fix setup to work with new numpy

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=41", "wheel", "setuptools_scm[toml]>=6.2", "numpy"]
+requires = ["setuptools>=41", "wheel", "setuptools_scm[toml]>=6.2", "numpy", "Cython"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools-git-versioning]

setup.py

@@ -1,20 +1,40 @@
 from setuptools import setup, Extension
+from Cython.Build import cythonize
+from Cython.Compiler import Options
 import numpy
 
-setup_args = dict(
-    ext_modules=[
-        Extension(
-            "chromatinhd.loaders.fragments_helpers",
-            ["src/chromatinhd/loaders/fragments_helpers.c"],
+# These are optional
+Options.docstrings = True
+Options.annotate = False
+
+# Modules to be compiled and include_dirs when necessary
+extensions = [
+    # Extension(
+    #     "pyctmctree.inpyranoid_c",
+    #     ["src/pyctmctree/inpyranoid_c.pyx"],
+    # ),
+    Extension(
+        "chromatinhd.loaders.fragments_helpers",
+            ["src/chromatinhd/loaders/fragments_helpers.pyx"],
             include_dirs=[numpy.get_include()],
             py_limited_api=True,
-        ),
+    ),
         Extension(
             "chromatinhd.data.motifscan.scan_helpers",
-            ["src/chromatinhd/data/motifscan/scan_helpers.c"],
+            ["src/chromatinhd/data/motifscan/scan_helpers.pyx"],
             include_dirs=[numpy.get_include()],
             py_limited_api=True,
         ),
-    ]
-)
-setup(**setup_args)
+]
+
+
+# This is the function that is executed
+setup(
+    name='chromatinhd',  # Required
+
+    # A list of compiler Directives is available at
+    # https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html#compiler-directives
+
+    # external to be compiled
+    ext_modules = cythonize(extensions, compiler_directives={"language_level": 3, "profile": False}),
+)