Just a word of warning to anyone using the Pynq-Z2 RPi header and basing their work on section 18 of the PYNQ-Z2 Reference Manual v1.0 (17 May 2018). The pin assignments shown in that document are incorrect.
The schematic has the correct pinout, but it requires a little more work to decipher. I noticed this because the pins that are shared between the PMOD A connector and the RPi connector are not where the Reference Manual says they are.