From 26f0dfa933f3a977700fb7a8b9194723a4edef0a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Szabolcs=20Horva=CC=81t?= Date: Thu, 7 Nov 2024 13:50:50 +0000 Subject: [PATCH] chore: Update vendored sources to igraph/igraph@a16619502b6c21d4883eeee992794b271e1035d9 chore: updated changelog chore: updated changelog chore: run pre-commit hooks chore: bump VERSION property in shared library fix: fix self-loops handling during simple cycle detection, closes igraph/igraph#2692 Revert "fix: temporary fix for simple cycle search mishandling self-loops, ref igraph/igraph#2692" fix: temporary fix for simple cycle search mishandling self-loops, ref igraph/igraph#2692 test: minimum cycle length for igraph_simple_cycles() refactor: do not use vector_get() in simple cycle finder refactor: cleaner parameter ordering in igraph_i_simple_cycles_circuit() refactor: support specifying a minimum cycle length in `igraph_simple_cycles()` interface: loops=True default for igraph_degree() chore: updated contributors list --- R/aaa-auto.R | 5 +- src/cpp11.cpp | 4 +- src/rinterface.c | 7 +- src/vendor/cigraph/.all-contributorsrc | 18 ++ src/vendor/cigraph/CHANGELOG.md | 5 +- src/vendor/cigraph/CONTRIBUTORS.md | 174 +++++++++--------- src/vendor/cigraph/CONTRIBUTORS.txt | 2 + src/vendor/cigraph/include/igraph_cycles.h | 11 +- src/vendor/cigraph/interfaces/functions.yaml | 6 +- src/vendor/cigraph/src/CMakeLists.txt | 2 +- src/vendor/cigraph/src/cycles/simple_cycles.c | 48 +++-- src/vendor/igraph_version.h | 6 +- 12 files changed, 167 insertions(+), 121 deletions(-) diff --git a/R/aaa-auto.R b/R/aaa-auto.R index 1ff5d31d69..a04fa1f187 100644 --- a/R/aaa-auto.R +++ b/R/aaa-auto.R @@ -3580,15 +3580,16 @@ find_cycle_impl <- function(graph, mode=c("out", "in", "all", "total")) { res } -simple_cycles_impl <- function(graph, mode=c("out", "in", "all", "total"), max.cycle.length=-1) { +simple_cycles_impl <- function(graph, mode=c("out", "in", "all", "total"), min.cycle.length=-1, max.cycle.length=-1) { # Argument checks ensure_igraph(graph) mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L) + min.cycle.length <- as.numeric(min.cycle.length) max.cycle.length <- as.numeric(max.cycle.length) on.exit( .Call(R_igraph_finalizer) ) # Function call - res <- .Call(R_igraph_simple_cycles, graph, mode, max.cycle.length) + res <- .Call(R_igraph_simple_cycles, graph, mode, min.cycle.length, max.cycle.length) if (igraph_opt("return.vs.es")) { res$vertices <- lapply(res$vertices, unsafe_create_vs, graph = graph, verts = V(graph)) } diff --git a/src/cpp11.cpp b/src/cpp11.cpp index db2c70976e..f5181f421d 100644 --- a/src/cpp11.cpp +++ b/src/cpp11.cpp @@ -401,7 +401,7 @@ extern SEXP R_igraph_similarity_inverse_log_weighted(SEXP, SEXP, SEXP); extern SEXP R_igraph_similarity_jaccard(SEXP, SEXP, SEXP, SEXP); extern SEXP R_igraph_similarity_jaccard_es(SEXP, SEXP, SEXP, SEXP); extern SEXP R_igraph_similarity_jaccard_pairs(SEXP, SEXP, SEXP, SEXP); -extern SEXP R_igraph_simple_cycles(SEXP, SEXP, SEXP); +extern SEXP R_igraph_simple_cycles(SEXP, SEXP, SEXP, SEXP); extern SEXP R_igraph_simple_interconnected_islands_game(SEXP, SEXP, SEXP, SEXP); extern SEXP R_igraph_simplify(SEXP, SEXP, SEXP, SEXP); extern SEXP R_igraph_simplify_and_colorize(SEXP); @@ -856,7 +856,7 @@ static const R_CallMethodDef CallEntries[] = { {"R_igraph_similarity_jaccard", (DL_FUNC) &R_igraph_similarity_jaccard, 