fix(docs+review): numpydoc See Also->Notes for C++ cross-refs; address CodeQL/CodeRabbit

- RTD build failed: numpydoc's strict See Also parser rejected the C++-twin
  cross-reference prose entries ('Error parsing See Also entry ...'). Move the
  cross-refs to Notes sections (free-form reST) in apply_pair_exclusion and
  apply_pair_exclusion_nlist.
- main.py: drop stale 'no type exclusion' from the graph-eligibility comment
  (exclude_types is now graph-native; matches the docstring + ValueError).
- test_graph_atomic_parity: remove dead ds/ft/am chain (CodeQL unused 'am').
- test_neighbor_graph_builder: drop redundant local 'import unittest' (CodeQL).

Author: Han Wang

deepmd/dpmodel/utils/neighbor_graph/graph.py

@@ -211,14 +211,15 @@ def apply_pair_exclusion(
         A ``dataclasses.replace`` copy (or the original ``graph`` on early
         exit) with the exclusion applied.
 
-    See Also
-    --------
-    C++ twin ``applyPairExclusion`` in ``source/api_cc/include/commonPT.h``
-        The inference-path mirror. Same argument order (edge_index, edge_mask,
-        atype, ...), same variable names (``type_ij``, ``keep``): it computes
-        ``type_ij = atype[dst]*(ntypes+1) + atype[src]`` and ANDs the flat
-        ``(ntypes+1)^2`` table lookup into ``edge_mask`` (mask-only mode; no
-        compact variant on the compiled path).
+    Notes
+    -----
+    The C++ inference-path mirror is ``applyPairExclusion`` in
+    ``source/api_cc/include/commonPT.h``. It uses the same argument order
+    (edge_index, edge_mask, atype, ...) and the same variable names
+    (``type_ij``, ``keep``): it computes
+    ``type_ij = atype[dst]*(ntypes+1) + atype[src]`` and ANDs the flat
+    ``(ntypes+1)^2`` table lookup into ``edge_mask`` (mask-only mode; no
+    compact variant on the compiled path).
     """
     import dataclasses
 

deepmd/dpmodel/utils/nlist.py

@@ -92,14 +92,6 @@ def apply_pair_exclusion_nlist(
     This is the nlist-representation counterpart of
     :func:`deepmd.dpmodel.utils.neighbor_graph.apply_pair_exclusion`.
 
-    See Also
-    --------
-    C++ twin ``applyPairExclusionNlist`` in ``source/api_cc/include/commonPT.h``
-        The inference-path mirror. Same argument order (nlist, atype_ext, ...),
-        same variable names (``type_ij``, ``keep``): it computes ``type_ij``
-        from the center/neighbor types via the flat ``(ntypes+1)^2`` table and
-        replaces excluded entries with ``-1``.
-
     Parameters
     ----------
     nlist : Array
@@ -115,6 +107,15 @@ def apply_pair_exclusion_nlist(
     Array
         Neighbor list of the same shape with excluded entries set to ``-1``.
         Erasing ``-1`` entries a second time is a no-op (idempotent).
+
+    Notes
+    -----
+    The C++ inference-path mirror is ``applyPairExclusionNlist`` in
+    ``source/api_cc/include/commonPT.h``. It uses the same argument order
+    (nlist, atype_ext, ...) and the same variable names (``type_ij``,
+    ``keep``): it computes ``type_ij`` from the center/neighbor types via
+    the flat ``(ntypes+1)^2`` table and replaces excluded entries with
+    ``-1``.
     """
     if pair_excl is None or len(pair_excl.exclude_types) == 0:
         return nlist

deepmd/pt_expt/entrypoints/main.py

@@ -569,7 +569,7 @@ def freeze(
     m.eval()
 
     # The graph lower is opt-in and only valid for graph-eligible models
-    # (dpa1 with concat tebd and no type exclusion; attention layers included
+    # (dpa1 with concat tebd, incl. attention layers and exclude_types
     # -- the carry-all pair enumeration exports via unbacked SymInts). Fail
     # fast with a clear message rather than emitting a broken .pt2. Enable the
     # per-atom virial for the graph form -- it is near-free there (one extra

source/tests/common/dpmodel/test_graph_atomic_parity.py

@@ -326,9 +326,6 @@ def test_apply_pair_exclusion_idempotent(pair_exclude_types):
     rng = np.random.default_rng(42)
     coord = rng.normal(size=(1, 5, 3)) * 1.5
     atype = np.array([[0, 1, 0, 1, 0]], dtype=np.int64)
-    ds = DescrptDPA1(rcut=4.0, rcut_smth=0.5, sel=[200], ntypes=2, attn_layer=0)
-    ft = InvarFitting("energy", 2, ds.get_dim_out(), 1, mixed_types=True)
-    am = DPAtomicModel(ds, ft, type_map=["a", "b"])
     ext_coord, ext_atype, mapping, nlist = extend_input_and_build_neighbor_list(
         coord, atype, 4.0, [200], mixed_types=True, box=None
     )

source/tests/common/dpmodel/test_neighbor_graph_builder.py

@@ -421,8 +421,6 @@ def setUpClass(cls) -> None:
         try:
             import ase  # noqa: F401
         except ImportError as e:
-            import unittest
-
             raise unittest.SkipTest("ase not installed") from e
 
     def setUp(self) -> None: