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diff --git a/dev-python/scipy/scipy-1.16.1.ebuild b/dev-python/scipy/scipy-1.16.1.ebuild
deleted file mode 100644
index a88dea60d034..000000000000
--- a/dev-python/scipy/scipy-1.16.1.ebuild
+++ /dev/null
@@ -1,171 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-FORTRAN_NEEDED=fortran
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=meson-python
-PYTHON_COMPAT=( pypy3_11 python3_{11..13} )
-PYTHON_REQ_USE="threads(+)"
-
-inherit flag-o-matic fortran-2 distutils-r1
-
-DESCRIPTION="Scientific algorithms library for Python"
-HOMEPAGE="
- https://scipy.org/
- https://github.com/scipy/scipy/
- https://pypi.org/project/scipy/
-"
-
-if [[ ${PV} == *9999* ]] ; then
- inherit git-r3
-
- # Need submodules, so git for now.
- EGIT_REPO_URI="https://github.com/scipy/scipy"
- EGIT_BRANCH="maintenance/$(ver_cut 1-2).x"
- EGIT_SUBMODULES=( '*' )
-else
- inherit pypi
-
- # Upstream is often behind with doc updates
- DOC_PV=${PV}
-
- SRC_URI+="
- doc? (
- https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip
- )"
-
- if [[ ${PV} != *rc* ]] ; then
- KEYWORDS="~amd64 ~arm ~arm64 ~loong ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86"
- fi
-fi
-
-LICENSE="BSD LGPL-2"
-SLOT="0"
-IUSE="doc +fortran test-rust"
-
-# pythran is needed in both BDEPEND (for /usr/bin/pythran) and in DEPEND
-# to actually compile code generated by pythran (headers and such needed).
-#
-# umfpack is technically optional but it's preferred to have it available.
-COMMON_DEPEND="
- >=dev-python/numpy-1.23.5:=[lapack,${PYTHON_USEDEP}]
- ~media-libs/qhull-2020.2:=
- sci-libs/arpack:=
- sci-libs/umfpack
- virtual/cblas
- >=virtual/lapack-3.8
-"
-# Only boost.math is used, and meson.build doesn't even look up specific boost modules.
-# Exact version is enforced upstream, so building will fail if subslot isn't enforced.
-DEPEND="
- ${COMMON_DEPEND}
- dev-libs/boost:0/1.88.0
-"
-RDEPEND="
- ${COMMON_DEPEND}
- dev-python/pillow[${PYTHON_USEDEP}]
-"
-DEPEND+="
- fortran? (
- >=dev-python/pythran-0.16.0[${PYTHON_USEDEP}]
- )
-"
-BDEPEND="
- dev-lang/swig
- >=dev-python/cython-3.0.8[${PYTHON_USEDEP}]
- >=dev-python/meson-python-0.15.0[${PYTHON_USEDEP}]
- >=dev-python/pybind11-2.13.2[${PYTHON_USEDEP}]
- >=dev-build/meson-1.5.0
- !kernel_Darwin? ( dev-util/patchelf )
- virtual/pkgconfig
- doc? ( app-arch/unzip )
- fortran? (
- >=dev-python/pythran-0.16.0[${PYTHON_USEDEP}]
- )
- test-rust? (
- dev-python/pooch[${PYTHON_USEDEP}]
- )
-"
-
-EPYTEST_PLUGINS=( hypothesis )
-EPYTEST_XDIST=1
-distutils_enable_tests pytest
-
-src_unpack() {
- default
-
- if use doc; then
- unzip -qo "${DISTDIR}"/${PN}-html-${DOC_PV}.zip -d html || die
- fi
-}
-
-python_configure_all() {
- DISTUTILS_ARGS=(
- -Dblas=blas
- -Dlapack=lapack
- -Duse-pythran=$(usex fortran true false)
- # note: recheck on version bumps, upstream is planning
- # to allow more
- '-Duse-system-libraries=boost.math,qhull'
- )
-
- # https://bugs.gentoo.org/932721
- has_version '>=dev-python/numpy-2.0.0' && filter-lto
-}
-
-python_test() {
- cd "${BUILD_DIR}/install$(python_get_sitedir)" || die
-
- local EPYTEST_DESELECT=(
- # Network
- scipy/datasets/tests/test_data.py::TestDatasets::test_existence_all
- scipy/datasets/tests/test_data.py::TestDatasets::test_ascent
- scipy/datasets/tests/test_data.py::TestDatasets::test_face
- scipy/datasets/tests/test_data.py::TestDatasets::test_electrocardiogram
-
- # Crashes with assertion, not a regression
- # https://github.com/scipy/scipy/issues/19321
- scipy/signal/tests/test_signaltools.py::test_lfilter_bad_object
-
- # Awfully slow tests
- scipy/interpolate/tests/test_bsplines.py::TestBatch::test_batch
- scipy/linalg/tests/test_basic.py::TestLstsq::test_random_complex_exact
- scipy/sparse/linalg/_eigen/tests/test_svds.py::test_small_sigma_sparse
-
- # TODO: minor precision errors
- 'scipy/linalg/tests/test_batch.py::TestBatch::test_solve[float32-bdim2]'
- 'scipy/linalg/tests/test_batch.py::TestBatch::test_lu_solve[float32-bdim2]'
-
- # Crashes, probably too big
- 'scipy/interpolate/tests/test_fitpack2.py::TestRectBivariateSpline::test_spline_large_2d_maxit'
- )
- local EPYTEST_IGNORE=()
-
- if ! has_version -b "dev-python/pooch[${PYTHON_USEDEP}]" ; then
- EPYTEST_IGNORE+=(
- scipy/datasets/tests/test_data.py
- )
- fi
-
- case ${EPYTHON} in
- pypy3*)
- EPYTEST_DESELECT+=(
- # TODO
- scipy/special/tests/test_data.py::test_boost
- scipy/_lib/tests/test_ccallback.py::test_callbacks
- )
- ;;
- esac
-
- # avoid other stuff being multithreaded when using xdist
- local -x PYTHON_CPU_COUNT=1
- epytest scipy
-}
-
-python_install_all() {
- use doc && local HTML_DOCS=( "${WORKDIR}"/html/. )
-
- distutils-r1_python_install_all
-}