sci-biology/mmseqs2: properly respect the cpu flags

Upstream PR is here: soedinglab/MMseqs2#533
See also: #1143

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <[email protected]>

Author: Nowa-Ammerlaan

sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch

@@ -0,0 +1,40 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1a677e3..df1d765 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -56,23 +56,29 @@ if (HAVE_AVX2)
+         set(MMSEQS_ARCH "${MMSEQS_ARCH} -mavx2 -mcx16 -Wa,-q")
+     endif ()
+     set(X64 1)
+-elseif (HAVE_SSE4_1)
++endif ()
++if (HAVE_SSE4_1)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse4.1 -mcx16")
+     set(X64 1)
+-elseif (HAVE_SSE2)
++endif ()
++if (HAVE_SSE2)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse2")
+     set(DISABLE_IPS4O 1)
+     set(X64 1)
+-elseif (HAVE_POWER9)
++endif ()
++if (HAVE_POWER9)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power9 -mvsx")
+     set(PPC64 1)
+-elseif (HAVE_POWER8)
++endif ()
++if (HAVE_POWER8)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power8 -mvsx")
+     set(PPC64 1)
+-elseif (HAVE_ARM8)
++endif ()
++if (HAVE_ARM8)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -march=armv8-a+simd")
+     set(ARM 1)
+-elseif (HAVE_S390X)
++endif ()
++if (HAVE_S390X)
+     set(MMSEQS_ARCH "${MMSEQS_ARCH} -mzarch -march=z14")
+     set(ZARCH 1)
+ endif ()

sci-biology/mmseqs2/mmseqs2-13.0.ebuild renamed to sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild

@@ -27,6 +27,10 @@ RDEPEND="
 "
 DEPEND="${RDEPEND}"
 
+PATCHES=(
+	"${FILESDIR}/${P}-properly-handle-cpuflags.patch"
+)
+
 src_configure() {
 	local mycmakeargs=(
 		# Need static libs: https://github.com/soedinglab/MMseqs2/issues/411