Helveg/binpack.md

## binpack.md

      
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              binpack.md
            
          
    Binary compatibility in Python packaging

As a user of scientific computing software packages, Python packages always trips over binary extensions that require cooperation with
binaries on the target system. Packaging things in wheels becomes impossible, because there is currently no way for a user to specify
that they want a wheel, but specifically the wheel that is compatible with their local library.
Take mpi4py, the most popular parallelization scheme in my field. It requires to know which MPI implementation is used: MPICH,
OpenMPI, ...? What mpi4py does is provide a source distribution that detects the local library at install time, and errors out if it can't. So the user is
tasked with installing the binary dependencies of a Python package, before they can install the Python package. Python users have by design 0 knowledge of building binary software, we pip install or riot ┬─┬ノ(ಠ_ಠノ).
To include the binary dependency, the maintainer of the package should be able to provide several choices to the installing user.

Do you want me to install a bundled MPI implementation for you?
Or, would you like me to detect a local library you already have, and build against that?

User's response:

I don't have MPI, don't know how to build it, please take the wheel bundled with OpenMPI: pip install mpi4py{mpi:openmpi}
I already have MPI, and am aware that mpi4py (or was made aware by mpi4py's docs) that it needs to cooperate with my local library: pip install mpi4py{mpi:local}

Same story for h5py: pip install h5py{hdf5:local}/pip install h5py{hdf5:bundled}/pip install h5py{hdf5:bundled, parallel:true}
Same for any neuroscience simulator that requires MPI, gpu, ...:

pip install arbor{mpi:local, gpu:nvidia}, pip install NEURON{mpi:local}, pip install nest{mpi:local}