diff --git a/ez_setup.py b/ez_setup.py
deleted file mode 100644
index 4ef3ee0..0000000
--- a/ez_setup.py
+++ /dev/null
@@ -1,426 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Setuptools bootstrapping installer.
-
-Maintained at https://github.com/pypa/setuptools/tree/bootstrap.
-
-Run this script to install or upgrade setuptools.
-"""
-
-import os
-import shutil
-import sys
-import tempfile
-import zipfile
-import optparse
-import subprocess
-import platform
-import textwrap
-import contextlib
-import json
-import codecs
-
-from distutils import log
-
-try:
-    from urllib.request import urlopen
-    from urllib.parse import urljoin
-except ImportError:
-    from urllib2 import urlopen
-    from urlparse import urljoin
-
-try:
-    from site import USER_SITE
-except ImportError:
-    USER_SITE = None
-
-LATEST = object()
-DEFAULT_VERSION = LATEST
-DEFAULT_URL = "https://pypi.io/packages/source/s/setuptools/"
-DEFAULT_SAVE_DIR = os.curdir
-
-
-def _python_cmd(*args):
-    """
-    Execute a command.
-
-    Return True if the command succeeded.
-    """
-    args = (sys.executable,) + args
-    return subprocess.call(args) == 0
-
-
-def _install(archive_filename, install_args=()):
-    """Install Setuptools."""
-    with archive_context(archive_filename):
-        # installing
-        log.warn('Installing Setuptools')
-        if not _python_cmd('setup.py', 'install', *install_args):
-            log.warn('Something went wrong during the installation.')
-            log.warn('See the error message above.')
-            # exitcode will be 2
-            return 2
-
-
-def _build_egg(egg, archive_filename, to_dir):
-    """Build Setuptools egg."""
-    with archive_context(archive_filename):
-        # building an egg
-        log.warn('Building a Setuptools egg in %s', to_dir)
-        _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
-    # returning the result
-    log.warn(egg)
-    if not os.path.exists(egg):
-        raise IOError('Could not build the egg.')
-
-
-class ContextualZipFile(zipfile.ZipFile):
-
-    """Supplement ZipFile class to support context manager for Python 2.6."""
-
-    def __enter__(self):
-        return self
-
-    def __exit__(self, type, value, traceback):
-        self.close()
-
-    def __new__(cls, *args, **kwargs):
-        """Construct a ZipFile or ContextualZipFile as appropriate."""
-        if hasattr(zipfile.ZipFile, '__exit__'):
-            return zipfile.ZipFile(*args, **kwargs)
-        return super(ContextualZipFile, cls).__new__(cls)
-
-
-@contextlib.contextmanager
-def archive_context(filename):
-    """
-    Unzip filename to a temporary directory, set to the cwd.
-
-    The unzipped target is cleaned up after.
-    """
-    tmpdir = tempfile.mkdtemp()
-    log.warn('Extracting in %s', tmpdir)
-    old_wd = os.getcwd()
-    try:
-        os.chdir(tmpdir)
-        with ContextualZipFile(filename) as archive:
-            archive.extractall()
-
-        # going in the directory
-        subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
-        os.chdir(subdir)
-        log.warn('Now working in %s', subdir)
-        yield
-
-    finally:
-        os.chdir(old_wd)
-        shutil.rmtree(tmpdir)
-
-
-def _do_download(version, download_base, to_dir, download_delay):
-    """Download Setuptools."""
-    py_desig = 'py{sys.version_info[0]}.{sys.version_info[1]}'.format(sys=sys)
-    tp = 'setuptools-{version}-{py_desig}.egg'
-    egg = os.path.join(to_dir, tp.format(**locals()))
-    if not os.path.exists(egg):
-        archive = download_setuptools(version, download_base,
-            to_dir, download_delay)
-        _build_egg(egg, archive, to_dir)
-    sys.path.insert(0, egg)
-
-    # Remove previously-imported pkg_resources if present (see
-    # https://bitbucket.org/pypa/setuptools/pull-request/7/ for details).
-    if 'pkg_resources' in sys.modules:
-        _unload_pkg_resources()
-
-    import setuptools
-    setuptools.bootstrap_install_from = egg
-
-
-def use_setuptools(
-        version=DEFAULT_VERSION, download_base=DEFAULT_URL,
-        to_dir=DEFAULT_SAVE_DIR, download_delay=15):
-    """
-    Ensure that a setuptools version is installed.
-
-    Return None. Raise SystemExit if the requested version
-    or later cannot be installed.
