diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml
index 094d40f58..b641fd520 100644
--- a/.github/workflows/conda.yml
+++ b/.github/workflows/conda.yml
@@ -32,7 +32,7 @@ jobs:
       - name: Install dependencies
         run: conda install -y python conda-build "grpcio-tools<1.62" conda-verify
       - name: Compiling the prototypes
-        run: python python-libraries/nanover-core/setup.py compile_proto --proto-dir=protocol
+        run: python ./python-libraries/compile_proto.py --proto-dir=./protocol --python-dir=./python-libraries/nanover-core/src
       - name: Building the Conda packages
         run: |
           $build_command \
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ee776ff22..2f7842a8e 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -44,8 +44,8 @@ jobs:
         run: conda install -y mpi4py openmm
       - name: Install tests dependancies
         run: python -m pip install -r python-libraries/requirements.test
-      - name: Compile
-        run: ./compile.sh --no-dotnet
+      - name: Compile (mypy requires --no-edit)
+        run: ./compile.sh --no-dotnet --no-edit
       - name: mypy
         run: |
           # Mypy accepts paths, modules or packages as inputs. However, only
diff --git a/compile.sh b/compile.sh
index 7ffce599e..d5c2b429b 100755
--- a/compile.sh
+++ b/compile.sh
@@ -63,13 +63,13 @@ if [[ $with_python == true ]]; then
 	python -m pip install -r ./python-libraries/requirements.test ${user_option}
 
 	announce "Compiling proto files to python"
-	python ./python-libraries/nanover-core/setup.py compile_proto
+	python ./python-libraries/compile_proto.py --proto-dir=./protocol --python-dir=./python-libraries/nanover-core/src
 
 	announce "Installing the python packages"
 	python -m pip install ${edit_option} ${nanover_user_option} ./python-libraries/nanover-core/
 
