colored logging messages added

conkit/command_line/__init__.py

@@ -34,6 +34,7 @@
 __version__ = "0.1"
 
 import logging
+import os
 
 
 def setup_logging(level='info', logfile=None):
@@ -54,6 +55,28 @@ def setup_logging(level='info', logfile=None):
        Instance of a :obj:`logger <logging.Logger>`
 
     """
+
+    class ColorFormatter(logging.Formatter):
+        """Formatter to color console logging output"""
+
+        # ANSI foreground color codes
+        colors = { 
+            logging.DEBUG: 34,           # blue
+            logging.INFO: 0   ,          # reset to default
+            logging.WARNING: 33,         # yellow
+            logging.ERROR: 31,           # red
+            logging.CRITICAL: 31,        # red
+        }
+
+        def format(self, record):
+            if record.exc_info is None:
+                # REM: get the ANSI FG color code
+                color = ColorFormatter.colors[record.levelno]
+                prefix = '\033[{}m'.format(color)
+                record.msg = os.linesep.join([prefix + l for l in str(record.msg).splitlines()])
+
+            return logging.Formatter.format(self, record)
+
     # Reset any Handlers or Filters already in the logger to start from scratch
     # https://stackoverflow.com/a/16966965
     map(logging.getLogger().removeHandler, logging.getLogger().handlers[:])
@@ -70,7 +93,7 @@ def setup_logging(level='info', logfile=None):
     # create console handler with a higher log level
     ch = logging.StreamHandler()
     ch.setLevel(logging_levels.get(level, logging.INFO))
-    ch.setFormatter(logging.Formatter('%(message)s'))
+    ch.setFormatter(ColorFormatter('%(message)s'))
     logging.getLogger().addHandler(ch)
 
     # create file handler which logs even debug messages
@@ -86,3 +109,4 @@ def setup_logging(level='info', logfile=None):
     logging.getLogger().debug('File logger level: %s', logging.NOTSET)
 
     return logging.getLogger()
+

conkit/command_line/conkit_convert.py

@@ -47,11 +47,12 @@
 __version__ = "0.1"
 
 import argparse
-import sys
 
 import conkit.command_line
 import conkit.io
 
+logger = None
+
 
 def main():
     parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -62,6 +63,7 @@ def main():
     args = parser.parse_args()
 
     # Setup the logger
+    global logger
     logger = conkit.command_line.setup_logging(level='info')
 
     # Perform the conversion
@@ -73,4 +75,13 @@ def main():
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    import sys 
+    import traceback
+    try:
+        main()
+        sys.exit(0)
+    except:
+        msg = "".join(traceback.format_exception(*sys.exc_info()))
+        logger.critical(msg)
+        sys.exit(1)
+

conkit/command_line/conkit_msatool.py

@@ -42,12 +42,13 @@
 __version__ = "0.1"
 
 import argparse
-import sys
 
 import conkit.command_line
 import conkit.io
 import conkit.plot
 
+logger = None
+
 
 def main():
     parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -56,6 +57,7 @@ def main():
     args = parser.parse_args()
 
     # Setup the logger
+    global logger
     logger = conkit.command_line.setup_logging(level='info')
 
     # Compute all the data
@@ -72,4 +74,13 @@ def main():
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    import sys 
+    import traceback
+    try:
+        main()
+        sys.exit(0)
+    except:
+        msg = "".join(traceback.format_exception(*sys.exc_info()))
+        logger.critical(msg)
+        sys.exit(1)
+

conkit/command_line/conkit_plot.py

@@ -43,11 +43,12 @@
 
 import argparse
 import inspect
-import sys
 
 import conkit.command_line
 import conkit.io
 import conkit.plot
+
+logger = None
 
 # Note:
 #     New subparsers can be added automatically as long as the convention is followed.
@@ -246,6 +247,7 @@ def main():
     args = parser.parse_args()
 
     # Setup the logger
+    global logger
     logger = conkit.command_line.setup_logging(level='info')
 
     if args.which == 'contact_map':
@@ -397,4 +399,13 @@ def altloc_remove(cmap):
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    import sys 
+    import traceback
+    try:
+        main()
+        sys.exit(0)
+    except:
+        msg = "".join(traceback.format_exception(*sys.exc_info()))
+        logger.critical(msg)
+        sys.exit(1)
+

conkit/command_line/conkit_precision.py

@@ -39,11 +39,12 @@
 __version__ = "0.1"
 
 import argparse
-import sys
 
 import conkit.command_line
 import conkit.io
 
+logger = None
+
 
 def main():
     parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -64,6 +65,7 @@ def main():
     args = parser.parse_args()
 
     # Setup the logger
+    global logger
     logger = conkit.command_line.setup_logging(level='info')
 
     # Compute all the data
@@ -93,5 +95,15 @@ def main():
 
     return 
 
+
 if __name__ == "__main__":
-    sys.exit(main())
+    import sys 
+    import traceback
+    try:
+        main()
+        sys.exit(0)
+    except:
+        msg = "".join(traceback.format_exception(*sys.exc_info()))
+        logger.critical(msg)
+        sys.exit(1)
+

conkit/command_line/conkit_predict.py

@@ -48,14 +48,15 @@
 
 import argparse
 import os
-import sys
 import time
 
 import conkit.applications
 import conkit.command_line
 import conkit.io
 import conkit.plot
 
+logger = None
+
 
 def add_default_args(parser):
     """Define default arguments"""
@@ -106,6 +107,7 @@ def main(argl=None):
     args = parser.parse_args(argl)
 
     # Setup the logger
+    global logger
     logger = conkit.command_line.setup_logging(level='info')
 
     logger.info('Prefix: %s', args.prefix)
@@ -224,4 +226,13 @@ def main(argl=None):
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    import sys 
+    import traceback
+    try:
+        main()
+        sys.exit(0)
+    except:
+        msg = "".join(traceback.format_exception(*sys.exc_info()))
+        logger.critical(msg)
+        sys.exit(1)
+