diff --git a/CHANGELOG.md b/CHANGELOG.md
index 63acc2b..0669c0b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+# [2.2.29] - 2024-02-16
+
+- Bump version with .toml
+
 # [2.2.28] - 2024-02-16
 
 - Removed dependencies (most importantly sklearn; which is optional now)
diff --git a/pyproject.toml b/pyproject.toml
index 1adaf18..ae69b86 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "deeplc"
-version = "2.2.27"
+version = "2.2.29"
 description = "DeepLC: Retention time prediction for (modified) peptides using Deep Learning."
 readme = "README.md"
 license = { file = "LICENSE" }
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 422b7f3..0000000
--- a/setup.py
+++ /dev/null
@@ -1,65 +0,0 @@
-from setuptools import find_packages, setup
-
-with open("README.md", "r") as fh:
-    LONG_DESCRIPTION = fh.read()
-
-
-setup(
-    name="deeplc",
-    version="2.2.28",
-    license="apache-2.0",
-    description="DeepLC: Retention time prediction for (modified) peptides using Deep Learning.",
-    long_description=LONG_DESCRIPTION,
-    long_description_content_type="text/markdown",
-    author="Robbin Bouwmeester, Niels Hulstaert, Arthur Declercq, Ralf Gabriels, Prof. Lennart Martens, Prof. Sven Degroeve",
-    author_email="Robbin.Bouwmeester@UGent.be",
-    url="http://compomics.github.io/projects/DeepLC",
-    project_urls={
-        "Documentation": "http://compomics.github.io/projects/DeepLC",
-        "Source": "https://github.com/compomics/DeepLC",
-        "Tracker": "https://github.com/compomics/DeepLC/issues",
-    },
-    packages=find_packages(),
-    include_package_data=True,
-    entry_points={
-        "console_scripts": [
-            "deeplc=deeplc.__main__:main",
-            "deeplc-gui=deeplc.gui:start_gui",
-        ]
-    },
-    keywords=[
-        "DeepLC",
-        "Proteomics",
-        "deep learning",
-        "peptides",
-        "retention time",
-        "prediction",
-    ],
-    classifiers=[
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: Apache Software License",
-        "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "Development Status :: 4 - Beta",
-    ],
-    install_requires=[
-        "setuptools>=42.0.1",
-        "tensorflow>=2.2,<2.13.0",
-        "scipy>=1.4.1,<2",
-        "numpy>=1.17,<2",
-        "pandas>=0.25,<2",
-        "matplotlib>=3,<4",
-        "h5py>=2.10.0,<4",
-        "pygam>=0.8.0,<1",
-        "scikit-learn>=0.24.0,<2",
-        "deeplcretrainer>=0.1,<1",
-        "psm_utils>=0.2.3,<1",
-        "hdf5plugin>=4.1.1",
-    ],
-    extras_require={
-        "gui": ["gooey>=1.0"],
-        "plot": ["plotly>=5"],
-    },
-    python_requires=">=3.7",
-)