 	for package in python-libraries/nanover-*/; do
-		if [[ -f "${package}/setup.py" ]]; then
+		if [[ -f "${package}/pyproject.toml" ]]; then
 			python -m pip install ${edit_option} ${nanover_user_option} ${package}
 		fi
 	done
diff --git a/python-libraries/compile_proto.py b/python-libraries/compile_proto.py
new file mode 100644
index 000000000..fe079434a
--- /dev/null
+++ b/python-libraries/compile_proto.py
@@ -0,0 +1,130 @@
+import argparse
+import os
+import textwrap
+from contextlib import contextmanager
+from importlib import resources
+from pathlib import Path
+
+
+def handle_user_arguments(args=None) -> argparse.Namespace:
+    """
+    Parse the arguments from the command line.
+
+    :return: The namespace of arguments read from the command line.
+    """
+    description = textwrap.dedent(
+        """\
+    Compile the gRPC protocol files to python.
+    """
+    )
+    parser = argparse.ArgumentParser(description=description)
+
+    parser.add_argument(
+        "--proto-dir",
+        required=True,
+        dest="proto_dir",
+        metavar="PATH",
+        help="The path to the directory containing the proto files",
+    )
+
+    parser.add_argument(
+        "--python-dir",
+        required=True,
+        dest="python_dir",
+        metavar="PATH",
+        help="The path to the directory where to generate the python files",
+    )
+
+    arguments = parser.parse_args(args)
+    return arguments
+
+
+def compile_protocol(proto_dir, python_dir):
+    """
+    Compile the protocol files to python.
+
+    :param proto_dir: The path to the directory containing the proto files.
+    :param python_dir: The path to the directory where to generate the python files.
+    """
+    from grpc_tools import protoc
+
+    try:
+        os.makedirs(python_dir)
+    except OSError:
+        pass
+
+    # Note on calling grpc_tools.protoc as a python function:
+    # grpc_tools.protoc.main is called by the command line with sys.argv and
+    # the include path for the default protobuf proto files. sys.argv is a list of
+    # the arguments passed to the command line, the first element of that list is
+    # the command itself; what is passed as a command does not matter, but the actual
+    # arguments must start at sys.argv[1] (hence "protoc" as first argument passed
+    # to the function).
+    proto_include = resources.files("grpc_tools") / "_proto"
+    with move_in_directory(proto_dir):
+        for protocol_file in Path(".").glob("**/*.proto"):
+            print(f"Compiling {protocol_file}")
+            protoc.main(
+                (
+                    "protoc",
+                    "--proto_path=.",
+                    f"--python_out={python_dir}",
+                    f"--grpc_python_out={python_dir}",
+                    str(protocol_file),
+                    f"--proto_path={proto_include}",
+                )
+            )
+    generated_protocol_directories = (
+        path for path in (python_dir / "nanover/protocol").glob("**/*") if path.is_dir()
+    )
+    for directory in generated_protocol_directories:
+        (directory / "__init__.py").touch()
+        contained_files = (file for file in directory.glob("*_pb2*.py"))
+        with open(directory / "__init__.py", "w+") as init_py:
+            for contained_file in contained_files:
+                file_name = os.path.splitext(os.path.split(contained_file)[1])[0]
+                init_py.write("from .%s import *\n" % file_name)
+
+
+@contextmanager
+def move_in_directory(destination):
+    """
+    Context manager that moves in the given directory.
+
+    When the interpreter enters the context manager, the working directory becomes
+    the given destination. When the interpreter exists the context manager, the
+    working directory is restored to where the working directory was before entering.
+
+    Example:
+    ========
+
+    >>> with move_in_directory("bar"):
+    >>>    # working directory is "bar"
+    >>>    pass
+    >>> # working directory is "foo" again
+
+    :param destination: The directory to use as working directory.
+    """
+    destination = Path(destination)
+    directory_to_restore = Path.cwd()
+    try:
+        os.chdir(str(destination))
+        yield
+    finally:
+        os.chdir(str(directory_to_restore))
+
+
+def main():
+    """
+    Entry point for the command line.
+    """
+    arguments = handle_user_arguments()
+
+    compile_protocol(
+        Path(arguments.proto_dir).resolve(),
+        Path(arguments.python_dir).resolve(),
+    )
+
+
+if __name__ == "__main__":
