minimap2 0.2.25.1 → 0.2.26.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 20d1a7f791311682922de7fcb3eef581102483c8791fbd63966d42ac1492169c
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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/Rakefile

@@ -37,7 +37,7 @@ namespace :minimap2 do
     end
   end
 
-  desc "Clean"
+  desc "`make clean`"
   task :clean do
     Dir.chdir(minimap2_dir) do
       sh "make clean"
@@ -46,7 +46,7 @@ namespace :minimap2 do
 
   task cleanall: [:clean]
 
-  desc "Clean all"
+  desc "`make clean` and remove shared lib"
   task :cleanall do
     Dir.chdir(minimap2_dir) do
       sh "rm #{target_path}" if File.exist?(target_path)

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 = "0.2.25.1"
+  VERSION = "0.2.26.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.25.1
+  version: 0.2.26.0
 platform: ruby
 authors:
 - kojix2
@@ -87,102 +87,6 @@ files:
 - ext/minimap2/kthread.h
 - ext/minimap2/kvec.h
 - ext/minimap2/lchain.c
-- ext/minimap2/lib/simde/CONTRIBUTING.md
-- ext/minimap2/lib/simde/COPYING
-- ext/minimap2/lib/simde/README.md
-- ext/minimap2/lib/simde/amalgamate.py
-- ext/minimap2/lib/simde/meson.build
-- ext/minimap2/lib/simde/netlify.toml
-- ext/minimap2/lib/simde/simde/arm/neon.h
-- ext/minimap2/lib/simde/simde/arm/neon/float32x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/float32x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/float64x1.h
-- ext/minimap2/lib/simde/simde/arm/neon/float64x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/int16x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/int16x8.h
-- ext/minimap2/lib/simde/simde/arm/neon/int32x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/int32x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/int64x1.h
-- ext/minimap2/lib/simde/simde/arm/neon/int64x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/int8x16.h
-- ext/minimap2/lib/simde/simde/arm/neon/int8x8.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h
-- ext/minimap2/lib/simde/simde/check.h
-- ext/minimap2/lib/simde/simde/debug-trap.h
-- ext/minimap2/lib/simde/simde/hedley.h
-- ext/minimap2/lib/simde/simde/simde-arch.h
-- ext/minimap2/lib/simde/simde/simde-common.h
-- ext/minimap2/lib/simde/simde/x86/avx.h
-- ext/minimap2/lib/simde/simde/x86/avx2.h
-- ext/minimap2/lib/simde/simde/x86/avx512bw.h
-- ext/minimap2/lib/simde/simde/x86/avx512f.h
-- ext/minimap2/lib/simde/simde/x86/avx512vl.h
-- ext/minimap2/lib/simde/simde/x86/fma.h
-- ext/minimap2/lib/simde/simde/x86/mmx.h
-- ext/minimap2/lib/simde/simde/x86/sse.h
-- ext/minimap2/lib/simde/simde/x86/sse2.h
-- ext/minimap2/lib/simde/simde/x86/sse3.h
-- ext/minimap2/lib/simde/simde/x86/sse4.1.h
-- ext/minimap2/lib/simde/simde/x86/sse4.2.h
-- ext/minimap2/lib/simde/simde/x86/ssse3.h
-- ext/minimap2/lib/simde/simde/x86/svml.h
-- ext/minimap2/lib/simde/test/CMakeLists.txt
-- ext/minimap2/lib/simde/test/arm/meson.build
-- ext/minimap2/lib/simde/test/arm/neon/meson.build
-- ext/minimap2/lib/simde/test/arm/neon/skel.c
-- ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h
-- ext/minimap2/lib/simde/test/arm/neon/test-neon.c
-- ext/minimap2/lib/simde/test/arm/neon/test-neon.h
-- ext/minimap2/lib/simde/test/arm/neon/vadd.c
-- ext/minimap2/lib/simde/test/arm/neon/vdup_n.c
-- ext/minimap2/lib/simde/test/arm/neon/vmul.c
-- ext/minimap2/lib/simde/test/arm/neon/vsub.c
-- ext/minimap2/lib/simde/test/arm/test-arm-internal.h
-- ext/minimap2/lib/simde/test/arm/test-arm.c
-- ext/minimap2/lib/simde/test/arm/test-arm.h
-- ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake
-- ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake
-- ext/minimap2/lib/simde/test/meson.build
-- ext/minimap2/lib/simde/test/munit/COPYING
-- ext/minimap2/lib/simde/test/munit/Makefile
-- ext/minimap2/lib/simde/test/munit/README.md
-- ext/minimap2/lib/simde/test/munit/example.c
-- ext/minimap2/lib/simde/test/munit/meson.build
-- ext/minimap2/lib/simde/test/munit/munit.c
-- ext/minimap2/lib/simde/test/munit/munit.h
-- ext/minimap2/lib/simde/test/run-tests.c
-- ext/minimap2/lib/simde/test/run-tests.h
-- ext/minimap2/lib/simde/test/x86/avx.c
-- ext/minimap2/lib/simde/test/x86/avx2.c
-- ext/minimap2/lib/simde/test/x86/avx512bw.c
-- ext/minimap2/lib/simde/test/x86/avx512f.c
-- ext/minimap2/lib/simde/test/x86/avx512vl.c
-- ext/minimap2/lib/simde/test/x86/fma.c
-- ext/minimap2/lib/simde/test/x86/meson.build
-- ext/minimap2/lib/simde/test/x86/mmx.c
-- ext/minimap2/lib/simde/test/x86/skel.c
-- ext/minimap2/lib/simde/test/x86/sse.c
-- ext/minimap2/lib/simde/test/x86/sse2.c
-- ext/minimap2/lib/simde/test/x86/sse3.c
-- ext/minimap2/lib/simde/test/x86/sse4.1.c
-- ext/minimap2/lib/simde/test/x86/sse4.2.c
-- ext/minimap2/lib/simde/test/x86/ssse3.c
-- ext/minimap2/lib/simde/test/x86/svml.c
-- ext/minimap2/lib/simde/test/x86/test-avx.h
-- ext/minimap2/lib/simde/test/x86/test-avx512.h
-- ext/minimap2/lib/simde/test/x86/test-mmx.h
-- ext/minimap2/lib/simde/test/x86/test-sse.h
-- ext/minimap2/lib/simde/test/x86/test-sse2.h
-- ext/minimap2/lib/simde/test/x86/test-x86-internal.h
-- ext/minimap2/lib/simde/test/x86/test-x86.c
-- ext/minimap2/lib/simde/test/x86/test-x86.h
 - ext/minimap2/main.c
 - ext/minimap2/map.c
 - ext/minimap2/minimap.h

