From fcb72ec49c2228e27730130eb06e6741e8b2eceb Mon Sep 17 00:00:00 2001
From: Clarence Mah <clarence.k.mah@gmail.com>
Date: Fri, 5 Apr 2024 22:15:26 +0000
Subject: [PATCH] more merge conflicts

---
 bento/_settings.py | 101 ---------------------------------------------
 bento/tools/_lp.py |   4 +-
 2 files changed, 2 insertions(+), 103 deletions(-)
 delete mode 100644 bento/_settings.py

diff --git a/bento/_settings.py b/bento/_settings.py
deleted file mode 100644
index 3aee303..0000000
--- a/bento/_settings.py
+++ /dev/null
@@ -1,101 +0,0 @@
-import logging
-from rich.logging import RichHandler
-
-
-class Settings:
-    """
-    Settings class for Bento.
-
-    Parameters
-    ----------
-    verbosity : int
-        Verbosity level for logging. Default is 0. See the logging module for more information (https://docs.python.org/3/howto/logging.html#logging-levels).
-    log : logging.Logger
-        Logger object for Bento.
-    """
-
-    def __init__(self, verbosity):
-        self._verbosity = verbosity
-        self._log = Logger(verbosity)
-
-    @property
-    def verbosity(self):
-        return self._verbosity
-
-    @verbosity.setter
-    def verbosity(self, value):
-        self._verbosity = value
-        self._log.setLevel(value)
-
-    @property
-    def log(self):
-        return self._log
-
-
-class Logger:
-    def __init__(self, verbosity):
-
-        FORMAT = "%(message)s"
-        logging.basicConfig(
-            level=verbosity, format=FORMAT, datefmt="[%X]", handlers=[RichHandler(markup=True)]
-        )
-        self._logger = logging.getLogger("rich")
-
-    def debug(self, text):
-        self._logger.debug(text)
-
-    def info(self, text):
-        self._logger.info(text)
-
-    def warn(self, text):
-        self._logger.warning(text)
-
-
-    def start(self, text):
-        """
-        Alias for self.info(). Start logging a method.
-
-        Parameters
-        ----------
-        text : str
-            Text to log.
-        """
-        self.info(f"[bold]{text}[/]")
-
-
-    def step(self, text):
-        """
-        Alias for self.info(). Step logging.
-
-        Parameters
-        ----------
-        text : str
-            Text to log.
-        """
-        self._logger.info(text)
-
-
-    def end(self, text):
-        """
-        End logging.
-
-        Parameters
-        ----------
-        text : str
-            Text to log.
-        """
-        self._logger.info(f"[bold]{text}[/]")
-
-    def setLevel(self, value):
-        """
-        Set the verbosity level of the logger.
-
-        Parameters
-        ----------
-        value : int
-            Verbosity level for logging.
-        """
-        self._logger.setLevel(value)
-
-
-settings = Settings(verbosity="WARNING")
diff --git a/bento/tools/_lp.py b/bento/tools/_lp.py
index bd3b4ce..82af1ba 100644
--- a/bento/tools/_lp.py
+++ b/bento/tools/_lp.py
@@ -87,8 +87,8 @@ def lp(
     X_df = sdata.table.uns[feature_key][pattern_features]
 
     # Load trained model
-    model_path = os.path.join(os.path.split(bento.__file__)[0], "models", "rf_calib_20220514.pkl")
-    model = pickle.load(open(model_path, "rb"))
+    model_dir = "/".join(bento.__file__.split("/")[:-1]) + "/models"
+    model = pickle.load(open(f"{model_dir}/rf_calib_20220514.pkl", "rb"))
 
     # Compatibility with newer versions of scikit-learn
     for cls in model.calibrated_classifiers_: