abpoa: fix build for version 1.5.2

BioArchLinux/abpoa/PKGBUILD

@@ -4,8 +4,8 @@ pkgname=('abpoa' 'pyabpoa')
 pkgname=abpoa
 pkgdesc="SIMD-based C library for fast partial order alignment. https://dx.doi.org/10.1093/bioinformatics/btaa963"
 _name=abPOA
-pkgver=1.5.1
-pkgrel=3
+pkgver=1.5.2
+pkgrel=1
 arch=(x86_64)
 url="https://github.com/yangao07/abPOA"
 license=('MIT')
@@ -18,13 +18,15 @@ source=("${pkgbase}-${pkgver}.tar.gz::https://github.com/yangao07/abPOA/archive/
         "series"
         "buildflags.patch"
         "simde.patch"
+        "relax-cython-dep.patch"
         )
 
-b2sums=('f95e35c7826334cd26f00ccd65ccc354c35c713da18fd3ed0e06528b87897eda2a9739f22bedaa81beb3dbe92830572cd998f0b2b43d21c6da8b3dc90dee79d7'
+b2sums=('d74a6a8b0cad57ee3849e2ca866e39a1c89090e6e2fa6d99f82559287248cb2f6747998d93adff70a94334e05c36663c42851c96bf19aaec440351b62ffd5b04'
         'ca47e595ff4d1b27e72ccb8ca900ba1524a23444198be4e9a05b8f49688832553d8e035f391f359d5fb3324ba23178ba5ac280069c46121f0c17e6d6050c66e2'
-        'bfee3142cc01cd8ab3547e61e3921b082557e0220a2d7809bf13a9d2274379547e9ad1131008b503705dc311aae78f51137eb0b282dbb6a5a359e3e5b4f0a9bd'
-        '8295d934f470b2bf4eff817eb0eb1ae6ab051942044ad77d76f2f9ae5aaab1baca04c622bfd68e866c7e86a3e519aff32172c4af84d8e3382d130a08da08381c'
-        '59ebf7e79f80bae90dea9b03e649ac21ea31a2759d0ca340ac5060927c758e3c09327d9074db3ad0abab16d2f15293a3dc611c67388d60b94aad61dfd4a12b99')
+        '6ef4e3d5f8a37bc103ca2b720bf4a064825b25382d2cb6d99edfeb5388fda821190dd0ebc35e0ab3e1507e4c27f6815f843419bcfbb9c017594165d377c49a02'
+        '531591beb6430dabb045167a96d901af2fc4945a88b17ca7ba369115bf6314b7d4aa1830a3ca9748ed0cf8a5b5e1a48389ac830bc1a1e5276be1b22ad1b8e11e'
+        '59ebf7e79f80bae90dea9b03e649ac21ea31a2759d0ca340ac5060927c758e3c09327d9074db3ad0abab16d2f15293a3dc611c67388d60b94aad61dfd4a12b99'
+        'd7b5054c4a4092e345bf1d893645eb3a3516faf2b0f76f13f022c01ae3deb6b7d4f871ded08d97d6a44372354aeebbfa8cfcc87cec145eb04514c336fc302e27')
 
 prepare() {
     # adapt patches from debian to make use SIMDe from Archlinux repo 

BioArchLinux/abpoa/buildflags.patch

@@ -1,61 +1,17 @@
---- abPOA-1.5.0/Makefile	2024-01-11 20:53:54.000000000 +0530
-+++ abPOA-1.5.0.new/Makefile	2024-01-13 20:48:42.551863612 +0530
-@@ -5,7 +5,7 @@
- OS          := $(shell uname)
- ARCH        := $(shell arch)
- EXTRA_FLAGS = -Wno-unused-function -Wno-misleading-indentation -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
--CFLAGS      = -Wall -O3 $(EXTRA_FLAGS)
-+CFLAGS      += $(CPPFLAGS) -Wall -O3 $(EXTRA_FLAGS) $(LDFLAGS)
+Description: inject standard debian build flags.
+Author: Étienne Mollier <emollier@debian.org>
+Forwarded: not-needed
+Last-Update: 2022-07-09
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- abpoa.orig/Makefile
++++ abpoa/Makefile
+@@ -23,7 +23,7 @@
+ 	OPT_FLAGS = -O3
+ endif
  
- # for debug
- ifneq ($(debug),)
-@@ -13,9 +13,9 @@
- endif
- # for gdb
- ifneq ($(gdb),)
--	CFLAGS   = -Wall -g ${DFLAGS} $(EXTRA_FLAGS)
-+	CFLAGS   += -Wall -g ${DFLAGS} $(EXTRA_FLAGS)
- else
--	CFLAGS   = -Wall -O3 ${DFLAGS} $(EXTRA_FLAGS)
-+	CFLAGS   += -Wall -O3 ${DFLAGS} $(EXTRA_FLAGS)
- endif
+-CFLAGS        = $(OPT_FLAGS) $(EXTRA_FLAGS)
++CFLAGS        = $(CPPFLAGS) $(OPT_FLAGS) $(EXTRA_FLAGS) $(LDFLAGS)
  
  # for gprof
-@@ -40,7 +40,7 @@
- OBJS = $(addprefix $(SRC_DIR)/, abpoa_align.o abpoa_graph.o abpoa_plot.o abpoa_seed.o abpoa_seq.o abpoa_output.o kalloc.o kstring.o simd_abpoa_align.o simd_check.o utils.o)
- 
- # Set default SIMD flags
--SIMD_FLAG   = -march=native
-+# SIMD_FLAG   = -march=native
- 
- # auto-detect some appropriate defaults -- this helps users in the common case of macOS with arm
- ifeq ($(ARCH), $(filter $(ARCH), aarch64 arm64))
-@@ -53,17 +53,17 @@
- endif
- 
- # override if user specified
--ifneq ($(armv7),) # for ARMv7
--	SIMD_FLAG   =  -march=armv7-a -mfpu=neon -D__AVX2__
--else
--ifneq ($(armv8),) # for ARMv8
--ifneq ($(aarch64),) # for Aarch64
--	SIMD_FLAG   =  -march=armv8-a+simd -D__AVX2__
--else # for Aarch32
--	SIMD_FLAG   =  -march=armv8-a+simd -mfpu=auto -D__AVX2__
--endif
--endif
--endif
-+#ifneq ($(armv7),) # for ARMv7
-+#	SIMD_FLAG   =  -march=armv7-a -mfpu=neon -D__AVX2__
-+##else
-+#ifneq ($(armv8),) # for ARMv8
-+#ifneq ($(aarch64),) # for Aarch64
-+#	SIMD_FLAG   =  -march=armv8-a+simd -D__AVX2__
-+#else # for Aarch32
-+#	SIMD_FLAG   =  -march=armv8-a+simd -mfpu=auto -D__AVX2__
-+#endif
-+#endif
-+#endif
- 
- # some more possible overrides
- FLAG_SSE2     = -msse2
+ ifneq ($(pg),)

BioArchLinux/abpoa/series

@@ -1,3 +1,4 @@
 simde.patch
 buildflags.patch
 baseline.patch
+relax-cython-dep.patch