git: f5f701c8a30e - main - science/agrum: update 3.1.1 → 3.2.1
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Date: Fri, 09 Oct 2026 23:44:30 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=f5f701c8a30ef60be9f62201ee87890342a437fb
commit f5f701c8a30ef60be9f62201ee87890342a437fb
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-10-09 23:23:48 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-10-09 23:44:26 +0000
science/agrum: update 3.1.1 → 3.2.1
---
science/agrum/Makefile | 8 +-
science/agrum/distinfo | 6 +-
...tunits_module__BN_GreedyHillClimbingTestSuite.h | 18 --
science/agrum/pkg-plist | 265 ++++++++++++---------
4 files changed, 161 insertions(+), 136 deletions(-)
diff --git a/science/agrum/Makefile b/science/agrum/Makefile
index 44a81ba51802..e7ea402ecd5b 100644
--- a/science/agrum/Makefile
+++ b/science/agrum/Makefile
@@ -1,6 +1,5 @@
PORTNAME= agrum
-DISTVERSION= 3.1.1
-PORTREVISION= 1
+DISTVERSION= 3.2.1
CATEGORIES= science math
MAINTAINER= yuri@FreeBSD.org
@@ -59,6 +58,9 @@ do-test:
@cd ${WRKSRC} && \
${SETENV} ${MAKE_ENV} ./act test release agrum -t all
-# tests as of 3.1.1: test cases: 2458 | 2458 passed | 0 failed | 0 skipped
+# tests as of 3.2.1: test cases: 2458 | 2458 passed | 0 failed | 0 skipped
+# [doctest] test cases: 2595 | 2595 passed | 0 failed | 0 skipped
+# [doctest] assertions: 1192401 | 1192401 passed | 0 failed |
+# [doctest] Status: SUCCESS!
.include <bsd.port.mk>
diff --git a/science/agrum/distinfo b/science/agrum/distinfo
index 79ac2f30475c..478cb31d549e 100644
--- a/science/agrum/distinfo
+++ b/science/agrum/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1788678431
-SHA256 (aGrUM-3.1.1.tar.bz2) = 48ac61ec6f3743f03c7c9e9e017ee98b9392559149115d059c808f4e3add6774
-SIZE (aGrUM-3.1.1.tar.bz2) = 21273215
+TIMESTAMP = 1791586548
+SHA256 (aGrUM-3.2.1.tar.bz2) = 6ab56ba944acababdfe17686721091a8cf08b11c3459587960bbc13d26aa7479
+SIZE (aGrUM-3.2.1.tar.bz2) = 22197279
diff --git a/science/agrum/files/patch-src_testunits_module__BN_GreedyHillClimbingTestSuite.h b/science/agrum/files/patch-src_testunits_module__BN_GreedyHillClimbingTestSuite.h
deleted file mode 100644
index 5436bfc115d9..000000000000
--- a/science/agrum/files/patch-src_testunits_module__BN_GreedyHillClimbingTestSuite.h
+++ /dev/null
@@ -1,18 +0,0 @@
--- 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 500821c8285a..d97e10ffb5e5 100644
--- a/science/agrum/pkg-plist
+++ b/science/agrum/pkg-plist
@@ -136,6 +136,7 @@ include/agrum/BN/io/net/netReader.h
include/agrum/BN/io/net/netReader_tpl.h
include/agrum/BN/io/net/netWriter.h
include/agrum/BN/io/net/netWriter_tpl.h
+include/agrum/BN/io/xml/XmlDocument.h
include/agrum/BN/learning/BNLearnUtils/BNLearnerListener.h
include/agrum/BN/learning/BNLearnUtils/IBNLearner.h
include/agrum/BN/learning/BNLearnUtils/IBNLearner_inl.h
@@ -210,18 +211,6 @@ include/agrum/BN/learning/paramUtils/paramEstimator_inl.h
include/agrum/BN/learning/paramUtils/paramEstimator_tpl.h
include/agrum/BN/learning/priors/DirichletPriorFromBN.h
include/agrum/BN/learning/priors/DirichletPriorFromBN_tpl.h
-include/agrum/BN/learning/priors/DirichletPriorFromDatabase.h
-include/agrum/BN/learning/priors/DirichletPriorFromDatabase_inl.h
-include/agrum/BN/learning/priors/K2Prior.h
-include/agrum/BN/learning/priors/K2Prior_inl.h
-include/agrum/BN/learning/priors/bdeuPrior.h
-include/agrum/BN/learning/priors/bdeuPrior_inl.h
-include/agrum/BN/learning/priors/noPrior.h
-include/agrum/BN/learning/priors/noPrior_inl.h
-include/agrum/BN/learning/priors/prior.h
-include/agrum/BN/learning/priors/prior_inl.h
-include/agrum/BN/learning/priors/smoothingPrior.h
-include/agrum/BN/learning/priors/smoothingPrior_inl.h
include/agrum/BN/learning/scores/score.h
include/agrum/BN/learning/scores/scoreAIC.h
include/agrum/BN/learning/scores/scoreAIC_inl.h
@@ -400,6 +389,21 @@ include/agrum/ID/io/IDReader.h
include/agrum/ID/io/IDReader_tpl.h
include/agrum/ID/io/IDWriter.h
include/agrum/ID/io/IDWriter_tpl.h
+include/agrum/KTBN/KTBN.h
+include/agrum/KTBN/KTBN_inl.h
+include/agrum/KTBN/KTBN_tpl.h
+include/agrum/KTBN/database/KTBNDatabaseGenerator.h
+include/agrum/KTBN/database/KTBNDatabaseGenerator_tpl.h
+include/agrum/KTBN/generator/KTBNGenerator.h
+include/agrum/KTBN/generator/KTBNGenerator_tpl.h
+include/agrum/KTBN/inference/KTBNInference.h
+include/agrum/KTBN/inference/KTBNInference_tpl.h
+include/agrum/KTBN/learning/IKTBNLearner.h
+include/agrum/KTBN/learning/IKTBNLearner_tpl.h
+include/agrum/KTBN/learning/KTBNAdaptiveLearner.h
+include/agrum/KTBN/learning/KTBNAdaptiveLearner_tpl.h
+include/agrum/KTBN/learning/KTBNLearner.h
+include/agrum/KTBN/learning/KTBNLearner_tpl.h
include/agrum/MRF/IMarkovRandomField.h
