Updated logging system: log formatting consistent across cli and direct

function calls, cli now includes log info from submodules, formatting
for clarity for warnings printing when progress bar is active.

src/pyscenic/__init__.py

@@ -2,3 +2,11 @@
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
+
+import logging
+from pyscenic.log import create_logging_handler
+LOGGER = logging.getLogger(__name__)
+# Set logging level.
+logging_debug_opt = False
+LOGGER.addHandler(create_logging_handler(logging_debug_opt))
+LOGGER.setLevel(logging.DEBUG)

src/pyscenic/cli/pyscenic.py

@@ -393,10 +393,6 @@ def create_argument_parser():
 
 
 def main(argv=None):
-    # Set logging level.
-    logging_debug_opt = False
-    LOGGER.addHandler(create_logging_handler(logging_debug_opt))
-    LOGGER.setLevel(logging.DEBUG)
 
     # Parse arguments.
     parser = create_argument_parser()

src/pyscenic/log.py

@@ -17,5 +17,5 @@ def create_logging_handler(debug: bool) -> logging.Handler:
     # to DEBUG, information will still be outputted. In addition, errors and warnings are more
     # severe than info and therefore will always be outputted to the log.
     ch.setLevel(logging.DEBUG if debug else logging.INFO)
-    ch.setFormatter(logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s'))
+    ch.setFormatter(logging.Formatter('\n%(asctime)s - %(name)s - %(levelname)s - %(message)s'))
     return ch