Fix compilation error with `clang` on some older OSX versions

.github/workflows/package.yml

@@ -76,9 +76,7 @@ jobs:
       run: python -m pip install --no-index --find-links=dist pyfastani
     - name: Install numpy
       run: python -m pip install numpy
-      if: ${{ !startsWith(matrix.python-version != 'pypy' }}
-    - name: Install tests requirements
-      run: python -m pip install -r pyfastani/tests/requirements.txt
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
     - name: Run tests without coverage
       run: python -m unittest pyfastani.tests -vv
 
@@ -144,9 +142,7 @@ jobs:
       run: python -m pip install --no-index --find-links=dist pyfastani
     - name: Install numpy
       run: python -m pip install numpy
-      if: ${{ !startsWith(matrix.python-version != 'pypy' }}
-    - name: Install tests requirements
-      run: python -m pip install -r pyfastani/tests/requirements.txt
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
     - name: Run tests without coverage
       run: python -m unittest pyfastani.tests -vv
 

.github/workflows/test.yml

@@ -66,7 +66,7 @@ jobs:
       run: python setup.py build_ext --inplace --debug
     - name: Install numpy
       run: python -m pip install numpy
-      if: ${{ !startsWith(matrix.python-version != 'pypy' }}
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
     - name: Install tests requirements
       run: python -m pip install -r pyfastani/tests/requirements.txt
     - name: Test with coverage
@@ -138,7 +138,7 @@ jobs:
     - name: Build C extension
       run: python setup.py build_ext --inplace --debug
     - name: Install numpy
-      if: ${{ matrix.python-impl != 'PyPy' }}
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
       run: python -m pip install numpy
     - name: Install tests requirements
       run: python -m pip install -r pyfastani/tests/requirements.txt

setup.cfg

@@ -52,6 +52,7 @@ setup_requires =
 
 [options.package_data]
 pyfastani = py.typed, *.pyi
+pyfastani.tests = requirements.txt
 
 [publicize_headers]
 sources = vendor/FastANI/src

setup.py

@@ -112,6 +112,30 @@ class build_ext(_build_ext):
     """A `build_ext` that disables optimizations if compiled in debug mode.
     """
 
+    # --- Autotools-like helpers ---
+
+    def _silent_spawn(self, cmd):
+        try:
+            subprocess.run(cmd, check=True, stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
+        except subprocess.CalledProcessError as err:
+            raise CompileError(err.stderr)
+
+    def _needs_clang_flags(self):
+        self.mkpath(self.build_temp)
+        testfile = os.path.join(self.build_temp, "testc++11.cpp")
+
+        with open(testfile, "w") as f:
+            f.write('#include <chrono>\n')
+        try:
+            with mock.patch.object(self.compiler, "spawn", new=self._silent_spawn):
+                objects = self.compiler.compile([testfile], debug=self.debug)
+        except CompileError as err:
+            log.warn('failed to include <chrono>, assuming we need clang flags')
+            return True
+        else:
+            log.info('successfully built a C++11 program with default flags')
+            return False
+
     def finalize_options(self):
         _build_ext.finalize_options(self)
         self._clib_cmd = self.get_finalized_command("build_clib")
@@ -179,6 +203,11 @@ class build_ext(_build_ext):
             ext.extra_compile_args.append("-std=c++11")
             ext.extra_link_args.append("-std=c++11")
 
+        # in case we are compiling with clang, make sure to use libstdc++
+        if self.compiler.compiler_type == "unix" and sys.platform == "darwin":
+            ext.extra_compile_args.append("-stdlib=libc++")
+            ext.extra_link_args.append("-stdlib=libc++")
+
         # build the rest of the extension as normal
         _build_ext.build_extension(self, ext)