diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 5d15ef3..a240fa6 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -27,6 +27,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install pytest
+        pip install pyopenms
+        pip install psims
         pip install -e .
     - name: Unzip system test file
       run: |
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..fbcbbdb
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,39 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "CsoDIAq"
+version = "2.0.0"
+authors = [
+  { name="Caleb Cranney", email="caleb.cranney.github@proton.me" },
+]
+description = "Bioinformatics software package for identifying peptides and proteins in DIA and DISPA mass spectrometry data files."
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+    'pyteomics>=4.4.1',
+    'matplotlib>=3.3.4',
+    'numba>=0.53.1',
+    'numpy>=1.20.1',
+    'pandas>=1.2.2',
+    'Bio>=0.4.1',
+    'PyQt5>=5.15.4',
+    'lxml>=4.6.2',
+    'scikit-learn>=1.1.2',
+]
+
+
+[project.urls]
+"Homepage" = "https://github.com/xomicsdatascience/CsoDIAq"
+"Bug Tracker" = "https://github.com/xomicsdatascience/CsoDIAq/issues"
+
+[project.scripts]
+csodiaq = "csodiaq.csodiaq:main"
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index a1dd95f..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-pyteomics==4.4.1
-matplotlib==3.3.4
-numba==0.53.1
-numpy==1.20.1
-pandas==1.2.2
-Bio==1.4.0
-PyQt5==5.15.4
diff --git a/setup.py b/setup.py
deleted file mode 100644
index d5d80ea..0000000
--- a/setup.py
+++ /dev/null
@@ -1,55 +0,0 @@
-import setuptools
-import os
-
-def readfile(filename):
-    with open(filename, 'r+') as f:
-        return f.read()
-
-
-def get_version(module_path: str) -> str:
-    """Gets the version from the specified file. Expected to be of format __version__ = 'x.y.z'"""
-    f = open(module_path, 'r')
-    lines = f.read().splitlines()
-    for l in lines:
-        if l.startswith('__version__'):
-            # Found version; parse
-            return l.split('=')[-1].strip().strip("'").strip('"')
-
-pwd = os.path.abspath(os.path.dirname(__file__))
-version = get_version(os.path.join(pwd, 'csodiaq/__init__.py'))
-
-setuptools.setup(
-    name="csodiaq",
-    version=version,
-    author="Meyer Lab",
-    author_email="",
-    description="CsoDIAq Package",
-    long_description=readfile('README.md'),
-    long_description_content_type="text/markdown",
-    url="",
-    classifiers=[
-        "Development Status :: 4 - Beta",
-        'Intended Audience :: Science/Research',
-        "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: MIT License"
-    ],
-    packages=setuptools.find_packages(),
-    python_requires='>=3.8',
-    license="MIT",
-    entry_points={
-        'console_scripts': [
-            'csodiaq = csodiaq.csodiaq:main'
-        ]
-    },
-    install_requires=[
-        'pyteomics>=4.4.1',
-        'matplotlib>=3.3.4',
-        'numba>=0.53.1',
-        'numpy>=1.20.1',
-        'pandas>=1.2.2',
-        'Bio>=0.4.1',
-        'PyQt5>=5.15.4',
-        'lxml>=4.6.2',
-        'scikit-learn>=1.1.2'
-    ],
-)
diff --git a/csodiaq/__init__.py b/src/csodiaq/__init__.py
similarity index 100%
rename from csodiaq/__init__.py
rename to src/csodiaq/__init__.py
diff --git a/csodiaq/csodiaq.py b/src/csodiaq/csodiaq.py
similarity index 100%
rename from csodiaq/csodiaq.py
rename to src/csodiaq/csodiaq.py
diff --git a/csodiaq/csodiaqParser.py b/src/csodiaq/csodiaqParser.py
similarity index 100%
rename from csodiaq/csodiaqParser.py
rename to src/csodiaq/csodiaqParser.py
diff --git a/csodiaq/gui/__init__.py b/src/csodiaq/gui/__init__.py
similarity index 100%
rename from csodiaq/gui/__init__.py
rename to src/csodiaq/gui/__init__.py
diff --git a/csodiaq/gui/gui.py b/src/csodiaq/gui/gui.py
similarity index 96%
rename from csodiaq/gui/gui.py
rename to src/csodiaq/gui/gui.py
index 6867913..64c58ae 100644
--- a/csodiaq/gui/gui.py
+++ b/src/csodiaq/gui/gui.py
@@ -2,7 +2,6 @@
     QApplication,
 )
 import sys
-import os
 