4}, {"R_igraph_similarity_jaccard_es", (DL_FUNC) &R_igraph_similarity_jaccard_es, 4}, {"R_igraph_similarity_jaccard_pairs", (DL_FUNC) &R_igraph_similarity_jaccard_pairs, 4}, - {"R_igraph_simple_cycles", (DL_FUNC) &R_igraph_simple_cycles, 3}, + {"R_igraph_simple_cycles", (DL_FUNC) &R_igraph_simple_cycles, 4}, {"R_igraph_simple_interconnected_islands_game", (DL_FUNC) &R_igraph_simple_interconnected_islands_game, 4}, {"R_igraph_simplify", (DL_FUNC) &R_igraph_simplify, 4}, {"R_igraph_simplify_and_colorize", (DL_FUNC) &R_igraph_simplify_and_colorize, 1}, diff --git a/src/rinterface.c b/src/rinterface.c index bec61580ac..0374a61fee 100644 --- a/src/rinterface.c +++ b/src/rinterface.c @@ -10968,12 +10968,13 @@ SEXP R_igraph_find_cycle(SEXP graph, SEXP mode) { /*-------------------------------------------/ / igraph_simple_cycles / /-------------------------------------------*/ -SEXP R_igraph_simple_cycles(SEXP graph, SEXP mode, SEXP max_cycle_length) { +SEXP R_igraph_simple_cycles(SEXP graph, SEXP mode, SEXP min_cycle_length, SEXP max_cycle_length) { /* Declarations */ igraph_t c_graph; igraph_vector_int_list_t c_vertices; igraph_vector_int_list_t c_edges; igraph_neimode_t c_mode; + igraph_integer_t c_min_cycle_length; igraph_integer_t c_max_cycle_length; SEXP vertices; SEXP edges; @@ -10986,10 +10987,12 @@ SEXP R_igraph_simple_cycles(SEXP graph, SEXP mode, SEXP max_cycle_length) { IGRAPH_R_CHECK(igraph_vector_int_list_init(&c_edges, 0)); IGRAPH_FINALLY(igraph_vector_int_list_destroy, &c_edges); c_mode = (igraph_neimode_t) Rf_asInteger(mode); + IGRAPH_R_CHECK_INT(min_cycle_length); + c_min_cycle_length = (igraph_integer_t) REAL(min_cycle_length)[0]; IGRAPH_R_CHECK_INT(max_cycle_length); c_max_cycle_length = (igraph_integer_t) REAL(max_cycle_length)[0]; /* Call igraph */ - IGRAPH_R_CHECK(igraph_simple_cycles(&c_graph, &c_vertices, &c_edges, c_mode, c_max_cycle_length)); + IGRAPH_R_CHECK(igraph_simple_cycles(&c_graph, &c_vertices, &c_edges, c_mode, c_min_cycle_length, c_max_cycle_length)); /* Convert output */ PROTECT(r_result=NEW_LIST(2)); diff --git a/src/vendor/cigraph/.all-contributorsrc b/src/vendor/cigraph/.all-contributorsrc index e031cc7cc4..65201c5342 100644 --- a/src/vendor/cigraph/.all-contributorsrc +++ b/src/vendor/cigraph/.all-contributorsrc @@ -594,6 +594,24 @@ "contributions": [ "code" ] + }, + { + "login": "GenieTim", + "name": "Tim Bernhard", + "avatar_url": "https://avatars.githubusercontent.com/u/8596965?v=4", + "profile": "https://github.com/GenieTim", + "contributions": [ + "code" + ] + }, + { + "login": "maelle", + "name": "Maëlle Salmon", + "avatar_url": "https://avatars.githubusercontent.com/u/8360597?v=4", + "profile": "https://masalmon.eu/", + "contributions": [ + "code" + ] } ], "contributorsPerLine": 7 diff --git a/src/vendor/cigraph/CHANGELOG.md b/src/vendor/cigraph/CHANGELOG.md index b8fe2d4c52..4130bc79cd 100644 --- a/src/vendor/cigraph/CHANGELOG.md +++ b/src/vendor/cigraph/CHANGELOG.md @@ -2,6 +2,8 @@ ## [master] +## [0.10.15] + ### Added - `igraph_bitset_update()` copies the contents of one bitset into another (experimental function). @@ -1445,7 +1447,8 @@ Some of the highlights are: - Provide proper support for Windows, using `__declspec(dllexport)` and `__declspec(dllimport)` for `DLL`s and static usage by using `#define IGRAPH_STATIC 1`. - Provided integer versions of `dqueue` and `stack` data types. -[master]: