diff --git a/sci-libs/onnxruntime/Manifest b/sci-libs/onnxruntime/Manifest
index 60caa90f41..a75478f1a9 100644
--- a/sci-libs/onnxruntime/Manifest
+++ b/sci-libs/onnxruntime/Manifest
@@ -1,4 +1,3 @@
 DIST eigen-3.4.0_p20250216.tar.bz2 2272941 BLAKE2B c86764a5c31b978d09f9f8f458a982fb16c2cdfd053e0c7a371fbe5b9c64bead42c25fb7d4cb795eb5ee7ff1800bb51fac6783ad0881dd69dee5d463ccd213e3 SHA512 3c9fab41bde1ee4b8f5ba21c991a75cc73e104cdb48f3377b5fc51afae8cbb5e891c39e4fd998c5263178a8962b09d9d907b9d125dfddc50bc2ec5171917d6b8
-DIST onnxruntime-1.25.1.tar.gz 284862475 BLAKE2B 82667031281285474feda951fe153c8000a2d4ed9ad4ee4f1ef8ee41f8334f0462608f938ca15f93a3369860a5078eb89b7ceeee791dcea23468b8d469e9122c SHA512 df760e30f1027b024d5a67aa3f36a6508609a58acc37e5e1066f919eaa42f9568c1c8218fbc80eeee0b9ec10307ea4778575b9ed3a1b312690f394b35d036e61
 DIST onnxruntime-1.26.0.tar.gz 285128576 BLAKE2B 825f73cf8aa5ecb185f7e77e825e78906666ddc6f194f4034e5443900e9d8e90b20173b0ba33c37b80650658e589078dad6f7c6c7c86ff5247bc797f4d4aa952 SHA512 14d629a14eb2161178c6babe49ed8a3adb15e8c6d26adc4c975261f9b5d43674e8a85bc4dbeb05a87917291d44b056140a1ac5a1c70ed80d92cb3f38cc670ebd
 DIST onnxruntime-1.27.0.tar.gz 285714570 BLAKE2B 2c25873f92ee144a567b5fdf745327c8f5c7c42010565db1d26856115dc2345c6b3304e235a17990e30278e30c4986b5d078688f64006f64f74c25927ceb75f6 SHA512 578ccf5321233bc65252b0bbfceaee183abc06175039fd6e0d044af0a4ae43b424c6f71c97b8e5bc6adb9992982d79e397eb4884f0370b4083b3b37d539a404d
diff --git a/sci-libs/onnxruntime/files/onnxruntime-1.24.3-use-system-libraries.patch b/sci-libs/onnxruntime/files/onnxruntime-1.24.3-use-system-libraries.patch
deleted file mode 100644
index 13a01a0dc0..0000000000
--- a/sci-libs/onnxruntime/files/onnxruntime-1.24.3-use-system-libraries.patch
+++ /dev/null
@@ -1,234 +0,0 @@
-From: Pavel Sobolev <contact@paveloom.dev>
-Subject: [PATCH] Use system libraries.
-
-Everything, except for Eigen3.
-
-Signed-off-by: Pavel Sobolev <contact@paveloom.dev>
-
---- a/cmake/external/abseil-cpp.cmake
-+++ b/cmake/external/abseil-cpp.cmake
-@@ -41,7 +41,7 @@ onnxruntime_fetchcontent_declare(
-     URL_HASH SHA1=${DEP_SHA1_abseil_cpp}
-     EXCLUDE_FROM_ALL
-     PATCH_COMMAND ${ABSL_PATCH_COMMAND}
--    FIND_PACKAGE_ARGS 20250814 NAMES absl
-+    FIND_PACKAGE_ARGS NAMES absl REQUIRED
- )
- 
- onnxruntime_fetchcontent_makeavailable(abseil_cpp)
---- a/cmake/external/onnxruntime_external_deps.cmake
-+++ b/cmake/external/onnxruntime_external_deps.cmake
-@@ -43,7 +43,7 @@ onnxruntime_fetchcontent_declare(
-     URL ${DEP_URL_re2}
-     URL_HASH SHA1=${DEP_SHA1_re2}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS NAMES re2
-+    FIND_PACKAGE_ARGS NAMES re2 REQUIRED
- )
- onnxruntime_fetchcontent_makeavailable(re2)
- 
-@@ -71,7 +71,7 @@ if (onnxruntime_BUILD_UNIT_TESTS)
-     URL ${DEP_URL_googletest}
-     URL_HASH SHA1=${DEP_SHA1_googletest}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS 1.14.0...<2.0.0 NAMES GTest
