Github Actions and PyPI Wheels

[dilawar]

This PR contains a lot of changes.

• Added cmake based build systems.
• Builds on Windows, Linux and OSX.
• Added Github Actions to generate wheels and upload to PyPi.

I'd be happy to handover the pypi packages if you are interested.

[joachimwolff]

Thanks a lot for your contribution; that is really awesome!

At the moment we have minimal time, therefore this late reply. Also, I fear that it will take a while (actually maybe a few weeks) until we have reviewed it and discussed a few things you propose here.

What I recognized we need to discuss:

• We don't support Windows. We don't test for this platform, nor do we develop on it or use it in production. All workflows and testing are based on Linux as the main software platform, simply because more or less all HPC/Cluster environments run on Linux. MacOS is only supported because many biomedical uses the Mac as a working device, and the overhead to support it is very limited.
• You are using techniques where I don't know if we want to support it, for example, brew on macOS. Our main package manager is Conda, and we don't want to change this. A few years back, I used brew on my Mac (maybe that was 2012 - 2014), and everything you wanted to install had to be compiled on the system. That was a very unpleasant experience; it simply took way too long. If this is still the case, I don't want to have this for our users, mainly biomedical people with no computer science background.
• PyPI: The reason we don't support this package manager is that certain dependencies are not resolvable with PyPI and the users need to take care of it on their own. The last time I checked, dependencies like boost c++ eigen c++have not been available, and I have not recognized that this changed. Again, our user base are biomedical people with no computer science background.

Maybe some of the things have changed in the meantime, and I am open to discuss the points listed!

Best,

Joachim

[dilawar]

Hi Joachim,

Thanks for the response. There is no hurry. Take your time.

I did this when a colleague was struggling to install https://github.com/deeptools/HiCExplorer which is available only via conda because of two of its dependencies (one is kr-balancing) are available via conda only. So I created pip installable packages (binary wheels) for both of them.

This PR builds binary wheels for amd64 architecture i.e., one can simply do python3 -m pip install kr-balancing on Linux, OSX and Windows without any need to build anything on end-user machine (more here https://pythonwheels.com/, and https://www.python.org/dev/peps/pep-0571/).

On OSX, brew is used to install dependencies to build the wheel (homebrew these days install pre-compiled binaries for most packages). I am happy to drop Windows support: I don't use it. The template I use to generate work on Windows as well.

At the end of the day, the purpose is to create a portable binary python package for amd64 architecture for almost all linuxes, OSX and optionally Windows.