diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..0586ecb
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,37 @@
+[build-system]
+requires = ["setuptools>=60.5", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "colint"
+version = "0.1"
+description = ""
+authors = [
+    { name = "Davide Colì", email = "davide.coli@secomind.com" },
+]
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "black>=25.1.0",
+    "exceptiongroup>=1.2.2",
+    "flake8-docstrings>=1.7.0",
+    "GitPython>=3.1.43",
+    "ipykernel>=6.29.5",
+    "isort>=6.0.1",
+    "tokenize-rt>=6.0.0",
+    "toml>=0.10.2",
+    "tomli>=2.0.1",
+    "typing-extensions>=4.12.2",
+]
+
+[project.scripts]
+colint = "colint.colinter:main"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"colint" = ["*.toml"]
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index e211846..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,48 +0,0 @@
-asttokens==2.4.1
-black==24.8.0
-click==8.1.7
-comm==0.2.2
-debugpy==1.8.5
-decorator==5.1.1
-exceptiongroup==1.2.2
-executing==2.1.0
-flake8==7.1.1
-flake8-docstrings==1.7.0
-gitdb==4.0.11
-GitPython==3.1.43
-ipykernel==6.29.5
-ipython==8.27.0
-isort==5.13.2
-jedi==0.19.1
-jupyter_client==8.6.3
-jupyter_core==5.7.2
-matplotlib-inline==0.1.7
-mccabe==0.7.0
-mypy-extensions==1.0.0
-nest-asyncio==1.6.0
-packaging==24.1
-parso==0.8.4
-pathspec==0.12.1
-pexpect==4.9.0
-platformdirs==4.3.2
-prompt_toolkit==3.0.47
-psutil==6.0.0
-ptyprocess==0.7.0
-pure_eval==0.2.3
-pycodestyle==2.12.1
-pydocstyle==6.3.0
-pyflakes==3.2.0
-Pygments==2.18.0
-python-dateutil==2.9.0.post0
-pyzmq==26.2.0
-six==1.16.0
-smmap==5.0.1
-snowballstemmer==2.2.0
-stack-data==0.6.3
-tokenize-rt==6.0.0
-toml==0.10.2
-tomli==2.0.1
-tornado==6.4.1
-traitlets==5.14.3
-typing_extensions==4.12.2
-wcwidth==0.2.13
diff --git a/setup.py b/setup.py
deleted file mode 100644
index b93101f..0000000
--- a/setup.py
+++ /dev/null
@@ -1,18 +0,0 @@
-from setuptools import find_packages, setup
-
-with open("requirements.txt") as f:
-    requirements = f.read().splitlines()
-setup(
-    name="colint",
-    version="0.1",
-    packages=find_packages(),
-    package_data={
-        "colint": ["pyproject.toml"],
-    },
-    install_requires=requirements,
-    entry_points={
-        "console_scripts": [
-            "colint=colint.colinter:main",
-        ],
-    },
-)
diff --git a/colint/__init__.py b/src/colint/__init__.py
similarity index 100%
rename from colint/__init__.py
rename to src/colint/__init__.py
diff --git a/colint/clean_jupyter/__init__.py b/src/colint/clean_jupyter/__init__.py
similarity index 100%
rename from colint/clean_jupyter/__init__.py
rename to src/colint/clean_jupyter/__init__.py
diff --git a/colint/clean_jupyter/clean_jupyter.py b/src/colint/clean_jupyter/clean_jupyter.py
similarity index 100%
rename from colint/clean_jupyter/clean_jupyter.py
rename to src/colint/clean_jupyter/clean_jupyter.py
diff --git a/colint/code_format/__init__.py b/src/colint/code_format/__init__.py
similarity index 100%
rename from colint/code_format/__init__.py
rename to src/colint/code_format/__init__.py
diff --git a/colint/code_format/code_format.py b/src/colint/code_format/code_format.py
similarity index 100%
rename from colint/code_format/code_format.py
rename to src/colint/code_format/code_format.py
diff --git a/colint/colinter.py b/src/colint/colinter.py
similarity index 98%
rename from colint/colinter.py
rename to src/colint/colinter.py
index d07d7e3..d525c13 100644
--- a/colint/colinter.py
+++ b/src/colint/colinter.py
@@ -10,7 +10,7 @@
 from .params.params import Params
 from .sort_libraries.sorter import sort_imports
 
