When trying to light up the right leds on the mini-Rainbow (8x4) with Python with x and y positions and set_pixel, both x and y seem to have a range with the length of 8 (0-7). Each second row of 4 leds seems to be a continuation of the first row of 4 leds.
Example:

import time
import rainbowhat as rainbow

rainbow.set_layout(rainbow.PHAT)
rainbow.rotation(0)
rainbow.brightness(0.3)

for x in range(8):
    for y in range(4):
        rainbow.set_pixel(x,y,255,255,255)
        rainbow.show()
        time.sleep(1)

Playing with rotation doesn't help. I'm using set_layout to set it to PHAT.

Example 2 (with rotation):

import time
import rainbowhat as rainbow

rainbow.set_layout(rainbow.PHAT)
rainbow.rotation(90)
rainbow.brightness(0.3)

for x in range(4):
    rainbow.set_pixel(x,0,255,255,255)
    rainbow.show()
    time.sleep(1)

for x in range(4):
    rainbow.set_pixel(x,1,255,0,0)
    rainbow.show()
    time.sleep(1)

results in this:

Traceback (most recent call last):
File "demo.py", line 7, in
import rainbowhat as rainbow
File "build/bdist.linux-armv7l/egg/rainbowhat.py", line 17, in
File "build/bdist.linux-armv7l/egg/neopixel.py", line 114, in begin
RuntimeError: ws2811_init failed with code -1
Exiting cleanly

I had issue with using sudo pip install rainbowhat as that installs the appropriate files for the Pimoroni Rainbow HAT, not the Allo Rainbow HAT/PHAT. Using your github install instructions however do work. I would suggest removing that from your README under https://github.com/allocom/Rainbow-HAT/tree/master/library/RainbowHat

sudo python demo.py
Traceback (most recent call last):
File "demo.py", line 7, in
import rainbowhat as rainbow
File "build/bdist.linux-armv7l/egg/rainbowhat.py", line 4, in
ImportError: No module named neopixel