git: 0c2c029ec6e0 - main - misc/py-xgboost: update 3.1.3 → 3.4.1

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sat, 19 Sep 2026 22:43:12 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=0c2c029ec6e0f64ef197b5a60ef11d25696d8fd9

commit 0c2c029ec6e0f64ef197b5a60ef11d25696d8fd9
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-09-19 22:34:34 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-09-19 22:42:25 +0000

    misc/py-xgboost: update 3.1.3 → 3.4.1
---
 misc/py-xgboost/Makefile                   | 38 +++++++++----
 misc/py-xgboost/distinfo                   |  6 +--
 misc/py-xgboost/files/patch-CMakeLists.txt | 85 ++++++++----------------------
 3 files changed, 53 insertions(+), 76 deletions(-)

diff --git a/misc/py-xgboost/Makefile b/misc/py-xgboost/Makefile
index 316a2adfd0d7..74675c2807b9 100644
--- a/misc/py-xgboost/Makefile
+++ b/misc/py-xgboost/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=	xgboost
 DISTVERSIONPREFIX=	v
-DISTVERSION=	3.1.3
-PORTREVISION=	2
+DISTVERSION=	3.4.1
 CATEGORIES=	misc # machine-learning
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
@@ -16,15 +15,25 @@ BROKEN_armv7=	compilation fails due to type conversion issues, like on i386, but
 BROKEN_i386=	compilation fails, see https://github.com/dmlc/xgboost/issues/10002
 
 BUILD_DEPENDS=	cmake:devel/cmake-core \
-		${PYTHON_PKGNAMEPREFIX}hatchling>=1.12.1:devel/py-hatchling@${PY_FLAVOR}
+		${PYTHON_PKGNAMEPREFIX}scikit-build-core>=0.11.0:devel/py-scikit-build-core@${PY_FLAVOR}
 LIB_DEPENDS=	libdmlc.so:devel/dmlc-core
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR}
-RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}pandas>=1.2:math/py-pandas@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}pyarrow>0:databases/py-pyarrow@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR}
+		${PYTHON_PKGNAMEPREFIX}scikit-learn>=0:science/py-scikit-learn@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>=0:science/py-scipy@${PY_FLAVOR}
+RUN_DEPENDS_dask=	\
+		${PYTHON_PKGNAMEPREFIX}dask>0:devel/py-dask@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}distributed>0:devel/py-distributed@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR}
+RUN_DEPENDS_plotting=	\
+		${PYTHON_PKGNAMEPREFIX}graphviz>0:graphics/py-graphviz@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>=2.1.0:math/py-matplotlib@${PY_FLAVOR}
+RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}pandas>=1.2:math/py-pandas@${PY_FLAVOR}
+RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR}
+RUN_DEPENDS+=	${RUN_DEPENDS_dask}
+RUN_DEPENDS+=	${RUN_DEPENDS_plotting}
+TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}loky>0:devel/py-loky@${PY_FLAVOR}
 
-USES=		compiler:c11 python localbase:ldflags
+USES=		compiler:c++17-lang python:3.12+ localbase:ldflags
 USE_PYTHON=	pep517 autoplist pytest
 USE_LDCONFIG=	yes
 
@@ -32,15 +41,24 @@ USE_GITHUB=	yes
 GH_ACCOUNT=	dmlc
 
 WRKSRC_SUBDIR=	python-package
-
 LDFLAGS+=	-lexecinfo \
 		-ldmlc
 
 PYDISTUTILS_INSTALLARGS=	--use-system-libxgboost # this is ignored so that setup.py has to be patched, see https://github.com/dmlc/xgboost/issues/6879
 
-TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
+TEST_ENV=	${MAKE_ENV} \
+		LD_LIBRARY_PATH=/lib \
+		PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
+TEST_ARGS=	--disable-plugin-autoload \
+		--deselect=python/test_tracker.py::test_rank_assignment \
+		--deselect=python/test_updaters.py::TestTreeMethod::test_approx
 TEST_WRKSRC=	${WRKSRC}/../tests/python
 
