Ingredient docstrings and hint types

[meganrm]

Problem

Add docstrings to the Ingredient module

Solution

So far I worked on Ingredient.py, agent.py, and single_sphere.py.

Some issues I ran into: typing env with Environment created a circlurlar import so I had to use a solution I found on stackoverflow https://stackoverflow.com/a/72324393

Types are inconsistent, it would be nice for instance to always have the rotMat be a np array.

I deleted unused code as I came across it. but there is still a lot of it.

Type of change

Please delete options that are not relevant.

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

• This change requires updated or new tests

[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

[Copilot]

Pull Request Overview

This pull request adds comprehensive docstrings and type hints to the Ingredient module and related components. The changes focus on improving code documentation and type safety across multiple ingredient-related files while addressing circular import issues and fixing spelling errors in method names and test expectations.

• Adds detailed docstrings to the Ingredient base class and subclasses with parameter descriptions
• Implements type annotations throughout ingredient classes and utility functions
• Fixes circular import issues using forward reference strings for Environment type
• Corrects spelling errors in method names and test assertion strings

Reviewed Changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
cellpack/autopack/ingredient/Ingredient.py	Comprehensive docstrings and type hints for base Ingredient class
cellpack/autopack/ingredient/single_sphere.py	Full documentation and type annotations for SingleSphereIngr class
cellpack/autopack/ingredient/agent.py	Added docstrings and type hints to Agent class methods
cellpack/autopack/ingredient/utils.py	Type annotations for utility functions
cellpack/autopack/ingredient/grow.py	Fixed method name from oneJitter to jitter_once
cellpack/autopack/ingredient/single_cylinder.py	Corrected get_cuttoff_value to get_cutoff_value
cellpack/autopack/ingredient/multi_cylinder.py	Fixed spelling and added docstring improvements
cellpack/autopack/ingredient/single_cube.py	Updated principal_vector default from tuple to list
cellpack/autopack/ingredient/multi_sphere.py	Changed principal_vector default type
cellpack/tests/test_ingredient.py	Updated test expectation to match new error message format
cellpack/tests/test_gradient_data.py	Updated test expectation for error message
cellpack/autopack/writers/init.py	Code formatting improvements
cellpack/autopack/loaders/recipe_loader.py	Code formatting improvements
cellpack/autopack/Graphics.py	Code formatting improvements
cellpack/autopack/GeometryTools.py	Code formatting improvements
cellpack/autopack/Environment.py	Parameter name fix and type annotation
cellpack/autopack/DBRecipeHandler.py	Code formatting improvements
cellpack/autopack/Analysis.py	Made env parameter optional with proper handling

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[rugeli]

nit: type casing might've been missing here?

near_by_ingredients: List[str],
placed_partners: List[List[Any]],
current_packing_position: List[int] = [0, 0, 0],

also line 86 with placed_partners: list

[rugeli]

i'm wondering if we should standardize all directional/3d/rgb values as tuples, that way it's clear they contain exactly three elements and stay immutable. when we need to update/edit the value, just replace the whole tuple.

[mogres]

i'm wondering if we should standardize all directional/3d/rgb values as tuples

I think we want to have at least some of these remain lists, or even better, numpy arrays since we use them in calculating rotations etc. by multiplying them together or performing other mathematical operations on them.