.join(
             OUTPUT_DIRECTORY, 'CRISPResso2Pooled_info.json',

diff --git a/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py b/CRISPResso2/CRISPRessoPooledWGSCompareCORE.py
@@ -17,16 +17,17 @@
 
 import logging
 logging.basicConfig(
-    level=logging.INFO,
     format='%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
     datefmt='%a, %d %b %Y %H:%M:%S',
     stream=sys.stderr,
     filemode="w"
 )
-error   = logging.critical
-warn    = logging.warning
-debug   = logging.debug
-info    = logging.info
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+error   = logger.critical
+warn    = logger.warning
+debug   = logger.debug
+info    = logger.info
 
 
 def check_library(library_name):
@@ -216,7 +217,7 @@ def main():
             warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
         log_filename = _jp('CRISPRessoPooledWGSCompare_RUNNING_LOG.txt')
-        logging.getLogger().addHandler(logging.FileHandler(log_filename))
+        logger.addHandler(logging.FileHandler(log_filename))
 
         with open(log_filename, 'w+') as outfile:
             outfile.write(

diff --git a/CRISPResso2/CRISPRessoWGSCORE.py b/CRISPResso2/CRISPRessoWGSCORE.py
@@ -24,16 +24,18 @@
 
 
 import logging
-logging.basicConfig(level=logging.INFO,
+logging.basicConfig(
                      format='%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
                      datefmt='%a, %d %b %Y %H:%M:%S',
                      stream=sys.stderr,
                      filemode="w"
                      )
-error   = logging.critical
-warn    = logging.warning
-debug   = logging.debug
-info    = logging.info
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+error   = logger.critical
+warn    = logger.warning
+debug   = logger.debug
+info    = logger.info
 
 
 _ROOT = os.path.abspath(os.path.dirname(__file__))
@@ -350,7 +352,7 @@ def print_stacktrace_if_debug():
                  warn('Folder %s already exists.' % OUTPUT_DIRECTORY)
 
         log_filename=_jp('CRISPRessoWGS_RUNNING_LOG.txt')
-        logging.getLogger().addHandler(logging.FileHandler(log_filename))
+        logger.addHandler(logging.FileHandler(log_filename))
 
         crispresso2_info_file = os.path.join(OUTPUT_DIRECTORY, 'CRISPResso2WGS_info.json')
         crispresso2_info = {'running_info': {}, 'results': {'alignment_stats': {}, 'general_plots': {}}} #keep track of all information for this run to be pickled and saved at the end of the run