Convert python install from build_ext to setuptools setup_requires.

[marcus1487]

This should make cython installation a bit more robust and allows python3.9 support (on my machine at least).

Resolves #719

[lh3]

Does the change require cython? The current setup.py makes cython optional. When you install with pip, cython is not required. I prefer that way.

[marcus1487]

With this change, if cython is not available at install time it will be installed before building the mappy extension as part of the full install command sequence. It does not require that cython is installed/available before pip install mappy or python setup.py install.

This also forces mappy.pyx to be compiled by cython with the version linked with the installing python environment. I think this might be the source of the python 3.9 issue. I'm not sure exactly why it is popping up with python 3.9 specifically, but I got the same error message as posted in the linked issue when trying to install in a python 3.9 environment.

[lh3]

I much prefer people can download the tar-ball and compile without any dependencies. Cython shouldn't be required. I will update the package at PyPI at some point.

[marcus1487]

I appreciate the concern. I am wondering how the mappy.c file is created without cython. It seems that the Makefile removes this file, but I am not following how this file is created without cython. Running the following raises an error indicating no such file or directory: 'python/mappy.c'

git clone https://github.com/lh3/minimap2
cd minimap2
make
pip install .

[lh3]

You create mappy.c with cython. The current setup.py submits this file to PyPI. This way, when users run pip install, they don't need cython as a dependency.

#719 is probably caused by the older cython that was used to create mappy.c.

[marcus1487]

I see. Thank you for the detailed explanation!

[lh3]

It seems that I am using TABs but you are using SPACEs. Could you change that? I will merge after that.

[marcus1487]

Done.

[lh3]

Just to confirm: with this PR, pip will automatically install cython. Is that right?

[marcus1487]

Yes. When pip install mappy is run cython will be installed automatically (if not already available) before the mappy source is compiled with cython.

[lh3]

Good. Thanks.