diff --git a/dev-python/pybedtools/Manifest b/dev-python/pybedtools/Manifest
index 7db62a4c423..b87b0f9e6a8 100644
--- a/dev-python/pybedtools/Manifest
+++ b/dev-python/pybedtools/Manifest
@@ -1 +1 @@
-DIST pybedtools-0.10.0.tar.gz 12497095 BLAKE2B d9fb44bd3afcb8748e0cadbe0c4d55c7325911331d0719b79bd04eff264bd6299d407dee7f511bc05a7e12dd46e92a9c25ce0607b8926e6542e4dd652cc9d23f SHA512 cec04464fcfaa12bb660f223d6f656a30ac5822ea9053455dbc5717d2afbc998db9fd4b7424d8458445450a6ce5aafb65463fa1274b2691b26bfda7fe84bef56
+DIST pybedtools-0.11.0.tar.gz 12498434 BLAKE2B c1157e172e94b565234c592e0c8379e46cb7ed4b5659bc6998dda10ee9654d262c60faf0214c5f90236f1c536cd48bc94f78ed6661612c7d84832831c0947861 SHA512 c06eaae64a9d175e434881cfcf084b4a20c488809c7091599b2eaa5113a6c84b59b89f9d3503e3f606856437c77d30d9364271d660bc675bf4c54ffa20bb5368
diff --git a/dev-python/pybedtools/pybedtools-0.10.0.ebuild b/dev-python/pybedtools/pybedtools-0.11.0.ebuild
similarity index 87%
rename from dev-python/pybedtools/pybedtools-0.10.0.ebuild
rename to dev-python/pybedtools/pybedtools-0.11.0.ebuild
index ae51c24ce68..70012c4ebc6 100644
--- a/dev-python/pybedtools/pybedtools-0.10.0.ebuild
+++ b/dev-python/pybedtools/pybedtools-0.11.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -6,7 +6,7 @@ EAPI=8
 PYTHON_COMPAT=( python3_{10..12} )
 DISTUTILS_USE_PEP517=setuptools
 DISTUTILS_EXT=1
-inherit distutils-r1
+inherit distutils-r1 flag-o-matic
 
 DESCRIPTION="Use BED and GFF files from python using BEDtools"
 HOMEPAGE="https://daler.github.io/pybedtools"
@@ -31,6 +31,11 @@ RDEPEND="
 #distutils_enable_sphinx docs/source
 distutils_enable_tests pytest
 
+python_compile() {
+	filter-lto
+	distutils-r1_python_compile
+}
+
 python_test() {
 	# Requires network
 	local EPYTEST_DESELECT=(