From 628a176e8123a0a552919d3034cb903c533e666a Mon Sep 17 00:00:00 2001
From: chase mateusiak <chase.mateusiak@gmail.com>
Date: Thu, 31 Aug 2023 18:18:57 -0500
Subject: [PATCH 1/2] fixing logging

---
 src/isocomp/__main__.py                | 31 +++++---------------------
 src/isocomp/utils/configure_logging.py | 19 +++++++---------
 2 files changed, 14 insertions(+), 36 deletions(-)

diff --git a/src/isocomp/__main__.py b/src/isocomp/__main__.py
index c05bae6..498a2f0 100644
--- a/src/isocomp/__main__.py
+++ b/src/isocomp/__main__.py
@@ -12,6 +12,7 @@
 # local imports
 from .Coordinates import create_comparison_windows
 from .Compare import find_unique_isoforms
+from .utils.configure_logging import configure_logging
 
 logger = logging.getLogger(__name__)
 
@@ -328,34 +329,14 @@ def main(args=None) -> None:
     # help message
     try:
         log_level = args.log_level.upper()
+        if log_level not in ['CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG']:
+            raise ValueError("The logging level must be one of debug, "
+                             "info, warning, error, "
+                             "or critical.")
     except AttributeError:
         sys.exit(arg_parser.print_help())
 
-    # set the logging details
-    log_config = {
-        "version": 1,
-        "root": {
-            "handlers": ["console"],
-            "level": f"{log_level}"
-        },
-        "handlers": {
-            "console": {
-                "formatter": "std_out",
-                "class": "logging.StreamHandler"
-            }
-        },
-        "formatters": {
-            "std_out": {
-                "format": "%(asctime)s : %(module)s : " +
-                "%(funcName)s : line: %(lineno)d\n" +
-                "\tprocess details : %(process)d, %(processName)s\n" +
-                "\tthread details : %(thread)d, %(threadName)s\n" +
-                "\t%(levelname)s : %(message)s",
-                "datefmt": "%Y-%m-%d %H:%M:%S"
-            }
-        }
-    }
-    dictConfig(log_config)
+    configure_logging(log_level)
     # log the cmd line arguments at the debug level
     logger.debug(sys.argv)
     logger.debug(str(args))
diff --git a/src/isocomp/utils/configure_logging.py b/src/isocomp/utils/configure_logging.py
index e3142b6..44f1aa5 100644
--- a/src/isocomp/utils/configure_logging.py
+++ b/src/isocomp/utils/configure_logging.py
@@ -27,18 +27,15 @@ def configure_logging(level=logging.INFO,
     >>> configure_logging(level=logging.DEBUG)
     >>> configure_logging(level=logging.INFO)
     """
-    if level not in [logging.DEBUG,
-                     logging.INFO,
-                     logging.WARNING,
-                     logging.ERROR,
-                     logging.CRITICAL]:
-        raise ValueError("The logging level must be one of logging.DEBUG, "
-                         "logging.INFO, logging.WARNING, logging.ERROR, "
-                         "or logging.CRITICAL.")
-    
+    log_level = level.upper()
+    if log_level not in ['CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG']:
+        raise ValueError("The logging level must be one of debug, "
+                         "info, warning, error, "
+                         "or critical.")
+
     if not isinstance(to_file, bool):
         raise ValueError("to_file must be a boolean.")
-    
+
     if to_file:
         if not filename:
             raise ValueError("filename must be provided when to_file is True.")
@@ -69,7 +66,7 @@ def configure_logging(level=logging.INFO,
         'handlers': handlers,
         'root': {
             'handlers': list(handlers.keys()),
-            'level': level,
+            'level': log_level,
         },
     }
 

From f6080eda2a363f7082f7d8c337eb9b3deccf1769 Mon Sep 17 00:00:00 2001
From: chase mateusiak <chase.mateusiak@gmail.com>
Date: Thu, 31 Aug 2023 18:19:13 -0500
Subject: [PATCH 2/2] bump to version 0.2.2

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2ccbc16..6e204f9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "isocomp"
-version = "0.2.1"
+version = "0.2.2"
 description = ""
 authors = ["Yutong Qiu <yutongq@andrew.cmu.edu>", "Chia Sin Liew <chiasin.liew@unl.edu>", "Rupesh Kesharwani <rupesh.kesharwani@bcm.edu>", 
            "Bida Gu <bidagu@usc.edu>", "chase mateusiak <chase.mateusiak@gmail.com>",