Expose n_recycle as inference sampler parameter

[Ubiquinone-dot]

Summary

• Exposes n_recycle through the inference sampler config so users can override the model default (2) at inference time via CLI: inference_sampler.n_recycle=3
• Adds num_timesteps and n_recycle to the "Other CLI Options" section in docs/input.md (they were missing from that list)
• Makes the InputSpecification reference more prominent in the README (upgraded from [!NOTE] to [!IMPORTANT], added direct link to docs/input.md)
• Includes a repo-wide ruff format pass (pre-commit hook required it)

Test plan

• Run inference with default config (no n_recycle override) — should behave identically to before (uses model default of 2)
• Run inference with inference_sampler.n_recycle=1 — verify fewer recycles are used (check logs)
• Run inference with inference_sampler.n_recycle=3 — verify more recycles are used
• Verify symmetry sampler also respects the override

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR exposes n_recycle as an inference-time sampler/config parameter for RFD3 so users can override the checkpoint default recycling count via CLI, and updates related documentation/configuration. It also includes a repo-wide ruff format pass that primarily reformats assertions and a few expressions without changing behavior.

Changes:

• Add inference_sampler.n_recycle (nullable) and thread it through the RFD3 inference sampler into the diffusion module’s recycle loop.
• Update RFD3 inference config (rfdiffusion3.yaml) and docs (docs/input.md, README) to surface n_recycle and num_timesteps.
• Apply ruff format across multiple packages/tests (mostly assert formatting).

Reviewed changes

Copilot reviewed 63 out of 63 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
src/foundry/utils/logging.py	Ruff formatting (assert formatting).
src/foundry/utils/ddp.py	Ruff formatting (assert formatting).
src/foundry/utils/datasets.py	Ruff formatting (assert formatting).
src/foundry/utils/alignment.py	Ruff formatting (assert formatting).
src/foundry/trainers/fabric.py	Ruff formatting (assert formatting).
src/foundry/metrics/metric.py	Ruff formatting (assert formatting).
src/foundry/metrics/losses.py	Ruff formatting (assert formatting).
src/foundry/inference_engines/base.py	Ruff formatting + touched assertion messages.
src/foundry/callbacks/metrics_logging.py	Ruff formatting (assert formatting).
models/rfd3/tests/transforms/test_pipeline_regression.py	Ruff formatting (assert formatting).
models/rfd3/tests/test_unindexing.py	Ruff formatting (assert formatting).
models/rfd3/tests/test_tokenization.py	Ruff formatting (assert formatting).
models/rfd3/tests/test_symmetry.py	Ruff formatting (assert formatting).
models/rfd3/tests/test_selections.py	Ruff formatting (assert formatting).
models/rfd3/tests/test_metrics.py	Ruff formatting (assert formatting).
models/rfd3/tests/test_glycines.py	Ruff formatting (assert formatting).
models/rfd3/tests/test_conditioning.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/utils/io.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/utils/inference.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/transforms/virtual_atoms.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/transforms/util_transforms.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/transforms/ppi_transforms.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/transforms/pipelines.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/transforms/conditioning_base.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/trainer/fabric_trainer.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/trainer/dump_validation_structures.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/train.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/model/RFD3_diffusion_module.py	Allow inference-time override of n_recycle when provided.
models/rfd3/src/rfd3/model/layers/chunked_pairwise.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/model/layers/block_utils.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/model/inference_sampler.py	Add n_recycle to sampler config and pass into diffusion module calls.
models/rfd3/src/rfd3/metrics/losses.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/metrics/hbonds_metrics.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/inference/symmetry/symmetry_utils.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/inference/symmetry/frames.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/inference/symmetry/checks.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/inference/legacy_input_parsing.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/inference/input_parsing.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/inference/datasets.py	Ruff formatting (assert formatting).
models/rfd3/src/rfd3/callbacks.py	Ruff formatting (assert formatting).
models/rfd3/README.md	Make InputSpecification reference more prominent and link to docs/input.md.
models/rfd3/docs/input.md	Document num_timesteps and n_recycle under CLI options.
models/rfd3/configs/inference_engine/rfdiffusion3.yaml	Add inference_sampler.n_recycle: null to allow CLI override.
models/rf3/tests/test_inference_regression.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/validate.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/utils/predicted_error.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/utils/io.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/train.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/symmetry/resolve.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/model/RF3.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/model/layers/mlff.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/model/layers/attention.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/diffusion_samplers/inference_sampler.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/data/pipelines.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/data/ground_truth_template.py	Ruff formatting (line wrapping).
models/rf3/src/rf3/data/extra_xforms.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/callbacks/metrics_logging.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/callbacks/dump_validation_structures.py	Ruff formatting (assert formatting).
models/rf3/src/rf3/alignment.py	Ruff formatting (assert formatting).
models/mpnn/tests/test_utils.py	Ruff formatting (assert formatting).
models/mpnn/tests/test_samplers.py	Ruff formatting (assert formatting).
models/mpnn/tests/test_pipeline.py	Ruff formatting (assert formatting / wrapping).
models/mpnn/tests/test_integration.py	Ruff formatting (assert formatting).

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[Copilot]

n_recycle is user-configurable now, but there’s no validation that it’s a positive integer. If a user sets inference_sampler.n_recycle=0 (or a negative / non-int), forward_with_recycle() will run zero iterations and downstream code will error when expected outputs are missing. Add an explicit validation (e.g., in a __post_init__ for SampleDiffusionConfig or in ConditionalDiffusionSampler.__init__) to require n_recycle is None or n_recycle >= 1 (and ideally an int).

[Copilot]

The assertion message has broken grammar ("Checkpoint provided not and not in registered checkpoints"), which makes this failure hard to understand. Please reword it to clearly indicate the checkpoint name isn’t registered and (optionally) list valid keys.