Trying setup_required.

Seems to work for cython/Cython. Attempt to use it for pysam and
pybedtools failed. Install of pybedtools from source (to use unmerged
fork providing headers) requires cythonizing, which might be done using
--global-option="cythonize" option. Now this needs to be checked, and
also: how to have it done as part of automatic dependency install?

install.sh

 #!/bin/sh
 #/usr/bin/env python3 setup.py build_ext
 # .egg-link does not work with PYTHONPATH ?
-/usr/bin/env python3 -m pip install -e .
-/usr/bin/env python3 -m pip install --no-deps --ignore-installed .
+/usr/bin/env python3 -m pip install --no-build-isolation -e .
+/usr/bin/env python3 -m pip install --no-build-isolation --no-deps --ignore-installed .

pyproject.toml

 [build-system]
-requires = ["setuptools", "Cython"]
+requires = [
+    #"wheel",
+    "pysam",
+    "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers",
+    #"Cython"
+]
 build-backend = "setuptools.build_meta"

setup.py

-from os import environ
+from os import environ, PathLike
 from setuptools import setup, find_packages
 # from glob import glob
 # If you have .pyx things to cythonize
 from distutils.extension import Extension
-from Cython.Build import cythonize
+#from Cython.Build import cythonize
 # https://github.com/daler/pybedtools/issues/253
 from pybedtools.helpers import get_includes as pybedtools_get_includes
 from pysam import get_include as pysam_get_include
@@ -11,14 +11,34 @@ from pysam import get_include as pysam_get_include
 name = "bam25prime"
 __version__ = "0.1"
 
+
+# https://stackoverflow.com/a/54138355/1878788
+# defer the import of these modules after setup_requires have been provided
+#class pysam_get_includes(str):
+#    def __str__(self):
+#        from pysam import get_include
+#        includes = get_include()
+#        print(*includes, sep="\n")
+#        return "|".join(includes)
+#
+#class pybedtools_get_includes(str):
+#    def __str__(self):
+#        from pybedtools.helpers import get_includes
+#        includes = get_includes()
+#        print(*includes, sep="\n")
+#        return "|".join(includes)
+
+
 # https://github.com/cython/cython/blob/master/docs/src/reference/compilation.rst#configuring-the-c-build
 extensions = [
     Extension(
         "bam25prime.libcollapsesam", ["bam25prime/libcollapsesam.pyx"],
+        #include_dirs=pysam_get_includes().split("|")),
         include_dirs=pysam_get_include()),
     Extension(
         "bam25prime.libcollapsebed", ["bam25prime/libcollapsebed.pyx"],
         #include_dirs=glob("%s/src/bedtools2-2.27.1/src/utils/*" % environ["HOME"]),
+        #include_dirs=pybedtools_get_includes().split("|"),
         include_dirs=pybedtools_get_includes(),
         language="c++"),
     ]
@@ -36,9 +56,20 @@ setup(
         "console_scripts": ["bam25prime = bam25prime.bam25prime:main",]
     },
     # scripts=["bin/%s" % name],
-    ext_modules = cythonize(extensions),
+    #ext_modules = cythonize(extensions),
+    ext_modules = extensions,
     #ext_modules = cythonize("bam25prime/libbam25prime.pyx", include_path=pysam_get_include()),
-    install_requires=["pysam", "pybedtools"])
+    setup_requires=[
+        "wheel",
+        "cython",
+        #"pysam",
+        #"pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers"
+    ],
+    install_requires=[
+        "pysam",
+        "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers"
+    ]
+)
 # If you have .pyx things to cythonize
     #ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
     #install_requires=["cytoolz"],