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* test: bootstrap mypy + pytest + coverage CI gates Wire up the tooling the upcoming test/annotation/refactor work depends on: - Add mypy>=1.13 to [dev] and a lenient [tool.mypy] config scoped to src/foundry + src/foundry_cli (ignore_missing_imports, no disallow_untyped_defs). The 14 modules with pre-existing type errors are pinned via [[tool.mypy.overrides]] ignore_errors=true and listed as the ratchet target — fix and remove, never add. - Add [tool.pytest.ini_options] (testpaths=["tests"], --strict-markers --strict-config) and [tool.coverage.*] (source = src/foundry + src/foundry_cli, branch = true) for opt-in gap finding. - Add .github/workflows/test.yaml with mypy and pytest jobs running on the same triggers as lint_production.yaml. Top-level tests/ only; per-model tests under models/*/tests/ may require GPU and checkpoints and stay out of CI for now. Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> * test(mypy): extend ignore list with 4 modules CI surfaced Local sanity-check ran mypy without foundry installed, so torch / lightning resolved to `Any` and errors that depend on knowing those types stayed invisible. First CI run installed the full deps and surfaced 6 errors in 4 additional modules: foundry.model.layers.blocks foundry.training.schedulers foundry.utils.logging foundry.utils.xpu.xpu_accelerator Same ratchet contract as the original 14: do not add, only remove (after fixing the errors and removing `ignore_errors = true`). Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> * style: ruff format 2 pre-existing files unrelated to bootstrap These files have been failing `ruff format --check` on production HEAD (merged via #275 and #281 without a pre-commit run). They block the existing `lint_production` workflow on every PR, including this bootstrap. Strictly out of scope for 0001 — kept in a separate commit so it can be cherry-picked or reverted cleanly. models/rfd3/src/rfd3/inference/input_parsing.py models/rfd3/tests/test_partial_diffusion.py No semantic changes — `ruff format` output only. Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> * ci: run test workflow on all pull requests Drop the base-branch filter on the pull_request trigger so PRs targeting stacked task branches are gated too, not only PRs into the mainline branches. Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> * test: unit tests for foundry geometry utils (alignment, rotation augmentation) Pin the numeric behaviour of weighted_rigid_align/get_rmsd and the rotation/centre/augment helpers used across the diffusion models: exact recovery of known rigid transforms, mask/weight exclusion from the fit, proper-rotation invariants, global-centroid centring, and distance-preserving augmentation. CPU-only, float32, 18 tests. Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> * fix: make weighted_rigid_align dtype-agnostic (accept float64) The determinant-correction matrix F was built with torch.eye's default dtype (float32), so float64 coordinate inputs raised at U @ F @ V. Pass dtype=X_L.dtype so F follows the input. Add a float64 regression test. Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> * Add test for float64 coords with float32 weights Add test for float64 coordinates with float32 weights to ensure correct output dtype and alignment. * Add additional blank line before functions Fix formatting by adding blank line before functions in test_alignment --------- Co-authored-by: Sergey Lyskov <sergey.lyskov@jhu.edu> Co-authored-by: Hope Woods <hope.woods@omsf.io>