Use multiple gradients on a single ingredient

[mogres]

Problem

Closes #262

Solution

Added support to allow multiple gradients on a single ingredient at the ingredient level.

Type of change

• New feature (non-breaking change which adds functionality)

Change summary:

• Allow the gradient attribute of an ingredient to be a List instance with multiple gradients.
• While creating an ingredient, check if it requires multiple gradients. If yes, add an attribute combined_weight that specifies the probabilities of the grid point to be picked to place the ingredient.
• Refactor functions in the Gradient class to be static methods.
• Add example recipe and edit config.

Steps to Verify:

Pack a recipe with an X and Y gradient combined:

pack -r cellpack/tests/recipes/v2/test_combined_gradient.json -c cellpack/tests/packing-configs/test_grid_plot_config.json

Screenshots:

Weight map:

Simularium screenshot

[github-actions]

Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name	Encapsulating radius	Average number packed
ext_A	25	236.0

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key	Pairwise distance distribution
ext_A

[rugeli]

I was able to run and see the combined gradient results, very cool! Just one minor suggestion, everything else look good

[rugeli]

nit: maybe simply reverse if and else statements for readability?

Suggested change

	if not isinstance(ingr.gradient, list):
	self.center = center = self.env.gradients[
	ingr.gradient
	].mode_settings.get("center", center)
	else:
	self.center = center
	if isinstance(ingr.gradient, list):
	self.center = center
	else:
	self.center = self.env.gradients[
	ingr.gradient
	].mode_settings.get("center", center)

[mogres]

Thanks Ruge! This reminded me of another edge case of a single gradient in a list so I added that in as well here.

[meganrm]

can you push the logic above into a generic Gradient.pick_point_from_weight that figures out wether it needs to combine weights and returns the ptInd

[mogres]

Good call! I added a static method Gradient.pick_point_for_ingredient here

[codecov-commenter]

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.73%. Comparing base (843dfec) to head (7a880a9).
Report is 11 commits behind head on main.

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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #270      +/-   ##
==========================================
- Coverage   98.75%   98.73%   -0.03%     
==========================================
  Files          19       18       -1     
  Lines         563      553      -10     
==========================================
- Hits          556      546      -10     
  Misses          7        7              

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