Merge pull request #8 from ACEnglish/master

pyproject.toml fixes pip installation

README.rst

@@ -29,7 +29,7 @@ Alignment of pattern and text strings can be performed by accessing WFA2-lib fun
 
 .. code-block:: python
 
-    from pywfa.align import WavefrontAligner
+    from pywfa import WavefrontAligner
 
     pattern = "TCTTTACTCGCGCGTTGGAGAAATACAATAGT"
     text =    "TCTATACTGCGCGTTTGGAGAAATAAAATAGT"
@@ -115,7 +115,7 @@ To configure the `WaveFrontAligner`, options can be provided during initializati
 
 .. code-block:: python
 
-    from pywfa.align import WavefrontAligner
+    from pywfa import WavefrontAligner
 
     a = WavefrontAligner(scope="score",
                          distance="affine2p",

_custom_build.py

@@ -0,0 +1,116 @@
+import os
+import glob
+import shutil
+import sysconfig
+import setuptools
+from subprocess import run
+from distutils import ccompiler
+from setuptools import Extension
+from Cython.Build import cythonize
+from setuptools.command.build_py import build_py as _build_py
+
+###########
+# Helpers #
+###########
+debug = False
+
+cy_options = {
+    'annotate': False,
+    'compiler_directives': {
+        'profile': debug,
+        'linetrace': debug,
+        'boundscheck': debug,
+        'wraparound': debug,
+        'nonecheck': debug,
+        'initializedcheck': debug,
+        'language_level': 3
+    }
+}
+
+cfg_vars = sysconfig.get_config_vars()
+for key, value in cfg_vars.items():
+    if type(value) == str:
+        cfg_vars[key] = value.replace("-Wstrict-prototypes", "")
+
+def has_flag(compiler, flagname):
+    """Return a boolean indicating whether a flag name is supported on
+    the specified compiler.
+    """
+    import tempfile
+    with tempfile.NamedTemporaryFile('w', suffix='.c') as f:
+        f.write('int main (int argc, char **argv) { return 0; }')
+        try:
+            compiler.compile([f.name], extra_postargs=[flagname])
+        except setuptools.distutils.errors.CompileError:
+            return False
+    return True
+
+def get_extra_args(flags):
+    compiler = ccompiler.new_compiler()
+    extra_compile_args = []
+    for f in flags:
+        if has_flag(compiler, f):
+            extra_compile_args.append(f)
+    return extra_compile_args
+
+##################
+# WFA2_lib build #
+##################
+extras = ["-Wno-unused-function", "-Wno-unused-result", '-Wno-ignored-qualifiers', "-Wno-deprecated-declarations"]
+extras_pywfa = get_extra_args(extras)
+
+root = os.path.abspath(os.path.dirname(__file__))
+wfa = os.path.join(root, "pywfa/WFA2_lib")
+libraries = [f"{wfa}/lib"]
+library_dirs = [f"{wfa}/lib"]
+include_dirs = [".", root, wfa, f"{wfa}/lib", f"{wfa}/utils", f"{wfa}/wavefront", f"{wfa}/bindings/cpp", f"{wfa}/system",
+                f"{wfa}/alignment", f"{root}/pywfa"]
+
+print("Libs", libraries)
+print("Library dirs", library_dirs)
+print("Include dirs", include_dirs)
+
+# Can't get openmp to behave. Whenever its on (1), the build fails.
+# this has happened on multiple OS with/without `libomp-dev`
+# compiler = ccompiler.new_compiler()
+omp = 0 #1 if has_flag(compiler, "-fopenmp") else 0
+ret = run(f"cd pywfa/WFA2_lib; make clean all BUILD_WFA_PARALLEL={omp} BUILD_MINIMAL=1; cd ../../", shell=True)
+if ret.returncode != 0:
+    print("Unable to build WFA2_lib")
+    print(ret)
+    exit(ret.returncode)
+
+##################
+# bindings build #
+##################
+m_ext_module = cythonize(Extension("pywfa.align",
+                                ["pywfa/align.pyx"],
+                                libraries=libraries,
+                                library_dirs=library_dirs,
+                                include_dirs=include_dirs,
+                                extra_compile_args=extras_pywfa,
+                                language="c",
+                                extra_objects=[f"{wfa}/lib/libwfa.a"]
+                                ),
+                        **cy_options)
+
+shared = glob.glob(f"{root}/build/lib*/pywfa/*.so") + glob.glob(f"{root}/build/lib*/pywfa/*.dll")
+[shutil.copy(i, f"{root}/pywfa") for i in shared]
+
+###################
+# Basic build_ext #
+###################
+# Thanks to https://stackoverflow.com/questions/73800736/pyproject-toml-and-cython-extension-module
+class build_py(_build_py):
+    def run(self):
+        self.run_command("build_ext")
+        return super().run()
+
+    def initialize_options(self):
+        super().initialize_options()
+        if self.distribution.ext_modules == None:
+            self.distribution.ext_modules = []
+
+        self.distribution.ext_modules.extend(
+            m_ext_module
+        )

pyproject.toml

@@ -0,0 +1,28 @@
+[build-system]
+requires = ["setuptools>=61.0", "cython"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name="pywfa"
+version='0.4.1'
+description="Align sequences using WFA2-lib"
+requires-python='>=3.7'
+readme = "README.rst"
+authors = [
+    { name = "Kez Cleal", email = "clealk@cardiff.ac.uk" }
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+[tool.setuptools]
+py-modules = ["_custom_build"]
+packages=["pywfa", "pywfa.tests", "pywfa.WFA2_lib"]
+
+[tool.setuptools.cmdclass]
+build_py = "_custom_build.build_py"
+
+[project.urls]
+Repository="https://github.com/kcleal/pywfa"

pywfa/__init__.py

@@ -1,3 +1,6 @@
-from __future__ import absolute_import
-from .align import WavefrontAligner, clip_cigartuples, cigartuples_to_str, elide_mismatches_from_cigar
-
+from pywfa.align import (
+    WavefrontAligner, 
+    clip_cigartuples, 
+    cigartuples_to_str,
+    elide_mismatches_from_cigar,
+)