This is what I do which is working fine for me on 10.11 and have been doing for many years.
Create a virtual port in the Audio MIDI Setup app and have Pd use it:
* open Audio MIDI Setup app (in /Applications/Utilities)
* Window->Show MIDI Studio
* Double click IAC Driver
* Make sure the “Device is online” checkbox is enabled
* Click the Plus button under the Ports list to add a virtual input (mine is named Pure Data In)
* Click Plus again and add a virtual output (mine is named Pure Data Out)
Next, open Pd and have it use the input & output virtual ports. Save the settings.
Download and install
MIDI Patchbay. You can then use it to route between the devices and Pd as well as save hot plug settings, kind of like the Alsa MIDI routing in qjackctl.
I’ve not actually connected to devices directly in Pd since the above handles everything.
Subject: [PD] OSX midi ports visibility
Date: October 8, 2016 at 3:04:27 PM MDT
Hi all,I have several students who are trying to use the old pd-extended and current pure-data and who are unable to connect to their internal general MIDI synth. Under MIDI settings there are no MIDI output devices found. I believe this pertains primarily to Yosemite and newer. I wonder if anyone has any ideas as to why this is so and whether you have a proposed solution?