commit: 7fdfd97f34314b9fb85bcbadb46efc07b94b67aa Author: Alfred Wingate <parona <AT> protonmail <DOT> com> AuthorDate: Mon Feb 10 19:14:46 2025 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Tue Feb 11 01:36:17 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7fdfd97f
sci-biology/augustus: add 3.5.0 * Add missing dependency on python with tests. * Wire up unittests. * Disable test comparing on musl. This follows upstream with non-amd64 and non-linux environments. Bug: https://bugs.gentoo.org/868363 Bug: https://bugs.gentoo.org/873025 Signed-off-by: Alfred Wingate <parona <AT> protonmail.com> Closes: https://github.com/gentoo/gentoo/pull/40521 Signed-off-by: Sam James <sam <AT> gentoo.org> sci-biology/augustus/Manifest | 1 + sci-biology/augustus/augustus-3.5.0.ebuild | 93 ++++++++++++++++++++++++++++++ 2 files changed, 94 insertions(+) diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest index 7ddb67b5c888..7bba72327fb5 100644 --- a/sci-biology/augustus/Manifest +++ b/sci-biology/augustus/Manifest @@ -1,2 +1,3 @@ DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab SHA512 ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6 +DIST augustus-3.5.0.tar.gz 225918930 BLAKE2B 26e934f3d3f50d183fb0ee7874352c5ac9af9877eaa40a9a6195ae79cfd9a78a321bd9261e8bd3435b1d4984589d0bdd4e0821ba6600c717d6afd95f511702de SHA512 0869e54b3126b3ab2f6fb2c28ff07b779265a139968e5277352f5230d3c317415324ca61dce4a0cd6c3f1fb5399447ae815bec7732a285ce652cf44e6cd23e5d DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B 3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f diff --git a/sci-biology/augustus/augustus-3.5.0.ebuild b/sci-biology/augustus/augustus-3.5.0.ebuild new file mode 100644 index 000000000000..481476e902c5 --- /dev/null +++ b/sci-biology/augustus/augustus-3.5.0.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DOCS_BUILDER="doxygen" +DOCS_CONFIG_NAME="doxygen.conf" + +PYTHON_COMPAT=( python3_{12..13} ) + +inherit docs python-any-r1 toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/"; +SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${P^}" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-db/sqlite:3 + dev-db/mysql++:= + dev-db/mysql-connector-c:= + dev-libs/boost:=[zlib] + sci-biology/bamtools:= + sci-biology/samtools:0 + sci-libs/gsl:= + sci-libs/htslib:= + sci-libs/suitesparse + sci-mathematics/lpsolve:= + sys-libs/zlib +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + ${PYTHON_DEPS} + ) +" + +PATCHES=( + "${FILESDIR}"/augustus-3.4.0-missing-cstdint.patch +) + +pkg_setup() { + use test && python-any-r1_pkg_setup +} + +src_compile() { + tc-export CC CXX AR + + emake + + # Vendored gtest + use test && emake -C src unittest + + docs_compile +} + +src_install() { + einstalldocs + # from upstream Makefile install: + dodir "opt/${P}" + cp -a config bin scripts "${ED}/opt/${P}" || die + local file + for file in bin/*; do + dosym "../${P}/${file}" "/opt/${file}" + done +} + +src_test() { + if use elibc_musl; then + # Upstream already does this for non-amd64 and non-linux environments + # Probably related https://github.com/Gaius-Augustus/Augustus/issues/247 + # bug #873025 + emake test TEST_COMPARE= TEST_HTML= + else + emake test + fi + + pushd src/unittests >/dev/null || die + if use elibc_musl; then + # Float issues + ./unittests --gtest_filter='-CodonEvoTest.CodonEvoRateReadWrite' || die + else + ./unittests || die + fi + popd >/dev/null || die +}
