So I turned debug mode on and look at the console in ST3 and see some curious bits:
SublimeLinter: user shell: /bin/zsh
SublimeLinter: computed PATH using /bin/zsh:
/Users/paltman/bin
/usr/local/share/npm/bin
/usr/local/share/python
/usr/local/bin
/usr/bin
/bin
/usr/local/sbin
/usr/sbin
/sbin
/usr/X11/bin
/Users/paltman/.local/bin
/usr/local/bin
/usr/bin
/bin
/usr/sbin
/sbin
and then:
SublimeLinter: find_posix_python: python => /usr/bin/python
SublimeLinter: find_python: system python = /usr/bin/python
SublimeLinter: find_python: available version = {'major': 2, 'minor': 7}
and then when I open a python file:
SublimeLinter: find_python(version=None, script='flake8', module=None)
SublimeLinter: find_python: default python = /usr/bin/python
SublimeLinter: find_python: available version = {'major': 2, 'minor': 7}
SublimeLinter: find_python: 'flake8' path = None
SublimeLinter: find_python: <= (None, None, 2, 7)
SublimeLinter: WARNING: flake8 deactivated, cannot locate 'flake8@python'