+    main()
diff --git a/python-libraries/nanover-ase/pyproject.toml b/python-libraries/nanover-ase/pyproject.toml
new file mode 100644
index 000000000..42ad61bcc
--- /dev/null
+++ b/python-libraries/nanover-ase/pyproject.toml
@@ -0,0 +1,24 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover-ase"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "ASE integration for NanoVer"
+readme = "README.md"
+requires-python = ">=3.11"
+dependencies = [
+    "nanover",
+    "ase >= 3.21",
+]
+dynamic = ["version"]
+
+[project.scripts]
+nanover-omm-ase = "nanover.ase.openmm.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*"]  # package names should match these glob patterns (["*"] by default)
diff --git a/python-libraries/nanover-ase/setup.py b/python-libraries/nanover-ase/setup.py
deleted file mode 100644
index 38135eba1..000000000
--- a/python-libraries/nanover-ase/setup.py
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env python
-
-from distutils.core import setup
-from setuptools import find_namespace_packages
-
-setup(
-    name="nanover-ase",
-    version="0.1.0",
-    description="ASE integration for NanoVer",
-    author="Intangible Realities Lab",
-    author_email="m.oconnor@bristol.ac.uk",
-    url="https://gitlab.com/intangiblerealities/",
-    packages=find_namespace_packages("src", include="nanover.*"),
-    package_dir={"": "src"},
-    package_data={"": ["py.typed"]},
-    install_requires=(
-        "nanover",
-        "ase>=3.21",
-    ),
-    entry_points={
-        "console_scripts": ["nanover-omm-ase=nanover.ase.openmm.cli:main"],
-    },
-)
diff --git a/python-libraries/nanover-core/conda/bld.bat b/python-libraries/nanover-core/conda/bld.bat
deleted file mode 100644
index 602113031..000000000
--- a/python-libraries/nanover-core/conda/bld.bat
+++ /dev/null
@@ -1,2 +0,0 @@
-"%PYTHON%" setup.py install
-if errorlevel 1 exit 1
\ No newline at end of file
diff --git a/python-libraries/nanover-core/pyproject.toml b/python-libraries/nanover-core/pyproject.toml
new file mode 100644
index 000000000..2afa88ebd
--- /dev/null
+++ b/python-libraries/nanover-core/pyproject.toml
@@ -0,0 +1,29 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "NanoVer python framework"
+requires-python = ">=3.11"
+dependencies = [
+    "setuptools>=40.1.1",
+    "grpcio>=1.63.0",
+    "grpcio-tools>=1.63.0",
+    "pytest",
+    "aiogrpc",
+    "numpy",
+    "hypothesis",
+    "typing_extensions",
+]
+dynamic = ["version"]
+
+[project.scripts]
+nanover-multiplayer = "nanover.multiplayer.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*", "nanover.protocol"]  # package names should match these glob patterns (["*"] by default)
diff --git a/python-libraries/nanover-core/setup.py b/python-libraries/nanover-core/setup.py
deleted file mode 100644
index 89c41cd65..000000000
--- a/python-libraries/nanover-core/setup.py
+++ /dev/null
@@ -1,161 +0,0 @@
-# !/usr/bin/env python
-
-
-import os
-from contextlib import contextmanager
-from pathlib import Path
-import distutils.cmd
-import distutils.log
-from distutils.core import setup
-from setuptools import find_namespace_packages
-from importlib import resources
-
-
-class CompileProtoCommand(distutils.cmd.Command):
-    """
-    Custom command to compile the protocol files.
-
-    To run the command, call::
-
-        python setup.py compile_proto
-
-    While it is not recommended, it is possible to run the compilation with a
-    different set of protocol files by passing the --proto-dir option:
-
-        python setup.py compile_proto --proto-dir=../other-proto-files
-
-    """
-
-    description = "Compile the protocol files."
-    user_options = [
-        # The format is (long option, short option, description)
-        ("proto-dir=", None, "Path to the directory containing the protocol files."),
-    ]
-
-    def initialize_options(self):
-        """
-        Set the default values for the options.
-        """
-        # By default, the setup.py file is in nanover-protocol/python-libraries/nanover-core,
-        # the protocol files are in nanover-protocol/protocol, which is ../../protocol relative
-        # to the directory of setup.py.
-        here = Path(__file__).parent
-        self.proto_dir = here / "../../protocol"
-
-    def finalize_options(self):
-        """
-        Post-process options.
-        """
-        self.proto_dir = Path(self.proto_dir)
-        assert (
-            self.proto_dir.exists
-        ), "The prototype directory {} does not exist.".format(self.proto_dir)
-
-    def run(self):
