Merge branch 'master' into feat/steiner

.all-contributorsrc

@@ -585,6 +585,15 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "gendelpiekel",
+      "name": "Michael",
+      "avatar_url": "https://avatars.githubusercontent.com/u/14215028?v=4",
+      "profile": "https://github.com/gendelpiekel",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7

.azure/build-win.yml

@@ -41,9 +41,14 @@ parameters:
   - name: vcpkg_target_triplet
     type: string
     default: 'x64-windows-static-md'
-  - name: vsver # for choosing a VS toolset, see https://en.wikipedia.org/wiki/Microsoft_Visual_C%2B%2B#Internal_version_numbering
+  - name: vsver
+    # For choosing a VS toolset, see https://en.wikipedia.org/wiki/Microsoft_Visual_C%2B%2B#Internal_version_numbering
+    # Generally, 14.1 is VS2017, 14.2 is VS2019, while 14.3 and 14.4 are VS2022. Use a single digit after the dot to\
+    # be flexible with the patch version the current runner has installed. Note that VS 2022 17.10 and later require
+    # a version of 14.4 instead of 14.3, see:
+    # https://devblogs.microsoft.com/cppblog/msvc-toolset-minor-version-number-14-40-in-vs-2022-v17-10/
     type: string
-    default: '14.1' # VS2017
+    default: '14.2' # VS2019
 
 steps:
   - task: Cache@2
@@ -96,8 +101,7 @@ steps:
       set CXX=cl.exe
       set CC=cl.exe
 
-      cmake .. -DCMAKE_PREFIX_PATH=%CONDA%\Library\lib ^
-               -DIGRAPH_USE_INTERNAL_BLAS=${{ parameters.int_blas }} ^
+      cmake .. -DIGRAPH_USE_INTERNAL_BLAS=${{ parameters.int_blas }} ^
                -DIGRAPH_USE_INTERNAL_LAPACK=${{ parameters.int_lapack }} ^
                -DIGRAPH_USE_INTERNAL_ARPACK=${{ parameters.int_arpack }} ^
                -DIGRAPH_USE_INTERNAL_GLPK=${{ parameters.int_glpk }} ^

.github/pull_request_template.md

@@ -0,0 +1 @@
+<!-- Please disclose any use of LLMs (ChatGPT, Copilot, Gemini, etc.) during the preparation of this PR. -->

.github/stale.yml

@@ -1,5 +1,5 @@
 # Number of days of inactivity before an issue becomes stale
-daysUntilStale: 60
+daysUntilStale: 28
 
 # Number of days of inactivity before a stale issue is closed
 daysUntilClose: 14

.github/workflows/cifuzz.yml

@@ -21,14 +21,14 @@ jobs:
        fuzz-seconds: 720
        output-sarif: true
    - name: Upload Crash
-     uses: actions/upload-artifact@v3
+     uses: actions/upload-artifact@v4
      if: failure() && steps.build.outcome == 'success'
      with:
        name: artifacts
        path: ./out/artifacts
    - name: Upload Sarif
      if: always() && steps.build.outcome == 'success'
-     uses: github/codeql-action/upload-sarif@v2
+     uses: github/codeql-action/upload-sarif@v3
      with:
       # Path to SARIF file relative to the root of the repository
       sarif_file: cifuzz-sarif/results.sarif

.github/workflows/codecov.yml

@@ -38,3 +38,5 @@ jobs:
 
     - name: Codecov.io
       uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/coverity.yml

@@ -13,6 +13,9 @@ jobs:
   coverity:
     runs-on: ubuntu-latest
 
+    # Do not run in forks
+    if: github.repository == 'igraph/igraph'
+
     steps:
     - name: Install dependencies
       run: sudo apt-get install bison flex libarpack2-dev libglpk-dev libgmp-dev libxml2-dev
@@ -21,6 +24,7 @@ jobs:
       uses: actions/checkout@v4
       with:
         fetch-depth: 0
+        ref: 'develop'
 
     - name: Create build environment
       run: cmake -E make_directory ${{github.workspace}}/build

.github/workflows/stimulus.yml

@@ -5,7 +5,7 @@ jobs:
   ci:
     runs-on: ubuntu-latest
     env:
-      STIMULUS_VERSION: "0.19.0"
+      STIMULUS_VERSION: "0.21.6"
     steps:
       # Use Clang for more informative error messages
       - name: Install Clang

