diff --git a/sdk_container/src/third_party/portage-stable/dev-python/cython/Manifest b/sdk_container/src/third_party/portage-stable/dev-python/cython/Manifest
index d4948a0948..204f84dc5f 100644
--- a/sdk_container/src/third_party/portage-stable/dev-python/cython/Manifest
+++ b/sdk_container/src/third_party/portage-stable/dev-python/cython/Manifest
@@ -1,3 +1 @@
-DIST cython-3.0.12.tar.gz 2757617 BLAKE2B 064549e36e03424065eab081b60e2761d198490cfd4d7836ea236b833ada3962e6ed42ba1710b33418f8a31ac282cdc156ceb544ee21be80ee34b7a3d3f6c7fb SHA512 c4e85596eeea444fae983d32ce8731cc5d0d612d1f96b998db3aa7946e8be151a7ea62c6df163d875111e306c870656b82a8468dd873cacf84c7bd5671a39bc3
-DIST cython-3.1.1.tar.gz 3175446 BLAKE2B 4a75df724e313220321b05b7839bd406e5e923eb860337b7819c31152859396e5bda65a0a06ace196839bed729e28e51a1349c178e615ba58cf9bc80dc706b0d SHA512 5c64b5d280b234d93d02e91ab22567342350671c605df30a3ac7b41b64e0605eb0aef7bc721f68d35d6048085eaa392cb0a803df32ca902e51e2009c987d962e
 DIST cython-3.1.2.tar.gz 3184825 BLAKE2B 8be6016f3e9a5a7db71fd1cab65424db1a1cd8e9d0118f01432964eb816135021f77542aff2b1f0fd2af8f657f952ebce2f420d7610ae37c6c6956f94e54a636 SHA512 c674027dae58377ea71d8d8b15601e6e0c80435807603251e685608218805fef2e6eac4bbebd3c50c319cd7da660ff9ce1a6daeb673eb40ce70bbfe7f0069600
diff --git a/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.0.12-r1.ebuild b/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.0.12-r1.ebuild
deleted file mode 100644
index 99a15f0d03..0000000000
--- a/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.0.12-r1.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_TESTED=( python3_{10..12} )
-PYTHON_COMPAT=( "${PYTHON_TESTED[@]}" pypy3 pypy3_11 python3_13 )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1 multiprocessing pypi toolchain-funcs
-
-DESCRIPTION="A Python to C compiler"
-HOMEPAGE="
-	https://cython.org/
-	https://github.com/cython/cython/
-	https://pypi.org/project/Cython/
-"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~alpha amd64 arm arm64 hppa ~loong ~m68k ~mips ppc ppc64 ~riscv ~s390 sparc x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-BDEPEND="
-	${RDEPEND}
-	test? (
-		$(python_gen_cond_dep '
-			<dev-python/numpy-2[${PYTHON_USEDEP}]
-		' "${PYTHON_TESTED[@]}")
-	)
-"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-0.29.22-spawn-multiprocessing.patch"
-	"${FILESDIR}/${PN}-0.29.23-test_exceptions-py310.patch"
-	"${FILESDIR}/${PN}-0.29.23-pythran-parallel-install.patch"
-)
-
-distutils_enable_sphinx docs \
-	dev-python/jinja2 \
-	dev-python/sphinx-issues \
-	dev-python/sphinx-tabs
-
-python_prepare_all() {
-	# Needs dev-python/pip and doesn't like 'externally-managed' (bug #927995)
-	rm tests/run/coverage_cmd_src_pkg_layout.srctree || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	# Python gets confused when it is in sys.path before build.
