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Sync public main into dev and retain CellNOpt updates - #62
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Rebuild CellNOpt inference around vectorized Boolean propagation, shared structural flow, and acyclic connectivity. Add CORNETO-integrated model and fit plotting, renderer improvements, outcome-based tests, and an executable signaling guide. Co-authored-by: Attila Gabor <3891745+gabora@users.noreply.github.com> Co-authored-by: Martin Garrido Rodriguez-Cordoba <61513563+martingarridorc@users.noreply.github.com>
release: CORNETO v1.0.0-rc.3
Release CORNETO 1.0.0 RC4
docs: prepare CORNETO 1.0.0 RC5
AnnNet renamed "vertex" to "node" across its public surface with no alias, so both bridges raise against a current AnnNet. add_cellnopt_conditions fails on its first statement, and from_annnet on the matrix and the positional lookup. corneto/contrib/annnet.py graph.vertices() -> graph.nodes() result.add_vertices(...) -> result.add_nodes(...) attrs.get_vertex_attrs(...) -> attrs.get_node_attrs(...) graph.X() -> graph.S graph.get_vertex(i) -> graph.N[i] the reserved key "vertex_id" -> "node_id" corneto/methods/signaling/annnet.py graph.vertices() -> graph.nodes() graph.add_vertices(...) -> graph.add_nodes(...) layers.set_vertex_layer_attrs -> layers.set_node_attrs layers.get_vertex_layer_attrs -> layers.node_attrs layers.layer_vertex_set -> layers.layer_node_set layers.set_layer_attrs -> layers.set_attrs CORNETO keeps its own word everywhere it owns the call: graph.V, get_attr_vertex, add_vertex, vertex_incidence_matrix and problem.expr.vertex_value are untouched. The two AnnNet test modules and the CellNOptDAG tutorial follow, and the interoperability guide says "node" for the AnnNet side of the conversion.
fix(annnet): follow the node rename in the AnnNet bridges
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Merge public main into public dev while retaining the newer CellNOptDAG implementation. Restore the AnnNet node API updates from PR #60 in a separate follow-up commit.