diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
index dfa8472..9fb8509 100644
--- a/.github/workflows/pytest.yaml
+++ b/.github/workflows/pytest.yaml
@@ -1,37 +1,41 @@
 ---
-name: pytest
+name: Run PyTest
 
 on:
   pull_request:
     branches:
       - main
+  push:
+    branches:
+      - main
+
 jobs:
   pytest:
     runs-on: ubuntu-latest
 
-    timeout-minutes: 15
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - "3.8"
+          - "3.12"
 
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .
-      - name: Test with pytest
+          python-version: ${{ matrix.python-version }}
+
+      - name: Run tests
         run: |
-          pytest test \
-            --doctest-modules \
-            --junitxml=junit/test-results.xml
+          pip install tox
+          tox -e py${{matrix.python-version}}
+
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
+        if: success() || failure()
         with:
-          name: test-results.xml
+          name: "pytest-${{ matrix.python-version }}.xml"
           path: junit/test-results.xml
           if-no-files-found: error
-        # Use always() to always run this step to publish test results when
-        # there are test failures
-        if: ${{ always() }}
diff --git a/.gitignore b/.gitignore
index b4b1eb0..5a35ec3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,3 +16,6 @@ build
 venv
 .env
 junit
+.tox/
+.pytest_cache/
+_version.py
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5d06350..948a80b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,9 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Added
 - Add `--report` flag to write out a summary JSON file
 
+### Changed
+- Migrate package definition to pyproject.toml
+
 ### Fixed
 - Properly catch failing test cases
 
diff --git a/nftest/__init__.py b/nftest/__init__.py
index 14bce41..a1fe93e 100644
--- a/nftest/__init__.py
+++ b/nftest/__init__.py
@@ -1,3 +1,10 @@
-"""nftest module"""
+"""NFTest module."""
 
-__version__ = "1.1.0"
+try:
+    from nftest._version import version as __version__  # noqa: F401
+except ModuleNotFoundError as err:
+    # The user is probably trying to run this without having installed
+    # the package, so complain.
+    raise RuntimeError(
+        "NFTest is not correctly installed. Please install it with pip."
+    ) from err
diff --git a/pyproject.toml b/pyproject.toml
index 35ae477..8d031cc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,51 @@
 [build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
 
-requires = [
-    "setuptools>=42",
-    "wheel"
+[project]
+name = "nftest"
+dynamic = ["version"]
+description = "CLI testing tool for Nextflow"
+readme = "README.md"
+authors = [
+    { name = "Chenghao Zhu", email = "ChenghaoZhu@mednet.ucla.edu" }
 ]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: GNU General Public License (GPL)",
+    "Operating System :: OS Independent"
+]
+requires-python = ">=3.8"
+dependencies = [
+    "PyYAML",
+    "python-dotenv",
+    "pytest",
+    "mock"
+]
+
+[project.optional-dependencies]
+dev = ["pytest", "mock"]
+
+[project.scripts]
+nftest = "nftest.__main__:main"
+
+[tool.hatch.metadata]
+package-data = { "nftest" = ["data/*"] }
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "nftest/_version.py"
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+env_list =
+    py3.8
+    py3.12
 
-build-backend = "setuptools.build_meta"
+[testenv]
+deps = pytest
+commands = pytest test --doctest-modules --junitxml=junit/test-results.xml
+"""
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 1165a95..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,38 +0,0 @@
-[metadata]
-# replace with your username:
-name = nftest
-version = attr: nftest.__version__
-author = 'Chenghao Zhu'
-author_email = 'ChenghaoZhu@mednet.ucla.edu'
-description = 'CLI testing tool for Nextflow'
-long_description = file: README.md
-long_description_content_type = text/markdown
-url =
-project_urls =
-    Bug Tracker =
-classifiers =
-    Programming Language :: Python :: 3
-    License :: OSI Approved :: GNU General Public License (GPL)
-    Operating System :: OS Independent
-
-[options]
-package_dir =
-    = .
-packages = find:
-python_requires = >=3.8
-
-install_requires =
-    PyYAML
-    python-dotenv
-    pytest
-    mock
-
-[options.packages.find]
-where = .
-
-[options.package_data]
-nftest = data/*
-
-[options.entry_points]
-console_scripts =
-    nftest = nftest.__main__:main
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 3460076..0000000
--- a/setup.py
+++ /dev/null
@@ -1,5 +0,0 @@
-"""setup"""
-
-from setuptools import setup
-
-setup()