-	local -x PYTHONPATH=
-
-	distutils-r1_python_compile
-}
-
-python_test() {
-	if ! has "${EPYTHON/./_}" "${PYTHON_TESTED[@]}"; then
-		einfo "Skipping tests on ${EPYTHON} (xfail)"
-		return
-	fi
-
-	# Needed to avoid confusing cache tests
-	unset CYTHON_FORCE_REGEN
-
-	tc-export CC
-	"${PYTHON}" runtests.py \
-		-vv \
-		-j "$(makeopts_jobs)" \
-		--work-dir "${BUILD_DIR}"/tests \
-		--no-examples \
-		--no-code-style \
-		|| die "Tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	local DOCS=( CHANGES.rst README.rst ToDo.txt USAGE.txt )
-	distutils-r1_python_install_all
-}
diff --git a/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.1.1.ebuild b/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.1.1.ebuild
deleted file mode 100644
index 0d005e35cf..0000000000
--- a/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.1.1.ebuild
+++ /dev/null
@@ -1,125 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_FULLY_TESTED=( python3_{11..14} )
-PYTHON_TESTED=( "${PYTHON_FULLY_TESTED[@]}" pypy3_11 )
-PYTHON_COMPAT=( "${PYTHON_TESTED[@]}" python3_{13,14}t )
-PYTHON_REQ_USE="threads(+)"
-
-inherit distutils-r1 multiprocessing pypi toolchain-funcs
-
-DESCRIPTION="A Python to C compiler"
-HOMEPAGE="
-	https://cython.org/
-	https://github.com/cython/cython/
-	https://pypi.org/project/Cython/
-"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~alpha amd64 arm arm64 ~hppa ~loong ~m68k ~mips ppc ppc64 ~riscv ~s390 ~sparc x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
-IUSE="test test-full"
-RESTRICT="!test? ( test )"
-
-BDEPEND="
-	${RDEPEND}
-	test? (
-		test-full? (
-			$(python_gen_cond_dep '
-				dev-python/numpy[${PYTHON_USEDEP}]
-			' "${PYTHON_FULLY_TESTED[@]}")
-		)
-	)
-"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-0.29.22-spawn-multiprocessing.patch"
-	"${FILESDIR}/${PN}-0.29.23-pythran-parallel-install.patch"
-)
-
-distutils_enable_sphinx docs \
-	dev-python/jinja2 \
-	dev-python/sphinx-issues \
-	dev-python/sphinx-tabs
-
-python_compile() {
-	# Python gets confused when it is in sys.path before build.
-	local -x PYTHONPATH=
-
-	if use elibc_musl ; then
-		# Workaround for bug #925318
-		local -x LDFLAGS="${LDFLAGS} -Wl,-z,stack-size=2097152"
-	fi
-
-	distutils-r1_python_compile
-}
-
-python_test() {
-	# PYTHON_TESTED controls whether we expect the testsuite to
-	# pass at all, while PYTHON_FULLY_TESTED allows skipping before
-	# numpy is ported (and possibly other deps in future).
-	if ! has "${EPYTHON/./_}" "${PYTHON_TESTED[@]}"; then
-		einfo "Skipping tests on ${EPYTHON} (xfail)"
-		return
-	fi
-
-	# Needed to avoid confusing cache tests
-	unset CYTHON_FORCE_REGEN
-
-	tc-export CC
-
-	local testargs=(
-		-vv
-		-j "$(makeopts_jobs)"
-		--work-dir "${BUILD_DIR}"/tests
-
-		--no-examples
-		--no-code-style
-
-		# Fails to find embedded.c
-		--exclude 'embedded'
-		# coverage_installed_pkg needs dev-python/pip and doesn't like
-		# 'externally-managed' (bug #927995), but we don't really
-		# want automagic test dependencies at all, so just skip
-		# unimportant-for-us coverage tests entirely.
-		--exclude 'run.coverage*'
-		--exclude 'Cython.Coverage'
-		# Automagic on dev-python/python-tests, could add this in future
-		--exclude 'run.test_exceptions'
-		# TODO: Unpackaged dev-python/interpreters-pep-734 (interpreters_backport)
-		# This only shows up as a failure with >=3.13.
-		--exclude 'subinterpreters_threading_stress_test'
-	)
-
-	if [[ ${EPYTHON} == pypy3* ]] ; then
-		testargs+=(
-			# Recursion issue
-			--exclude 'run.if_else_expr'
-			--exclude 'run.test_patma*'
-			# Slight output difference (missing '<')
-			--exclude 'run.cpp_exception_ptr_just_handler'
-
-		)
-	fi
-
-	# Keep test-full for numpy as it's large and doesn't pass tests itself
-	# on niche arches.
