You can draw lines using the connector object versus the shape object, (Shape requires x,y, height, and width and powerpoint can't deal with negative heights)
From the docs
Lines are a sub-category of auto shape that differ in certain properties and behaviors. In particular, they have a start point and end point in addition to extents (left, top, width, height).
Connectors are based on the element and have one of a handful of different preset geometry values, such as line. Freeform connectors, despite the name, are not connectors, and are a custom geometry shape based on the p:sp element.
Connectors can be “connected” to an auto shape such that a connected end point remains connected when the auto shape is moved. This relies on a concept of “connection points” on the auto shape. These connections points are preset features of the auto shape, similar to how adjustment points are pre-defined. Connection points are identified by index.
Using the code below allows you to draw a straight line from x = 4 inches to x= 2 inches.
from pptx.enum.shapes import MSO_CONNECTOR
from pptx import Presentation
# Make sure you have a presentation called test1.pptx in your working directory
prs = Presentation(pptx='test1.pptx')
slide = prs.slides.add_slide(prs.slide_layouts[1])
#shapes.add_connector(MSO_CONNECTOR.STRAIGHT, start_x, start_y, end_x, end_y
line1=slide.shapes.add_connector(MSO_CONNECTOR.STRAIGHT, Inches(4), Inches(2), Inches(1), Inches(2))
prs.save('test2.pptx')