From f780cd42a077c6045cef868e472d7726c267eb55 Mon Sep 17 00:00:00 2001
From: Tor Solli-Nowlan <tor.solli-nowlan@medisin.uio.no>
Date: Tue, 21 Sep 2021 13:50:04 +0200
Subject: [PATCH] remove use_2to3 for new setuptools

---
 setup.py | 91 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 45 insertions(+), 46 deletions(-)

diff --git a/setup.py b/setup.py
index b865b8dd..63b250a4 100644
--- a/setup.py
+++ b/setup.py
@@ -4,77 +4,76 @@
 
 try:
     from Cython.Distutils import build_ext
+
     CYTHON = True
 except:
     CYTHON = False
 
-DEPENDENCIES = ['setuptools']
+DEPENDENCIES = ["setuptools"]
 
 # get the version without an import
 VERSION = "Undefined"
 DOC = ""
 inside_doc = False
-for line in open('vcf/__init__.py'):
+for line in open("vcf/__init__.py"):
     if "'''" in line:
         inside_doc = not inside_doc
     if inside_doc:
         DOC += line.replace("'''", "")
 
-    if (line.startswith('VERSION')):
+    if line.startswith("VERSION"):
         exec(line.strip())
 
 extras = {}
 if CYTHON:
-    extras['cmdclass'] = {'build_ext': build_ext}
-    extras['ext_modules'] = [Extension("vcf.cparse", ["vcf/cparse.pyx"])]
+    extras["cmdclass"] = {"build_ext": build_ext}
+    extras["ext_modules"] = [Extension("vcf.cparse", ["vcf/cparse.pyx"])]
 
 setup(
-    name='PyVCF',
-    packages=['vcf', 'vcf.test'],
-    scripts=['scripts/vcf_melt', 'scripts/vcf_filter.py',
-             'scripts/vcf_sample_filter.py'],
-    author='James Casbon and @jdoughertyii',
-    author_email='casbon@gmail.com',
-    description='Variant Call Format (VCF) parser for Python',
+    name="PyVCF",
+    packages=["vcf", "vcf.test"],
+    scripts=["scripts/vcf_melt", "scripts/vcf_filter.py", "scripts/vcf_sample_filter.py"],
+    author="James Casbon and @jdoughertyii",
+    author_email="casbon@gmail.com",
+    description="Variant Call Format (VCF) parser for Python",
     long_description=DOC,
-    test_suite='vcf.test.test_vcf.suite',
+    test_suite="vcf.test.test_vcf.suite",
     install_requires=DEPENDENCIES,
-    entry_points = {
-        'vcf.filters': [
-            'site_quality = vcf.filters:SiteQuality',
-            'vgq = vcf.filters:VariantGenotypeQuality',
-            'eb = vcf.filters:ErrorBiasFilter',
-            'dps = vcf.filters:DepthPerSample',
-            'avg-dps = vcf.filters:AvgDepthPerSample',
-            'snp-only = vcf.filters:SnpOnly',
+    entry_points={
+        "vcf.filters": [
+            "site_quality = vcf.filters:SiteQuality",
+            "vgq = vcf.filters:VariantGenotypeQuality",
+            "eb = vcf.filters:ErrorBiasFilter",
+            "dps = vcf.filters:DepthPerSample",
+            "avg-dps = vcf.filters:AvgDepthPerSample",
+            "snp-only = vcf.filters:SnpOnly",
         ]
     },
-    url='https://github.com/jamescasbon/PyVCF',
+    url="https://github.com/jamescasbon/PyVCF",
     version=VERSION,
-    classifiers = [
-        'Development Status :: 4 - Beta',
-        'Intended Audience :: Developers',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
-        'License :: OSI Approved :: MIT License',
-        'Operating System :: OS Independent',
-        'Programming Language :: Cython',
-        'Programming Language :: Python',
-        'Programming Language :: Python :: 2',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.4',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: Implementation :: CPython',
-        'Programming Language :: Python :: Implementation :: PyPy',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',
-      ],
-    keywords='bioinformatics',
-    use_2to3=True,
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+        "Programming Language :: Cython",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 2",
+        "Programming Language :: Python :: 2.7",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.4",
+        "Programming Language :: Python :: 3.5",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: Implementation :: CPython",
+        "Programming Language :: Python :: Implementation :: PyPy",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+    ],
+    keywords="bioinformatics",
     include_package_data=True,
-    package_data = {
-        '': ['*.vcf', '*.gz', '*.tbi'],
-        },
+    package_data={
+        "": ["*.vcf", "*.gz", "*.tbi"],
+    },
     **extras
 )