added arm and aarch64 builds (#51184)

* added arm and arch64 builds

* simplifying CMake command

* patch for S_ZEROFILL issue with asmlib on osx

* moved patch to sources section

* another patch to avoid asmlib on osx

* typo fixed

* forgotten modification in patch

recipes/mbgc/asmlib_off.patch

@@ -0,0 +1,113 @@
+Subject: [PATCH] turned off asmlib for mac to avoid build problems
+---
+Index: mbgccoder/MBGC_Encoder.cpp
+IDEA additional info:
+Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
+<+>UTF-8
+===================================================================
+diff --git a/mbgccoder/MBGC_Encoder.cpp b/mbgccoder/MBGC_Encoder.cpp
+--- a/mbgccoder/MBGC_Encoder.cpp	(revision 3f75674bef8463fbfb38e5c13b2760001c82db2a)
++++ b/mbgccoder/MBGC_Encoder.cpp	(date 1728303373036)
+@@ -15,7 +15,7 @@
+     ( params->checkIfDNAisWellFormed ? (seq->dnaLineLen == DNA_NOT_WELLFORMED ? 0 : seq->dnaLineLen )  \
+         : seq->maxLastDnaLineLen ) : 0)
+
+-#if !defined(__arm__) && !defined(__aarch64__) && !defined(__ARM_ARCH)
++#if false
+ #include "../libs/asmlib.h"
+ #endif
+ #include "../coders/PropsLibrary.h"
+Index: matching/SlidingWindowSparseEMMatcher.cpp
+IDEA additional info:
+Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
+<+>UTF-8
+===================================================================
+diff --git a/matching/SlidingWindowSparseEMMatcher.cpp b/matching/SlidingWindowSparseEMMatcher.cpp
+--- a/matching/SlidingWindowSparseEMMatcher.cpp	(revision 3f75674bef8463fbfb38e5c13b2760001c82db2a)
++++ b/matching/SlidingWindowSparseEMMatcher.cpp	(date 1728303373000)
+@@ -28,7 +28,7 @@
+ * ================================================================= */
+
+ #include "SlidingWindowSparseEMMatcher.h"
+-#if !defined(__arm__) && !defined(__aarch64__) && !defined(__ARM_ARCH)
++#if false
+ #include "../libs/asmlib.h"
+ #endif
+ #include <algorithm>
+Index: mbgccoder/MBGC_Decoder.cpp
+IDEA additional info:
+Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
+<+>UTF-8
+===================================================================
+diff --git a/mbgccoder/MBGC_Decoder.cpp b/mbgccoder/MBGC_Decoder.cpp
+--- a/mbgccoder/MBGC_Decoder.cpp	(revision 3f75674bef8463fbfb38e5c13b2760001c82db2a)
++++ b/mbgccoder/MBGC_Decoder.cpp	(date 1728303418036)
+@@ -1,7 +1,7 @@
+ #include "MBGC_Decoder.h"
+
+ #include "../coders/CodersLib.h"
+-#if !defined(__arm__) && !defined(__aarch64__) && !defined(__ARM_ARCH)
++#if false
+ #include "../libs/asmlib.h"
+ #endif
+ #include "../matching/SimpleSequenceMatcher.h"
+Index: utils/helper.h
+IDEA additional info:
+Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
+<+>UTF-8
+===================================================================
+diff --git a/utils/helper.h b/utils/helper.h
+--- a/utils/helper.h	(revision 3f75674bef8463fbfb38e5c13b2760001c82db2a)
++++ b/utils/helper.h	(date 1728303373072)
+@@ -338,7 +338,7 @@
+
+ }
+
+-#if defined(__arm__) || defined(__aarch64__) || defined(__ARM_ARCH)
++#if true
+
+ void A_memcpy(void *dest, const void *src, size_t n);
+
+Index: utils/helper.cpp
+IDEA additional info:
+Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
+<+>UTF-8
+===================================================================
+diff --git a/utils/helper.cpp b/utils/helper.cpp
+--- a/utils/helper.cpp	(revision 3f75674bef8463fbfb38e5c13b2760001c82db2a)
++++ b/utils/helper.cpp	(date 1728303373058)
+@@ -582,7 +582,7 @@
+ #endif
+ }
+
+-#if defined(__arm__) || defined(__aarch64__) || defined(__ARM_ARCH)
++#if true
+
+ void A_memcpy(void *dest, const void *src, size_t n) {
+     memcpy(dest, src, n);
+Index: CMakeLists.txt
+IDEA additional info:
+Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
+<+>UTF-8
+===================================================================
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+--- a/CMakeLists.txt	(revision 3f75674bef8463fbfb38e5c13b2760001c82db2a)
++++ b/CMakeLists.txt	(date 1728303558182)
+@@ -99,17 +99,6 @@
+     set(CMAKE_BUILD_TYPE Release)
+ endif()
+
+-if(CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64|AMD64)")
+-    if(CYGWIN OR MINGW)
+-        set(ASM_LIB ${CMAKE_SOURCE_DIR}/libs/libacof64.lib)
+-    elseif(UNIX AND NOT APPLE)
+-        set(ASM_LIB ${CMAKE_SOURCE_DIR}/libs/libaelf64.a)
+-    elseif(APPLE)
+-        set(ASM_LIB ${CMAKE_SOURCE_DIR}/libs/libamac64.a)
+-    endif()
+-    link_libraries(${ASM_LIB})
+-endif()
+-
+ link_libraries(pthread)
+
+ if(CYGWIN OR MINGW)

