Background svg shading

[hyanwong]

To be considered after #555 (on which this is based - the only new stuff is in the last commit in this PR). New (default) behaviour is equivalent to ts.draw_svg(x_scale="physical"), old behaviour is gained by ts.draw_svg(x_scale="treewise"). x_scale="physical" produces tree sequence SVG plots like the one below. There are some hard-coded margin values etc that could probably be improved, and suggestions as to better parameter nomenclature welcome.

[codecov]

Codecov Report

Merging #563 into master will decrease coverage by 0.02%.
The diff coverage is 77.41%.

@@            Coverage Diff             @@
##           master     #563      +/-   ##
==========================================
- Coverage   87.30%   87.27%   -0.03%     
==========================================
  Files          22       22              
  Lines       16718    16735      +17     
  Branches     3267     3272       +5     
==========================================
+ Hits        14595    14605      +10     
- Misses       1040     1043       +3     
- Partials     1083     1087       +4     

Flag	Coverage Δ
#c_tests	88.47% <77.41%> (-0.05%)	⬇️
#python_c_tests	90.37% <77.41%> (-0.07%)	⬇️
#python_tests	?

Impacted Files	Coverage Δ
python/tskit/trees.py	98.18% <ø> (ø)
python/tskit/drawing.py	98.67% <77.41%> (-1.16%)	⬇️

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[jeromekelleher]

Beautiful! I think the parameter names are just right.

[hyanwong]

Beautiful! I think the parameter names are just right.

Thanks @jeromekelleher. I guess the only missing thing is a check on the two allowed values (I was waiting until this seemed like a good nomenclature). I coded x_scale as a text string in case we want to leave the option to scale e.g. by genetic distance in the future.

[jeromekelleher]

Sound good. Let's look at it again when the stuff it depends on is merged.

[benjeffery]

This one is the next SVG PR to go in. It's rebased to master, just needs some coverage of the "tree-wise" path and an error thrown when a bad x_scale is passed.

[jeromekelleher]

Yes, let's get this one merged ASAP, just needs some small updates. The pattern used for other string constants like this has been

x_scale = check_xscale(x_scale)

where check_xscale() decides the defaults, etc. There's a bunch of these functions at the top of the file.

[hyanwong]

There's a bunch of these functions at the top of the file.

Yep, perfect. Do you want me to do this @benjeffery, or can you do it (I think you said you might!)?

[benjeffery]

I can fix it up, squash and rebase.

[benjeffery]

I've added the extra coverage and x_scale check. Unless you want a final review @jeromekelleher @hyanwong this is ready to merge.

[jeromekelleher]

Merge away I'd say @benjeffery

[benjeffery]

Hmm, travis is AWOL. Checking.

[jeromekelleher]

Feel free to just merge stuff if CI has passed on Circle and we know that it'll pass on the others (i.e., it's already pass n times before)