Specify setup time dependency with `--global-option` for a python package

I'm trying to package a python library that has setup-time (and also run-time) dependencies: it imports the modules so that the modules can inform the setup process of the location of some provided C headers:

from distutils.extension import Extension
from pybedtools.helpers import get_includes as pybedtools_get_includes
from pysam import get_include as pysam_get_include
# [...]
extensions = [
    Extension(
        "bam25prime.libcollapsesam", ["bam25prime/libcollapsesam.pyx"],
        include_dirs=pysam_get_include()),
    Extension(
        "bam25prime.libcollapsebed", ["bam25prime/libcollapsebed.pyx"],
        include_dirs=pybedtools_get_includes(),
        language="c++"),
    ]
# [...]

However, one of the dependencies (pybedtools) needs to be installed with a specific --global-option pip option (see at the end of the post what happens when the option is not provided).

If I understand correctly, the currently up-to-date way to automatically have some dependencies available before setup.py is used is to indicate them in the [build-system] section of a pyproject.toml file.

I tried the following pyproject.toml:

[build-system]
requires = [
    "pysam",
    "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option='cythonize'",
]
build-backend = "setuptools.build_meta"

(By the way, it took me quite some time to figure out how to specify the build-backend, the documentation is not easily discoverable.)

However, this generates the following error upon pip install:

  ERROR: Invalid requirement: "pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option='cythonize'"
  Hint: It looks like a path. File 'pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option='cythonize'' does not exist.

How can I correctly specify options for dependencies ?

If I simply specify the package and its URL ("pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers), the install fails as follows:

    Exception:
                            Cython-generated file 'pybedtools/cbedtools.cpp' not found.

                            Please install Cython and run

                                python setup.py cythonize

It was while trying to tackle the above error that I found out about the --global-option pip option. I can manually run pip install --global-option="cythonize" git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers, and the install works, provided the dependencies of that package are already installed, otherwise their install fails because of an unrecognized "cythonize" option (which is another issue...).

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