Installing from source via pip

[moravveji]

I would like to propose an update to your installation guide (https://alleninstitute.github.io/bmtk/installation.html) when building from source. Currently, the proposed installation step is python setup.py install. However, in the latest versions of Python, using .egg files is deprecated. When I try this on our HPC clusters, I ended up with only .egg files under the lib folder, and not a working copy of the actual bmtk module and its other dependencies.

Instead, simply using pip(3) comes to the rescue, e.g.

cd bmtk-1.0.8     # i.e. the top folder for a specific version
pip3 install --prefix=<path/to/software/folder> .

mind the ending dot . which enforces pip3 to use the local setup.py file.

I hope this helps.