Support python 3.13/cython 3

.github/workflows/main.yml

@@ -13,7 +13,7 @@ jobs:
   build-and-test:
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
@@ -42,7 +42,7 @@ jobs:
       # with pip to make sure it works.
       run: |
         source "${HOME}/conda/etc/profile.d/conda.sh"
-        conda create -p ./cython-env -y "cython>=0.29.30,<3.0" python=${{ matrix.python-version }} gxx zlib --channel conda-forge
+        conda create -p ./cython-env -y "cython>3.0" python=${{ matrix.python-version }} gxx zlib setuptools --channel conda-forge
         conda activate ./cython-env
         python setup.py clean cythonize sdist
         (cd dist && pip install pybedtools-*.tar.gz && cd $TMPDIR && python -c 'import pybedtools; print(pybedtools.__file__)')

pybedtools/__init__.py

@@ -12,6 +12,7 @@
     Attributes,
     MalformedBedLineError,
     IntervalIterator,
+    create_interval_from_list,
 )
 from . import contrib
 from .helpers import (

pybedtools/cbedtools.pxd

@@ -1,3 +1,4 @@
+# cython: language_level=3str
 from cpython cimport bool
 from libcpp.vector cimport vector
 from libcpp.string cimport string

pybedtools/featurefuncs.pyx

@@ -1,7 +1,7 @@
 # cython: language_level=2
 # distutils: language = c++
 from cbedtools cimport Interval
-from cbedtools import create_interval_from_list
+from pybedtools.cbedtools import create_interval_from_list
 
 
 cpdef extend_fields(Interval feature, int n):

pybedtools/version.py

@@ -1,4 +1,4 @@
 
 # THIS FILE IS GENERATED FROM SETUP.PY
-version = '0.11.0'
+version = '0.12.0'
 __version__ = version

pyproject.toml

@@ -1,3 +1,15 @@
 [build-system]
-requires = ["setuptools>=61.0", "wheel", "Cython>=0.29.30,<3.0"]
-build-backend = "setuptools.build_meta:__legacy__"
+requires = ["setuptools>=61.0", "wheel", "Cython>=3.0"]
+build-backend = "setuptools.build_meta:__legacy__"
+
+[project]
+name = "pybedtools"
+dynamic = ["version", "maintainers", "license", "classifiers", "readme"]
+description='Wrapper around BEDTools for bioinformatics work'
+dependencies = [
+    "numpy",
+    "pysam",
+    "pandas"
+]
+[tool.pytest.ini_options]
+testpaths = ["pybedtools"]

setup.cfg

@@ -1,5 +1,5 @@
-[wheel]
-universal = 1
+[bdist_wheel]
+
 [nosetests]
 detailed-errors = 1
 doctest-extension = .pyx .py

setup.py

@@ -26,7 +26,6 @@
 """
 
 try:
-    from Cython.Build import build_ext as cython_build_ext
     from Cython.Build import cythonize
     HAVE_CYTHON = True
 except ImportError:
@@ -52,12 +51,7 @@
 # Try bootstrapping setuptools if it doesn't exist. This is for using the
 # `develop` command, which is very useful for in-place development work.
 try:
-    import pkg_resources
-    try:
-        pkg_resources.require("setuptools>=0.6c5")
-    except pkg_resources.VersionConflict:
-        from ez_setup import use_setuptools
-        use_setuptools(version="0.6c5")
+    import setuptools
     from setuptools import setup, Command
 except ImportError:
     sys.exit(
@@ -68,15 +62,15 @@
 curdir = os.path.abspath(os.path.dirname(__file__))
 
 # These imports need to be here; setuptools needs to be imported first.
-from distutils.extension import Extension  # noqa: E402
-from distutils.command.build import build  # noqa: E402
-from distutils.command.build_ext import build_ext  # noqa: E402
-from distutils.command.sdist import sdist  # noqa: E402
-import distutils.log
-
+from setuptools.extension import Extension  # noqa: E402
+from setuptools.command.build import build  # noqa: E402
+from setuptools.command.build_ext import build_ext  # noqa: E402
+from setuptools.command.sdist import sdist  # noqa: E402
+import setuptools.logging
+setuptools.logging.configure()
 
 MAJ = 0
-MIN = 11
+MIN = 12
 REV = 0
 VERSION = '%d.%d.%d' % (MAJ, MIN, REV)
 
@@ -209,7 +203,7 @@ def build_extensions(self):
                         ''')
                 self.announce(
                     "Trying to generate the following missing files:\n%s" % "\n".join(missing_src),
-                    level=distutils.log.INFO)
+                    level=0)
                 for src in missing_src:
                     assert src in ext.sources
                     (root, extn) = os.path.splitext(src)
@@ -266,7 +260,6 @@ def run(self):
 }
 
 if USE_CYTHON:
-    cmdclass['build_ext'] = cython_build_ext
     cmdclass['cythonize'] = Cythonize
 else:
     cmdclass['build_ext'] = InformativeBuildExt
@@ -296,7 +289,6 @@ def run(self):
         long_description=README,
         zip_safe=False,
         setup_requires=[],
-        install_requires=['pysam', 'numpy'],
         classifiers=[
             'Development Status :: 5 - Production/Stable',
             'Intended Audience :: Science/Research',
@@ -324,6 +316,5 @@ def run(self):
                                      "*.h"],
                       'src': ['src/*'],
                       },
-        include_package_data=True,
-        language_level=2,
+        include_package_data=True
     )