From 3a1256691216e53576464942ee7e827cc55419e4 Mon Sep 17 00:00:00 2001
From: BenTenmann <benji.tenmann@me.com>
Date: Sun, 2 Jan 2022 11:22:27 +0000
Subject: [PATCH 1/2] fix: add openmp macOS

---
 .gitignore     |  2 ++
 pyproject.toml |  3 +++
 setup.py       | 66 +++++++++++++++++++++++++++++++++++++++++++-------
 3 files changed, 62 insertions(+), 9 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/.gitignore b/.gitignore
index b09d791..80100b2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -36,3 +36,5 @@ nosetests.xml
 .project
 .pydevproject
 .python-version
+build-test.sh
+.idea
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..8fe2f47
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
index c0ef96a..00e30e4 100644
--- a/setup.py
+++ b/setup.py
@@ -1,20 +1,68 @@
-from setuptools import setup, Extension
-
+import logging
 import os
+import platform
+import shutil
+import subprocess
+
+from setuptools import setup, Extension
 
 OPENMP_DISABLED = os.environ.get('OPENMP_DISABLED', False)
-libraries=['clustalo', 'stdc++']
-extra_compile_args = []
+libraries = ['clustalo', 'stdc++']
+
+# if not OPENMP_DISABLED:
+#     libraries.append('gomp')
+
+
+class BuildFlags:
+    _tools_formulae = {
+        'Darwin': ('brew', 'libomp'),
+    }
+    _args = {
+        'Darwin': {
+            'compiler': ['-Xpreprocessor', '-fopenmp'],
+            'linker': ['-lomp']
+        }
+    }
+    _default_args = {
+        'compiler': ['-fopenmp'],
+        'linker': ['-fopenmp']
+    }
+    compiler: list
+    linker: list
+
+    def __init__(self):
+        self._system = platform.system()
+        tool, formula = self._tools_formulae.get(self._system, ('apt', 'libomp-dev'))
+        args = self._args.get(self._system, self._default_args)
+
+        not_found = self._libomp_check(tool, formula)
+        if not_found is not None:
+            logging.warning(f'{repr(not_found)} not found -- cannot compile parallelized code')
+            for key in args:
+                args[key] = []
+
+        for key, val in args.items():
+            self.__setattr__(key, val)
+
+    @staticmethod
+    def _libomp_check(tool, formula):
+        if shutil.which(tool) is None:
+            return tool
+
+        formulae = subprocess.check_output([tool, 'list']).decode()
+        if formula not in formulae:
+            return formula
+
+        return None
 
-if not OPENMP_DISABLED:
-    libraries.append('gomp')
-    extra_compile_args.append('-fopenmp')
 
+flags = BuildFlags()
 module = Extension('clustalo',
-                   sources = ['clustalo.c'],
+                   sources=['clustalo.c'],
                    include_dirs=['/usr/include/clustalo', '/usr/local/include/clustalo'],
                    libraries=libraries,
-                   extra_compile_args=extra_compile_args)
+                   extra_compile_args=flags.compiler,
+                   extra_link_args=flags.linker)
 
 setup(name='clustalo',
       version='0.1.2',

From 6a16073a3fee60d9bb41c0995f40b6afecdaf1b0 Mon Sep 17 00:00:00 2001
From: BenTenmann <benji.tenmann@me.com>
Date: Sun, 2 Jan 2022 12:05:35 +0000
Subject: [PATCH 2/2] fix: add library path

---
 setup.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/setup.py b/setup.py
index 00e30e4..9d71ed4 100644
--- a/setup.py
+++ b/setup.py
@@ -9,9 +9,6 @@
 OPENMP_DISABLED = os.environ.get('OPENMP_DISABLED', False)
 libraries = ['clustalo', 'stdc++']
 
-# if not OPENMP_DISABLED:
-#     libraries.append('gomp')
-
 
 class BuildFlags:
     _tools_formulae = {
@@ -60,6 +57,7 @@ def _libomp_check(tool, formula):
 module = Extension('clustalo',
                    sources=['clustalo.c'],
                    include_dirs=['/usr/include/clustalo', '/usr/local/include/clustalo'],
+                   library_dirs=['/usr/local/lib'],
                    libraries=libraries,
                    extra_compile_args=flags.compiler,
                    extra_link_args=flags.linker)