diff --git a/interfaces/cython/SConscript b/interfaces/cython/SConscript
index 71403a4c4..f2cd3054b 100644
--- a/interfaces/cython/SConscript
+++ b/interfaces/cython/SConscript
@@ -84,6 +84,9 @@ if localenv['OS'] == 'Windows':
         compilerOpt = ' --compiler=mingw32'
 else:
     compilerOpt = ''
+    if '-fprofile-arcs' in localenv['CCFLAGS']:
+        localenv['py_extra_compiler_args'] = repr(['-fprofile-arcs', '-ftest-coverage'])
+        localenv['py_extra_link_args'] = repr(['-fprofile-arcs', '-ftest-coverage'])
 
 dataFiles = localenv.RecursiveInstall('#interfaces/cython/cantera/data',
                                       '#build/data')
diff --git a/platform/posix/coverage.py b/platform/posix/coverage.py
index 6e4a2dc2a..3075b2c0f 100755
--- a/platform/posix/coverage.py
+++ b/platform/posix/coverage.py
@@ -66,8 +66,9 @@ def collect():
     # Filter to remove non-Cantera code
     subprocess.call(['lcov',
                      '-o', 'coverage.info',
-                     '-r', 'coverage-raw.info',
-                     '/usr/include/*', '*/ext/*'])
+                     '-e', 'coverage-raw.info',
+                     os.getcwd() + '/include/*',
+                     os.getcwd() + '/src/*'])
     os.remove('coverage-raw.info')
 
 def genhtml():