diff --git a/setup.py b/setup.py
index 28fa8423..b79346ba 100644
--- a/setup.py
+++ b/setup.py
@@ -17,53 +17,57 @@
 
 # Compile the list of packages available, because distutils doesn't have
 # an easy way to do this.
-packages, data_files = [], []
-
-root_dir = os.path.dirname(__file__)
-len_root_dir = len(root_dir)
-
-biskit_dir = os.path.join(root_dir, 'biskit')
-doc_dir    = os.path.join(root_dir, 'doc')
-script_dir = os.path.join(root_dir, 'scripts')
-
-for dirpath, dirnames, filenames in os.walk(biskit_dir):
-    # Ignore dirnames that start with '.'
-    for i, dirname in enumerate(dirnames):
-        if dirname.startswith('.'): del dirnames[i]
-
-    if '__init__.py' in filenames:
-        package = dirpath[len_root_dir:].lstrip('/').replace('/', '.')
-        packages.append(package)
-    else:
-        data_files.append([dirpath, [os.path.join(dirpath, f) for f in filenames]])
-
-## docs and scripts are moved from the root of the project into
-## the package folder. That's why the separate treatment.
-## First item in the data_files entry is the target folder, second item
-## is the relative path in the svn project.
-for dirpath, dirnames, filenames in os.walk( doc_dir ):
-    # Ignore dirnames that start with '.'
-    for i, dirname in enumerate(dirnames):
-        if dirname.startswith('.'): del dirnames[i]
-    data_files.append([os.path.join( 'biskit', dirpath ),
-                       [os.path.join(dirpath, f) for f in filenames]])
-
-for dirpath, dirnames, filenames in os.walk( script_dir ):
-    # Ignore dirnames that start with '.'
-    for i, dirname in enumerate(dirnames):
-        if dirname.startswith('.'): del dirnames[i]
-    data_files.append([os.path.join( 'biskit', dirpath ),
-                       [os.path.join(dirpath, f) for f in filenames]])
+
+
+def get_packages(target):
+    packages = [
+        dirpath.replace("/", ".").lstrip(".")
+        for dirpath, _, filenames in os.walk(os.path.join(".", target))
+        if "__init__.py" in filenames
+    ]
+    return [package for package in packages if len(package) > 0]
+
+
+def get_files(target, prefix):
+    data_files = [
+        [
+            os.path.join(prefix, dirpath),
+            [os.path.join(dirpath, f) for f in filenames if "__init__.py" not in f],
+        ]
+        for dirpath, _, filenames in os.walk(target)
+    ]
+    return data_files
+
+
+def get_data_files_and_packages():
+    root_dir = os.path.dirname(__file__)
+
+    biskit_dir = "biskit"
+    doc_dir = "doc"
+    script_dir = "scripts"
+
+    cwd = os.getcwd()
+    os.chdir(root_dir)
+    packages = get_packages(biskit_dir)
+    print(packages)
+    data_files = get_files(biskit_dir, ".")
+    data_files += get_files(doc_dir, biskit_dir)
+    data_files += get_files(script_dir, biskit_dir)
+    os.chdir(cwd)
+    return packages, data_files
+
+
+packages, data_files = get_data_files_and_packages()
 
 # Small hack for working with bdist_wininst.
 # See http://mail.python.org/pipermail/distutils-sig/2004-August/004134.html
-if len(sys.argv) > 1 and sys.argv[1] == 'bdist_wininst':
+if len(sys.argv) > 1 and sys.argv[1] == "bdist_wininst":
     for file_info in data_files:
-        file_info[0] = '/PURELIB/%s' % file_info[0]
+        file_info[0] = "/PURELIB/%s" % file_info[0]
 
 
 long_description = \
- """ Biskit is a modular, object-oriented Python library for structural
+""" Biskit is a modular, object-oriented Python library for structural
  bioinformatics research. It facilitates the manipulation and analysis
  of macromolecular structures, protein complexes, and molecular
  dynamics trajectories. For efficient number crunching, Biskit objects
@@ -75,31 +79,30 @@
 
 
 setup(
-    name = "biskit",
-    version = "3.0.0a0",
-    url = 'http://biskit.pasteur.fr',
-    download_url= 'https://github.com/graik/biskit/archive/v3.0.0.tar.gz',
-    author = 'Raik Gruenberg, Johan Leckner and others',
-    author_email = 'raik.gruenberg@crg.es',
-    description = 'A Python platform for structural bioinformatics',
-    long_description = long_description,
-    provides=['biskit'],
-
+    name="biskit",
+    version="3.0.0a0",
+    url="http://biskit.pasteur.fr",
+    download_url="https://github.com/graik/biskit/archive/v3.0.0.tar.gz",
+    author="Raik Gruenberg, Johan Leckner and others",
+    author_email="raik.gruenberg@crg.es",
+    description="A Python platform for structural bioinformatics",
+    long_description=long_description,
+    provides=["biskit"],
     ## available on PyPi
-    install_requires=['numpy', 'scipy', 'biopython'],
-    packages = packages,
+    install_requires=["numpy", "scipy", "biopython"],
+    packages=packages,
     include_package_data=True,
-    data_files = data_files,
-    scripts = ['scripts/bis.py'],
-
-    classifiers= ['License :: OSI Approved :: GNU General Public License (GPL)',
-                  'Topic :: Scientific/Engineering :: Bio-Informatics',
-                  'Topic :: Scientific/Engineering :: Physics',
-                  'Programming Language :: Python',
-                  'Operating System :: OS Independent',
-                  'Operating System :: POSIX',
-                  'Operating System :: MacOS :: MacOS X',
-                  'Intended Audience :: Science/Research',
-                  'Development Status :: 5 - Production/Stable'
-                  ]
+    data_files=data_files,
+    scripts=["scripts/bis.py"],
+    classifiers=[
+        "License :: OSI Approved :: GNU General Public License (GPL)",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Scientific/Engineering :: Physics",
+        "Programming Language :: Python",
+        "Operating System :: OS Independent",
+        "Operating System :: POSIX",
+        "Operating System :: MacOS :: MacOS X",
+        "Intended Audience :: Science/Research",
+        "Development Status :: 5 - Production/Stable",
+    ],
 )