refactor: move the flat-layout research core under grl_snam/ - #103
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sdf_nav / material_nav / train_coef_energy / eval_coef_energy / surrogate_robust were top-level modules at the repo root, imported absolutely (import sdf_nav) by the package + tests + scripts + experiments and shipped via explicit pyproject py-module includes — a flat-layout legacy. Move all five under grl_snam/ and rewrite every import site (78 files) to grl_snam.<module> (aliased imports and a docstring reference preserved; the surrogate_robust<->train_coef_energy try/except cycle survives). pyproject: drop the 5 top-level includes (now under the grl_snam package); add them to the coverage omit list to keep the 80% gate scope unchanged. Verified: all modules import, every .py compiles, and the full test suite passes (378 passed, 26 skipped — the native-lib-gated ones).
Moving the five modules under grl_snam/ pulled them into the black+ruff gate (they were unlinted at the repo root). Rather than carve them back out, bring them up to standard: black-format all five, ruff --fix (44 auto-fixes: import sort, pyupgrade, unused-import cleanup — noqa re-exports preserved), and drop two dead F841 unused locals (surrogate_robust dev, train_coef_energy W) by hand. Lint now clean across the whole grl_snam package with the five IN scope; full suite still 378 passed / 26 skipped.
The cp313 CI leg uses a newer black (its cvcpkg closure is mislaid -> pip-latest) than cp312's pinned black; black 24.x formatting of the moved modules was rejected by cp313's newer black. Reformat the three with black 26.x — verified accepted by BOTH 26.5.1 and 24.10.0 (a fixed point across the matrix), ruff still clean, AST-preserving so behavior is unchanged.
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The five research-core modules —
sdf_nav.py,material_nav.py,train_coef_energy.py,eval_coef_energy.py,surrogate_robust.py— lived at the repo root as top-level modules, imported absolutely (import sdf_nav) by the package, tests, scripts, and experiments, and shipped via explicit[tool.poetry] packagespy-module includes. That flat layout pollutes the global module namespace and is easy to mistake for stray leftovers.What
grl_snam/(git renames, history preserved).grl_snam.<module>(import grl_snam.sdf_nav as sdf_nav,from grl_snam.sdf_nav import …). Aliased imports (import material_nav as mnav) and a docstring reference are preserved; thesurrogate_robust↔train_coef_energytry/except import cycle still resolves.{ include = "grl_snam" }); add them to the coverageomitlist so the 80% gate scope is unchanged (they were outside the gate before, as top-level modules).Verification
.pycompile.Pure move + import-rewrite — no behavior change.