Add CPU unit tests and tighten type-checking (foundry rigid.py + rf3 helpers)#317
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…_module Cover the pure numeric helpers in rf3.loss.loss and rf3.util_module: - calc_ddihedralmse_dxyz: the hand-derived closed-form dihedral-loss gradient, pinned against torch.autograd of a mirrored forward, plus zero-at-truth and leading-dim shape preservation. - calc_chiral_grads_flat_impl: empty-centres, scatter routing onto only the centre atoms, index_add_ accumulation for shared atoms, and the no_grad_on_chiral_center flag. - rbf: Gaussian distance-encoding (feature dim, exact values, [0,1]). - init_lecun_normal: module returned, Parameter weight, +/-2*stddev bound, and Lecun std sqrt(scale/fan_in). Test-only; both modules are already mypy-clean. Tests run in float32 (the production coordinate dtype). Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
…duct layer Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
…helpers Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
Replace the central pyproject ignore_errors override for rf3.data.paired_msa with a file-level '# mypy: ignore-errors' directive in the module itself. The module is broken against the installed atomworks (subclasses a now-function) and needs a PandasDataset-API refactor to clear honestly; keeping it in mypy's files scope with an in-file directive makes the suppression visible at the point of breakage and re-enables checking the moment the directive is removed. Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
…it tests Bring src/foundry/utils/rigid.py under a per-module disallow_untyped_defs + check_untyped_defs override (the first Track 1 direction-(b) strictness slice) by annotating its ~47 previously-untyped Rotation/Rigid methods and quaternion/matrix helpers. Annotation-only, no behaviour change; self-references use string forward-refs and the identity helpers' shape params are widened to Tuple[int, ...]. Add tests/test_rigid.py: 33 fixture-backed CPU unit tests pinning the pure geometry (quat<->matrix round-trips, compose/invert, apply, the 4x4/7-vector encodings, and from_3_points) against independent references. Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
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Adds CPU unit tests and tightens type-checking across the shared
foundrylayer and therf3model. No runtime behaviour changes — the source edits are type annotations plus a relocation of one type-check suppression; everything else is new tests.foundry/utils/rigid.py— type annotations + testsRotation/Rigidmethods and the module-level quaternion/matrix helpers, and enabled strict type-checking for the module (disallow_untyped_defs+check_untyped_defs). Annotation-only. Also widened theidentity_*/identityshapeparameters fromTuple[int]toTuple[int, ...](they accept arbitrary-rank shapes).tests/test_rigid.py(33 tests) pinning the geometry: quaternion↔rotation-matrix round-trips, composition/inversion, point application, the 4×4 and 7-vector encodings, andfrom_3_pointsframe construction — all against independent references (Rodrigues, einsum, QR-built rotations).rf3— CPU unit testsNew fixture-backed CPU tests (no cluster data / GPU / checkpoints) for pure
rf3logic: loss gradients and utilities, model-layer shape helpers (layer_utils,mlff, attention, outer-product), the diffusion sampler's noise schedule and initial structure, theaf3_lossessymmetry-resolution geometry, and the chiral / iPTM metric orchestration.rf3.data.paired_msa— type-check hygieneMoved the module's mypy suppression out of the central
pyproject.tomlreject-list into a file-level# mypy: ignore-errorsdirective, so the suppression is visible at the broken code and deleting one line re-enables checking. (The module is broken against the installedatomworksand needs a data-loader refactor validated on cluster data — tracked separately.)