-+    FIND_PACKAGE_ARGS 1.14.0...<2.0.0 NAMES GTest REQUIRED
-   )
-   FetchContent_MakeAvailable(googletest)
- endif()
-@@ -87,7 +87,7 @@ if (onnxruntime_BUILD_BENCHMARKS)
-     URL ${DEP_URL_google_benchmark}
-     URL_HASH SHA1=${DEP_SHA1_google_benchmark}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS NAMES benchmark
-+    FIND_PACKAGE_ARGS NAMES benchmark REQUIRED
-   )
-   onnxruntime_fetchcontent_makeavailable(google_benchmark)
- endif()
-@@ -105,7 +105,7 @@ if(onnxruntime_USE_MIMALLOC)
-     URL ${DEP_URL_mimalloc}
-     URL_HASH SHA1=${DEP_SHA1_mimalloc}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS NAMES mimalloc
-+    FIND_PACKAGE_ARGS NAMES mimalloc REQUIRED
-   )
-   FetchContent_MakeAvailable(mimalloc)
- endif()
-@@ -199,7 +199,7 @@ onnxruntime_fetchcontent_declare(
-   URL_HASH SHA1=${DEP_SHA1_protobuf}
-   PATCH_COMMAND ${ONNXRUNTIME_PROTOBUF_PATCH_COMMAND}
-   EXCLUDE_FROM_ALL
--  FIND_PACKAGE_ARGS NAMES Protobuf protobuf
-+  FIND_PACKAGE_ARGS NAMES Protobuf protobuf REQUIRED
- )
- 
- set(protobuf_BUILD_TESTS OFF CACHE BOOL "Build protobuf tests" FORCE)
-@@ -274,7 +274,7 @@ onnxruntime_fetchcontent_declare(
-   URL ${DEP_URL_date}
-   URL_HASH SHA1=${DEP_SHA1_date}
-   EXCLUDE_FROM_ALL
--  FIND_PACKAGE_ARGS 3...<4 NAMES date
-+  FIND_PACKAGE_ARGS 3...<4 NAMES date REQUIRED
- )
- onnxruntime_fetchcontent_makeavailable(date)
- 
-@@ -288,12 +288,11 @@ if(NOT TARGET Boost::mp11)
-      mp11
-      URL ${DEP_URL_mp11}
-      EXCLUDE_FROM_ALL
--     FIND_PACKAGE_ARGS NAMES Boost
-+     FIND_PACKAGE_ARGS NAMES Boost REQUIRED
-     )
--    FetchContent_Populate(mp11)
-+    onnxruntime_fetchcontent_makeavailable(mp11)
-     if(NOT TARGET Boost::mp11)
--      add_library(Boost::mp11 IMPORTED INTERFACE)
--      target_include_directories(Boost::mp11 INTERFACE $<BUILD_INTERFACE:${mp11_SOURCE_DIR}/include>)
-+      add_library(Boost::mp11 ALIAS Boost::headers)
-     endif()
-   endif()
- endif()
-@@ -306,7 +305,7 @@ onnxruntime_fetchcontent_declare(
-     URL ${DEP_URL_json}
-     URL_HASH SHA1=${DEP_SHA1_json}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS 3.10 NAMES nlohmann_json
-+    FIND_PACKAGE_ARGS 3.10 NAMES nlohmann_json REQUIRED
- )
- onnxruntime_fetchcontent_makeavailable(nlohmann_json)
- 
-@@ -372,7 +371,7 @@ if (CPUINFO_SUPPORTED)
-         ${Patch_EXECUTABLE} -p1 < ${PROJECT_SOURCE_DIR}/patches/cpuinfo/patch_vcpkg_arm64ec_support.patch &&
-         # https://github.com/pytorch/cpuinfo/pull/348
-         ${Patch_EXECUTABLE} -p1 < ${PROJECT_SOURCE_DIR}/patches/cpuinfo/win_arm_fp16_detection_fallback.patch
--      FIND_PACKAGE_ARGS NAMES cpuinfo
-+      FIND_PACKAGE_ARGS NAMES cpuinfo REQUIRED
-     )
-   else()
-     onnxruntime_fetchcontent_declare(
-@@ -380,7 +379,7 @@ if (CPUINFO_SUPPORTED)
-       URL ${DEP_URL_pytorch_cpuinfo}
-       URL_HASH SHA1=${DEP_SHA1_pytorch_cpuinfo}
-       EXCLUDE_FROM_ALL
--      FIND_PACKAGE_ARGS NAMES cpuinfo