-	if ! use test-full || ! has "${EPYTHON/./_}" "${PYTHON_FULLY_TESTED[@]}"; then
-		testargs+=(
-			--exclude 'run.numpy*'
-			--exclude 'run.ufunc'
-			--exclude 'numpy*'
-		)
-	fi
-
-	"${PYTHON}" runtests.py "${testargs[@]}" || die "Tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	local DOCS=( CHANGES.rst README.rst ToDo.txt USAGE.txt )
-	distutils-r1_python_install_all
-}
diff --git a/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.1.2.ebuild b/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.1.2-r1.ebuild
similarity index 93%
rename from sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.1.2.ebuild
rename to sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.1.2-r1.ebuild
index 24a437ad5c..6145478e66 100644
--- a/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.1.2.ebuild
+++ b/sdk_container/src/third_party/portage-stable/dev-python/cython/cython-3.1.2-r1.ebuild
@@ -21,7 +21,7 @@ HOMEPAGE="
 
 LICENSE="Apache-2.0"
 SLOT="0"
-KEYWORDS="~alpha amd64 ~arm arm64 ~hppa ~loong ~m68k ~mips ppc ppc64 ~riscv ~s390 ~sparc x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
+KEYWORDS="~alpha amd64 arm arm64 hppa ~loong ~m68k ~mips ppc ppc64 ~riscv ~s390 sparc x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
 IUSE="test test-full"
 RESTRICT="!test? ( test )"
 
@@ -39,6 +39,8 @@ BDEPEND="
 PATCHES=(
 	"${FILESDIR}/${PN}-0.29.22-spawn-multiprocessing.patch"
 	"${FILESDIR}/${PN}-0.29.23-pythran-parallel-install.patch"
+	# https://github.com/cython/cython/pull/6957
+	"${FILESDIR}/${P}-odr.patch"
 )
 
 distutils_enable_sphinx docs \
diff --git a/sdk_container/src/third_party/portage-stable/dev-python/cython/files/cython-0.29.23-test_exceptions-py310.patch b/sdk_container/src/third_party/portage-stable/dev-python/cython/files/cython-0.29.23-test_exceptions-py310.patch
deleted file mode 100644
index 0c9fb2c9ea..0000000000
--- a/sdk_container/src/third_party/portage-stable/dev-python/cython/files/cython-0.29.23-test_exceptions-py310.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- a/tests/run/test_exceptions.pyx
-+++ b/tests/run/test_exceptions.pyx
-@@ -188,7 +188,10 @@
- 
-         # should not apply to subclasses, see issue #31161
-         s = '''if True:\nprint "No indent"'''
--        ckmsg(s, "expected an indented block", IndentationError)
-+        if sys.version_info >= (3, 10):
-+            ckmsg(s, "expected an indented block after 'if' statement on line 1", IndentationError)
-+        else:
-+            ckmsg(s, "expected an indented block", IndentationError)
- 
-         s = '''if True:\n        print()\n\texec "mixed tabs and spaces"'''
-         ckmsg(s, "inconsistent use of tabs and spaces in indentation", TabError)
diff --git a/sdk_container/src/third_party/portage-stable/dev-python/cython/files/cython-3.1.2-odr.patch b/sdk_container/src/third_party/portage-stable/dev-python/cython/files/cython-3.1.2-odr.patch
new file mode 100644
index 0000000000..f5dacc748d
--- /dev/null
+++ b/sdk_container/src/third_party/portage-stable/dev-python/cython/files/cython-3.1.2-odr.patch
@@ -0,0 +1,35 @@
+From 269dea7ac6f10566c3b1ea3850f6a45538e998ee Mon Sep 17 00:00:00 2001
+From: Ray Speth <yarmond@gmail.com>
+Date: Tue, 10 Jun 2025 03:09:03 -0400
+Subject: [PATCH] Mark utility function static to avoid ODR violations (#6957)
+
+PR #6882 introduces a new method `__pyx_CommonTypesMetaclass_get_module`
+in `CommonStructures.c`. Unlike other functions in this file, it is not
+marked `static`, which causes one-definition-rule violations when trying
+to compile multiple `.pyx` files into a single extension module.
+
+For context, this module structure is used in
+[Cantera](https://github.com/Cantera/cantera). We build the combined
+module
+[here](https://github.com/Cantera/cantera/blob/b308592776130d82eaac4949283fc87c031cdc97/interfaces/cython/SConscript#L46-L81),
+and then use a custom "finder" to load the submodules as defined
+[here](https://github.com/Cantera/cantera/blob/main/interfaces/cython/cantera/_cantera.pyx).
+
+Marking this function `static` restores the previous capability.
+---
+ Cython/Utility/CommonStructures.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Cython/Utility/CommonStructures.c b/Cython/Utility/CommonStructures.c
+index 94f7cc89066..3f1ce6d8408 100644
+--- a/Cython/Utility/CommonStructures.c
++++ b/Cython/Utility/CommonStructures.c
+@@ -161,7 +161,7 @@ static int __pyx_CommonTypesMetaclass_init(PyObject *module); /* proto */
+ //@requires: FetchCommonType
+ //@substitute: naming
+ 
+-PyObject* __pyx_CommonTypesMetaclass_get_module(CYTHON_UNUSED PyObject *self, CYTHON_UNUSED void* context) {
++static PyObject* __pyx_CommonTypesMetaclass_get_module(CYTHON_UNUSED PyObject *self, CYTHON_UNUSED void* context) {
+     return PyUnicode_FromString(__PYX_ABI_MODULE_NAME);
+ }
+