data/ext/minimap2/lib/simde/CONTRIBUTING.md

@@ -1,114 +0,0 @@
-# Contributing to SIMDe
-
-First off, if you're even reading this, thank you!  There is a lot of
-work to do, and any help is appreciated.
-
-If you haven't already, please read the
-[README](https://github.com/nemequ/simde/blob/master/README.md).  The
-[wiki](https://github.com/nemequ/simde/wiki) also has some good
-information, especially the
-[FAQ](https://github.com/nemequ/simde/wiki/FAQ) and a guide on how to
-[implement a new
-function](https://github.com/nemequ/simde/wiki/Implementing-a-New-Function).
-
-For information on developing for architectures you don't have access
-to, please see the [Development
-Environment](https://github.com/nemequ/simde/wiki/Development-Environment)
-page on the wiki.
-
-If you still have questions, or if anything below doesn't make sense
-to you, please feel free to use the [issue
-tracker](https://github.com/nemequ/simde/issues) or the [mailing
-list](https://groups.google.com/forum/#!forum/simde) to ask.  I know
-the SIMDe documentation needs a lot of improvement, and asking
-questions will help us understand what is missing, so please don't be
-shy!
-
-## Building the Tests
-
-SIMDe contains an extensive test suite used for development.  Most
-users will never need to build the suite, but if you're contributing
-code to SIMDe you'll need to build them.
-
-Here is the basic procedure for compiling the tests:
-
-```bash
-mkdir test/build
-cd test/build
-CFLAGS="-march=native" CXXFLAGS="-march=native" cmake ..
-make -j
-./run-tests
-```
-
-Note that `-march=native` may not be the right flag for your compiler.
-That should work for most compilers on x86/x86_64, though MSVC is an
-exception (try `/arch:AVX2` instead of `-march=native`).  On other
-architectures please consult your compiler documentation to find out
-what flags you should use to enable the SIMD extension for your target
-platform.  Here are a few to try:
-
- * ARM:
-   * `-march=armv8-a+simd` (for ARMv8)
-   * `-march=armv7-a -mfpu=neon` (for ARMv7)
- * POWER
-   * `-mcpu=native`
-
-If you need a flag not listed above, please let us know so we can add
-it to the list.
-
-## Coding Style
-
-SIMDe uses two spaces for indentation.  Please adjust your editor
-accordingly.
-
-The coding style for preprocessor macros is a bit mixed since I made
-some changes mid-project.  For new code, please indent the
-preprocessor conditions before the hash to the same level as the
-normal code would be, and indent the code inside of preprocessor
-conditions as if the conditions were normal code.  For example:
-
-```c
-int
-foo(void) {
-  #if 1
-    bar();
-  #else
-    baz();
-  #endif
-}
-```
-
-Other than that, please just try to follow the existing style.  We'll
-add new rules here as the need arises.
-
-## Commit Messages
-
-Git commit messages should contain lines no longer than 72 characters.
-The first line should always be a one-line summary of the commit, with
-the relevant component followed by a colon and a space (if
-applicable), then the summary.
-
-If the one-line summary is insufficient to fully describe the changes
-further descriptive paragraphs should be added, separated by blank
-lines.
-
-For example:
-
-```
-sse: add magical code to make everything go fast
-
-Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur
-interdum scelerisque risus non ultricies. Vivamus id tristique mauris.
-Mauris et augue vel urna aliquam posuere. Morbi in sem nec ante
-ullamcorper ultrices in quis nibh. In felis velit, semper a mauris sed,
-congue ullamcorper enim. Vestibulum ante ipsum primis in faucibus orci
-luctus et ultrices posuere cubilia Curae; Nulla facilisi. Donec
-scelerisque elit dui, et aliquet magna tincidunt eu.
-
-Curabitur rhoncus lacus ac elit pulvinar, quis posuere ante ultrices.
-Suspendisse at mauris vitae justo pretium tempor et in mauris. Nunc
-facilisis nulla a ante tincidunt, imperdiet rhoncus metus interdum.
-Vivamus sed nunc vel tellus porta consequat. Donec quis porttitor elit,
-et cursus urna. Donec et sapien lorem. In imperdiet magna at aliquet
-hendrerit.
-```

data/ext/minimap2/lib/simde/COPYING

@@ -1,20 +0,0 @@
-Copyright (c) 2017 Evan Nemerson <evan@nemerson.com>
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.