-+      FIND_PACKAGE_ARGS NAMES cpuinfo REQUIRED
-     )
-   endif()
-   set(ONNXRUNTIME_CPUINFO_PROJ pytorch_cpuinfo)
-@@ -398,7 +397,7 @@ if(onnxruntime_USE_CUDA)
-     URL_HASH SHA1=${DEP_SHA1_microsoft_gsl}
-     PATCH_COMMAND ${Patch_EXECUTABLE} --binary --ignore-whitespace -p1 < ${PROJECT_SOURCE_DIR}/patches/gsl/1064.patch
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS 4.0 NAMES Microsoft.GSL
-+    FIND_PACKAGE_ARGS 4.0 NAMES Microsoft.GSL REQUIRED
-   )
- else()
-   onnxruntime_fetchcontent_declare(
-@@ -406,7 +405,7 @@ else()
-     URL ${DEP_URL_microsoft_gsl}
-     URL_HASH SHA1=${DEP_SHA1_microsoft_gsl}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS 4.0 NAMES Microsoft.GSL
-+    FIND_PACKAGE_ARGS 4.0 NAMES Microsoft.GSL REQUIRED
-   )
- endif()
- set(GSL_TARGET "Microsoft.GSL::GSL")
-@@ -420,7 +419,7 @@ if (NOT GSL_FOUND AND NOT onnxruntime_BUILD_SHARED_LIB)
-   RUNTIME  DESTINATION ${CMAKE_INSTALL_BINDIR})
- endif()
- 
--find_path(safeint_SOURCE_DIR NAMES "SafeInt.hpp")
-+find_path(safeint_SOURCE_DIR NAMES "SafeInt.hpp" REQUIRED)
- if(NOT safeint_SOURCE_DIR)
-   unset(safeint_SOURCE_DIR)
-   onnxruntime_fetchcontent_declare(
-@@ -462,10 +461,14 @@ onnxruntime_fetchcontent_declare(
-     URL_HASH SHA1=${DEP_SHA1_flatbuffers}
-     PATCH_COMMAND ${ONNXRUNTIME_FLATBUFFERS_PATCH_COMMAND}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS 23.5.9 NAMES Flatbuffers flatbuffers
-+    FIND_PACKAGE_ARGS 23.5.9 NAMES Flatbuffers flatbuffers REQUIRED
- )
- 
- onnxruntime_fetchcontent_makeavailable(flatbuffers)
-+if(TARGET flatbuffers::flatbuffers_shared AND NOT TARGET flatbuffers::flatbuffers)
-+  message(STATUS "Aliasing flatbuffers::flatbuffers to flatbuffers::flatbuffers_shared")
-+  add_library(flatbuffers::flatbuffers ALIAS flatbuffers::flatbuffers_shared)
-+endif()
- if(NOT flatbuffers_FOUND)
-   if(NOT TARGET flatbuffers::flatbuffers)
-     add_library(flatbuffers::flatbuffers ALIAS flatbuffers)
-@@ -527,7 +530,7 @@ onnxruntime_fetchcontent_declare(
-   URL_HASH SHA1=${DEP_SHA1_onnx}
-   PATCH_COMMAND ${ONNXRUNTIME_ONNX_PATCH_COMMAND}
-   EXCLUDE_FROM_ALL
--  FIND_PACKAGE_ARGS NAMES ONNX onnx
-+  FIND_PACKAGE_ARGS NAMES ONNX onnx REQUIRED
- )
- 
- onnxruntime_fetchcontent_makeavailable(onnx)
-@@ -602,7 +605,7 @@ if(onnxruntime_ENABLE_DLPACK)
-     URL ${DEP_URL_dlpack}
-     URL_HASH SHA1=${DEP_SHA1_dlpack}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS NAMES dlpack
-+    FIND_PACKAGE_ARGS NAMES dlpack REQUIRED
-   )
-   onnxruntime_fetchcontent_makeavailable(dlpack)
- endif()
-@@ -615,7 +618,7 @@ if(onnxruntime_ENABLE_TRAINING OR (onnxruntime_ENABLE_TRAINING_APIS AND onnxrunt
-     URL ${DEP_URL_cxxopts}
-     URL_HASH SHA1=${DEP_SHA1_cxxopts}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS NAMES cxxopts
-+    FIND_PACKAGE_ARGS NAMES cxxopts REQUIRED
-   )
-   set(CXXOPTS_BUILD_EXAMPLES OFF CACHE BOOL "" FORCE)
-   set(CXXOPTS_BUILD_TESTS OFF CACHE BOOL "" FORCE)