 from csodiaq.gui.windows import MainWindow
 
diff --git a/csodiaq/gui/windows/MainWindow.py b/src/csodiaq/gui/windows/MainWindow.py
similarity index 92%
rename from csodiaq/gui/windows/MainWindow.py
rename to src/csodiaq/gui/windows/MainWindow.py
index 5f1b80f..395bd50 100644
--- a/csodiaq/gui/windows/MainWindow.py
+++ b/src/csodiaq/gui/windows/MainWindow.py
@@ -1,7 +1,6 @@
 from PyQt5.QtWidgets import (
     QMainWindow,
 )
-from PyQt5.QtCore import Qt
 from csodiaq.gui.windows.TableWindow import TableWindow
 
 
diff --git a/csodiaq/gui/windows/TableWindow.py b/src/csodiaq/gui/windows/TableWindow.py
similarity index 100%
rename from csodiaq/gui/windows/TableWindow.py
rename to src/csodiaq/gui/windows/TableWindow.py
diff --git a/csodiaq/gui/windows/__init__.py b/src/csodiaq/gui/windows/__init__.py
similarity index 100%
rename from csodiaq/gui/windows/__init__.py
rename to src/csodiaq/gui/windows/__init__.py
diff --git a/csodiaq/gui/windows/tabs/IdentificationTabWindow.py b/src/csodiaq/gui/windows/tabs/IdentificationTabWindow.py
similarity index 100%
rename from csodiaq/gui/windows/tabs/IdentificationTabWindow.py
rename to src/csodiaq/gui/windows/tabs/IdentificationTabWindow.py
diff --git a/csodiaq/gui/windows/tabs/ScoringTabWindow.py b/src/csodiaq/gui/windows/tabs/ScoringTabWindow.py
similarity index 100%
rename from csodiaq/gui/windows/tabs/ScoringTabWindow.py
rename to src/csodiaq/gui/windows/tabs/ScoringTabWindow.py
diff --git a/csodiaq/gui/windows/tabs/TabWindow.py b/src/csodiaq/gui/windows/tabs/TabWindow.py
similarity index 100%
rename from csodiaq/gui/windows/tabs/TabWindow.py
rename to src/csodiaq/gui/windows/tabs/TabWindow.py
diff --git a/csodiaq/gui/windows/tabs/TargetedReanalysisTabWindow.py b/src/csodiaq/gui/windows/tabs/TargetedReanalysisTabWindow.py
similarity index 100%
rename from csodiaq/gui/windows/tabs/TargetedReanalysisTabWindow.py
rename to src/csodiaq/gui/windows/tabs/TargetedReanalysisTabWindow.py
diff --git a/csodiaq/gui/windows/tabs/__init__.py b/src/csodiaq/gui/windows/tabs/__init__.py
similarity index 100%
rename from csodiaq/gui/windows/tabs/__init__.py
rename to src/csodiaq/gui/windows/tabs/__init__.py
diff --git a/csodiaq/identification/__init__.py b/src/csodiaq/identification/__init__.py
similarity index 100%
rename from csodiaq/identification/__init__.py
rename to src/csodiaq/identification/__init__.py
diff --git a/csodiaq/identification/identifier.py b/src/csodiaq/identification/identifier.py
similarity index 100%
rename from csodiaq/identification/identifier.py
rename to src/csodiaq/identification/identifier.py
diff --git a/csodiaq/identification/matchingFunctions.py b/src/csodiaq/identification/matchingFunctions.py
similarity index 100%
rename from csodiaq/identification/matchingFunctions.py
rename to src/csodiaq/identification/matchingFunctions.py
diff --git a/csodiaq/identification/outputFormattingFunctions.py b/src/csodiaq/identification/outputFormattingFunctions.py
similarity index 93%
rename from csodiaq/identification/outputFormattingFunctions.py
rename to src/csodiaq/identification/outputFormattingFunctions.py
index bab1dad..968f03b 100644
--- a/csodiaq/identification/outputFormattingFunctions.py
+++ b/src/csodiaq/identification/outputFormattingFunctions.py
@@ -1,9 +1,5 @@
 import pandas as pd
 import numpy as np
-from csodiaq.scoring.scoringFunctions import (
-    calculate_fdr_rates_of_decoy_array,
-)
-from csodiaq.utils import format_protein_list_to_string, format_protein_string_to_list
 