include/agrum/MRF/IMarkovRandomField_tpl.h
include/agrum/MRF/MarkovRandomField.h
@@ -998,6 +1002,18 @@ include/agrum/base/stattests/independenceTest_inl.h
include/agrum/base/stattests/independenceTest_tpl.h
include/agrum/base/stattests/kNML.h
include/agrum/base/stattests/kNML_inl.h
+include/agrum/base/stattests/priors/DirichletPriorFromDatabase.h
+include/agrum/base/stattests/priors/DirichletPriorFromDatabase_inl.h
+include/agrum/base/stattests/priors/K2Prior.h
+include/agrum/base/stattests/priors/K2Prior_inl.h
+include/agrum/base/stattests/priors/bdeuPrior.h
+include/agrum/base/stattests/priors/bdeuPrior_inl.h
+include/agrum/base/stattests/priors/noPrior.h
+include/agrum/base/stattests/priors/noPrior_inl.h
+include/agrum/base/stattests/priors/prior.h
+include/agrum/base/stattests/priors/prior_inl.h
+include/agrum/base/stattests/priors/smoothingPrior.h
+include/agrum/base/stattests/priors/smoothingPrior_inl.h
include/agrum/base/stattests/pseudoCount.h
include/agrum/base/stattests/pseudoCount_inl.h
include/agrum/base/stattests/recordCounter.h
@@ -1033,6 +1049,7 @@ include/agrum/cm.h
include/agrum/cn.h
include/agrum/config.h
include/agrum/id.h
+include/agrum/ktbn.h
include/agrum/mrf.h
lib/cmake/aGrUM/aGrUMConfig.cmake
lib/cmake/aGrUM/aGrUMConfigVersion.cmake
@@ -1049,6 +1066,8 @@ lib/cmake/aGrUM/agrumFMDP-targets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/aGrUM/agrumFMDP-targets.cmake
lib/cmake/aGrUM/agrumID-targets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/aGrUM/agrumID-targets.cmake
+lib/cmake/aGrUM/agrumKTBN-targets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/aGrUM/agrumKTBN-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
@@ -1071,110 +1090,132 @@ lib/libagrumFMDP.so.%%VERSION%%
lib/libagrumID.so
lib/libagrumID.so.3
lib/libagrumID.so.%%VERSION%%
+lib/libagrumKTBN.so
+lib/libagrumKTBN.so.3
+lib/libagrumKTBN.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
-%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/METADATA
-%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/WHEEL
-%%PYTHON_SITELIBDIR%%/pyagrum/__init__.py
-%%PYTHON_SITELIBDIR%%/pyagrum/_pyagrum.so
-%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/BNMInference.py
-%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/BNMLearning.py
-%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/BNMixture.py
-%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/__init__.py
-%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/notebook.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causal/__init__.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causal/notebook.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_CausalEffectEstimation.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_IVEstimators.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_RCTEstimators.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/__init__.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_backdoorEstimators.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_causalBNEstimator.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_frontdoorEstimators.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_learners.py
-%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_utils.py
-%%PYTHON_SITELIBDIR%%/pyagrum/clg/CLG.py
-%%PYTHON_SITELIBDIR%%/pyagrum/clg/GaussianVariable.py
-%%PYTHON_SITELIBDIR%%/pyagrum/clg/SEM.py
-%%PYTHON_SITELIBDIR%%/pyagrum/clg/__init__.py
-%%PYTHON_SITELIBDIR%%/pyagrum/clg/canonicalForm.py
-%%PYTHON_SITELIBDIR%%/pyagrum/clg/forwardSampling.py
-%%PYTHON_SITELIBDIR%%/pyagrum/clg/learning.py
-%%PYTHON_SITELIBDIR%%/pyagrum/clg/notebook.py
-%%PYTHON_SITELIBDIR%%/pyagrum/clg/variableElimination.py
-%%PYTHON_SITELIBDIR%%/pyagrum/common.py
-%%PYTHON_SITELIBDIR%%/pyagrum/config.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CIM.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CTBN.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CTBNGenerator.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CTBNInference.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/CTBNLearner.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/SamplesStats.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/StatsIndepTest.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/__init__.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/constants.py
-%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/notebook.py
-%%PYTHON_SITELIBDIR%%/pyagrum/defaults.ini