-    """
-    version = _resolve_version(version)
-    to_dir = os.path.abspath(to_dir)
-
-    # prior to importing, capture the module state for
-    # representative modules.
-    rep_modules = 'pkg_resources', 'setuptools'
-    imported = set(sys.modules).intersection(rep_modules)
-
-    try:
-        import pkg_resources
-        pkg_resources.require("setuptools>=" + version)
-        # a suitable version is already installed
-        return
-    except ImportError:
-        # pkg_resources not available; setuptools is not installed; download
-        pass
-    except pkg_resources.DistributionNotFound:
-        # no version of setuptools was found; allow download
-        pass
-    except pkg_resources.VersionConflict as VC_err:
-        if imported:
-            _conflict_bail(VC_err, version)
-
-        # otherwise, unload pkg_resources to allow the downloaded version to
-        #  take precedence.
-        del pkg_resources
-        _unload_pkg_resources()
-
-    return _do_download(version, download_base, to_dir, download_delay)
-
-
-def _conflict_bail(VC_err, version):
-    """
-    Setuptools was imported prior to invocation, so it is
-    unsafe to unload it. Bail out.
-    """
-    conflict_tmpl = textwrap.dedent("""
-        The required version of setuptools (>={version}) is not available,
-        and can't be installed while this script is running. Please
-        install a more recent version first, using
-        'easy_install -U setuptools'.
-
-        (Currently using {VC_err.args[0]!r})
-        """)
-    msg = conflict_tmpl.format(**locals())
-    sys.stderr.write(msg)
-    sys.exit(2)
-
-
-def _unload_pkg_resources():
-    sys.meta_path = [
-        importer
-        for importer in sys.meta_path
-        if importer.__class__.__module__ != 'pkg_resources.extern'
-    ]
-    del_modules = [
-        name for name in sys.modules
-        if name.startswith('pkg_resources')
-    ]
-    for mod_name in del_modules:
-        del sys.modules[mod_name]
-
-
-def _clean_check(cmd, target):
-    """
-    Run the command to download target.
-
-    If the command fails, clean up before re-raising the error.
-    """
-    try:
-        subprocess.check_call(cmd)
-    except subprocess.CalledProcessError:
-        if os.access(target, os.F_OK):
-            os.unlink(target)
-        raise
-
-
-def download_file_powershell(url, target):
-    """
-    Download the file at url to target using Powershell.
-
-    Powershell will validate trust.
-    Raise an exception if the command cannot complete.
-    """
-    target = os.path.abspath(target)
-    ps_cmd = (
-        "[System.Net.WebRequest]::DefaultWebProxy.Credentials = "
-        "[System.Net.CredentialCache]::DefaultCredentials; "
-        '(new-object System.Net.WebClient).DownloadFile("%(url)s", "%(target)s")'
-        % locals()
-    )
-    cmd = [
-        'powershell',
-        '-Command',
-        ps_cmd,
-    ]
-    _clean_check(cmd, target)
-
-
-def has_powershell():
-    """Determine if Powershell is available."""
-    if platform.system() != 'Windows':
-        return False
-    cmd = ['powershell', '-Command', 'echo test']
-    with open(os.path.devnull, 'wb') as devnull:
-        try:
-            subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
-        except Exception:
-            return False
-    return True
-download_file_powershell.viable = has_powershell
-
-
-def download_file_curl(url, target):
-    cmd = ['curl', url, '--location', '--silent', '--output', target]
-    _clean_check(cmd, target)
-
-
-def has_curl():
-    cmd = ['curl', '--version']
-    with open(os.path.devnull, 'wb') as devnull:
-        try:
-            subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
-        except Exception:
-            return False
-    return True
-download_file_curl.viable = has_curl
-
-
-def download_file_wget(url, target):
-    cmd = ['wget', url, '--quiet', '--output-document', target]
-    _clean_check(cmd, target)
-
-
-def has_wget():
-    cmd = ['wget', '--version']
-    with open(os.path.devnull, 'wb') as devnull:
-        try:
-            subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
-        except Exception:
-            return False
-    return True
-download_file_wget.viable = has_wget
-
-
-def download_file_insecure(url, target):
-    """Use Python to download the file, without connection authentication."""
-    src = urlopen(url)
-    try:
-        # Read all the data in one block.
-        data = src.read()
-    finally:
-        src.close()
-
-    # Write all the data in one block to avoid creating a partial file.
