Add radians option to angle_between_vectors and add value ranges to bond distribution functions.

[chrisjonesBSU]

This PR does a couple of things:

Adds a parameter so that geometry.angle_between_vectors can return the angle in degrees or radians. It defaults to degrees

Adds a radians option to the bond and angle distribution functions.

Adds min and max options to the distribution functions, so that it can work similar to the gsd_rdf function

[codecov]

Codecov Report

Merging #35 (75922d0) into master (e96dd7f) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master      #35   +/-   ##
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  Coverage   99.68%   99.69%           
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  Files           7        7           
  Lines         318      328   +10     
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+ Hits          317      327   +10     
  Misses          1        1           

Impacted Files	Coverage Δ
cmeutils/geometry.py	100.00% <100.00%> (ø)
cmeutils/plotting.py	100.00% <100.00%> (ø)
cmeutils/structure.py	100.00% <100.00%> (ø)

[jennyfothergill]

Might want to add tests for theta_min/theta_max and l_min/l_max just to validate that these values don't break anything. Also what happens if the min and max are set such that they are outside the distribution?

[jennyfothergill]

Suggested change

	else:
	return angle
	return angle

[chrisjonesBSU]

Might want to add tests for theta_min/theta_max and l_min/l_max just to validate that these values don't break anything. Also what happens if the min and max are set such that they are outside the distribution?

Yeah, I can add a test. To your question, that's kind of the point of having the min and max values. For example, say some bond distribution only has values between 1 and 2, but you want the distribution to go from zero to 3, so you'd set min=0, max=3 and the distribution would include the entire range from min to max, even if a good portion of it is zero. Unless I'm not understanding what you mean by outside the distribution.

[jennyfothergill]

Might want to add tests for theta_min/theta_max and l_min/l_max just to validate that these values don't break anything. Also what happens if the min and max are set such that they are outside the distribution?

Yeah, I can add a test. To your question, that's kind of the point of having the min and max values. For example, say some bond distribution only has values between 1 and 2, but you want the distribution to go from zero to 3, so you'd set min=0, max=3 and the distribution would include the entire range from min to max, even if a good portion of it is zero. Unless I'm not understanding what you mean by outside the distribution.

What I mean using your example of a bond distribution with values between 1 and 2, what if you set the min and max to 1.5 to 3? Some of the distribution isn't captured. Is there anything we should do to handle that? (I don't mean these as leading questions, I'm just thinking about possible hangups.)

[chrisjonesBSU]

If that's the case then I'm pretty sure numpy.histogram just trims the distribution based on the range you give it. We could maybe add a warning if any part of the array of values returned (bond lengths, angles) lies outside of either min or max values, but it wouldn't error out.

[jennyfothergill]

LGTM 🙌