-%%PYTHON_SITELIBDIR%%/pyagrum/deprecated.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ComputationCausal.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ComputationConditional.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ComputationMarginal.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_CustomShapleyCache.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_Explainer.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_Explanation.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_FIFOCache.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallCausalValues.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallConditionalValues.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallMarginalValues.py
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-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShapConditionalValues.py
-%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShapMarginalValues.py
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-%%PYTHON_SITELIBDIR%%/pyagrum/lib/ipython.py
-%%PYTHON_SITELIBDIR%%/pyagrum/lib/jt2graph.py
-%%PYTHON_SITELIBDIR%%/pyagrum/lib/mrf2graph.py
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-%%PYTHON_SITELIBDIR%%/pyagrum/skbn/_learningMethods.py
-%%PYTHON_SITELIBDIR%%/pyagrum/skbn/_utils.py
-%%PYTHON_SITELIBDIR%%/pyagrum/skbn/bnclassifier.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSE.md
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSES/LGPL-3.0-or-later.txt
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/LICENSES/MIT.txt
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/METADATA
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum-%%VERSION%%.dist-info/WHEEL
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/_pyagrumcpp.so
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/BNMInference.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/BNMLearning.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/BNMixture.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/bnmixture/notebook.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causal/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causal/notebook.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_CausalEffectEstimation.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_IVEstimators.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_RCTEstimators.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_backdoorEstimators.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_causalBNEstimator.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_frontdoorEstimators.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_learners.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causalEffectEstimation/_utils.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causal_model/__init__.py
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+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/causal_model/cmcpp.py
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+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/clg/GaussianVariable.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/clg/SEM.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/clg/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/clg/canonicalForm.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/clg/forwardSampling.py
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+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/common.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/config.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/credal_net/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/credal_net/_cncpp.so
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+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/StatsIndepTest.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/constants.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/ctbn/notebook.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/defaults.ini
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/deprecated.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ComputationCausal.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ComputationConditional.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ComputationMarginal.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_CustomShapleyCache.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_Explainer.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_Explanation.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_FIFOCache.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallCausalValues.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallConditionalValues.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallMarginalValues.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pyagrum/explain/_ShallValues.py
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libdata/pkgconfig/agrum.pc