refactor: file changes to requirements.txt

Author: Benji918

requirements.txt

@@ -84,7 +84,6 @@ pydantic-settings==2.1.0
 pydantic_core==2.14.1
 pyflakes==3.1.0
 pyparsing==3.2.3
-pypdfium2==4.30.0
 pytest==7.4.3
 pytest-asyncio==0.21.1
 pytest-cov==4.1.0
@@ -100,7 +99,7 @@ requests==2.31.0
 rsa==4.9.1
 seaborn==0.13.0
 sentry-sdk==1.38.0
-shapely==1.8.5
+shapely==2.1.1
 six==1.17.0
 sniffio==1.3.1
 SQLAlchemy==2.0.23