https://github.com/igraph/igraph/compare/0.10.13..master +[master]: https://github.com/igraph/igraph/compare/0.10.15..master +[0.10.15]: https://github.com/igraph/igraph/compare/0.10.13..0.10.15 [0.10.13]: https://github.com/igraph/igraph/compare/0.10.12..0.10.13 [0.10.12]: https://github.com/igraph/igraph/compare/0.10.11..0.10.12 [0.10.11]: https://github.com/igraph/igraph/compare/0.10.10..0.10.11 diff --git a/src/vendor/cigraph/CONTRIBUTORS.md b/src/vendor/cigraph/CONTRIBUTORS.md index 3d2f470665..349ec3150e 100644 --- a/src/vendor/cigraph/CONTRIBUTORS.md +++ b/src/vendor/cigraph/CONTRIBUTORS.md @@ -6,91 +6,95 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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Michael
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Gábor Csárdi
Gábor Csárdi
💻		Tamás Nepusz
Tamás Nepusz
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Szabolcs Horvát
💻		Vincent Traag
Vincent Traag
💻		GroteGnoom
GroteGnoom
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Fabio Zanini
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Jan Katins
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Sancar Adali
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Ferran Parés
💻		mvngu
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Dr. Nick
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💻		Jérôme Benoit
Jérôme Benoit
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Frederik Harwath
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AdamKorcz
AdamKorcz
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Antonio Rojas
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Árpád Horváth
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Peter Scott
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Andreas Beham
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Bart Kastermans
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Erik Welch
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Hong Xu
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Jean Monlong
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Min Kim
Min Kim
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Nikolay Khitrin
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Peter Schmiedeskamp
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Philipp A.
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Robert Schütz
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Ryan Duffin
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Tomasz Kłoczko
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alexperrone
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Georgica Bors
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kwofach
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Kevin Zhu
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Pradeep Krishnamurthy
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flange-ipb
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Juan Julián Merelo Guervós
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Radoslav Fulek
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professorcode1
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larah19
larah19
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Biswapriyo Nath
💻		Gwyn Ciesla
Gwyn Ciesla
💻		aagon
aagon
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Quinn Buratynski
💻		Arnar Bjarni Arnarson
Arnar Bjarni Arnarson