 
 def format_output_line(libMetadata, queMetadata, matchMetadata):
diff --git a/csodiaq/identification/poolingFunctions.py b/src/csodiaq/identification/poolingFunctions.py
similarity index 88%
rename from csodiaq/identification/poolingFunctions.py
rename to src/csodiaq/identification/poolingFunctions.py
index bdefc05..8eed35c 100644
--- a/csodiaq/identification/poolingFunctions.py
+++ b/src/csodiaq/identification/poolingFunctions.py
@@ -1,6 +1,3 @@
-from csodiaq.loaders.library.libraryLoaderContext import LibraryLoaderContext
-from csodiaq.loaders.query.queryLoaderContext import QueryLoaderContext
-import pandas as pd
 import warnings
 from bisect import bisect
 
diff --git a/csodiaq/loaders/__init__.py b/src/csodiaq/loaders/__init__.py
similarity index 100%
rename from csodiaq/loaders/__init__.py
rename to src/csodiaq/loaders/__init__.py
index b1bd748..6f8d5c4 100644
--- a/csodiaq/loaders/__init__.py
+++ b/src/csodiaq/loaders/__init__.py
@@ -1,2 +1,2 @@
-from csodiaq.loaders.query import QueryLoaderContext
 from csodiaq.loaders.library import LibraryLoaderContext
+from csodiaq.loaders.query import QueryLoaderContext
diff --git a/csodiaq/loaders/library/__init__.py b/src/csodiaq/loaders/library/__init__.py
similarity index 100%
rename from csodiaq/loaders/library/__init__.py
rename to src/csodiaq/loaders/library/__init__.py
diff --git a/csodiaq/loaders/library/libraryLoaderContext.py b/src/csodiaq/loaders/library/libraryLoaderContext.py
similarity index 94%
rename from csodiaq/loaders/library/libraryLoaderContext.py
rename to src/csodiaq/loaders/library/libraryLoaderContext.py
index 5652a5d..e39255b 100644
--- a/csodiaq/loaders/library/libraryLoaderContext.py
+++ b/src/csodiaq/loaders/library/libraryLoaderContext.py
@@ -4,7 +4,6 @@
 from csodiaq.loaders.library.libraryLoaderStrategyMgf import (
     LibraryLoaderStrategyMgf as Mgf,
 )
-from csodiaq.loaders.library.libraryLoaderStrategy import LibraryLoaderStrategy
 import os
 
 
diff --git a/csodiaq/loaders/library/libraryLoaderStrategy.py b/src/csodiaq/loaders/library/libraryLoaderStrategy.py
similarity index 100%
rename from csodiaq/loaders/library/libraryLoaderStrategy.py
rename to src/csodiaq/loaders/library/libraryLoaderStrategy.py
diff --git a/csodiaq/loaders/library/libraryLoaderStrategyMgf.py b/src/csodiaq/loaders/library/libraryLoaderStrategyMgf.py
similarity index 99%
rename from csodiaq/loaders/library/libraryLoaderStrategyMgf.py
rename to src/csodiaq/loaders/library/libraryLoaderStrategyMgf.py
index ae91d52..333b0b6 100644
--- a/csodiaq/loaders/library/libraryLoaderStrategyMgf.py
+++ b/src/csodiaq/loaders/library/libraryLoaderStrategyMgf.py
@@ -4,7 +4,6 @@
     remove_low_intensity_peaks_below_max_peak_num,
     finalVariableNames,
 )
-import pandas as pd
 import os
 from pyteomics import mgf
 import re
diff --git a/csodiaq/loaders/library/libraryLoaderStrategyTable.py b/src/csodiaq/loaders/library/libraryLoaderStrategyTable.py
similarity index 100%
rename from csodiaq/loaders/library/libraryLoaderStrategyTable.py
rename to src/csodiaq/loaders/library/libraryLoaderStrategyTable.py
diff --git a/csodiaq/loaders/library/mappings.py b/src/csodiaq/loaders/library/mappings.py
similarity index 100%
rename from csodiaq/loaders/library/mappings.py
rename to src/csodiaq/loaders/library/mappings.py
diff --git a/csodiaq/loaders/query/__init__.py b/src/csodiaq/loaders/query/__init__.py
similarity index 100%
rename from csodiaq/loaders/query/__init__.py
rename to src/csodiaq/loaders/query/__init__.py
diff --git a/csodiaq/loaders/query/queryLoaderContext.py b/src/csodiaq/loaders/query/queryLoaderContext.py
similarity index 100%
rename from csodiaq/loaders/query/queryLoaderContext.py
rename to src/csodiaq/loaders/query/queryLoaderContext.py
diff --git a/csodiaq/loaders/query/queryLoaderStrategy.py b/src/csodiaq/loaders/query/queryLoaderStrategy.py
similarity index 100%
rename from csodiaq/loaders/query/queryLoaderStrategy.py
rename to src/csodiaq/loaders/query/queryLoaderStrategy.py
diff --git a/csodiaq/loaders/query/queryLoaderStrategyMzxml.py b/src/csodiaq/loaders/query/queryLoaderStrategyMzxml.py
similarity index 100%
rename from csodiaq/loaders/query/queryLoaderStrategyMzxml.py
rename to src/csodiaq/loaders/query/queryLoaderStrategyMzxml.py
diff --git a/csodiaq/plotting/__init__.py b/src/csodiaq/plotting/__init__.py
similarity index 100%
rename from csodiaq/plotting/__init__.py
rename to src/csodiaq/plotting/__init__.py
diff --git a/csodiaq/plotting/spectra.py b/src/csodiaq/plotting/spectra.py
similarity index 97%
rename from csodiaq/plotting/spectra.py
rename to src/csodiaq/plotting/spectra.py
index 51b0efd..8ea1342 100644
--- a/csodiaq/plotting/spectra.py
+++ b/src/csodiaq/plotting/spectra.py
@@ -1,5 +1,5 @@
 from matplotlib import pyplot as plt
-from csodiaq.plotting.spectrum import Spectrum
+from src.csodiaq.plotting.spectrum import Spectrum
 