-        """
-        Run the compilation.
-        """
-        self.announce("Compile protocol files.", level=distutils.log.INFO)
-        setup_path = Path(__file__).parent.resolve()
-        compile_protocol(self.proto_dir, setup_path / "src", self)
-
-
-def compile_protocol(proto_dir, python_dir, logger):
-    """
-    Compile the protocol files to python.
-
-    :param proto_dir: The path to the directory containing the proto files.
-    :param python_dir: The path to the directory where to generate the python files.
-    :param logger: The logger instance used by distutils.
-    """
-    from grpc_tools import protoc
-
-    # Note on calling grpc_tools.protoc as a python function:
-    # grpc_tools.protoc.main is called by the command line with sys.argv and
-    # the include path for the default protobuf proto files. sys.argv is a list of
-    # the arguments passed to the command line, the first element of that list is
-    # the command itself; what is passed as a command does not matter, but the actual
-    # arguments must start at sys.argv[1] (hence "protoc" as first argument passed
-    # to the function).
-    proto_include = resources.files("grpc_tools") / "_proto"
-    with move_in_directory(proto_dir):
-        for protocol_file in Path(".").glob("**/*.proto"):
-            logger.announce(
-                "Compiling {}".format(protocol_file), level=distutils.log.INFO
-            )
-            protoc.main(
-                (
-                    "protoc",
-                    "--proto_path=.",
-                    "--python_out=" + str(python_dir),
-                    "--grpc_python_out=" + str(python_dir),
-                    str(protocol_file),
-                    "--proto_path={}".format(proto_include),
-                )
-            )
-    generated_protocol_directories = (
-        path for path in (python_dir / "nanover/protocol").glob("**/*") if path.is_dir()
-    )
-    for directory in generated_protocol_directories:
-        (directory / "__init__.py").touch()
-        contained_files = (file for file in directory.glob("*_pb2*.py"))
-        with open(directory / "__init__.py", "w+") as init_py:
-            for contained_file in contained_files:
-                file_name = os.path.splitext(os.path.split(contained_file)[1])[0]
-                init_py.write("from .%s import *\n" % file_name)
-
-
-@contextmanager
-def move_in_directory(destination):
-    """
-    Context manager that moves in the given directory.
-
-    When the interpreter enters the context manager, the working directory becomes
-    the given destination. When the interpreter exists the context manager, the
-    working directory is restored to where the working directory was before entering.
-
-    Example:
-    ========
-
-    >>> with move_in_directory("bar"):
-    >>>    # working directory is "bar"
-    >>>    pass
-    >>> # working directory is "foo" again
-
-    :param destination: The directory to use as working directory.
-    """
-    destination = Path(destination)
-    directory_to_restore = Path.cwd()
-    try:
-        os.chdir(str(destination))
-        yield
-    finally:
-        os.chdir(str(directory_to_restore))
-
-
-# Avoid repeating the content of requirements.txt here.
-# The requirements.txt file is in the same directory as this setup.py,
-# we then should now were the setup lies to be independent of the working
-# directory.
-requirements_path = Path(__file__).parent.resolve() / "requirements.txt"
-with open(str(requirements_path)) as f:
-    requirements = f.readlines()
-
-setup(
-    name="nanover",
-    version="1.0",
-    description="NanoVer python framework",
-    author="Intangible Realities Lab",
-    author_email="m.oconnor@bristol.ac.uk",
-    url="https://gitlab.com/intangiblerealities/",
-    packages=find_namespace_packages("src", include="nanover.*") + ["nanover.protocol"],
-    package_dir={"": "src"},
-    package_data={"": ["py.typed"]},
-    install_requires=requirements,
-    cmdclass={
-        "compile_proto": CompileProtoCommand,
-    },
-    entry_points={
-        "console_scripts": ["nanover-multiplayer=nanover.multiplayer.cli:main"],
-    },
-)
diff --git a/python-libraries/nanover-core/tests/core/test_nanover_client_server_state.py b/python-libraries/nanover-core/tests/core/test_nanover_client_server_state.py
index 42412151b..ac0be4d63 100644
--- a/python-libraries/nanover-core/tests/core/test_nanover_client_server_state.py
+++ b/python-libraries/nanover-core/tests/core/test_nanover_client_server_state.py
@@ -3,6 +3,8 @@
 
