git: a2fa5f70fb02 - main - science/agrum: update 3.0.0 → 3.1.1
Date: Sun, 06 Sep 2026 06:19:49 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=a2fa5f70fb02ffae669bf345df2119afea3b4845
commit a2fa5f70fb02ffae669bf345df2119afea3b4845
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-09-06 06:16:49 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-09-06 06:18:31 +0000
science/agrum: update 3.0.0 → 3.1.1
---
science/agrum/Makefile | 6 +++---
science/agrum/distinfo | 6 +++---
..._testunits_module__BN_GreedyHillClimbingTestSuite.h | 18 ++++++++++++++++++
science/agrum/pkg-plist | 9 +++++++++
4 files changed, 33 insertions(+), 6 deletions(-)
diff --git a/science/agrum/Makefile b/science/agrum/Makefile
index da1addfe2d01..86b8ad6aa499 100644
--- a/science/agrum/Makefile
+++ b/science/agrum/Makefile
@@ -1,5 +1,5 @@
PORTNAME= agrum
-DISTVERSION= 3.0.0
+DISTVERSION= 3.1.1
CATEGORIES= science math
MAINTAINER= yuri@FreeBSD.org
@@ -20,7 +20,7 @@ LLD_UNSAFE= yes
USE_GITLAB= yes
GL_ACCOUNT= agrumery
GL_PROJECT= aGrUM
-GL_TAGNAME= 9c28852d
+GL_TAGNAME= c8d35dae
SHEBANG_FILES= act
@@ -62,6 +62,6 @@ do-test:
@cd ${WRKSRC} && \
${SETENV} ${MAKE_ENV} ./act test release agrum -t all
-# tests as of 3.0.0: test cases: 1188 | 1187 passed | 1 failed | 702 skipped
+# tests as of 3.1.1: test cases: 2458 | 2458 passed | 0 failed | 0 skipped
.include <bsd.port.mk>
diff --git a/science/agrum/distinfo b/science/agrum/distinfo
index 65c816e372ec..83cf25c7f53d 100644
--- a/science/agrum/distinfo
+++ b/science/agrum/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1785087754
-SHA256 (aGrUM-9c28852d.tar.bz2) = fac4ba8e0d8cf7ed4885c3896a6f0a79387f0a2dcc84268ae450fb34a4de5029
-SIZE (aGrUM-9c28852d.tar.bz2) = 20982859
+TIMESTAMP = 1788631607
+SHA256 (aGrUM-c8d35dae.tar.bz2) = 2ef8b2f62878bacf48d89190451b6d26698017e44c7479019e6bf4eec368bad2
+SIZE (aGrUM-c8d35dae.tar.bz2) = 21263367
diff --git a/science/agrum/files/patch-src_testunits_module__BN_GreedyHillClimbingTestSuite.h b/science/agrum/files/patch-src_testunits_module__BN_GreedyHillClimbingTestSuite.h
new file mode 100644
index 000000000000..5436bfc115d9
--- /dev/null
+++ b/science/agrum/files/patch-src_testunits_module__BN_GreedyHillClimbingTestSuite.h
@@ -0,0 +1,18 @@
+-- Fix out-of-bounds vector access in the GreedyHillClimbing test helper.
+-- The rank vector was sized to total_order.size(), but node IDs used as
+-- indices can be as large as nb_vars - 1. With libc++ hardening this
+-- triggered a SIGILL (ud2) trap, crashing the _K2_asia test case.
+--
+-- Upstream: https://gitlab.com/agrumery/aGrUM
+--
+--- src/testunits/module_BN/GreedyHillClimbingTestSuite.h.orig 2026-09-05 18:56:31 UTC
++++ src/testunits/module_BN/GreedyHillClimbingTestSuite.h
+@@ -124,7 +124,7 @@ namespace gum_tests {
+
+ std::vector< int > rank;
+ if (!total_order.empty()) {
+- rank.resize(total_order.size());
++ rank.resize(nb_vars);
+ int i = 0;
+ for (const auto node: total_order) {
+ rank[node] = i++;
diff --git a/science/agrum/pkg-plist b/science/agrum/pkg-plist
index 3e8a8d20f746..500821c8285a 100644
--- a/science/agrum/pkg-plist
+++ b/science/agrum/pkg-plist
@@ -23,6 +23,8 @@ include/agrum/BN/algorithms/divergence/BNdistance.h
include/agrum/BN/algorithms/divergence/BNdistance_tpl.h
include/agrum/BN/algorithms/divergence/GibbsBNdistance.h
include/agrum/BN/algorithms/divergence/GibbsBNdistance_tpl.h
+include/agrum/BN/algorithms/divergence/MCBNDistance.h
+include/agrum/BN/algorithms/divergence/MCBNDistance_tpl.h
include/agrum/BN/algorithms/divergence/exactBNdistance.h
include/agrum/BN/algorithms/divergence/exactBNdistance_tpl.h
include/agrum/BN/algorithms/essentialGraph.h
@@ -826,6 +828,8 @@ include/agrum/base/graphs/cliqueGraph.h
include/agrum/base/graphs/cliqueGraph_inl.h
include/agrum/base/graphs/diGraph.h
include/agrum/base/graphs/diGraph_inl.h
+include/agrum/base/graphs/fastGraph.h
+include/agrum/base/graphs/fastGraph_tpl.h
include/agrum/base/graphs/graphConcepts.h
include/agrum/base/graphs/graphConcepts_inl.h
include/agrum/base/graphs/graphElements.h
@@ -1047,6 +1051,8 @@ lib/cmake/aGrUM/agrumID-targets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/aGrUM/agrumID-targets.cmake
lib/cmake/aGrUM/agrumMRF-targets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/aGrUM/agrumMRF-targets.cmake
+lib/cmake/aGrUM/agrumPRM-targets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/aGrUM/agrumPRM-targets.cmake
lib/libagrumBASE.so
lib/libagrumBASE.so.3
lib/libagrumBASE.so.%%VERSION%%
@@ -1068,6 +1074,9 @@ lib/libagrumID.so.%%VERSION%%
lib/libagrumMRF.so
lib/libagrumMRF.so.3
lib/libagrumMRF.so.%%VERSION%%
+lib/libagrumPRM.so
+lib/libagrumPRM.so.3
+lib/libagrumPRM.so.%%VERSION%%
%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE.md
%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSES/LGPL-3.0-or-later.txt
%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSES/MIT.txt