├── .github └── workflows │ └── rhub.yaml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R └── leidenbase.R ├── cleanup ├── cleanup.win ├── configure ├── configure.ac ├── configure.win ├── inst ├── doc │ ├── leidenbase.R │ ├── leidenbase.Rmd │ └── leidenbase.html └── testdata │ ├── expected_values.txt │ ├── igraph_n1500_edgelist.txt.gz │ ├── test01_file01.txt │ ├── test02_file01.txt │ ├── test03_file01.txt │ ├── test04_file01.txt │ ├── test05_file01.txt │ ├── test06_file01.txt │ ├── test07_file01.txt │ ├── test08_file01.txt │ ├── test09_file01.txt │ └── test10_file01.txt ├── man └── leiden_find_partition.Rd ├── src ├── Makevars.in ├── Makevars.ucrt ├── Makevars.win ├── config.h ├── config.h.in ├── core │ ├── centrality │ │ ├── betweenness.c │ │ ├── centrality_other.c │ │ ├── centralization.c │ │ ├── closeness.c │ │ ├── coreness.c │ │ ├── prpack.cpp │ │ ├── prpack │ │ │ ├── prpack.h │ │ │ ├── prpack_base_graph.cpp │ │ │ ├── prpack_base_graph.h │ │ │ ├── prpack_csc.h │ │ │ ├── prpack_csr.h │ │ │ ├── prpack_edge_list.h │ │ │ ├── prpack_igraph_graph.cpp │ │ │ ├── prpack_igraph_graph.h │ │ │ ├── prpack_preprocessed_ge_graph.cpp │ │ │ ├── prpack_preprocessed_ge_graph.h │ │ │ ├── prpack_preprocessed_graph.h │ │ │ ├── prpack_preprocessed_gs_graph.cpp │ │ │ ├── prpack_preprocessed_gs_graph.h │ │ │ ├── prpack_preprocessed_scc_graph.cpp │ │ │ ├── prpack_preprocessed_scc_graph.h │ │ │ ├── prpack_preprocessed_schur_graph.cpp │ │ │ ├── prpack_preprocessed_schur_graph.h │ │ │ ├── prpack_result.cpp │ │ │ ├── prpack_result.h │ │ │ ├── prpack_solver.cpp │ │ │ ├── prpack_solver.h │ │ │ ├── prpack_utils.cpp │ │ │ └── prpack_utils.h │ │ └── prpack_internal.h │ ├── cliques │ │ ├── cliquer │ │ │ ├── cliquer.c │ │ │ ├── cliquer.h │ │ │ ├── cliquer_graph.c │ │ │ ├── cliquerconf.h │ │ │ ├── graph.h │ │ │ ├── misc.h │ │ │ ├── reorder.c │ │ │ ├── reorder.h │ │ │ └── set.h │ │ ├── cliquer_internal.h │ │ ├── cliquer_wrapper.c │ │ ├── cliques.c │ │ ├── glet.c │ │ ├── maximal_cliques.c │ │ └── maximal_cliques_template.h │ ├── community │ │ ├── community_misc.c │ │ ├── edge_betweenness.c │ │ ├── fast_modularity.c │ │ ├── fluid.c │ │ ├── infomap │ │ │ ├── infomap.cc │ │ │ ├── infomap_FlowGraph.cc │ │ │ ├── infomap_FlowGraph.h │ │ │ ├── infomap_Greedy.cc │ │ │ ├── infomap_Greedy.h │ │ │ ├── infomap_Node.cc │ │ │ └── infomap_Node.h │ │ ├── label_propagation.c │ │ ├── leading_eigenvector.c │ │ ├── leiden.c │ │ ├── louvain.c │ │ ├── modularity.c │ │ ├── optimal_modularity.c │ │ ├── spinglass │ │ │ ├── NetDataTypes.cpp │ │ │ ├── NetDataTypes.h │ │ │ ├── NetRoutines.cpp │ │ │ ├── NetRoutines.h │ │ │ ├── clustertool.cpp │ │ │ ├── pottsmodel_2.cpp │ │ │ └── pottsmodel_2.h │ │ └── walktrap │ │ │ ├── walktrap.cpp │ │ │ ├── walktrap_communities.cpp │ │ │ ├── walktrap_communities.h │ │ │ ├── walktrap_graph.cpp │ │ │ ├── walktrap_graph.h │ │ │ ├── walktrap_heap.cpp │ │ │ └── walktrap_heap.h │ ├── connectivity │ │ ├── cohesive_blocks.c │ │ ├── components.c │ │ └── separators.c │ ├── constructors │ │ ├── adjacency.c │ │ ├── atlas-edges.h │ │ ├── atlas.c │ │ ├── basic_constructors.c │ │ ├── de_bruijn.c │ │ ├── famous.c │ │ ├── full.c │ │ ├── kautz.c │ │ ├── lcf.c │ │ ├── linegraph.c │ │ ├── prufer.c │ │ └── regular.c │ ├── core │ │ ├── array.c │ │ ├── array.pmt │ │ ├── buckets.c │ │ ├── buckets.h │ │ ├── cutheap.c │ │ ├── cutheap.h │ │ ├── dqueue.c │ │ ├── dqueue.pmt │ │ ├── error.c │ │ ├── estack.c │ │ ├── estack.h │ │ ├── exceptions.h │ │ ├── fixed_vectorlist.c │ │ ├── fixed_vectorlist.h │ │ ├── grid.c │ │ ├── grid.h │ │ ├── heap.c │ │ ├── heap.pmt │ │ ├── indheap.c │ │ ├── indheap.h │ │ ├── interruption.c │ │ ├── interruption.h │ │ ├── marked_queue.c │ │ ├── marked_queue.h │ │ ├── math.h │ │ ├── matrix.c │ │ ├── matrix.pmt │ │ ├── memory.c │ │ ├── printing.c │ │ ├── progress.c │ │ ├── psumtree.c │ │ ├── set.c │ │ ├── set.h │ │ ├── sparsemat.c │ │ ├── spmatrix.c │ │ ├── stack.c │ │ ├── stack.pmt │ │ ├── statusbar.c │ │ ├── strvector.c │ │ ├── trie.c │ │ ├── trie.h │ │ ├── vector.c │ │ ├── vector.pmt │ │ └── vector_ptr.c │ ├── f2c.h │ ├── flow │ │ ├── flow.c │ │ ├── flow_internal.h │ │ └── st-cuts.c │ ├── games │ │ ├── barabasi.c │ │ ├── callaway_traits.c │ │ ├── citations.c │ │ ├── correlated.c │ │ ├── degree_sequence.c │ │ ├── degree_sequence_vl │ │ │ ├── gengraph_box_list.cpp │ │ │ ├── gengraph_box_list.h │ │ │ ├── gengraph_definitions.h │ │ │ ├── gengraph_degree_sequence.cpp │ │ │ ├── gengraph_degree_sequence.h │ │ │ ├── gengraph_graph_molloy_hash.cpp │ │ │ ├── gengraph_graph_molloy_hash.h │ │ │ ├── gengraph_graph_molloy_optimized.cpp │ │ │ ├── gengraph_graph_molloy_optimized.h │ │ │ ├── gengraph_hash.h │ │ │ ├── gengraph_header.h │ │ │ ├── gengraph_mr-connected.cpp │ │ │ ├── gengraph_powerlaw.cpp │ │ │ ├── gengraph_powerlaw.h │ │ │ ├── gengraph_qsort.h │ │ │ ├── gengraph_random.cpp │ │ │ ├── gengraph_random.h │ │ │ └── gengraph_vertex_cover.h │ │ ├── dotproduct.c │ │ ├── erdos_renyi.c │ │ ├── establishment.c │ │ ├── forestfire.c │ │ ├── grg.c │ │ ├── growing_random.c │ │ ├── islands.c │ │ ├── k_regular.c │ │ ├── preference.c │ │ ├── recent_degree.c │ │ ├── sbm.c │ │ ├── static_fitness.c │ │ ├── tree.c │ │ └── watts_strogatz.c │ ├── graph │ │ ├── adjlist.c │ │ ├── attributes.c │ │ ├── attributes.h │ │ ├── basic_query.c │ │ ├── cattributes.c │ │ ├── iterators.c │ │ ├── neighbors.h │ │ ├── type_indexededgelist.c │ │ └── visitors.c │ ├── hrg │ │ ├── dendro.h │ │ ├── graph.h │ │ ├── graph_simp.h │ │ ├── hrg.cc │ │ ├── hrg_types.cc │ │ ├── rbtree.h │ │ └── splittree_eq.h │ ├── internal │ │ ├── glpk_support.c │ │ ├── glpk_support.h │ │ ├── gmp_internal.h │ │ ├── hacks.c │ │ ├── hacks.h │ │ ├── lsap.c │ │ ├── pstdint.h │ │ ├── qsort.c │ │ ├── qsort_r.c │ │ └── zeroin.c │ ├── io │ │ ├── dimacs.c │ │ ├── dl-header.h │ │ ├── dl-lexer.c │ │ ├── dl-lexer.h │ │ ├── dl-lexer.l │ │ ├── dl-parser.c │ │ ├── dl-parser.h │ │ ├── dl-parser.y │ │ ├── dl.c │ │ ├── dot.c │ │ ├── edgelist.c │ │ ├── gml-header.h │ │ ├── gml-lexer.c │ │ ├── gml-lexer.h │ │ ├── gml-lexer.l │ │ ├── gml-parser.c │ │ ├── gml-parser.h │ │ ├── gml-parser.y │ │ ├── gml-tree.c │ │ ├── gml-tree.h │ │ ├── gml.c │ │ ├── gml.c.orig │ │ ├── graphdb.c │ │ ├── graphml.c │ │ ├── leda.c │ │ ├── lgl-header.h │ │ ├── lgl-lexer.c │ │ ├── lgl-lexer.h │ │ ├── lgl-lexer.l │ │ ├── lgl-parser.c │ │ ├── lgl-parser.h │ │ ├── lgl-parser.y │ │ ├── lgl.c │ │ ├── ncol-header.h │ │ ├── ncol-lexer.c │ │ ├── ncol-lexer.h │ │ ├── ncol-lexer.l │ │ ├── ncol-parser.c │ │ ├── ncol-parser.h │ │ ├── ncol-parser.y │ │ ├── ncol.c │ │ ├── pajek-header.h │ │ ├── pajek-lexer.c │ │ ├── pajek-lexer.h │ │ ├── pajek-lexer.l │ │ ├── pajek-parser.c │ │ ├── pajek-parser.h │ │ ├── pajek-parser.y │ │ └── pajek.c │ ├── isomorphism │ │ ├── bliss.cc │ │ ├── bliss │ │ │ ├── bignum.hh │ │ │ ├── defs.cc │ │ │ ├── defs.hh │ │ │ ├── graph.cc │ │ │ ├── graph.hh │ │ │ ├── heap.cc │ │ │ ├── heap.hh │ │ │ ├── igraph-changes.md │ │ │ ├── kqueue.hh │ │ │ ├── kstack.hh │ │ │ ├── orbit.cc │ │ │ ├── orbit.hh │ │ │ ├── partition.cc │ │ │ ├── partition.hh │ │ │ ├── stats.hh │ │ │ ├── uintseqhash.cc │ │ │ ├── uintseqhash.hh │ │ │ ├── utils.cc │ │ │ └── utils.hh │ │ ├── isoclasses.c │ │ ├── isoclasses.h │ │ ├── isomorphism_misc.c │ │ ├── lad.c │ │ ├── queries.c │ │ └── vf2.c │ ├── layout │ │ ├── circular.c │ │ ├── davidson_harel.c │ │ ├── drl │ │ │ ├── DensityGrid.cpp │ │ │ ├── DensityGrid.h │ │ │ ├── DensityGrid_3d.cpp │ │ │ ├── DensityGrid_3d.h │ │ │ ├── drl_Node.h │ │ │ ├── drl_Node_3d.h │ │ │ ├── drl_graph.cpp │ │ │ ├── drl_graph.h │ │ │ ├── drl_graph_3d.cpp │ │ │ ├── drl_graph_3d.h │ │ │ ├── drl_layout.cpp │ │ │ ├── drl_layout.h │ │ │ ├── drl_layout_3d.cpp │ │ │ ├── drl_layout_3d.h │ │ │ ├── drl_parse.cpp │ │ │ └── drl_parse.h │ │ ├── fruchterman_reingold.c │ │ ├── gem.c │ │ ├── graphopt.c │ │ ├── kamada_kawai.c │ │ ├── large_graph.c │ │ ├── layout_bipartite.c │ │ ├── layout_grid.c │ │ ├── layout_internal.h │ │ ├── layout_random.c │ │ ├── mds.c │ │ ├── merge_dla.c │ │ ├── merge_grid.c │ │ ├── merge_grid.h │ │ ├── reingold_tilford.c │ │ └── sugiyama.c │ ├── linalg │ │ ├── arpack.c │ │ ├── arpack_internal.h │ │ ├── blas.c │ │ ├── blas_internal.h │ │ ├── eigen.c │ │ ├── lapack.c │ │ └── lapack_internal.h │ ├── math │ │ ├── bfgs.c │ │ ├── complex.c │ │ └── utils.c │ ├── misc │ │ ├── bipartite.c │ │ ├── chordality.c │ │ ├── cocitation.c │ │ ├── coloring.c │ │ ├── conversion.c │ │ ├── conversion_internal.h │ │ ├── degree_sequence.cpp │ │ ├── embedding.c │ │ ├── feedback_arc_set.c │ │ ├── feedback_arc_set.h │ │ ├── graphicality.c │ │ ├── matching.c │ │ ├── microscopic_update.c │ │ ├── mixing.c │ │ ├── motifs.c │ │ ├── other.c │ │ ├── scan.c │ │ ├── sir.c │ │ └── spanning_trees.c │ ├── operators │ │ ├── add_edge.c │ │ ├── complementer.c │ │ ├── compose.c │ │ ├── connect_neighborhood.c │ │ ├── contract.c │ │ ├── difference.c │ │ ├── disjoint_union.c │ │ ├── intersection.c │ │ ├── misc_internal.c │ │ ├── misc_internal.h │ │ ├── permute.c │ │ ├── rewire.c │ │ ├── rewire_edges.c │ │ ├── rewire_internal.h │ │ ├── simplify.c │ │ ├── subgraph.c │ │ ├── subgraph.h │ │ └── union.c │ ├── paths │ │ ├── all_shortest_paths.c │ │ ├── bellman_ford.c │ │ ├── dijkstra.c │ │ ├── distances.c │ │ ├── eulerian.c │ │ ├── histogram.c │ │ ├── johnson.c │ │ ├── random_walk.c │ │ ├── shortest_paths.c │ │ ├── simple_paths.c │ │ └── unweighted.c │ ├── properties │ │ ├── basic_properties.c │ │ ├── constraint.c │ │ ├── convergence_degree.c │ │ ├── dag.c │ │ ├── degrees.c │ │ ├── girth.c │ │ ├── loops.c │ │ ├── multiplicity.c │ │ ├── neighborhood.c │ │ ├── properties_internal.h │ │ ├── spectral.c │ │ ├── trees.c │ │ ├── triangles.c │ │ ├── triangles_template.h │ │ └── triangles_template1.h │ ├── random │ │ └── random.c │ ├── scg │ │ ├── scg.c │ │ ├── scg_approximate_methods.c │ │ ├── scg_exact_scg.c │ │ ├── scg_headers.h │ │ ├── scg_kmeans.c │ │ ├── scg_optimal_method.c │ │ └── scg_utils.c │ └── version.c ├── doc │ ├── issue_report_install.md │ └── issue_report_run.md ├── dummy.cpp ├── f2c.h ├── include │ ├── igraph.h │ ├── igraph_adjlist.h │ ├── igraph_arpack.h │ ├── igraph_array.h │ ├── igraph_array_pmt.h │ ├── igraph_attributes.h │ ├── igraph_bipartite.h │ ├── igraph_blas.h │ ├── igraph_centrality.h │ ├── igraph_cliques.h │ ├── igraph_cocitation.h │ ├── igraph_cohesive_blocks.h │ ├── igraph_coloring.h │ ├── igraph_community.h │ ├── igraph_complex.h │ ├── igraph_components.h │ ├── igraph_constants.h │ ├── igraph_constructors.h │ ├── igraph_conversion.h │ ├── igraph_datatype.h │ ├── igraph_decls.h │ ├── igraph_dqueue.h │ ├── igraph_dqueue_pmt.h │ ├── igraph_eigen.h │ ├── igraph_embedding.h │ ├── igraph_epidemics.h │ ├── igraph_error.h │ ├── igraph_eulerian.h │ ├── igraph_export.h │ ├── igraph_flow.h │ ├── igraph_foreign.h │ ├── igraph_games.h │ ├── igraph_graphicality.h │ ├── igraph_graphlets.h │ ├── igraph_heap.h │ ├── igraph_heap_pmt.h │ ├── igraph_hrg.h │ ├── igraph_interface.h │ ├── igraph_interrupt.h │ ├── igraph_iterators.h │ ├── igraph_lapack.h │ ├── igraph_layout.h │ ├── igraph_lsap.h │ ├── igraph_matching.h │ ├── igraph_matrix.h │ ├── igraph_matrix_pmt.h │ ├── igraph_memory.h │ ├── igraph_microscopic_update.h │ ├── igraph_mixing.h │ ├── igraph_motifs.h │ ├── igraph_neighborhood.h │ ├── igraph_nongraph.h │ ├── igraph_operators.h │ ├── igraph_paths.h │ ├── igraph_pmt.h │ ├── igraph_pmt_off.h │ ├── igraph_progress.h │ ├── igraph_psumtree.h │ ├── igraph_qsort.h │ ├── igraph_random.h │ ├── igraph_scan.h │ ├── igraph_scg.h │ ├── igraph_separators.h │ ├── igraph_sparsemat.h │ ├── igraph_spmatrix.h │ ├── igraph_stack.h │ ├── igraph_stack_pmt.h │ ├── igraph_statusbar.h │ ├── igraph_structural.h │ ├── igraph_strvector.h │ ├── igraph_threading.h │ ├── igraph_threading.h.in │ ├── igraph_topology.h │ ├── igraph_transitivity.h │ ├── igraph_types.h │ ├── igraph_vector.h │ ├── igraph_vector_pmt.h │ ├── igraph_vector_ptr.h │ ├── igraph_vector_type.h │ ├── igraph_version.h │ ├── igraph_version.h.in │ └── igraph_visitor.h ├── leidenalg │ ├── CPMVertexPartition.cpp │ ├── CPMVertexPartition.h │ ├── GraphHelper.cpp │ ├── GraphHelper.h │ ├── LinearResolutionParameterVertexPartition.cpp │ ├── LinearResolutionParameterVertexPartition.h │ ├── ModularityVertexPartition.cpp │ ├── ModularityVertexPartition.h │ ├── MutableVertexPartition.cpp │ ├── MutableVertexPartition.h │ ├── Optimiser.cpp │ ├── Optimiser.h │ ├── RBConfigurationVertexPartition.cpp │ ├── RBConfigurationVertexPartition.h │ ├── RBERVertexPartition.cpp │ ├── RBERVertexPartition.h │ ├── ResolutionParameterVertexPartition.cpp │ ├── ResolutionParameterVertexPartition.h │ ├── SignificanceVertexPartition.cpp │ ├── SignificanceVertexPartition.h │ ├── SurpriseVertexPartition.cpp │ └── SurpriseVertexPartition.h ├── leidenbase │ ├── leidenFindPartition.cpp │ ├── leidenFindPartition.h │ └── leidenFindPartitionR2C.cpp └── vendor │ ├── arpack │ ├── debug.h │ ├── dgetv0.f │ ├── dlaqrb.f │ ├── dmout.f │ ├── dnaitr.f │ ├── dnapps.f │ ├── dnaup2.f │ ├── dnaupd.f │ ├── dnconv.f │ ├── dneigh.f │ ├── dneupd.f │ ├── dngets.f │ ├── dsaitr.f │ ├── dsapps.f │ ├── dsaup2.f │ ├── dsaupd.f │ ├── dsconv.f │ ├── dseigt.f │ ├── dsesrt.f │ ├── dseupd.f │ ├── dsgets.f │ ├── dsortc.f │ ├── dsortr.f │ ├── dstatn.f │ ├── dstats.f │ ├── dstqrb.f │ ├── dvout.f │ ├── ivout.f │ ├── second.f │ ├── stat.h │ └── wrap.f │ ├── cs │ ├── SuiteSparse_config.h │ ├── cs.h │ ├── cs_add.c │ ├── cs_amd.c │ ├── cs_chol.c │ ├── cs_cholsol.c │ ├── cs_compress.c │ ├── cs_counts.c │ ├── cs_cumsum.c │ ├── cs_dfs.c │ ├── cs_dmperm.c │ ├── cs_droptol.c │ ├── cs_dropzeros.c │ ├── cs_dupl.c │ ├── cs_entry.c │ ├── cs_ereach.c │ ├── cs_etree.c │ ├── cs_fkeep.c │ ├── cs_gaxpy.c │ ├── cs_happly.c │ ├── cs_house.c │ ├── cs_ipvec.c │ ├── cs_leaf.c │ ├── cs_load.c │ ├── cs_lsolve.c │ ├── cs_ltsolve.c │ ├── cs_lu.c │ ├── cs_lusol.c │ ├── cs_malloc.c │ ├── cs_maxtrans.c │ ├── cs_multiply.c │ ├── cs_norm.c │ ├── cs_permute.c │ ├── cs_pinv.c │ ├── cs_post.c │ ├── cs_print.c │ ├── cs_pvec.c │ ├── cs_qr.c │ ├── cs_qrsol.c │ ├── cs_randperm.c │ ├── cs_reach.c │ ├── cs_scatter.c │ ├── cs_scc.c │ ├── cs_schol.c │ ├── cs_spsolve.c │ ├── cs_sqr.c │ ├── cs_symperm.c │ ├── cs_tdfs.c │ ├── cs_transpose.c │ ├── cs_updown.c │ ├── cs_usolve.c │ ├── cs_util.c │ └── cs_utsolve.c │ ├── mini-gmp │ ├── mini-gmp.c │ └── mini-gmp.h │ ├── plfit │ ├── arithmetic_ansi.h │ ├── arithmetic_sse_double.h │ ├── arithmetic_sse_float.h │ ├── gss.c │ ├── gss.h │ ├── hzeta.c │ ├── hzeta.h │ ├── kolmogorov.c │ ├── kolmogorov.h │ ├── lbfgs.c │ ├── lbfgs.h │ ├── mt.c │ ├── options.c │ ├── platform.c │ ├── platform.h │ ├── plfit.c │ ├── plfit.h │ ├── plfit_error.c │ ├── plfit_error.h │ ├── plfit_mt.h │ ├── plfit_sampling.h │ ├── plfit_version.h │ ├── rbinom.c │ └── sampling.c │ ├── simpleraytracer │ ├── Color.cpp │ ├── Color.h │ ├── Light.cpp │ ├── Light.h │ ├── Point.cpp │ ├── Point.h │ ├── RIgraphRay.cpp │ ├── Ray.cpp │ ├── Ray.h │ ├── RayTracer.cpp │ ├── RayTracer.h │ ├── RayVector.cpp │ ├── RayVector.h │ ├── Shape.cpp │ ├── Shape.h │ ├── Sphere.cpp │ ├── Sphere.h │ ├── Triangle.cpp │ ├── Triangle.h │ ├── unit_limiter.cpp │ └── unit_limiter.h │ └── uuid │ ├── COPYING │ ├── Makevars.in │ ├── Makevars.win │ ├── R.c │ ├── clear.c │ ├── compare.c │ ├── config.h.in │ ├── copy.c │ ├── gen_uuid.c │ ├── isnull.c │ ├── pack.c │ ├── parse.c │ ├── unpack.c │ ├── unparse.c │ ├── uuid.h │ ├── uuidP.h │ ├── uuidd.h │ └── win32 │ └── config.h ├── tests ├── cpp_tests │ ├── Makefile │ ├── NOTES │ ├── edge_weights.txt │ ├── edgelist.edg │ ├── igraph_edgelist.txt.gz │ ├── initial_memberships.txt │ ├── leiden.cpp │ ├── leidenalg_refs.py │ ├── leidenalg_test.py │ ├── node_sizes.txt │ ├── test_files │ │ ├── equals │ │ │ ├── test_set_1.txt │ │ │ ├── test_set_2.txt │ │ │ ├── test_set_3.txt │ │ │ ├── test_set_4.txt │ │ │ └── test_set_5.txt │ │ ├── test_set_1.txt │ │ ├── test_set_2.txt │ │ ├── test_set_3.txt │ │ ├── test_set_4.txt │ │ └── test_set_5.txt │ └── tests_out │ │ ├── edge_weights.txt │ │ ├── edgelist.edg │ 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