fix KeyError: 'weight_mode' when packing v2.1 recipes with under-specified gradients

[rugeli]

Problem

closes #465

Sorry for the delay on this one, after tracing it back through the packing pipeline, I figured the gradient packing error is not a problem with our Pydantic schema. The root cause is a data-pipeline gap. Gradient defaults were only ever filled in one place: the v2.0→v2.1 migration. But recipe_loader._read only runs migration when format_version != current_version. A recipe hand-authored directly as 2.1 skips migration entirely, so its gradients reach Gradient.__init__ still missing keys.

In short, without the changes in this pr, relabeling format_version as 2.0, everything else stays the same, the recipe cellpack/tests/recipes/v2/test_peroxisome_combined_gradient.json would pass.

Solution

in recipe_loader:

• added gradient normalization that converts list-of-dict form and fill missing top-level keys. Made this conversion happen before validation.
• removed now-redundant gradient dict to list block

with @mogres

Note: If we want to further refactor, we can:

1. make use of the validator output. validate_recipe builds a normalized copy that _read currently discards, we currently only use validator for validating which makes sense to me. But if we want to, we can make the validated recipe source of truth. This will be a larger pr so I'd keep this separate.
2. unify version migration scripts(default filling, structure flatten&nested, etc). more files involved, so better be another separate pr

Type of change

• Bug fix (non-breaking change which fixes an issue)

Steps to Verify:

1. run pack -r cellpack/tests/recipes/v2/test_peroxisome_combined_gradient.json -c cellpack/tests/packing-configs/test_gradient_mixing.json

[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

Fixes a packing-time KeyError: 'weight_mode' for v2.1 recipes whose gradients are under-specified (i.e., they skip v2.0→v2.1 migration, so gradient defaults never get filled). The core change is to normalize gradients earlier in RecipeLoader._read() so gradients are consistently list-of-dicts and have required top-level keys before validation and before constructing Gradient instances.

Changes:

• Add RecipeLoader._normalize_gradients() to convert dict→list gradient format and fill missing top-level gradient keys from defaults prior to validation.
• Remove the older late-stage “gradients dict→list” conversion block and move serializable_recipe_data capture to occur after dict-level normalization.
• Add a reproduction recipe/config under cellpack/tests/ for manual verification of gradient-mixing packing.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

File	Description
cellpack/autopack/loaders/recipe_loader.py	Adds gradient normalization + reorders normalization/validation/serialization to avoid missing gradient keys in v2.1 recipes.
cellpack/tests/recipes/v2/test_peroxisome_combined_gradient.json	Adds a v2.1 recipe fixture demonstrating combined gradients / under-specified gradient keys.
cellpack/tests/packing-configs/test_gradient_mixing.json	Adds a packing config used to reproduce the gradient-mixing scenario.

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[mogres]

Thanks Ruge! I ran the verification successfully.