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ exclude: "(^vendor/|\\.patch$)"
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.6.0
     hooks:
       - id: mixed-line-ending
         args: ["--fix=lf"]

CHANGELOG.md

@@ -2,11 +2,100 @@
 
 ## [master]
 
+### Fixed
+
+ - `igraph_layout_drl()` and `igraph_layout_drl_3d()` would crash with an assertion failure when interrupted. This is now fixed.
+ - Removed broken interruption support from `igraph_community_spinglass_single()`.
+
+### Deprecated
+
+ - `igraph_minimum_spanning_tree_prim()` and `igraph_minimum_spanning_tree_unweighted()` are deprecated. Use `igraph_minimum_spanning_tree()` in conjunction with `igraph_subgraph_from_edges()` instead.
+
+### Other
+
+ - Fixed multiple memory leaks in benchmark programs.
+ - Documentation improvements.
+
+## [0.10.13]
+
+### Added
+
+ - `igraph_bitset_fill()` sets all elements of a bitset to the same value (experimental function).
+ - `igraph_bitset_null()` clears all elements of a bitset (experimental function).
+ - `igraph_bitset_is_all_zero()`, `igraph_bitset_is_all_one()`, `igraph_bitset_is_any_zero()`, `igraph_bitset_is_any_one()` check if any/all elements of a bitset are zeros/ones (experimental functions).
+ - `igraph_chung_lu_game()` implements the classic Chung-Lu model, as well as a number of its variants (experimental function).
+ - `igraph_mean_degree()` computes the average of vertex degrees (experimental function).
+ - `igraph_count_loops()` counts self-loops in the graph (experimental function).
+ - `igraph_is_clique()` checks if all pairs within a set of vertices are connected (experimental function).
+ - `igraph_is_independent_vertex_set()` checks if no pairs within a set of vertices are connected (experimental function).
+ - `igraph_hypercube()` creates a hypercube graph (experimental function).
+ - `igraph_vector_intersection_size_sorted()` counts elements common to two sorted vectors (experimental function).
+ - `igraph_stack_capacity()` returns the allocated capacity of a stack.
+ - `igraph_vector_is_all_finite()` checks if all elements in a vector are finite (i.e. neither NaN nor Inf).
+
+### Fixed
+
+ - Fixed a bug that incorrectly cached that a graph has no multiple edges when `igraph_init_adjlist()` was called with `IGRAPH_NO_LOOPS` and `IGRAPH_NO_MULTIPLE` and all the multi-edges were loop edges.
+ - `igraph_is_forest()` would fail to set the result variable when testing for a directed forest, and it was already cached that the graph was not an undirected forest.
+ - `igraph_hub_and_authority_scores()` no longer clips negative results to zeros when negative weights are present.
+ - Fixed an assertion failure in `igraph_realize_bipartite_degree_sequence()` with some non-graphical degree sequences when requesting simple bipartite graphs.
+ - `igraph_static_fitness_game()` checks the input more carefully, and avoids an infinite loop in rare edge cases, such as when (almost) all fitness scores are zero.
+ - `igraph_arpack_rnsolve()` used the incorrect error message text for some errors. This is now corrected.
+ - Corrected the detection of some MSVC-specific bitset intrinsics during configuration.
+ - Corrected a bug in the fallback implementation of `igraph_bitset_countl_zero()` when `IGRAPH_INTEGER_SIZE` was set to 32. This fallback implementation was _not_ used with GCC, Clang, or MSVC.
+
+### Changed
+
+ - `igraph_is_graphical()` and `igraph_is_bigraphical()` are now linear-time in all cases, and generally several times faster than before (thanks to @gendelpiekel, contributed in #2605).
+ - `igraph_erdos_renyi_game_gnp()` can now generate graphs with more than a hundred million vertices.
+ - `igraph_hub_and_authority_scores()` now warns when negative edge weights are present.
+ - `igraph_layout_lgl()` now uses a BFS tree rooted in the vertex specified as `proot` to guide the layout. Previously it used an unspecified (arbitrary) spanning tree.
+ - Updated the internal heuristics used by igraph's ARPACK interface, `igraph_arpack_rssolve()` and `igraph_arpack_rnsolve()`, to improve the robustness of calculations.
+ - Updated the initial vector construction in `igraph_hub_and_authority_scores()`, `igraph_eigenvector_centrality()` and `igraph_(personalized_)pagerank()` with `IGRAPH_PAGERANK_ALGO_ARPACK`. This improves the robustness and convergence of calculations.
+
+### Other
+
+ - Documentation improvements.
+ - Reduced the memory usage of several functions by using bitsets instead of boolean vectors.
+ - `igraph_vector_intersect_sorted()` has better performance when the input vector sizes are similar.
+
+## [0.10.12] - 2024-05-06
+
+### Added
+
+ - `igraph_transitive_closure()` computes the transitive closure of a graph (experimental function).
+ - `igraph_reachability()` determines which vertices are reachable from each other in a graph (experimental function).
+ - `igraph_count_reachable()` counts how many vertices are reachable from each vertex (experimental function).
+ - Added a bitset data structure, `igraph_bitset_t`, and a set of corresponding functions (experimental functionality).
+
+### Fixed
+
+ - `igraph_community_label_propagation()` is now interruptible.
+ - `igraph_is_bipartite()` would on rare occasions return invalid results when the cache was employed.
+ - `igraph_weighted_adjacency()` correctly passes through NaN values with `IGRAPH_ADJ_MAX`, and correctly recognizes symmetric adjacency matrices containing NaN values with `IGRAPH_ADJ_UNDIRECTED`.
+ - `igraph_read_graph_gml()` can now read GML files that use ids larger than what is representable on 32 bits, provided that igraph was configured with a 64-bit `igraph_integer_t` size.
+ - Fixed a performance issue in `igraph_read_graph_graphml()` with files containing a very large number of entities, such as `>`.
+ - `igraph_read_graph_pajek()` has improved vertex ID validation that better matches that of Pajek's own behavior.
+
+### Changed
+
+ - `igraph_eigenvector_centrality()` no longer issues a warning when the input is directed and weighted. When using this function, keep in mind that eigenvector centrality is well-defined only for (strongly) connected graphs, and edges with a zero weights are effectively treated as absent.
+
+### Deprecated
+
+ - `igraph_transitive_closure_dag()` is deprecated in favour of `igraph_transitive_closure()`
+
+### Other
+
+ - Documentation improvements.
+ - `igraph_strength()` and `igraph_degree(loops=false)` are now faster when calculating values for all vertices (contributed by @gendelpiekel in #2602)
+
 ## [0.10.11] - 2024-04-02
 