💻		David Seifert
David Seifert
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Kirill Müller
Kirill Müller
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Michael
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Tim Bernhard
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Maëlle Salmon
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diff --git a/src/vendor/cigraph/CONTRIBUTORS.txt b/src/vendor/cigraph/CONTRIBUTORS.txt index 92702f357d..826271e153 100644 --- a/src/vendor/cigraph/CONTRIBUTORS.txt +++ b/src/vendor/cigraph/CONTRIBUTORS.txt @@ -65,6 +65,8 @@ Arnar Bjarni Arnarson (@Tagl) David Seifert (@SoapGentoo) Kirill Müller (@krlmlr) Michael (@gendelpiekel) +Tim Bernhard (@GenieTim) +Maëlle Salmon (@maelle) This project follows the [all-contributors][1] specification. Contributions of any kind welcome! diff --git a/src/vendor/cigraph/include/igraph_cycles.h b/src/vendor/cigraph/include/igraph_cycles.h index 060ed4f77f..2f38aa8d14 100644 --- a/src/vendor/cigraph/include/igraph_cycles.h +++ b/src/vendor/cigraph/include/igraph_cycles.h @@ -71,13 +71,18 @@ typedef igraph_error_t igraph_cycle_handler_t( IGRAPH_EXPORT igraph_error_t igraph_simple_cycles_callback( const igraph_t *graph, - igraph_neimode_t mode, igraph_integer_t max_cycle_length, + igraph_neimode_t mode, + igraph_integer_t min_cycle_length, + igraph_integer_t max_cycle_length, igraph_cycle_handler_t *callback, void *arg); IGRAPH_EXPORT igraph_error_t igraph_simple_cycles( const igraph_t *graph, - igraph_vector_int_list_t *vertices, igraph_vector_int_list_t *edges, - igraph_neimode_t mode, igraph_integer_t max_cycle_length); + igraph_vector_int_list_t *vertices, + igraph_vector_int_list_t *edges, + igraph_neimode_t mode, + igraph_integer_t min_cycle_length, + igraph_integer_t max_cycle_length); __END_DECLS diff --git a/src/vendor/cigraph/interfaces/functions.yaml b/src/vendor/cigraph/interfaces/functions.yaml index 232608bb8b..e6e923e805 100644 --- a/src/vendor/cigraph/interfaces/functions.yaml +++ b/src/vendor/cigraph/interfaces/functions.yaml @@ -59,7 +59,7 @@ igraph_is_directed: igraph_degree: PARAMS: |- GRAPH graph, OUT VECTOR_INT res, VERTEX_SELECTOR vids=ALL, NEIMODE mode=ALL, - BOOLEAN loops + BOOLEAN loops=True DEPS: vids ON graph igraph_edge: @@ -2542,13 +2542,13 @@ igraph_simple_cycles: PARAMS: |- GRAPH graph, OPTIONAL OUT VERTEXSET_LIST vertices, OPTIONAL OUT EDGESET_LIST edges, - NEIMODE mode=OUT, INTEGER max_cycle_length=-1 + NEIMODE mode=OUT, INTEGER min_cycle_length=-1, INTEGER max_cycle_length=-1 DEPS: vertices ON graph, edges ON graph igraph_simple_cycles_callback: PARAMS: |- GRAPH graph, - NEIMODE mode=OUT, INTEGER max_cycle_length=-1, + NEIMODE mode=OUT, INTEGER min_cycle_length=-1, INTEGER max_cycle_length=-1, CYCLE_FUNC cycle_handler, OPTIONAL EXTRA arg ####################################### diff --git a/src/vendor/cigraph/src/CMakeLists.txt b/src/vendor/cigraph/src/CMakeLists.txt index e59bc9200c..ac95f94179 100644 --- a/src/vendor/cigraph/src/CMakeLists.txt +++ b/src/vendor/cigraph/src/CMakeLists.txt @@ -332,7 +332,7 @@ add_library( add_dependencies(igraph parsersources) # Set soname for the library -set_target_properties(igraph PROPERTIES VERSION "3.1.8") +set_target_properties(igraph PROPERTIES VERSION "3.1.9") set_target_properties(igraph PROPERTIES SOVERSION 3) # Add extra compiler definitions if needed diff --git