step pulse and dir are not smooth

That looks about right.
You might want to lengthen the step time, especially if using chinese drives, that will improve smoothness a lot.

What you are seeing there is likely an artefact of measurement due to the sample time of the halscope, you are only sampling at 1kHz
Click the button that says "2000 samples at 1kHz" and put the Halscope sampler into the base-thread and you stand a better chance of seeing the real pulse shapes.

You probably don't even see most of the pulses. The fact that you can see any at all may mean that (unusually) your step pulses are too _long_