recipes/mbgc/build.sh

@@ -1,18 +1,22 @@
-#! /bin/bash
+#!/bin/bash
 
 mkdir -p $PREFIX/bin
-mkdir build
-cd build
-export CPATH=${BUILD_PREFIX}/include
-export CXXPATH=${BUILD_PREFIX}/include
-export CFLAGS="$CFLAGS -I$BUILD_PREFIX/include"
-export CXXFLAGS="$CFLAGS -I$BUILD_PREFIX/include"
-export LDFLAGS="$LDFLAGS -L$BUILD_PREFIX/lib"
-cmake ..
-if [[ "$(uname)" == "Linux" ]]; then
-  make mbgc
-else 
-  make mbgc-noavx
-  mv mbgc-noavx mbgc
-fi
-cp mbgc $PREFIX/bin
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi	
+
+cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=Release \
+	"${CONFIG_ARGS}"
+cmake --build build --target mbgc -j "${CPU_COUNT}" -v
+
+chmod 0755 build/mbgc
+cp -rf build/mbgc $PREFIX/bin

recipes/mbgc/meta.yaml

@@ -5,13 +5,15 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('mbgc', max_pin="x") }}
 
 source:
   url: https://github.com/kowallus/mbgc/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: fb422fc89aa95d82dab0b1431b7f220d5f4cdab2dfc1141218e74668461fa530 
+  sha256: fb422fc89aa95d82dab0b1431b7f220d5f4cdab2dfc1141218e74668461fa530
+  patches:
+    - asmlib_off.patch  #  [osx and x86_64]
 
 requirements:
   build:
@@ -20,21 +22,28 @@ requirements:
     - make
   host:
     - llvm-openmp  # [osx]
+    - libgomp  # [linux]
   run:
-    - llvm-openmp  # [osx]   
-
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
+
 test:
   commands:
     - mbgc -v 2>&1 | grep -F {{ version }}
 
 about:
   home: https://github.com/kowallus/mbgc
-  license: GPL3
+  license: "GPL-3.0-or-later"
   license_file: LICENSE
-  license_family: GPL
-  summary: A tool for compressing collection of genomes in FASTA format
+  license_family: GPL3
+  summary: "A tool for compressing collection of genomes in FASTA format."
+  dev_url: https://github.com/kowallus/mbgc
 
 extra:
-  maintainers:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
     - kowallus
-
+  identifiers:
+    - doi:10.1093/gigascience/giab099