a/src/vendor/cigraph/src/cycles/simple_cycles.c b/src/vendor/cigraph/src/cycles/simple_cycles.c index 0c505e3f59..2b562951d2 100644 --- a/src/vendor/cigraph/src/cycles/simple_cycles.c +++ b/src/vendor/cigraph/src/cycles/simple_cycles.c @@ -134,10 +134,10 @@ static igraph_error_t igraph_i_simple_cycles_unblock( * \param arg: argument to pass to the callback function */ static igraph_error_t igraph_i_simple_cycles_circuit( - igraph_i_simple_cycle_search_state_t *state, - igraph_integer_t V, - igraph_cycle_handler_t *callback, - igraph_integer_t max_cycle_length, void *arg) { + igraph_i_simple_cycle_search_state_t *state, igraph_integer_t V, + igraph_integer_t max_cycle_length, + igraph_integer_t min_cycle_length, + igraph_cycle_handler_t *callback, void *arg) { const igraph_vector_int_t *neighbors; const igraph_vector_int_t *incident_edges; @@ -178,7 +178,7 @@ static igraph_error_t igraph_i_simple_cycles_circuit( // printf("Pushing %" IGRAPH_PRId " to stack, stack size is %" IGRAPH_PRId // ", result size is %" IGRAPH_PRId "\n", // V, igraph_vector_int_size(&state->vertex_stack), - // igraph_vector_int_list_size(vertices)); + // igraph_stack_int_size(&v_stack)); VECTOR(state->v_blocked)[V] = true; } else { // back to what we were doing before @@ -206,16 +206,17 @@ static igraph_error_t igraph_i_simple_cycles_circuit( if ((!state->directed && igraph_vector_int_size(&state->edge_stack) == 1 && - igraph_vector_int_get(&state->edge_stack, 0) == WE)) { - // printf("Skipping cycle to prevent self-loop: \n"); + VECTOR(state->edge_stack)[0] == WE)) { + // printf("Skipping cycle to %" IGRAPH_PRId " via %" IGRAPH_PRId " to prevent self-loop.\n", W, WE); continue; } // prevent duplicates in undirected graphs by forcing a direction for // the closing edge if ((!state->directed && - igraph_vector_int_get(&state->edge_stack, 0) > WE)) { - // printf("Skipping cycle to prevent duplicates: \n"); + igraph_vector_int_size(&state->edge_stack) > 0 && + VECTOR(state->edge_stack)[0] > WE)) { + // printf("Skipping cycle to %" IGRAPH_PRId " via %" IGRAPH_PRId " to prevent duplicates.\n", W, WE); continue; } @@ -225,16 +226,16 @@ static igraph_error_t igraph_i_simple_cycles_circuit( // printf("Found cycle with size %" IGRAPH_PRId "\n", // igraph_vector_int_size(&state->vertex_stack)); - IGRAPH_CHECK_CALLBACK(callback(&state->vertex_stack, &state->edge_stack, arg), &ret); - if (ret == IGRAPH_STOP) { - state->stop_search = true; - break; + if (igraph_vector_int_size(&state->edge_stack) >= min_cycle_length) { + IGRAPH_CHECK_CALLBACK(callback(&state->vertex_stack, &state->edge_stack, arg), &ret); + if (ret == IGRAPH_STOP) { + state->stop_search = true; + break; + } } igraph_vector_int_pop_back(&state->edge_stack); } else if (!(VECTOR(state->v_blocked)[W])) { - // printf("Recursing deeper from %" IGRAPH_PRId " to %" IGRAPH_PRId - // "\n", - // V, W); + // printf("Recursing deeper from %" IGRAPH_PRId " to %" IGRAPH_PRId "\n", V, W); recurse_deeper = ((max_cycle_length < 0) || (igraph_vector_int_size(&state->vertex_stack) <= max_cycle_length - 1)); @@ -432,6 +433,7 @@ static igraph_error_t igraph_i_append_simple_cycle_result( static igraph_error_t igraph_i_simple_cycles_search_callback_from_one_vertex( igraph_i_simple_cycle_search_state_t *state, igraph_integer_t s, + igraph_integer_t min_cycle_length, igraph_integer_t max_cycle_length, igraph_cycle_handler_t *callback, void *arg) { @@ -442,7 +444,9 @@ static igraph_error_t igraph_i_simple_cycles_search_callback_from_one_vertex( igraph_vector_int_clear(igraph_adjlist_get(&state->B, i)); } - IGRAPH_CHECK(igraph_i_simple_cycles_circuit(state, s, callback, max_cycle_length, arg)); + IGRAPH_CHECK(igraph_i_simple_cycles_circuit(state, s, + max_cycle_length, min_cycle_length, + callback, arg)); for (igraph_integer_t i = 0; i < state->N; ++i) { // We want to remove the vertex with value s, not at position s. @@ -488,6 +492,8 @@ static igraph_error_t igraph_i_simple_cycles_search_callback_from_one_vertex( * \c IGRAPH_IN, follows the opposite directions; and * \c IGRAPH_ALL, ignores edge directions. This argument is * ignored for undirected graphs. + * \param max_cycle_length Limit the minimum length of cycles to search for. + * Pass a negative value to search for all cycles. * \param max_cycle_length Limit the maximum length of cycles to search for. * Pass a negative value to search for all cycles. * \param callback A function to call for each cycle that is found. @@ -505,6 +511,7 @@ static igraph_error_t igraph_i_simple_cycles_search_callback_from_one_vertex( igraph_error_t igraph_simple_cycles_callback( const igraph_t *graph, igraph_neimode_t mode, + igraph_integer_t min_cycle_length, igraph_integer_t max_cycle_length, igraph_cycle_handler_t *callback, void *arg) { @@ -523,7 +530,7 @@ igraph_error_t igraph_simple_cycles_callback( for (igraph_integer_t i = 0; i < state.N; i++) { if (!igraph_vector_int_empty(igraph_adjlist_get(&state.AK, i))) { IGRAPH_CHECK(igraph_i_simple_cycles_search_callback_from_one_vertex( - &state, i, max_cycle_length, callback, arg)); + &state, i, min_cycle_length, max_cycle_length, callback, arg)); IGRAPH_ALLOW_INTERRUPTION(); } if (state.stop_search) { @@ -566,6 +573,8 @@ igraph_error_t igraph_simple_cycles_callback( * \c IGRAPH_IN, follows the opposite directions; and * \c IGRAPH_ALL, ignores edge directions. This argument is * ignored for undirected graphs. + * \param max_cycle_length Limit the minimum length of cycles to search for. + * Pass a negative value to search for all cycles. * \param max_cycle_length Limit the maximum length of cycles to search for. * Pass a negative value to search for all cycles. * @@ -582,6 +591,7 @@ igraph_error_t igraph_simple_cycles( igraph_vector_int_list_t *vertices, igraph_vector_int_list_t *edges, igraph_neimode_t mode, + igraph_integer_t min_cycle_length, igraph_integer_t max_cycle_length) { igraph_i_simple_cycle_results_t result_list; @@ -595,7 +605,7 @@ igraph_error_t igraph_simple_cycles( igraph_vector_int_list_clear(edges); } - igraph_simple_cycles_callback(graph, mode, max_cycle_length, + igraph_simple_cycles_callback(graph, mode, min_cycle_length, max_cycle_length, &igraph_i_append_simple_cycle_result, &result_list); diff --git a/src/vendor/igraph_version.h b/src/vendor/igraph_version.h index a1c72365ab..fea50a9275 100644 --- a/src/vendor/igraph_version.h +++ b/src/vendor/igraph_version.h @@ -28,11 +28,11 @@ __BEGIN_DECLS -#define IGRAPH_VERSION "0.10.13-154-ga6441e7a0" +#define IGRAPH_VERSION "0.10.15-1-ga16619502" #define IGRAPH_VERSION_MAJOR 0 #define IGRAPH_VERSION_MINOR 10 -#define IGRAPH_VERSION_PATCH 13 -#define IGRAPH_VERSION_PRERELEASE "154-ga6441e7a0" +#define IGRAPH_VERSION_PATCH 15 +#define IGRAPH_VERSION_PRERELEASE "1-ga16619502" IGRAPH_EXPORT void igraph_version(const char **version_string, int *major,