fcose 0.1.0

A pure Dart port of the fCoSE compound graph layout algorithm.

0.1.0-dev.1

• Start an experimental pure Dart port of cytoscape-fcose.
• Add deterministic spectral initialization and CoSE-style force refinement.
• Add compound nodes, disconnected component packing, and placement constraints.
• Add CoSE leaf reduction, staged tree regrowth, sparse-side placement, and post-growth cooling.
• Connect disconnected root and nested compound child components through upstream-compatible spectral dummy nodes.
• Add CoSE-style randomized zero-degree grouping and bottom-up clearing and repopulation of fully tiled compound subtrees.
• Add layout-utilities-compatible randomized polyomino component packing, original-center relocation, and explicit typed packing controls.
• Add layout-utilities-compatible incremental POSE component packing for randomize: false.
• Add uniformNodeDimensions force semantics and custom tilingCompareBy ordering with upstream-compatible ideal-row-width tiling.
• Add typed constraint-pipeline debug stages and make draft quality bypass CoSE constraint preprocessing and zero-degree tiling.
• Recenter non-fixed transformed-stage results to their original graph bounds without perturbing full-layout coordinates.
• Add typed per-node and per-edge force resolvers, evaluated once per layout run with explicit element values taking precedence.
• Match upstream first-edge filtering before callback evaluation and use the average resolved ideal edge length for implicit relative-placement gaps.
• Match cose-base's cross-axis alignment dummy collision during constrained displacement relaxation and add a deeply nested compound differential case.
• Match cose-base's dimension-aware defaults for omitted relative-placement gaps and cover mixed-size flat and nested compound differentials.
• Add typed zero-argument tiling-padding resolvers with run-scoped upstream semantics across flat and nested tiling.
• Add per-node compound padding across bounds, nested tiling, force geometry, and component packing while retaining the layout-wide fallback.
• Match CoSE's ten-pixel internal ideal-length floor when calculating sparse repulsion-grid neighborhoods without changing configured spring lengths.
• Measure draft-quality recentering on leaf bounds, as upstream does when it never builds the cose-base graph.
• Draw spectral samples and eigenvector guesses from the layout's own random stream, matching upstream's single sequence of Math.random calls.
• Replace the spectral pseudo-inverse with a transcription of the JAMA singular value decomposition that layout-base uses, so compound spectral layouts now match upstream to about 1e-13.
• Untile before relocating and packing, so a tiled layout now returns each component to its original center and takes part in component packing instead of keeping the coordinates the spring embedder left it with.
• Treat the components without an edge as the single tiled pseudo-component upstream packs, appended after the components that kept their edges.
• Run one spectral pass and one spring embedder per connected component when packing is enabled, in upstream's order, so a component is no longer embedded alongside the components it is only packed beside.
• Keep each leaf's top-left corner authoritative through the spring embedder, as LNode does, and derive its center from that corner. Accumulating displacements on a center instead lost the low bits of every tick, which calcRepulsionForce's minimum-distance sign snap turned into whole pixels on symmetric graphs; every oracle fixture now matches upstream to about 1e-13.
• Skip the spectral embedding for a debug step of a randomized run. Upstream calls its spectral routine whenever randomize is on, but the routine only embeds anything for a draft run or the whole pipeline, and otherwise reads back the positions it was given.
• Measure the bounding box that the closing relocation aims at the way the host reports it, adding FcoseOptions.compoundBorderWidth. A compound's box stands half a border and an antialiasing pixel outside its children's, so a graph mixing compounds with plain nodes settled three quarters of a pixel away from upstream.
• Guard both packers at eight hundred components: the polyomino packer against overlap and a moved center, the POSE packer against non-finite or irreproducible shifts, and both against a change of complexity class.
• Document the polyomino packing grid's sizing on FcoseOptions.polyominoGridSizeFactor: it follows layout-utilities, so many small components spread far apart can ask for a grid too large to allocate, which the packer refuses with an ArgumentError.