Pymake

.github/workflows/python.yml

@@ -0,0 +1,48 @@
+name: Build
+
+on: [push, pull_request]
+
+# doing as cibuildwheel docs says leads to frankenstein arm builds on macos
+# so lets be more explicit, no linux arm build as not available on github
+
+jobs:
+  build_wheels:
+    name: Wheel ${{ matrix.python }}-${{ matrix.buildplat[1] }}
+    runs-on: ${{ matrix.buildplat[0] }}
+    strategy:
+      fail-fast: false
+      matrix:
+        buildplat:
+        - [ubuntu-latest, manylinux_x86_64, auto]
+        - [macos-13, macosx_x86_64, x86_64]
+        - [macos-14, macosx_arm64, arm64]
+        python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.20.0
+        env:
+          CIBW_ARCHS: ${{ matrix.buildplat[2] }}
+          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.python }}-${{ matrix.buildplat[1] }}
+          path: ./wheelhouse/*.whl
+
+
+  build-sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Build sdist
+        run: python setup.py sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist

MANIFEST.in

@@ -1,7 +1,6 @@
 include *.h
+include *.c
 include Makefile
-include ksw2_dispatch.c
-include main.c
 include README.md
 include sse2neon/emmintrin.h
 include python/cmappy.h

Makefile

@@ -38,6 +38,13 @@ ifneq ($(tsan),)
 	LIBS+=-fsanitize=thread -ldl
 endif
 
+ifneq ($(python),)
+	# this allows us to build libminimap2.a here and then link to
+	# it in the python extension build, rather than doing
+	CFLAGS+=-fPIC
+endif
+
+
 .PHONY:all extra clean depend
 .SUFFIXES:.c .o
 

setup.py

@@ -1,26 +1,37 @@
 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
+import sys, platform, subprocess
 
-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 = ["python=1"]
+		if platform.machine() in ["aarch64", "arm64"]:
+			options += ["arm_neon=1", "aarch64=1"]
+		self.execute(
+			compile_libminimap2, options,
+			f'Compiling libminimap2 using Makefile with options: {options}')
+		build_ext.run(self)
+
+
 setup(
 	name = 'mappy',
 	version = '2.28',
@@ -32,16 +43,15 @@ def readme():
 	license = 'MIT',
 	keywords = 'sequence-alignment',
 	scripts = ['python/minimap2.py'],
-	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'])],
+	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'])],
 	classifiers = [
 		'Development Status :: 5 - Production/Stable',
 		'License :: OSI Approved :: MIT License',