+do-test:
+	@${MKDIR} ${WRKDIR}/.bin
+	@${LN} -sf ${PYTHON_CMD} ${WRKDIR}/.bin/python
+	cd ${WRKSRC}/.. && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -c 'import ctypes, pytest, sys; raise SystemExit(pytest.main(sys.argv[1:] + ["--ignore=tests/python/test_with_arrow.py", "tests/python"]))' ${TEST_ARGS}
+
 post-install:
 	@${PYTHON_CMD} -m compileall -d ${PYTHON_SITELIBDIR} ${STAGEDIR}${PYTHON_SITELIBDIR}
 	@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/xgboost/lib/libxgboost.so
diff --git a/misc/py-xgboost/distinfo b/misc/py-xgboost/distinfo
index d44192f5a83a..efa72d38afe2 100644
--- a/misc/py-xgboost/distinfo
+++ b/misc/py-xgboost/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1768210996
-SHA256 (dmlc-xgboost-v3.1.3_GH0.tar.gz) = 17c545f43ca543979dcafdfeb4921240ba3673d1464ec4c2f592733af12ad578
-SIZE (dmlc-xgboost-v3.1.3_GH0.tar.gz) = 2388327
+TIMESTAMP = 1789676928
+SHA256 (dmlc-xgboost-v3.4.1_GH0.tar.gz) = cb3a0c786144025acf5b1ff48c81198aa2124813e677cbdda9f2f6271a5dbc1a
+SIZE (dmlc-xgboost-v3.4.1_GH0.tar.gz) = 2449877
diff --git a/misc/py-xgboost/files/patch-CMakeLists.txt b/misc/py-xgboost/files/patch-CMakeLists.txt
index 10ec5aecd063..106656a01f35 100644
--- a/misc/py-xgboost/files/patch-CMakeLists.txt
+++ b/misc/py-xgboost/files/patch-CMakeLists.txt
@@ -1,67 +1,26 @@
---- ../CMakeLists.txt.orig	2026-01-08 13:54:31 UTC
+-- Build against the system dmlc-core package instead of the bundled
+-- submodule. XGBoost 3.4.1 gained an option for this, but the default still
+-- expects the missing submodule and one upstream typo links against a
+-- non-existent variable instead of the imported dmlc::dmlc CMake target.
+--- ../CMakeLists.txt.orig
 +++ ../CMakeLists.txt
-@@ -162,11 +162,11 @@ endif()
- if(PLUGIN_RMM AND NOT (CMAKE_SYSTEM_NAME STREQUAL "Linux"))
-   message(SEND_ERROR "`PLUGIN_RMM` must be used with Linux.")
- endif()
--if(ENABLE_ALL_WARNINGS)
--  if((NOT CMAKE_CXX_COMPILER_ID MATCHES "Clang") AND (NOT CMAKE_CXX_COMPILER_ID STREQUAL "GNU"))
--    message(SEND_ERROR "ENABLE_ALL_WARNINGS is only available for Clang and GCC.")
--  endif()
--endif()
-+#if(ENABLE_ALL_WARNINGS)
-+#  if((NOT CMAKE_CXX_COMPILER_ID MATCHES "Clang") AND (NOT CMAKE_CXX_COMPILER_ID STREQUAL "GNU"))
-+#    message(SEND_ERROR "ENABLE_ALL_WARNINGS is only available for Clang and GCC.")
-+#  endif()
-+#endif()
- if(BUILD_STATIC_LIB AND (R_LIB OR JVM_BINDINGS))
-   message(SEND_ERROR "Cannot build a static library libxgboost.a when R or JVM packages are enabled.")
- endif()
-@@ -289,7 +289,7 @@ set(DMLC_FORCE_SHARED_CRT ${FORCE_SHARED_CRT})
- 
- # dmlc-core
- set(DMLC_FORCE_SHARED_CRT ${FORCE_SHARED_CRT})
--add_subdirectory(${xgboost_SOURCE_DIR}/dmlc-core)
-+#add_subdirectory(${xgboost_SOURCE_DIR}/dmlc-core)
- 
- if(MSVC)
-   if(TARGET dmlc_unit_tests)
-@@ -302,7 +302,7 @@ add_subdirectory(${xgboost_SOURCE_DIR}/src)
- 
+@@ -54,7 +54,7 @@
+ option(BUILD_DEPRECATED_CLI "Build the deprecated command line interface" OFF)
+ option(FORCE_SHARED_CRT "Build with dynamic CRT on Windows (/MD)" OFF)
+ option(BUILD_WITH_GIT_HASH "Add a short git hash to the build info." OFF)
+-option(BUILD_WITH_SYSTEM_DMLC "Use system package for dmlc." OFF)
++option(BUILD_WITH_SYSTEM_DMLC "Use system package for dmlc." ON)
+ ## Bindings
+ option(JVM_BINDINGS "Build JVM bindings" OFF)
+ option(R_LIB "Build shared library for R package" OFF)
+@@ -323,8 +323,8 @@
  # core xgboost
  add_subdirectory(${xgboost_SOURCE_DIR}/src)
--target_link_libraries(objxgboost PUBLIC dmlc)
-+#target_link_libraries(objxgboost PUBLIC dmlc)
- 
- # Link -lstdc++fs for GCC 8.x
- if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS "9.0")
-@@ -391,7 +391,7 @@ if(BUILD_DEPRECATED_CLI)
-   target_include_directories(runxgboost
-     PRIVATE
-     ${xgboost_SOURCE_DIR}/include
--    ${xgboost_SOURCE_DIR}/dmlc-core/include
-+    #${xgboost_SOURCE_DIR}/dmlc-core/include
-   )
-   set_target_properties(runxgboost PROPERTIES OUTPUT_NAME xgboost)
-   xgboost_target_properties(runxgboost)
-@@ -407,7 +407,7 @@ endif()
- #-- End CLI for xgboost
- 
- # Common setup for all targets
--foreach(target xgboost objxgboost dmlc)
-+foreach(target xgboost objxgboost)
-   xgboost_target_properties(${target})
-   xgboost_target_link_libraries(${target})
-   xgboost_target_defs(${target})
-@@ -469,9 +469,9 @@ if(BUILD_STATIC_LIB)
- # https://github.com/dmlc/xgboost/issues/6085
- if(BUILD_STATIC_LIB)
-   if(BUILD_DEPRECATED_CLI)
--    set(INSTALL_TARGETS xgboost runxgboost objxgboost dmlc)
-+    set(INSTALL_TARGETS xgboost runxgboost objxgboost)
-   else()
--    set(INSTALL_TARGETS xgboost objxgboost dmlc)
-+    set(INSTALL_TARGETS xgboost objxgboost)
-   endif()
+ # dmlc-core
+-if(BUILD_WTIH_SYSTEM_DMLC)
+-  target_link_libraries(objxgboost PUBLIC ${dmlc-LIBRARIES})
++if(BUILD_WITH_SYSTEM_DMLC)
++  target_link_libraries(objxgboost PUBLIC dmlc::dmlc)
  else()
-   if(BUILD_DEPRECATED_CLI)
+   target_link_libraries(objxgboost PUBLIC dmlc)
+ endif()