If installing from git, you must have setuptools_git installed, or setuptools won't realize the scaffold's template directory is part of the package.
Pyramid Alembic/SQLAlchemy project scaffold using url dispatch and Mako templates
Use alembic to generate revisions before you run initializedb. Example:
alembic -c development.ini revision --autogenerate -m "starting"
Then you can use alembic to upgrade to that revision:
alembic -c development.ini upgrade head
Or initializedb:
initialize_myapp_db development.ini