Add CPU unit tests and tighten type-checking (foundry utils + rf3 helpers)#319
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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>
…g tests Bring src/foundry/utils/components.py under the per-module disallow_untyped_defs + check_untyped_defs override by annotating the contig parsers and mask getters. Annotation-only apart from two behaviour-preserving refactors (collapse a str->int variable reuse in split_contig; store fixed_parts as tuples to avoid object-typed heterogeneous lists). Also widen get_name_mask's query_names to str | list[str] to match the isinstance branch and docstring. Add tests/test_components.py: 25 unit tests pinning the contig/component parsing grammar (split_contig, extract_pn_unit_info, get_motif_components_and_breaks, get_design_pattern_with_constraints) and the get_name_mask atom selector. Co-authored-by: lyskov-ai <277346777+lyskov-ai@users.noreply.github.com>
Bring src/foundry/utils/torch.py under the per-module disallow_untyped_defs + check_untyped_defs override by annotating map_to's kwargs, the tracer-warning contextmanager, assert_shape, and the Timer/Timers methods. Annotation-only; the two warnings.filters mutations carry a documented type: ignore[attr-defined] (typeshed types it immutable, but it is a list at runtime). Extend tests/test_torch_utils.py with 12 tests for the untested pure helpers: scatter_mean, assert_shape/assert_same_shape, device_of, and Timer/Timers. 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 two behaviour-preserving refactors and one relocated type-check suppression); everything else is new tests.foundryshared layer — type annotations + testsutils/rigid.py— annotated theRotation/Rigidmethods and quaternion/matrix helpers and enabled strict type-checking for the module. Newtests/test_rigid.py(33 tests): quaternion↔rotation-matrix round-trips, composition/inversion, point application, the 4×4 and 7-vector encodings, andfrom_3_points.utils/components.py— annotated the contig/component parsers and atom-name mask getters and enabled strict type-checking (plus astr→intcollapse insplit_contig, a tuple-typedfixed_parts, and wideningget_name_mask'squery_namestostr | list[str]to match itsisinstancebranch). Newtests/test_components.py(25 tests) pinning the parsing grammar andget_name_mask.utils/torch.py— annotated the remaining untyped helpers (map_to, the tracer-warning contextmanager,assert_shape,Timer/Timers) and enabled strict type-checking; the twowarnings.filtersmutations carry a documented# type: ignore[attr-defined](typeshed types it immutable, but it is a list at runtime). Extendedtests/test_torch_utils.py(+12 tests):scatter_mean,assert_shape/assert_same_shape,device_of, andTimer/Timers.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.