Type-check and unit-test the mpnn, rfd3na, and rfd3 model packages#361

Merged

woodsh17 merged 36 commits into

RosettaCommons:productionfrom

lyskov-ai:0095-rfd3-mypy-strict-2error-tier

Jul 8, 2026

Commits on Jul 7, 2026

Bring rfd3 FabricTrainer under the mypy type-check gate

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Bring rfd3 legacy_input_parsing under the mypy type-check gate

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Clear the final rfd3 modules from the mypy ratchet (engine, vizualize)

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Bring models/mpnn into the mypy gate behind an ignore_errors ratchet

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Wire mpnn's CPU-portable tests into the pytest gate

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Clear the small-tier mpnn modules from the mypy ratchet

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Clear the inference/pipeline-glue mpnn modules from the mypy ratchet

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Clear the mpnn feature-collator and train modules from the mypy ratchet

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Clear mpnn.utils.weights from the mypy ratchet

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Type-check mpnn.utils.inference; fully clear the mpnn mypy ratchet

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Bring models/rfd3na into the mypy gate behind an ignore_errors ratchet

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Clear the 1-error-tier rfd3na modules from the mypy ratchet

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Clear the 2-3-error-tier rfd3na modules from the mypy ratchet

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Clear the io / trainer-utils / dump / run_inference rfd3na modules from the ratchet

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Clear the na_geom / pipelines / design_transforms / RFD3 rfd3na modules

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Clear the engine / inference_sampler / trainer rfd3na modules from the ratchet

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Clear the utils.inference / hbonds / na_geom_utils rfd3na modules

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Clear rfd3na.constants from the mypy ratchet

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Clear rfd3na legacy_input_parsing; port _check_has_backbone helper from rfd3

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Clear rfd3na input_parsing from the mypy ratchet

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Type-check rfd3na fabric_trainer; fully clear the rfd3na mypy ratchet

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Wire rfd3na tests into the pytest gate; add CPU unit tests

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Add rfd3na CPU tests for cfg_utils and symmetry checks

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Add rfd3na CPU tests for the NA dot-bracket parser and dict flattener

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Add rfd3na CPU tests for the symmetry atom_array helpers

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Add rfd3na CPU tests for symmetry check and Kabsch alignment

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Add rfd3na CPU tests for conditioning_utils pure helpers

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Reclaim mpnn test_inference_utils.py into the pytest gate

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Bring mpnn small-tier modules under strict mypy

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Bring mpnn 3-error-tier modules under strict mypy

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Bring mpnn pipelines and message_passing under strict mypy

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Bring mpnn metrics modules under strict mypy

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Bring mpnn model.mpnn under strict mypy

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Bring mpnn graph_embeddings under strict mypy; collapse override to mpnn.*

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Bring rfd3 small-tier modules under strict mypy

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Bring rfd3 2-error-tier modules under strict mypy

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