-config_file = Path(__file__).parent / "pyproject.toml"
+config_file = Path(__file__).parent / "config.toml"
 params = Params.from_toml(config_file)
 
 COMMANDS = {
diff --git a/colint/pyproject.toml b/src/colint/config.toml
similarity index 100%
rename from colint/pyproject.toml
rename to src/colint/config.toml
diff --git a/colint/docformat/__init__.py b/src/colint/docformat/__init__.py
similarity index 100%
rename from colint/docformat/__init__.py
rename to src/colint/docformat/__init__.py
diff --git a/colint/docformat/apply_google_style.py b/src/colint/docformat/apply_google_style.py
similarity index 100%
rename from colint/docformat/apply_google_style.py
rename to src/colint/docformat/apply_google_style.py
diff --git a/colint/docformat/docformat.py b/src/colint/docformat/docformat.py
similarity index 100%
rename from colint/docformat/docformat.py
rename to src/colint/docformat/docformat.py
diff --git a/colint/docformat/format_commented_lines.py b/src/colint/docformat/format_commented_lines.py
similarity index 100%
rename from colint/docformat/format_commented_lines.py
rename to src/colint/docformat/format_commented_lines.py
diff --git a/colint/docformat/format_docstring.py b/src/colint/docformat/format_docstring.py
similarity index 100%
rename from colint/docformat/format_docstring.py
rename to src/colint/docformat/format_docstring.py
diff --git a/colint/docformat/format_text.py b/src/colint/docformat/format_text.py
similarity index 100%
rename from colint/docformat/format_text.py
rename to src/colint/docformat/format_text.py
diff --git a/colint/grammar_libraries/__init__.py b/src/colint/grammar_libraries/__init__.py
similarity index 100%
rename from colint/grammar_libraries/__init__.py
rename to src/colint/grammar_libraries/__init__.py
diff --git a/colint/grammar_libraries/flake8error.py b/src/colint/grammar_libraries/flake8error.py
similarity index 100%
rename from colint/grammar_libraries/flake8error.py
rename to src/colint/grammar_libraries/flake8error.py
diff --git a/colint/grammar_libraries/get_custom_style_guide.py b/src/colint/grammar_libraries/get_custom_style_guide.py
similarity index 100%
rename from colint/grammar_libraries/get_custom_style_guide.py
rename to src/colint/grammar_libraries/get_custom_style_guide.py
diff --git a/colint/grammar_libraries/grammar_check.py b/src/colint/grammar_libraries/grammar_check.py
similarity index 100%
rename from colint/grammar_libraries/grammar_check.py
rename to src/colint/grammar_libraries/grammar_check.py
diff --git a/colint/newline_fix/__init__.py b/src/colint/newline_fix/__init__.py
similarity index 100%
rename from colint/newline_fix/__init__.py
rename to src/colint/newline_fix/__init__.py
diff --git a/colint/newline_fix/newline_fix.py b/src/colint/newline_fix/newline_fix.py
similarity index 100%
rename from colint/newline_fix/newline_fix.py
rename to src/colint/newline_fix/newline_fix.py
diff --git a/colint/params/__init__.py b/src/colint/params/__init__.py
similarity index 100%
rename from colint/params/__init__.py
rename to src/colint/params/__init__.py
diff --git a/colint/params/black_params.py b/src/colint/params/black_params.py
similarity index 100%
rename from colint/params/black_params.py
rename to src/colint/params/black_params.py
diff --git a/colint/params/exceptions.py b/src/colint/params/exceptions.py
similarity index 100%
rename from colint/params/exceptions.py
rename to src/colint/params/exceptions.py
diff --git a/colint/params/flake8_params.py b/src/colint/params/flake8_params.py
similarity index 100%
rename from colint/params/flake8_params.py
rename to src/colint/params/flake8_params.py
diff --git a/colint/params/isort_params.py b/src/colint/params/isort_params.py
similarity index 100%
rename from colint/params/isort_params.py
rename to src/colint/params/isort_params.py
diff --git a/colint/params/params.py b/src/colint/params/params.py
similarity index 100%
rename from colint/params/params.py
rename to src/colint/params/params.py
diff --git a/colint/sort_libraries/__init__.py b/src/colint/sort_libraries/__init__.py
similarity index 100%
rename from colint/sort_libraries/__init__.py
rename to src/colint/sort_libraries/__init__.py
diff --git a/colint/sort_libraries/sorter.py b/src/colint/sort_libraries/sorter.py
similarity index 92%
rename from colint/sort_libraries/sorter.py
rename to src/colint/sort_libraries/sorter.py
index a312161..92db1c2 100644
--- a/colint/sort_libraries/sorter.py
+++ b/src/colint/sort_libraries/sorter.py
@@ -1,11 +1,12 @@
 import io
+import os
 from pathlib import Path
 
