Remove `arm64` compilation flags from OSX in `setup.py`

.github/workflows/test.yml

@@ -137,13 +137,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Show Python build environment
-      run: python -m sysconfig
+      run: arch -x86_64 python -m sysconfig
     - name: Update pip
       run: python -m pip install -U pip wheel setuptools
     - name: Install Python requirements
       run: python -m pip install -r .github/workflows/requirements.txt
     - name: Build C extension
-      run: python setup.py build_ext --inplace --debug
+      run: arch -x86_64 python setup.py build_ext --inplace --debug
     - name: Install test requirements
       run: python -m pip install -r pyhmmer/tests/requirements.txt
       if: matrix.python-impl == 'CPython'

setup.py

@@ -11,6 +11,7 @@ import platform
 import re
 import sys
 import subprocess
+from pprint import pprint
 from unittest import mock
 
 import setuptools
@@ -36,6 +37,17 @@ def _split_multiline(value):
 def _eprint(*args, **kwargs):
     print(*args, **kwargs, file=sys.stderr)
 
+def _patch_osx_compiler(compiler):
+    # On newer OSX, Python has been compiled as a universal binary, so
+    # it will attempt to pass universal binary flags when building the
+    # extension. This will not work because the code makes use of SSE2.
+    for tool in ("compiler", "compiler_so", "linker_so"):
+        flags = getattr(compiler, tool)
+        i = next((i for i in range(1, len(flags)) if flags[i-1] == "-arch" and flags[i] == "arm64"), None)
+        if i is not None:
+            flags.pop(i)
+            flags.pop(i-1)
+
 # --- `setup.py` commands ----------------------------------------------------
 
 class sdist(_sdist):
@@ -143,6 +155,10 @@ class build_ext(_build_ext):
         else:
             ext.define_macros.append(("CYTHON_WITHOUT_ASSERTIONS", 1))
 
+        # remove universal binary CFLAGS from the compiler if any
+        if platform.system() == "Darwin":
+            _patch_osx_compiler(self.compiler)
+
         # update link and include directories
         ext.include_dirs.append(self._clib_cmd.build_clib)
         ext.library_dirs.append(self._clib_cmd.build_clib)
@@ -318,6 +334,10 @@ class configure(_build_clib):
         # ensure the output directory exists, otherwise create it
         self.mkpath(self.build_clib)
 
+        # remove universal binary CFLAGS from the compiler if any
+        if platform.system() == "Darwin":
+            _patch_osx_compiler(self.compiler)
+
         # run the `configure_library` method sequentially on each library,
         # unless the header already exists and the configuration has not
         # been edited
@@ -471,6 +491,10 @@ class build_clib(_build_clib):
         _build_clib.run(self)
 
     def build_libraries(self, libraries):
+        # remove universal binary CFLAGS from the compiler if any
+        if platform.system() == "Darwin":
+            _patch_osx_compiler(self.compiler)
+        # build extensions sequentially
         self.mkpath(self.build_clib)
         for library in libraries:
             self.make_file(