Pygame rotating cubes around axis

It is not sufficient to sort the faces of each cube separately by its depth. You’ve to sort the faces of all objects of the entire scene by its depth.

Create a list of tuples, which consists of the projected (transformed) points ofa face and the average depth (z value):

polygons = []
for cube in self._cubes:
    transformed_vectors = cube.transform_vectors(self._angle)
    avg_z = cube.calculate_average_z(transformed_vectors)
    for z in avg_z:
        face_index = z[0]
        face = cube._faces[face_index]
        pointlist = cube.create_polygon(face, transformed_vectors)
        polygons.append((pointlist, z[1]))

Draw the faces of all objects in (reverse) sorted order:

for poly in sorted(polygons, key=lambda x: x[1], reverse=True):
    pygame.draw.polygon(self.screen, Color.SILVER.value,poly[0])
    pygame.draw.polygon(self.screen, Color.BLACK.value, poly[0], 3)

---

Minimal example: repl.it/@Rabbid76/PyGame-3D

import math
import pygame

def project(vector, w, h, fov, distance):
    factor = math.atan(fov / 2 * math.pi / 180) / (distance + vector.z)
    x = vector.x * factor * w + w / 2
    y = -vector.y * factor * w + h / 2
    return pygame.math.Vector3(x, y, vector.z)

def rotate_vertices(vertices, angle, axis):
    return [v.rotate(angle, axis) for v in vertices]
def scale_vertices(vertices, s):
    return [pygame.math.Vector3(v[0]*s[0], v[1]*s[1], v[2]*s[2]) for v in vertices]
def translate_vertices(vertices, t):
    return [v + pygame.math.Vector3(t) for v in vertices]
def project_vertices(vertices, w, h, fov, distance):
    return [project(v, w, h, fov, distance) for v in vertices]

class Mesh():

    def __init__(self, vertices, faces):
        self.__vertices = [pygame.math.Vector3(v) for v in vertices]
        self.__faces = faces

    def rotate(self, angle, axis):
        self.__vertices = rotate_vertices(self.__vertices, angle, axis)
    def scale(self, s):
        self.__vertices = scale_vertices(self.__vertices, s)
    def translate(self, t):
        self.__vertices = translate_vertices(self.__vertices, t)

    def calculate_average_z(self, vertices):
        return [(i, sum([vertices[j].z for j in f]) / len(f)) for i, f in enumerate(self.__faces)]

    def get_face(self, index):
        return self.__faces[index]
    def get_vertices(self):
        return self.__vertices

    def create_polygon(self, face, vertices):
        return [(vertices[i].x, vertices[i].y) for i in [*face, face[0]]]
       
class Scene:
    def __init__(self, mehses, fov, distance):
        self.meshes = mehses
        self.fov = fov
        self.distance = distance 
        self.euler_angles = [0, 0, 0]

    def transform_vertices(self, vertices, width, height):
        transformed_vertices = vertices
        axis_list = [(1, 0, 0), (0, 1, 0), (0, 0, 1)]
        for angle, axis in reversed(list(zip(list(self.euler_angles), axis_list))):
            transformed_vertices = rotate_vertices(transformed_vertices, angle, axis)
        transformed_vertices = project_vertices(transformed_vertices, width, height, self.fov, self.distance)
        return transformed_vertices

    def draw(self, surface):
        
        polygons = []
        for mesh in self.meshes:
            transformed_vertices = self.transform_vertices(mesh.get_vertices(), *surface.get_size())
            avg_z = mesh.calculate_average_z(transformed_vertices)
            for z in avg_z:
            #for z in sorted(avg_z, key=lambda x: x[1], reverse=True):
                pointlist = mesh.create_polygon(mesh.get_face(z[0]), transformed_vertices)
                polygons.append((pointlist, z[1]))
                #pygame.draw.polygon(surface, (128, 128, 192), pointlist)
                #pygame.draw.polygon(surface, (0, 0, 0), pointlist, 3)

        for poly in sorted(polygons, key=lambda x: x[1], reverse=True):
            pygame.draw.polygon(surface, (128, 128, 192), poly[0])
            pygame.draw.polygon(surface, (0, 0, 0), poly[0], 3)
        

vertices = [(-1,-1,1), (1,-1,1), (1,1,1), (-1,1,1), (-1,-1,-1), (1,-1,-1), (1,1,-1), (-1,1,-1)]
faces = [(0,1,2,3), (1,5,6,2), (5,4,7,6), (4,0,3,7), (3,2,6,7), (1,0,4,5)]

cube_origins = [(-1, -1, 0), (0, -1, 0), (1, -1, 0), (1, 0, 0), (1, 1, 0), (0, 1, 0), (-1, 1, 0), (-1, 0, 0)]
meshes = []
for origin in cube_origins:
    cube = Mesh(vertices, faces)
    cube.scale((0.5, 0.5, 0.5))
    cube.translate(origin)
    meshes.append(cube)

scene = Scene(meshes, 90, 5)

pygame.init()
window = pygame.display.set_mode((400, 300))
clock = pygame.time.Clock()

run = True
while run:
    clock.tick(60)
    for event in pygame.event.get():
        if event.type == pygame.QUIT:
            run = False

    window.fill((255, 255, 255))
    scene.draw(window)
    scene.euler_angles[1] += 1
    pygame.display.flip()

pygame.quit()