V2.0

[ckmah]

Major release aligned with version 2 of the preprint 🎉

Overall goals for this upgrade:

• 3 core analyses: RNAforest (spatial patterns), RNAflux (spatial gradient embedding), Colocation analysis (cell, gene and compartment aware)
• break up monolith plotting function into separate functions for plotting each "layer"
• speed up shape and point feature computations
• more granular tutorials
• technical docs
• general stability

[codecov-commenter]

Codecov Report

Patch coverage: 76.38% and project coverage change: +10.14 🎉

Comparison is base (92cf5ce) 61.70% compared to head (90f4ab4) 71.84%.

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Additional details and impacted files

@@             Coverage Diff             @@
##           master      #96       +/-   ##
===========================================
+ Coverage   61.70%   71.84%   +10.14%     
===========================================
  Files          24       35       +11     
  Lines        1290     2252      +962     
===========================================
+ Hits          796     1618      +822     
- Misses        494      634      +140     

Impacted Files	Coverage Δ
bento/io/_io.py	17.39% <7.69%> (-8.50%)	⬇️
bento/tools/_flux_enrichment.py	22.41% <22.41%> (ø)
bento/tools/_composition.py	27.02% <27.02%> (ø)
bento/plotting/_multidimensional.py	53.42% <53.42%> (ø)
bento/tools/_lp.py	39.16% <61.36%> (-2.06%)	⬇️
bento/plotting/_layers.py	62.16% <62.16%> (ø)
bento/plotting/_utils.py	84.21% <66.66%> (ø)
bento/tools/_neighborhoods.py	67.30% <67.30%> (ø)
bento/plotting/_plotting.py	70.07% <68.21%> (+54.92%)	⬆️
bento/plotting/_lp.py	70.00% <70.00%> (ø)
... and 25 more

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