Unify coordinate systems for use in electrodes, light, and neurons

[kjohnsen]

One module for generating coords, with units.

• shank coords
• combining coords
• repeating coords
• random cylinders, prisms
• grid cylinders, prisms
• assign_coords_to_neurons

Need to decide whether to return x, y, z tuple or nx3 array

[kjohnsen]

coords everywhere should be nx3 array with units

[kjohnsen]

previously:

def assign_coords_uniform_cylinder(
    neuron_group: NeuronGroup,
    xyz_start: Tuple[float, float, float],
    xyz_end: Tuple[float, float, float],
    radius: float,
    unit: Unit = mm,
) -> None:

want to replace assign_... functions with the single assign_coords function and have separate functions to generate coords

def uniform_cylinder(
    n: int,
    xyz_start: Quantity,  # (3,) vector with units
    xyz_end: Quantity,# (3,) vector with units
    radius: Quantity, # e.g., with units
) -> Quantity:  # (n x 3) array with units