 
 def spectrum_lineplot(spectrum: Spectrum,
diff --git a/csodiaq/plotting/spectrum.py b/src/csodiaq/plotting/spectrum.py
similarity index 100%
rename from csodiaq/plotting/spectrum.py
rename to src/csodiaq/plotting/spectrum.py
diff --git a/csodiaq/scoring/__init__.py b/src/csodiaq/scoring/__init__.py
similarity index 100%
rename from csodiaq/scoring/__init__.py
rename to src/csodiaq/scoring/__init__.py
diff --git a/csodiaq/scoring/fdrCalculationFunctions.py b/src/csodiaq/scoring/fdrCalculationFunctions.py
similarity index 100%
rename from csodiaq/scoring/fdrCalculationFunctions.py
rename to src/csodiaq/scoring/fdrCalculationFunctions.py
diff --git a/csodiaq/scoring/idpickerFunctions.py b/src/csodiaq/scoring/idpickerFunctions.py
similarity index 100%
rename from csodiaq/scoring/idpickerFunctions.py
rename to src/csodiaq/scoring/idpickerFunctions.py
diff --git a/csodiaq/scoring/scoringFunctions.py b/src/csodiaq/scoring/scoringFunctions.py
similarity index 100%
rename from csodiaq/scoring/scoringFunctions.py
rename to src/csodiaq/scoring/scoringFunctions.py
diff --git a/csodiaq/targetedReanalysis/__init__.py b/src/csodiaq/targetedReanalysis/__init__.py
similarity index 100%
rename from csodiaq/targetedReanalysis/__init__.py
rename to src/csodiaq/targetedReanalysis/__init__.py
diff --git a/csodiaq/targetedReanalysis/targetedReanalysisFunctions.py b/src/csodiaq/targetedReanalysis/targetedReanalysisFunctions.py
similarity index 100%
rename from csodiaq/targetedReanalysis/targetedReanalysisFunctions.py
rename to src/csodiaq/targetedReanalysis/targetedReanalysisFunctions.py
diff --git a/csodiaq/utils/Printer.py b/src/csodiaq/utils/Printer.py
similarity index 100%
rename from csodiaq/utils/Printer.py
rename to src/csodiaq/utils/Printer.py
diff --git a/csodiaq/utils/__init__.py b/src/csodiaq/utils/__init__.py
similarity index 100%
rename from csodiaq/utils/__init__.py
rename to src/csodiaq/utils/__init__.py
diff --git a/csodiaq/utils/utils.py b/src/csodiaq/utils/utils.py
similarity index 100%
rename from csodiaq/utils/utils.py
rename to src/csodiaq/utils/utils.py