---- a/cmake/external/pybind11.cmake
-+++ b/cmake/external/pybind11.cmake
-@@ -6,6 +6,6 @@ onnxruntime_fetchcontent_declare(
-     URL ${DEP_URL_pybind11}
-     URL_HASH SHA1=${DEP_SHA1_pybind11}
-     EXCLUDE_FROM_ALL
--    FIND_PACKAGE_ARGS 3.0 NAMES pybind11
-+    FIND_PACKAGE_ARGS 3.0 NAMES pybind11 REQUIRED
- )
- onnxruntime_fetchcontent_makeavailable(pybind11_project)
---- a/cmake/external/wil.cmake
-+++ b/cmake/external/wil.cmake
-@@ -8,7 +8,7 @@ onnxruntime_fetchcontent_declare(
-   URL ${DEP_URL_microsoft_wil}
-   URL_HASH SHA1=${DEP_SHA1_microsoft_wil}
-   EXCLUDE_FROM_ALL
--  FIND_PACKAGE_ARGS NAMES wil
-+  FIND_PACKAGE_ARGS NAMES wil REQUIRED
- )
- 
- if(WIN32)
---- a/cmake/external/xnnpack.cmake
-+++ b/cmake/external/xnnpack.cmake
-@@ -17,11 +17,11 @@ if(CMAKE_ANDROID_ARCH_ABI STREQUAL armeabi-v7a)
- endif()
- 
- # pthreadpool depends on fxdiv
--onnxruntime_fetchcontent_declare(fxdiv URL ${DEP_URL_fxdiv} URL_HASH SHA1=${DEP_SHA1_fxdiv} EXCLUDE_FROM_ALL FIND_PACKAGE_ARGS NAMES fxdiv)
-+onnxruntime_fetchcontent_declare(fxdiv URL ${DEP_URL_fxdiv} URL_HASH SHA1=${DEP_SHA1_fxdiv} EXCLUDE_FROM_ALL FIND_PACKAGE_ARGS NAMES fxdiv REQUIRED)
- onnxruntime_fetchcontent_makeavailable(fxdiv)
- set(FXDIV_SOURCE_DIR ${fxdiv_SOURCE_DIR})
- 
--onnxruntime_fetchcontent_declare(pthreadpool URL ${DEP_URL_pthreadpool} URL_HASH SHA1=${DEP_SHA1_pthreadpool} EXCLUDE_FROM_ALL FIND_PACKAGE_ARGS NAMES unofficial-pthreadpool)
-+onnxruntime_fetchcontent_declare(pthreadpool URL ${DEP_URL_pthreadpool} URL_HASH SHA1=${DEP_SHA1_pthreadpool} EXCLUDE_FROM_ALL FIND_PACKAGE_ARGS NAMES unofficial-pthreadpool REQUIRED)
- onnxruntime_fetchcontent_makeavailable(pthreadpool)
- 
- # ---  Determine target processor
-@@ -84,7 +84,7 @@ endif()
- onnxruntime_fetchcontent_declare(googlexnnpack URL ${DEP_URL_googlexnnpack} URL_HASH SHA1=${DEP_SHA1_googlexnnpack}
-                      PATCH_COMMAND ${Patch_EXECUTABLE} --binary --ignore-whitespace -p1 < ${PROJECT_SOURCE_DIR}/patches/xnnpack/AddEmscriptenAndIosSupport.patch
- 		     EXCLUDE_FROM_ALL
--		     FIND_PACKAGE_ARGS NAMES xnnpack
-+		     FIND_PACKAGE_ARGS NAMES xnnpack REQUIRED
-                     )
- onnxruntime_fetchcontent_makeavailable(googlexnnpack)
- set(XNNPACK_DIR ${googlexnnpack_SOURCE_DIR})
-
diff --git a/sci-libs/onnxruntime/onnxruntime-1.25.1.ebuild b/sci-libs/onnxruntime/onnxruntime-1.25.1.ebuild
deleted file mode 100644
index c313c4c995..0000000000
--- a/sci-libs/onnxruntime/onnxruntime-1.25.1.ebuild
+++ /dev/null
@@ -1,148 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{12..14} )
-
-inherit cmake edo flag-o-matic python-r1
-
-EIGEN_COMMIT="1d8b82b0740839c0de7f1242a3585e3390ff5f33"
-
-DESCRIPTION="Cross-platform, high performance ML inferencing and training accelerator"
-HOMEPAGE="
-	https://onnxruntime.ai
-	https://github.com/microsoft/onnxruntime
-"
-SRC_URI="
-	https://github.com/microsoft/onnxruntime/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz
-	https://gitlab.com/libeigen/eigen/-/archive/${EIGEN_COMMIT}/eigen-${EIGEN_COMMIT}.tar.bz2 ->
-		eigen-3.4.0_p20250216.tar.bz2
-"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="python test"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	dev-cpp/abseil-cpp:=
-	dev-libs/cpuinfo
-	dev-libs/protobuf:=
-	dev-libs/re2:=
-	sci-ml/onnx[disableStaticReg]
-
-	python? (
-		${PYTHON_DEPS}
-		dev-python/coloredlogs[${PYTHON_USEDEP}]
-		dev-python/flatbuffers[${PYTHON_USEDEP}]
-		>=dev-python/numpy-2[${PYTHON_USEDEP}]
-		dev-python/packaging[${PYTHON_USEDEP}]
-		dev-python/protobuf[${PYTHON_USEDEP}]
-		dev-python/sympy[${PYTHON_USEDEP}]
-	)
-"
-DEPEND="
-	${RDEPEND}
-	dev-cpp/ms-gsl
-	dev-cpp/nlohmann_json
-	dev-cpp/safeint
-	dev-libs/boost
-	dev-libs/date
-	dev-libs/flatbuffers
-
-	python? (
-		dev-python/pybind11[${PYTHON_USEDEP}]
-		sci-libs/dlpack
-	)
-"
-BDEPEND="
-	${PYTHON_DEPS}
-
-	test? (
-		dev-cpp/gtest
-
-		python? ( dev-python/pytest[${PYTHON_USEDEP}] )
-	)
-"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-1.22.2-relax-the-dependency-on-flatbuffers.patch"
-	"${FILESDIR}/${PN}-1.24.3-use-system-libraries.patch"
-	"${FILESDIR}/${PN}-1.24.4-no-werror.patch"
-)
-
-CMAKE_USE_DIR="${S}/cmake"
-
-src_configure() {
-	# Python is used at build time unconditionally
-	python_setup
-
-	local mycmakeargs=(
-		-Donnxruntime_BUILD_SHARED_LIB=on
-
-		-Donnxruntime_BUILD_UNIT_TESTS=$(usex test)
-		-Donnxruntime_ENABLE_PYTHON=$(usex python)
-
-		# This is required until a newer version of Eigen3 comes out
-		-DFETCHCONTENT_SOURCE_DIR_EIGEN3="${WORKDIR}/eigen-${EIGEN_COMMIT}"
-
-		# This makes it possible for `find_path` to find the `onnx-ml.proto` file
-		-DCMAKE_INCLUDE_PATH="$(python_get_sitedir)"
-
-		-Wno-dev
-	)
-
-	append-ldflags -Wl,-z,noexecstack
-	cmake_src_configure
-}
-
-# Adapted from `run_onnxruntime_tests` in `tools/ci_build/build.py`
-python_test() {
-	cd "${S}/cmake_build" || die
-	epytest --pyargs \
-		onnxruntime_test_python.py \
-		onnxruntime_test_python_backend.py \
-		onnxruntime_test_python_mlops.py \
-		onnxruntime_test_python_sparse_matmul.py
-}
-
-src_test() {
-	local -x GTEST_FILTER="*:-ActivationOpNoInfTest.Softsign:LayoutTransformationPotentiallyAddedOpsTests.OpsHaveLatestVersions"
-	cmake_src_test
-
-	if use python ; then
-		python_test
-	fi
-}
-
-# There is some custom logic in `setup.py`
-python_install() {
-	cd "${S}/cmake_build" || die
-	edo "${EPYTHON}" ../setup.py install \
-		--prefix="${EPREFIX}/usr" \
-		--root="${D}"
-
-	local libs=(
-		"libonnxruntime.so.${PV}"
-		"libonnxruntime_providers_shared.so"
-	)
-	for lib in "${libs[@]}"; do
-		ln -fsr "${ED}/usr/$(get_libdir)/${lib}" "${D}/$(python_get_sitedir)/onnxruntime/capi/${lib}" || die
-	done
-
-	rm -rf "${D}/$(python_get_sitedir)"/*.egg-info || die
-	python_optimize
-}
-
-src_install() {
-	cmake_src_install
-
-	if use python ; then
-		python_foreach_impl python_install
-	fi
-
-	dodoc "${S}/"{README.md,LICENSE}
-}