chore: fix deprecation warnings

pyprobe/cell.py

@@ -428,7 +428,7 @@ def archive(self, path: str) -> None:
         ":func:`~Cell.import_from_cycler` method. To only process cycler files into the"
         " PyProBE format, use the :func:`process_cycler_data` function.",
         plain_reason="For integrated cycler file processing and data import, use the "
-        "import_from_cycler method`.To only process cycler files into the "
+        "import_from_cycler method. To only process cycler files into the "
         "PyProBE format, use the pyprobe.process_cycler_data function.",
         version="2.0.1",
     )
@@ -516,7 +516,7 @@ def process_cycler_file(
         "To only process cycler files into the "
         "PyProBE format, use the :func:`process_cycler_data` function.",
         plain_reason="For integrated cycler file processing and data import, use the "
-        "import_from_cycler method` using the 'generic' cycler. "
+        "import_from_cycler method using the 'generic' cycler. "
         "To only process cycler files into the "
         "PyProBE format, use the pyprobe.process_cycler_data function.",
         version="2.0.1",

pyprobe/utils.py

@@ -1,11 +1,13 @@
 """A collection of utility functions for PyProBE."""
 
 import functools
-import warnings
+import logging
 from typing import Any, Protocol
 
 from pydantic import ValidationError
 
+logger = logging.getLogger(__name__)
+
 
 def flatten_list(lst: int | list[Any]) -> list[int]:
     """Flatten a list of lists into a single list.
@@ -73,10 +75,8 @@ def deprecated(*, reason: str, version: str, plain_reason: str | None = None) ->
     def decorator(func: Any) -> Any:
         @functools.wraps(func)
         def wrapper(*args: Any, **kwargs: Any) -> Any:
-            warnings.warn(
-                plain_reason if plain_reason else reason,
-                DeprecationWarning,
-                stacklevel=2,
+            logger.warning(
+                "Deprecation Warning: " + plain_reason if plain_reason else reason,
             )
             return func(*args, **kwargs)