minimap2 0.2.25.2 → 0.2.26.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -169,6 +169,15 @@ Run tests.
 bundle exec rake test
 ```
 
+Release a Gem.
+
+```
+bundle exec rake minimap2:cleanall
+bundle exec rake build
+ls -l pkg # Check the size of the Gem and make sure it does not contain any unused code such as shared libraries or lib/simde.
+bundle exec rake release
+```
+
 </details>
 
 ruby-minimap2 is a library under development and there are many points to be improved.

data/ext/minimap2/NEWS.md

@@ -1,3 +1,12 @@
+Release 2.26-r1175 (29 April 2023)
+----------------------------------
+
+Fixed the broken Python package. This is the only change.
+
+(2.25: 25 April 2023, r1173)
+
+
+
 Release 2.25-r1173 (25 April 2023)
 ----------------------------------
 

data/ext/minimap2/README.md

@@ -74,8 +74,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
 Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
 the [release page][release] with:
 ```sh
-curl -L https://github.com/lh3/minimap2/releases/download/v2.25/minimap2-2.25_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.25_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.26_x64-linux/minimap2
 ```
 If you want to compile from the source, you need to have a C compiler, GNU make
 and zlib development files installed. Then type `make` in the source code

data/ext/minimap2/cookbook.md

@@ -31,8 +31,8 @@ To acquire the data used in this cookbook and to install minimap2 and paftools,
 please follow the command lines below:
 ```sh
 # install minimap2 executables
-curl -L https://github.com/lh3/minimap2/releases/download/v2.25/minimap2-2.25_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.25_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.26_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
 export PATH="$PATH:"`pwd`                               # put the current directory on PATH
 # download example datasets
 curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -

data/ext/minimap2/minimap.h

@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.25-r1173"
+#define MM_VERSION "2.26-r1175"
 
 #define MM_F_NO_DIAG       (0x001LL) // no exact diagonal hit
 #define MM_F_NO_DUAL       (0x002LL) // skip pairs where query name is lexicographically larger than target name

data/ext/minimap2/minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "25 April 2023" "minimap2-2.25 (r1173)" "Bioinformatics tools"
+.TH minimap2 1 "29 April 2023" "minimap2-2.26 (r1175)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

data/ext/minimap2/misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.25-r1173';
+var paftools_version = '2.26-r1175';
 
 /*****************************
  ***** Library functions *****

data/ext/minimap2/python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.25'
+__version__ = '2.26'
 
 cmappy.mm_reset_timer()
 

data/ext/minimap2/setup.py

@@ -1,40 +1,29 @@
 try:
 	from setuptools import setup, Extension
-	from setuptools.command.build_ext import build_ext
 except ImportError:
 	from distutils.core import setup
 	from distutils.extension import Extension
-	from distutils.command.build_ext import build_ext
 
-import sys, platform, subprocess
+import sys, platform
 
+sys.path.append('python')
+
+extra_compile_args = ['-DHAVE_KALLOC']
+include_dirs = ["."]
+
+if platform.machine() in ["aarch64", "arm64"]:
+	include_dirs.append("sse2neon/")
+	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
+else:
+	extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
 
 def readme():
 	with open('python/README.rst') as f:
 		return f.read()
 
-
-class LibMM2Build(build_ext):
-	# Uses Makefile to build library, avoids duplicating logic
-	# determining which objects to compile but does require
-	# end users to have Make (since precompiled wheels are not
-	# distributed on PyPI).
-	def run(self):
-		def compile_libminimap2(*args, **kwargs):
-			cmd = ['make', 'libminimap2.a'] + list(args)
-			subprocess.check_call(cmd)
-		options = []
-		if platform.machine() in ["aarch64", "arm64"]:
-			options = ["arm_neon=1", "aarch64=1"]
-		self.execute(
-			compile_libminimap2, options,
-			'Compiling libminimap2 using Makefile')
-		build_ext.run(self)
-
-
 setup(
 	name = 'mappy',
-	version = '2.25',
+	version = '2.26',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),
@@ -43,15 +32,16 @@ setup(
 	license = 'MIT',
 	keywords = 'sequence-alignment',
 	scripts = ['python/minimap2.py'],
-	cmdclass = {'build_ext': LibMM2Build},
-	ext_modules = [
-		Extension(
-			'mappy',
-			sources = ['python/mappy.pyx'],
-			depends = ['python/cmappy.h', 'python/cmappy.pxd'],
-			include_dirs = ['.'],
-			extra_objects = ['libminimap2.a'],
-			libraries = ['z', 'm', 'pthread'])],
+	ext_modules = [Extension('mappy',
+		sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'lchain.c', 'seed.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'options.c',
+				   'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
+				   'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c', 'splitidx.c'],
+		depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
+				   'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
+				   'python/cmappy.h', 'python/cmappy.pxd'],
+		extra_compile_args = extra_compile_args,
+		include_dirs = include_dirs,
+		libraries = ['z', 'm', 'pthread'])],
 	classifiers = [
 		'Development Status :: 5 - Production/Stable',
 		'License :: OSI Approved :: MIT License',

data/lib/minimap2/version.rb

@@ -2,5 +2,5 @@
 
 module Minimap2
   # Minimap2-2.25 (r1173)
-  VERSION = "0.2.25.2"
+  VERSION = "0.2.26.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.25.2
+  version: 0.2.26.0
 platform: ruby
 authors:
 - kojix2