-    with open(target, "wb") as dst:
-        dst.write(data)
-download_file_insecure.viable = lambda: True
-
-
-def get_best_downloader():
-    downloaders = (
-        download_file_powershell,
-        download_file_curl,
-        download_file_wget,
-        download_file_insecure,
-    )
-    viable_downloaders = (dl for dl in downloaders if dl.viable())
-    return next(viable_downloaders, None)
-
-
-def download_setuptools(
-        version=DEFAULT_VERSION, download_base=DEFAULT_URL,
-        to_dir=DEFAULT_SAVE_DIR, delay=15,
-        downloader_factory=get_best_downloader):
-    """
-    Download setuptools from a specified location and return its filename.
-
-    `version` should be a valid setuptools version number that is available
-    as an sdist for download under the `download_base` URL (which should end
-    with a '/'). `to_dir` is the directory where the egg will be downloaded.
-    `delay` is the number of seconds to pause before an actual download
-    attempt.
-
-    ``downloader_factory`` should be a function taking no arguments and
-    returning a function for downloading a URL to a target.
-    """
-    version = _resolve_version(version)
-    # making sure we use the absolute path
-    to_dir = os.path.abspath(to_dir)
-    zip_name = "setuptools-%s.zip" % version
-    url = download_base + zip_name
-    saveto = os.path.join(to_dir, zip_name)
-    if not os.path.exists(saveto):  # Avoid repeated downloads
-        log.warn("Downloading %s", url)
-        downloader = downloader_factory()
-        downloader(url, saveto)
-    return os.path.realpath(saveto)
-
-
-def _resolve_version(version):
-    """
-    Resolve LATEST version
-    """
-    if version is not LATEST:
-        return version
-
-    meta_url = urljoin(DEFAULT_URL, '/pypi/setuptools/json')
-    resp = urlopen(meta_url)
-    with contextlib.closing(resp):
-        try:
-            charset = resp.info().get_content_charset()
-        except Exception:
-            # Python 2 compat; assume UTF-8
-            charset = 'UTF-8'
-        reader = codecs.getreader(charset)
-        doc = json.load(reader(resp))
-
-    return str(doc['info']['version'])
-
-
-def _build_install_args(options):
-    """
-    Build the arguments to 'python setup.py install' on the setuptools package.
-
-    Returns list of command line arguments.
-    """
-    return ['--user'] if options.user_install else []
-
-
-def _parse_args():
-    """Parse the command line for options."""
-    parser = optparse.OptionParser()
-    parser.add_option(
-        '--user', dest='user_install', action='store_true', default=False,
-        help='install in user site package')
-    parser.add_option(
-        '--download-base', dest='download_base', metavar="URL",
-        default=DEFAULT_URL,
-        help='alternative URL from where to download the setuptools package')
-    parser.add_option(
-        '--insecure', dest='downloader_factory', action='store_const',
-        const=lambda: download_file_insecure, default=get_best_downloader,
-        help='Use internal, non-validating downloader'
-    )
-    parser.add_option(
-        '--version', help="Specify which version to download",
-        default=DEFAULT_VERSION,
-    )
-    parser.add_option(
-        '--to-dir',
-        help="Directory to save (and re-use) package",
-        default=DEFAULT_SAVE_DIR,
-    )
-    options, args = parser.parse_args()
-    # positional arguments are ignored
-    return options
-
-
-def _download_args(options):
-    """Return args for download_setuptools function from cmdline args."""
-    return dict(
-        version=options.version,
-        download_base=options.download_base,
-        downloader_factory=options.downloader_factory,
-        to_dir=options.to_dir,
-    )
-
-
-def main():
-    """Install or upgrade setuptools and EasyInstall."""