 import numpy
 import pytest
+
+from nanover.testing import assert_in_soon
 from nanover.utilities.change_buffers import DictionaryChange
 from nanover.utilities.key_lockable_map import ResourceLockedError
 
@@ -80,7 +82,8 @@ def test_client_copy_state_is_independent(client_server):
     client, server = client_server
     client.subscribe_all_state_updates(0)
 
-    time.sleep(IMMEDIATE_REPLY_WAIT_TIME)
+    # wait for first update
+    assert_in_soon(lambda: "test", lambda: client.copy_state())
 
     copy = client.copy_state()
     copy["test"]["baby"] = "shark"
diff --git a/python-libraries/nanover-essd/conda/meta.yaml b/python-libraries/nanover-essd/conda/meta.yaml
index e60293a1a..b42fc6720 100644
--- a/python-libraries/nanover-essd/conda/meta.yaml
+++ b/python-libraries/nanover-essd/conda/meta.yaml
@@ -8,6 +8,8 @@ source:
 build:
   noarch: python
   number: 0
+  entry_points:
+    - nanover-essd-list = nanover.essd.list_cli:main
 
 requirements:
   build:
diff --git a/python-libraries/nanover-essd/pyproject.toml b/python-libraries/nanover-essd/pyproject.toml
new file mode 100644
index 000000000..779bc11f1
--- /dev/null
+++ b/python-libraries/nanover-essd/pyproject.toml
@@ -0,0 +1,22 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover-essd"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "Extremely Simple Server Discovery, for use with NanoVer"
+requires-python = ">=3.11"
+dependencies = [
+    "netifaces",
+]
+dynamic = ["version"]
+
+[project.scripts]
+nanover-essd-list = "nanover.essd.list_cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*"]  # package names should match these glob patterns (["*"] by default)
diff --git a/python-libraries/nanover-essd/setup.py b/python-libraries/nanover-essd/setup.py
deleted file mode 100644
index ea31fb80a..000000000
--- a/python-libraries/nanover-essd/setup.py
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env python
-
-from distutils.core import setup
-from setuptools import find_namespace_packages
-
-setup(
-    name="nanover-essd",
-    version="1.0.0",
-    description="Extremely Simple Server Discovery, for use with NanoVer",
-    author="Intangible Realities Lab",
-    author_email="m.oconnor@bristol.ac.uk",
-    url="https://gitlab.com/intangiblerealities/",
-    packages=find_namespace_packages("src", include="nanover.*"),
-    package_data={"": ["py.typed"]},
-    install_requires=("netifaces",),
-    entry_points={
-        "console_scripts": ["nanover-essd-list=nanover.essd.list_cli:main"],
-    },
-    package_dir={"": "src"},
-)
diff --git a/python-libraries/nanover-jupyter/pyproject.toml b/python-libraries/nanover-jupyter/pyproject.toml
new file mode 100644
index 000000000..304c2f0c3
--- /dev/null
+++ b/python-libraries/nanover-jupyter/pyproject.toml
@@ -0,0 +1,22 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover-jupyter"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "Utilities for using Jupyter with NanoVer"
+requires-python = ">=3.11"
+dependencies = [
+    "nanover",
+    "MDAnalysis",
+    "numpy",
+    "nglview",
+]
+dynamic = ["version"]
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*"]  # package names should match these glob patterns (["*"] by default)
diff --git a/python-libraries/nanover-jupyter/setup.py b/python-libraries/nanover-jupyter/setup.py
deleted file mode 100644
index 5ec51ac13..000000000
--- a/python-libraries/nanover-jupyter/setup.py
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env python
-
-
-from distutils.core import setup
-from setuptools import find_namespace_packages
-
-setup(
-    name="nanover-jupyter",
-    version="0.1.0",
-    description="NGLView python client for NanoVer",
-    author="Intangible Realities Lab",
-    author_email="harry.stroud@usc.es",
-    url="https://github.com/IRL2/",
-    packages=find_namespace_packages("src", include="nanover.*"),
-    package_dir={"": "src"},
-    package_data={"": ["py.typed"]},
-    install_requires=(
-        "nanover",
-        "MDAnalysis",
-        "numpy",
-        "nglview",
-    ),
-)
diff --git a/python-libraries/nanover-lammps/pyproject.toml b/python-libraries/nanover-lammps/pyproject.toml
new file mode 100644
index 000000000..21be654bd
--- /dev/null
+++ b/python-libraries/nanover-lammps/pyproject.toml
@@ -0,0 +1,21 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover-lammps"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "LAMMPS integration for NanoVer"
+requires-python = ">=3.11"
+dependencies = [
+    "nanover",
+    "mpi4py",
+    "numpy",
+]
+dynamic = ["version"]
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*"]  # package names should match these glob patterns (["*"] by default)
diff --git a/python-libraries/nanover-lammps/setup.py b/python-libraries/nanover-lammps/setup.py
deleted file mode 100644
index cbaf8b4e9..000000000
--- a/python-libraries/nanover-lammps/setup.py
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-
-from distutils.core import setup
-from setuptools import find_namespace_packages
-
-setup(
-    name="nanover-lammps",
-    version="0.1.0",
-    description="LAMMPS integration for NanoVer",
-    author="Intangible Realities Lab",
-    author_email="simonbennie@gmail.com",
-    url="https://gitlab.com/intangiblerealities/",
-    packages=find_namespace_packages("src", include="nanover.*"),
-    package_dir={"": "src"},
-    package_data={"": ["py.typed"]},
-    install_requires=(
-        "nanover",
-        "mpi4py",
-        "numpy",
-    ),
-)
