ENH: add SIMD everywhere for non-x86 support

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "simde"]
+	path = simde
+	url = https://github.com/nemequ/simde-no-tests

CHANGELOG.md

@@ -28,6 +28,8 @@
 
 * Update hdmedians package to a version which doesn't require an initial manual numpy install.
 
+* Now buildable on non-x86 platforms due to use of the [SIMD Everywhere](https://github.com/nemequ/simde) library.
+
 ## Version 0.5.6
 
 ### Features

MANIFEST.in

@@ -10,6 +10,7 @@ include RELEASE.md
 include REVIEWING.md
 include checklist.py
 include asv.conf.json
+recursive-include simde *.h COPYING *.md
 
 graft assets
 graft ci
@@ -26,3 +27,5 @@ global-exclude *.pyo
 global-exclude *.so
 global-exclude .*.swp
 global-exclude .coverage
+
+exclude .gitmodules

setup.py

@@ -13,6 +13,8 @@
 import re
 import ast
 import sys
+import sysconfig
+import subprocess
 
 from setuptools import find_packages, setup
 from setuptools.extension import Extension
@@ -24,6 +26,29 @@
     sys.exit("scikit-bio can only be used with Python 3. You are currently "
              "running Python %d." % sys.version_info.major)
 
+clang = False
+icc = False
+try:
+    if os.environ['CC'] == "clang":
+        clang = True
+except KeyError:
+    pass
+
+if not clang:
+    try:
+        if subprocess.check_output(
+                ["gcc", "--version"], text=True).find("clang") != -1:
+            clang = True
+    except subprocess.CalledProcessError:
+        pass
+
+
+try:
+    if os.environ['CC'] == "icc":
+        icc = True
+except KeyError:
+    pass
+
 # version parsing from __init__ pulled from Flask's setup.py
 # https://github.com/mitsuhiko/flask/blob/master/setup.py
 _version_re = re.compile(r'__version__\s+=\s+(.*)')
@@ -65,9 +90,14 @@
 # the compilation of the interpreter. See http://bugs.python.org/issue21121 for
 # details. This acts as a workaround until the next Python 3 release -- thanks
 # Wolfgang Maier (wolma) for the workaround!
-ssw_extra_compile_args = ['-Wno-error=declaration-after-statement']
-if sys.platform == 'win32':
-    ssw_extra_compile_args = []
+ssw_extra_compile_args = ['-I.']
+if sys.platform != 'win32':
+    ssw_extra_compile_args.append('-Wno-error=declaration-after-statement')
+
+if icc or sysconfig.get_config_vars()['CC'] == 'icc':
+    ssw_extra_compile_args.extend(['-qopenmp-simd', '-DSIMDE_ENABLE_OPENMP'])
+elif not (clang or sysconfig.get_config_vars()['CC'] == 'clang'):
+    ssw_extra_compile_args.extend(['-fopenmp-simd', '-DSIMDE_ENABLE_OPENMP'])
 
 # Users with i686 architectures have reported that adding this flag allows
 # SSW to be compiled. See https://github.com/biocore/scikit-bio/issues/409 and

skbio/alignment/_lib/ssw.c

@@ -35,7 +35,8 @@
  *
  */
 
-#include <emmintrin.h>
+#define SIMDE_ENABLE_NATIVE_ALIASES
+#include "simde/x86/sse2.h"
 #include <stdint.h>
 #include <stdlib.h>
 #include <stdio.h>

skbio/alignment/_lib/ssw.h

@@ -14,7 +14,8 @@
 #include <stdio.h>
 #include <stdint.h>
 #include <string.h>
-#include <emmintrin.h>
+#define SIMDE_ENABLE_NATIVE_ALIASES
+#include "simde/x86/sse2.h"
 
 /*! @typedef    structure of the query profile  */
 struct _profile;
@@ -127,4 +128,4 @@ void align_destroy (s_align* a);
 }
 #endif  // __cplusplus
 
-#endif  // SSW_H
+#endif  // SSW_H