 ### Added
 
  - `igraph_is_complete()` checks whether there is a connection between all pairs of vertices (experimental function, contributed by Aymeric Agon-Rambosson @aagon in #2510).
+ - `igraph_join()` creates the _join_ of two graphs (experimental function, contributed by Quinn Buratynski @GanzuraTheConsumer in #2508).
 
 ### Fixed
 
@@ -1320,7 +1409,9 @@ 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/0.10.11..master
+[master]: https://github.com/igraph/igraph/compare/0.10.13..master
+[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
 [0.10.10]: https://github.com/igraph/igraph/compare/0.10.9..0.10.10
 [0.10.9]: https://github.com/igraph/igraph/compare/0.10.8..0.10.9

CITATION.cff

@@ -27,7 +27,7 @@ authors:
     family-names: Noom
 identifiers:
   - type: doi
-    value: 10.5281/zenodo.4319996
+    value: 10.5281/zenodo.3630268
     description: Zenodo
 repository-code: 'https://github.com/igraph/igraph'
 url: 'https://igraph.org'

CMakeLists.txt

@@ -5,7 +5,7 @@
 #  * SKIP_REGULAR_EXPRESSION to handle skipped tests properly (3.16)
 #  * CheckLinkerFlag for HAVE_NEW_DTAGS test (3.18)
 #  * cmake -E cat (3.18)
-cmake_minimum_required(VERSION 3.18...3.27)
+cmake_minimum_required(VERSION 3.18...3.29)
 
 # Add etc/cmake to CMake's search path so we can put our private stuff there
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/etc/cmake)
@@ -113,10 +113,11 @@ endif()
 check_symbol_exists(_configthreadlocale locale.h HAVE__CONFIGTHREADLOCALE)
 cmake_pop_check_state()
 
-# Check for 128-bit integer multiplication support, floating-point endianness
-# and support for built-in overflow detection.
+# Check for 128-bit integer multiplication support, floating-point endianness,
+# support for built-in overflow detection and fast bit operation support.
 include(ieee754_endianness)
 include(uint128_support)
+include(bit_operations_support)
 include(safe_math_support)
 
 if(NOT HAVE_USELOCALE AND NOT HAVE__CONFIGTHREADLOCALE)