diff --git a/python-libraries/nanover-mdanalysis/pyproject.toml b/python-libraries/nanover-mdanalysis/pyproject.toml
new file mode 100644
index 000000000..a538c473c
--- /dev/null
+++ b/python-libraries/nanover-mdanalysis/pyproject.toml
@@ -0,0 +1,20 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover-mdanalysis"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "MDAnalysis integration for NanoVer"
+requires-python = ">=3.11"
+dependencies = [
+    "nanover",
+    "MDAnalysis",
+]
+dynamic = ["version"]
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*"]  # package names should match these glob patterns (["*"] by default)
diff --git a/python-libraries/nanover-mdanalysis/setup.py b/python-libraries/nanover-mdanalysis/setup.py
deleted file mode 100644
index 3f9c26aa4..000000000
--- a/python-libraries/nanover-mdanalysis/setup.py
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-
-
-from distutils.core import setup
-from setuptools import find_namespace_packages
-
-setup(
-    name="nanover-mdanalysis",
-    version="0.1.0",
-    description="MDAnalysis integration for NanoVer",
-    author="Intangible Realities Lab",
-    author_email="m.oconnor@bristol.ac.uk",
-    url="https://gitlab.com/intangiblerealities/",
-    packages=find_namespace_packages("src", include="nanover.*"),
-    package_dir={"": "src"},
-    package_data={"": ["py.typed"]},
-    install_requires=(
-        "nanover",
-        "MDAnalysis",
-    ),
-)
diff --git a/python-libraries/nanover-omni/pyproject.toml b/python-libraries/nanover-omni/pyproject.toml
new file mode 100644
index 000000000..5e804a05c
--- /dev/null
+++ b/python-libraries/nanover-omni/pyproject.toml
@@ -0,0 +1,23 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover-omni"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "Multi-simulation server for NanoVer"
+requires-python = ">=3.11"
+dependencies = [
+    "nanover",
+    "openmm",
+]
+dynamic = ["version"]
+
+[project.scripts]
+nanover-omni = "nanover.omni.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*"]  # package names should match these glob patterns (["*"] by default)
diff --git a/python-libraries/nanover-omni/setup.py b/python-libraries/nanover-omni/setup.py
deleted file mode 100644
index 096bffa49..000000000
--- a/python-libraries/nanover-omni/setup.py
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env python
-
-from distutils.core import setup
-from setuptools import find_namespace_packages
-
-setup(
-    name="nanover-omni",
-    version="0.1.0",
-    description="Omni server for NanoVer",
-    author="Intangible Realities Lab",
-    author_email="m.oconnor@bristol.ac.uk",
-    url="https://gitlab.com/intangiblerealities/",
-    packages=find_namespace_packages("src", include="nanover.*"),
-    package_dir={"": "src"},
-    package_data={"": ["py.typed"]},
-    install_requires=(
-        "nanover",
-        "openmm",
-    ),
-    entry_points={
-        "console_scripts": ["nanover-omni=nanover.omni.cli:main"],
-    },
-)
diff --git a/python-libraries/nanover-openmm/pyproject.toml b/python-libraries/nanover-openmm/pyproject.toml
new file mode 100644
index 000000000..5204466aa
--- /dev/null
+++ b/python-libraries/nanover-openmm/pyproject.toml
@@ -0,0 +1,23 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nanover-openmm"
+authors = [
+    {name = "Intangible Realities Lab"},
+]
+description = "Multi-simulation server for NanoVer"
+requires-python = ">=3.11"
+dependencies = [
+    "nanover",
+    "openmm",
+]
+dynamic = ["version"]
+
+[project.scripts]
+nanover-omm-server = "nanover.openmm.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["nanover.*"]  # package names should match these glob patterns (["*"] by default)
diff --git a/python-libraries/nanover-openmm/setup.py b/python-libraries/nanover-openmm/setup.py
deleted file mode 100644
index ff19c138c..000000000
--- a/python-libraries/nanover-openmm/setup.py
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env python
-
-from distutils.core import setup
-from setuptools import find_namespace_packages
-
-setup(
-    name="nanover-openmm",
-    version="0.1.0",
-    description="OpenMM server for NanoVer",
-    author="Intangible Realities Lab",
-    author_email="m.oconnor@bristol.ac.uk",
-    url="https://gitlab.com/intangiblerealities/",
-    packages=find_namespace_packages("src", include="nanover.*"),
-    package_dir={"": "src"},
-    package_data={"": ["py.typed"]},
-    install_requires=(
-        "nanover",
-        "openmm",
-    ),
-    entry_points={
-        "console_scripts": ["nanover-omm-server=nanover.openmm.cli:main"],
-    },
-)
diff --git a/win_compile.ps1 b/win_compile.ps1
index 73371725a..e73ac34c5 100644
--- a/win_compile.ps1
+++ b/win_compile.ps1
@@ -38,13 +38,13 @@ announce "Installing python test requirements"
 python -m pip install -r ./python-libraries/requirements.test ${user_option}
 
 announce "Compiling proto files to python"
-python ./python-libraries/nanover-core/setup.py compile_proto
+python ./python-libraries/compile_proto.py --proto-dir=./protocol --python-dir=./python-libraries/nanover-core/src
 
 announce "Installing the python packages"
 python -m pip install ${edit_option} ${user_option} ./python-libraries/nanover-core/
 
 Get-ChildItem -Directory python-libraries/nanover-* | ForEach-Object {
-    if (Test-Path -Path "$($_.FullName)/setup.py") {
+    if (Test-Path -Path "$($_.FullName)/pyproject.toml") {
         Write-Host "$($_.FullName)"
         pip install ${edit_option} ${user_option} ""$($_.FullName)""
     }