commit: 14bc51e9759c448132391901ff1eb528fe0f5a0c Author: Eli Schwartz <eschwartz93 <AT> gmail <DOT> com> AuthorDate: Fri Apr 5 00:37:31 2024 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Sun Apr 7 06:16:09 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=14bc51e9
sci-biology/kallisto: port to catch2 version 3 Which is the current default distributed version. Nicer than requiring people to downgrade to an old version. Closes: https://bugs.gentoo.org/877887 Signed-off-by: Eli Schwartz <eschwartz93 <AT> gmail.com> Signed-off-by: Sam James <sam <AT> gentoo.org> sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch | 10 +++++----- sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch | 2 +- sci-biology/kallisto/kallisto-0.46.2.ebuild | 10 +++++++--- 3 files changed, 13 insertions(+), 9 deletions(-) diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch index 7566966c1c68..3ff6a0c33be0 100644 --- a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch +++ b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch @@ -3,12 +3,12 @@ @@ -1,2 +1,2 @@ #define CATCH_CONFIG_MAIN -#include "catch.hpp" -+#include <catch2/catch.hpp> ++#include <catch2/catch_all.hpp> --- a/unit_tests/test_index.cpp +++ b/unit_tests/test_index.cpp @@ -1,4 +1,4 @@ -#include "catch.hpp" -+#include <catch2/catch.hpp> ++#include <catch2/catch_all.hpp> #include "common.h" #include "KmerIndex.h" @@ -16,7 +16,7 @@ +++ b/unit_tests/test_kmerhashtable.cpp @@ -1,4 +1,4 @@ -#include "catch.hpp" -+#include <catch2/catch.hpp> ++#include <catch2/catch_all.hpp> #include <random> #include <string> @@ -24,7 +24,7 @@ +++ b/unit_tests/test_multinomial.cpp @@ -1,4 +1,4 @@ -#include "catch.hpp" -+#include <catch2/catch.hpp> ++#include <catch2/catch_all.hpp> #include <iostream> #include <vector> @@ -32,7 +32,7 @@ +++ b/unit_tests/test_weights.cpp @@ -1,4 +1,4 @@ -#include "catch.hpp" -+#include <catch2/catch.hpp> ++#include <catch2/catch_all.hpp> #include <vector> diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch index ba6114a9164f..6516f162e906 100644 --- a/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch +++ b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch @@ -142,7 +142,7 @@ +find_package( Catch2 REQUIRED ) +include_directories( ${Catch2_INCLUDE_DIRS} ) -+target_link_libraries( tests ${Catch2_LIBRARIES} ) ++target_link_libraries( tests Catch2::Catch2WithMain ) + find_package( ZLIB REQUIRED ) if ( ZLIB_FOUND ) diff --git a/sci-biology/kallisto/kallisto-0.46.2.ebuild b/sci-biology/kallisto/kallisto-0.46.2.ebuild index 293cf9f76ed0..a1926bbd10fe 100644 --- a/sci-biology/kallisto/kallisto-0.46.2.ebuild +++ b/sci-biology/kallisto/kallisto-0.46.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 -inherit cmake +inherit cmake flag-o-matic DESCRIPTION="Near-optimal RNA-Seq quantification" HOMEPAGE="http://pachterlab.github.io/kallisto/"; @@ -28,7 +28,7 @@ RDEPEND=" DEPEND=" ${RDEPEND} test? ( - dev-cpp/catch:0 + >=dev-cpp/catch-3:0 sci-libs/hdf5 )" BDEPEND="virtual/pkgconfig" @@ -51,6 +51,10 @@ src_prepare() { # specific builddir nesting structure. sed -e "s|../test/input/short_reads.fastq|$(readlink -f unit_tests/input/short_reads.fastq)|g" \ -i unit_tests/test_kmerhashtable.cpp || die + + # This randomly hardcodes a particular std, which unfortunately is too old for catch2. + sed -i '/CMAKE_CXX_STANDARD/d' CMakeLists.txt || die + append-cxxflags -std=c++14 } src_configure() {