 import isort
 
 from ..params.isort_params import IsortParams
 from ..utils.jupyter_utils import JupyterNotebokParser
-from ..utils.os_utils import get_valid_files
+from ..utils.os_utils import get_git_repo, get_valid_files
 from ..utils.text_styling_utils import TextModifiers, style_text
 
 FILE_SORTED_MESSAGE = "! File has been sorted: "
@@ -89,6 +90,12 @@ def sort_imports(path: str, only_check: bool, params: IsortParams) -> bool:
         bool: Boolean indicating if any imports have been sorted in any file.
     """
     files = get_valid_files(path)
+    git_repo = get_git_repo(path)
+    current_directory = os.getcwd()
+
+    if git_repo is not None:
+        new_dir = Path(git_repo.git_dir).parent.absolute()
+        os.chdir(str(new_dir))
 
     some_file_has_been_sorted = False
 
@@ -125,4 +132,7 @@ def sort_imports(path: str, only_check: bool, params: IsortParams) -> bool:
         if file_not_linted:
             print(__style_message(f, only_check))
 
+    if os.getcwd() != current_directory:
+        os.chdir(current_directory)
+
     return some_file_has_been_sorted
diff --git a/colint/utils/__init__.py b/src/colint/utils/__init__.py
similarity index 100%
rename from colint/utils/__init__.py
rename to src/colint/utils/__init__.py
diff --git a/colint/utils/exceptions.py b/src/colint/utils/exceptions.py
similarity index 100%
rename from colint/utils/exceptions.py
rename to src/colint/utils/exceptions.py
diff --git a/colint/utils/jupyter_utils.py b/src/colint/utils/jupyter_utils.py
similarity index 100%
rename from colint/utils/jupyter_utils.py
rename to src/colint/utils/jupyter_utils.py
diff --git a/colint/utils/os_utils.py b/src/colint/utils/os_utils.py
similarity index 85%
rename from colint/utils/os_utils.py
rename to src/colint/utils/os_utils.py
index 3dbdd3c..0262762 100644
--- a/colint/utils/os_utils.py
+++ b/src/colint/utils/os_utils.py
@@ -52,8 +52,12 @@ def get_valid_files(path: str | Path) -> list[str]:
         str(f) for f in Path(path).rglob("*") if f.is_file() and ".git" not in f.parts
     ]
 
+    valid_files = set(files)
+
     if repo:  # If a git repository exists, remove files in gitignore
-        repo_ignore = set(repo.ignored(files))
-        files = list(set(files).difference(repo_ignore))
+        batch_size = 100
+        for k in range(0, len(files), batch_size):
+            repo_ignore = set(repo.ignored(files[k : k + batch_size]))
+            valid_files.difference_update(repo_ignore)
 
-    return sorted(files)
+    return sorted(list(valid_files))
diff --git a/colint/utils/text_styling_utils.py b/src/colint/utils/text_styling_utils.py
similarity index 100%
rename from colint/utils/text_styling_utils.py
rename to src/colint/utils/text_styling_utils.py