-    options = _parse_args()
-    archive = download_setuptools(**_download_args(options))
-    return _install(archive, _build_install_args(options))
-
-if __name__ == '__main__':
-    sys.exit(main())
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..b0c3a2f
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,51 @@
+[build-system]
+requires = ["setuptools>=42", "setuptools-scm", "cython"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "umi_tools"
+description = "umi_tools: Tools for UMI analyses"
+dynamic = ["version"]
+authors = [
+    {name = "Ian Sudbery", email = "i.sudbery@sheffield.ac.uk" }
+]
+license = "MIT"
+keywords = ["computational", "genomics"]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "Intended Audience :: Developers",
+  "Programming Language :: Python",
+  "Topic :: Software Development",
+  "Topic :: Scientific/Engineering",
+  "Operating System :: POSIX",
+  "Operating System :: Unix",
+  "Operating System :: MacOS"
+]
+dependencies = [
+    "numpy>=1.7",
+    "pandas>=0.12.0",
+    "pysam>=0.16.0.1",
+    "future",
+    "regex",
+    "scipy",
+    "matplotlib",
+    "pybktree",
+]
+
+[tool.setuptools]
+ext-modules = [
+    {name = "umi_tools._dedup_umi", sources = ["umi_tools/_dedup_umi.pyx"]}
+]
+
+[tool.setuptools.packages.find]
+
+
+[tool.setuptools_scm]
+
+[project.urls]
+Homepage = "https://github.com/CGATOxford/UMI-tools"
+Repository = "https://github.com/CGATOxford/UMI-tools"
+
+[project.scripts]
+umi_tools = "umi_tools.umi_tools:main"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index f91b83d..0000000
--- a/setup.py
+++ /dev/null
@@ -1,122 +0,0 @@
-from __future__ import absolute_import
-
-import sys
-import os
-import glob
-
-from ez_setup import use_setuptools
-use_setuptools("10.0")
-import setuptools
-
-from umi_tools import __version__
-from setuptools import setup, find_packages, Extension
-
-from distutils.version import LooseVersion
-if LooseVersion(setuptools.__version__) < LooseVersion('1.1'):
-    print ("Version detected:", LooseVersion(setuptools.__version__))
-    raise ImportError(
-        "umi_tools requires setuptools 1.1 higher")
-
-###############################################################
-###############################################################
-# Define dependencies 
-# Perform a umi_tools Installation
-
-major, minor1, minor2, s, tmp = sys.version_info
-
-if major < 3:
-    raise SystemExit("""umi_tools requires Python 3 or later.""")
-
-umi_tools_packages = ["umi_tools"]
-umi_tools_package_dirs = {'umi_tools': 'umi_tools'}
-
-# debugging pip installation
-#install_requires = []
-#for requirement in (
-#        l.strip() for l in open('requirements.txt') if not l.startswith("#")):
-#    install_requires.append(requirement)
-
-install_requires = [
-    "setuptools>=1.1",
-    "numpy>=1.7",
-    "pandas>=0.12.0",
-    "future",
-    "regex",
-    "scipy",
-    "matplotlib",
-    "pybktree"]
-
-# This is a hack. When Pysam is installed from source, the recorded
-# version is 0.2.3, even though a more recent version is actaully
-# installed. In the following, if pysam is not detected, pysam will be
-# install, presumably this will be the lastest version. If pysam is
-# present detect its version with pysam.__version__.  The only problem
-# with this is that if pysam is present, but out of date, the system
-# will not recognise the update
-
-try:
-    import pysam
-    if LooseVersion(pysam.__version__) < LooseVersion('0.16.0.1'):
-        print("""
-        
-    ######################################################################
-    #
-    # WARNING:
-    # Pysam is installed, but not recent enough. We will update pysam, but
-    # the system may fail to detect that pysam has been updated. If this
-    # happens please run setup again"
-    #
-    ######################################################################
-
-        """)
-
-        install_requires.append("pysam>=0.16.0.1")
-
-except ImportError:
-    install_requires.append("pysam")
-
-##########################################################
-##########################################################
-# Classifiers
-classifiers = """
-Development Status :: 3 - Alpha
-Intended Audience :: Science/Research
-Intended Audience :: Developers
-License :: OSI Approved
-Programming Language :: Python
-Topic :: Software Development
-Topic :: Scientific/Engineering
-Operating System :: POSIX
-Operating System :: Unix
-Operating System :: MacOS
-"""
-
-setup(
-    # package information
-    name='umi_tools',
-    version=__version__,
-    description='umi_tools: Tools for UMI analyses',
-    author='Ian Sudbery',
-    author_email='i.sudbery@sheffield.ac.uk',
-    license="MIT",
-    platforms=["any"],
-    keywords="computational genomics",
-    long_description='umi_tools: Tools for UMI analyses',
-    classifiers=list(filter(None, classifiers.split("\n"))),
-    url="https://github.com/CGATOxford/UMI-tools",
-    download_url="https://github.com/CGATOxford/UMI-tools/tarball/%s" % __version__,
-    # package contents
-    packages=umi_tools_packages,
-    package_dir=umi_tools_package_dirs,
-    include_package_data=True,
-    # dependencies
-    #setup_requires=['cython'],
-    install_requires=install_requires,
-    # extension modules
-    ext_modules=[Extension("umi_tools._dedup_umi", ["umi_tools/_dedup_umi.c"])],
-    entry_points={
-        'console_scripts': ['umi_tools = umi_tools.umi_tools:main']
-    },
-    # other options
-    zip_safe=False,
-)
