I came across this and don't really have any answers or suggestions but in reading I wanted to make a comment about Stepper Monkey's suggestion.
Safe machine building practice suggests that controls intended to stop operation be logic LOW when in the tripped status. If your BOB doesn't support this then there are possibly some work arounds I'll mention at the end.
The underlying theory of the tripped state being a logic LOW state is that if a wire is cut, broken or shorts out to the machine (which 99.9% of the time is going to be ground - though whether referenced to logic ground or not making a difference could be debated with all the EMI generated by the movement of the machine but that's a larger and more complex debate) or if a power source separate from the controller fails - in my setup a charge pump switches power to everything other than the computer and the opto isolator dedicated to the charge pump so if that or anything after it fails there is no voltage at the limits, the drives, the spindle, anything - the control software - in my case EMC - see's a wholesale lack of "SAFE" signals since they are all expected to be HIGH under normal operating conditions.
Not trying to be a burr under anyones saddle, just trying to save a few fingers if I can.
The work arounds for the limits, if your BOB doesn't have the flexibility to let you run a switches as a high condition as the normal good to go condition, would be to utilize the PC 5V power supply (fused of course) and wire it through each switch using the normally closed terminals so that if the switch isn't activated the logic 5V of the PC is run back to the parallel port as the limit signal. If your software doesn't let you look for them as high being the go state then you're stuck with that limitation (and then I'd suggest looking at using EMC or Mach if that makes you more comfortable).
I hope I didn't offend anyone and everyone had the patience to read through this whole post, and that at least the concept makes sense. I would hate to see someone's part, or worst case scenario a finger, hand, etc. ruined because a wall wort died and there was no 5V signal to be seen so everything kept running because the software saw no 5V signal to tell it to stop doing what it was doing.
My .02 - and I hope your mileage doesn't vary If you have definitive reasons not to wire it as such I'd love to hear them, but in my years servicing, rebuilding and a few design tasks on a lot of equipment of many different types, any mechanical limit or interlock was HIGH in the safe to run state and LOW in the stop everything state.
HTH
Every day is a learning process, whether you remember yesterday or not is the hard part.
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