mdacli doesn't loop over single frames

[hejamu]

If one is using an AnalysisClass on a trajectory with only one frame, the AnalysisBaseClass from MDA will happily do exactly that. This is because at initialization (
https://github.com/MDAnalysis/mdanalysis/blob/3769ee29e5907221527ff0ec88a8c5acf9f86dee/package/MDAnalysis/analysis/base.py#L247
), if start, stop and step are None, and the trajectory is ONE frame long, it sets them to 0, 1 and 1 respectively.

mdacli however sets the default values to start = 0, stop = -1 and step = 1. This does not result in the same behaviour, since for array of length 1:

a[0:-1:1] != a[0:1:1]

This difference in behaviour finally matters at this point: https://github.com/MDAnalysis/mdanalysis/blob/3769ee29e5907221527ff0ec88a8c5acf9f86dee/package/MDAnalysis/analysis/base.py#L296

Maybe setting the defaults to None would be an option?

[PicoCentauri]

Good idea of changing these. Would you be able to do it? The lines are here:

mdacli/src/mdacli/libcli.py

Lines 182 to 204 in cd90206

	run_group.add_argument(
	"-b",
	dest="start",
	type=str,
	default="0",
	help="start frame or time for evaluation (default: %(default)s)"
	)
	run_group.add_argument(
	"-e",
	dest="stop",
	type=str,
	default="-1",
	help="end frame or time for evaluation (default: %(default)s)"
	)
	run_group.add_argument(
	"-dt",
	dest="step",
	type=str,
	default="1",
	help="step or time step for evaluation (default: %(default)s)"
	)

We ran through a test to check the units and maybe the function

mdacli/src/mdacli/utils.py

Line 25 in cd90206

def split_time_unit(s):

will breaks. An additional test for None would be sufficient I guess.

[PicoCentauri]

Closed by #99