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overview.md: rewrite — remove rotting external image links, simplify acknowledgements, add numerical scheme section. quickstart.md: fix verbose default (true not false), add savedir kwarg, replace prose with tables for output format and convergence stats. config.md: fix inaccuracies — inlet_file optional (defaults to <project_name>_inlet.dat), gamma_profile underscore, wk3 inferred from R2 presence not outlet: key, add visco-elastic/initial condition params, rewrite template. examples.md: model table, runnable Julia snippet, result-reading snippet, minimal single-vessel config. plotting.md (new): matplotlib and Julia plotting examples with unit conversion table. benchmarking.md (new): PkgBenchmark workflow and manual harness usage. index.md: fix two typos (accompaigning, backgound, accompaining). make.jl: add plotting and benchmarking pages, remove stale TODO.
overview.md: rewrite — remove rotting external image links, simplify acknowledgements, add numerical scheme section. quickstart.md: fix verbose default (true not false), add savedir kwarg, replace prose with tables for output format and convergence stats. config.md: fix inaccuracies — inlet_file optional (defaults to <project_name>_inlet.dat), gamma_profile underscore, wk3 inferred from R2 presence not outlet: key, add visco-elastic/initial condition params, rewrite template. examples.md: model table, runnable Julia snippet, result-reading snippet, minimal single-vessel config. plotting.md (new): matplotlib and Julia plotting examples with unit conversion table. benchmarking.md (new): PkgBenchmark workflow and manual harness usage. index.md: fix two typos (accompaigning, backgound, accompaining). make.jl: add plotting and benchmarking pages, remove stale TODO.
Adds test/test_golden_master.jl covering bifurcation (ibif), conjunction + bifurcation (adan56), and anastomosis (circle_of_willis). Each run is compared against the pre-existing serialised references (test/ref_*.jls) with a 1e-12 relative tolerance on all saved waveform fields. Adds Serialization stdlib to Project.toml so the test environment can load the .jls reference files.
Introduces src/junction.jl with the Junction struct and its constructor. Validates that k ≥ 2, sides are :inlet/:outlet, lengths match, and that every junction has at least one vessel of each side. Preallocates work arrays (x, F, J, dx) to avoid per-step allocation once the solver lands. Exports Junction from openBF.jl. No behavioural change — existing solver path is untouched.
Adds the full Newton solver to src/junction.jl: - pack_initial_guess! reads (A, Q) from each vessel's boundary face - residual! builds the 2k-component F: characteristic invariants (block 1), mass conservation (block 2), pressure continuity (block 3) - jacobian! fills the analytic 2k×2k Jacobian; no finite-differences - solve_junction! drives Newton to norm(F) < 1e-5 (matching legacy tolerance) - unpack_solution! writes converged (A, Q, u) back to each vessel face use_total_pressure=true switches pressure continuity from static to static+dynamic, matching the existing conjunction solver (join_vessels!/2). test/test_junction_k2.jl verifies that solve_junction! with use_total_pressure=true reproduces join_vessels! to 1e-10 relative on A, Q, u.
test_junction_k3_bifurcation.jl: constructs a synthetic 1-parent/2-daughter setup with ibif-like vessel parameters, runs join_vessels!(v1,v2,v3) and solve_junction! from the same initial state, asserts A/Q/u agree to 1e-10 relative on all three vessels. test_junction_k3_anastomosis.jl: same pattern for a 2-parent/1-daughter junction, comparing against solveAnastomosis. Both use use_total_pressure=false (static pressure), matching the legacy bifurcation and anastomosis solvers.
…flag Phase 4 of nfork plan. Adds Junction struct and solve_junction! using (u, α) parameterisation matching the legacy NR solvers exactly. The generic path is opt-in via run_simulation(yaml; use_generic_junctions=true) and verified to agree with legacy waveforms to within 1e-10 relative on ibif.
Phase 5: use_generic_junctions defaults to true in both Network and run_simulation. Legacy path remains reachable via use_generic_junctions=false.
Phase 6. Removes bifurcations.jl, conjunctions.jl, anastomosis.jl and all associated dead code (anastomosis_solved, use_generic_junctions flag, _apply_junctions!, legacy solve! branch). Also drops the unused StaticArrays dependency. Test count grows from 30 to 42 with the ibif smoke test.
Phase 7. Verifies Junction struct allocates correctly (8-element work arrays, 8×8 Jacobian) for a 1-outlet / 3-inlet junction.
Phase 8. validate_network() checks self-loops, missing inlet/outlet, all-inlet/all-outlet junctions, high-k junctions, and disconnected subgraphs. Exported from the module; run.jl wires it as `julia run.jl --validate <yaml>`.
MMatrix (mutable) allocates on the heap. Switch to reading jc.J/jc.F into an SMatrix/SVector (immutable, stack-allocated) for the linear solve, then copy the SVector result back to the pre-allocated jc.dx. Also precompute Wstar into a new jc.Wstar field instead of ntuple+collect. Result: solve_junction! is 0-alloc for k=2 and k=3 (all real models). Benchmarks vs baseline: cca -19% time, ibif -15% time / -25% allocs; adan56 -10% time (more convergence cycles due to parallel vs sequential junction update order; per-cycle cost is not regressed).
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