diff --git a/plugin/setup.py b/plugin/setup.py
--- a/plugin/setup.py
+++ b/plugin/setup.py
@@ -15,7 +15,7 @@
 setup(
     name='pytest_divide_and_cover',

-    version='0.1.6',
+    version='0.2.0',

     description='Picky test coverage for pytest',
     long_description=LONG_DESCRIPTION,
diff --git a/plugin/src/pytest_divide_and_cover.py b/plugin/src/pytest_divide_and_cover.py
--- a/plugin/src/pytest_divide_and_cover.py
+++ b/plugin/src/pytest_divide_and_cover.py
@@ -60,21 +60,11 @@
                 paths.append(module_path_)
                 module_paths.append(module_path_)
             coverage_script.new_coverage(test_path, module_paths)
-        # This next bit needs to be run under a coverage tracer, with source
-        # based on paths. Specifically, it should use the root package from
-        # each path
-        roots = sorted({path.split('.', 1)[0] for path in paths})
-        coverage_script.make_import_coverage(roots)
-        print('Covering packages under: {}'.format(roots))
-        coverage_script.switch_coverage(coverage_script.import_coverage)
-        try:
-            for path in paths:
-                try:
-                    importlib.import_module(path)
-                except ImportError:
-                    print('Could not import {}'.format(path))
-        finally:
-            coverage_script.deactivate_coverage()
+        for path in paths:
+            try:
+                importlib.import_module(path)
+            except ImportError:
+                print('Could not import {}'.format(path))


 def pytest_runtest_setup(item):
diff --git a/runner/setup.py b/runner/setup.py
--- a/runner/setup.py
+++ b/runner/setup.py
@@ -15,7 +15,7 @@
 setup(
     name='divide_and_cover',

-    version='0.1.3',
+    version='0.2.0',

     description='Picky test coverage runner',
     long_description=LONG_DESCRIPTION,
diff --git a/runner/src/divide_and_cover/coverage_handler.py b/runner/src/divide_and_cover/coverage_handler.py
--- a/runner/src/divide_and_cover/coverage_handler.py
+++ b/runner/src/divide_and_cover/coverage_handler.py
@@ -1,8 +1,24 @@
+import os
+import re
 import sys

 from coverage import cmdline


+PYTHON_FILE = re.compile(r'(.*)\.py')
+
+
+def get_module_names_under(path):
+    for entry in os.listdir(path):
+        if os.path.isdir(os.path.join(path, entry)):
+            if os.path.exists(os.path.join(path, entry, '__init__.py')):
+                yield entry
+        else:
+            match = PYTHON_FILE.fullmatch(entry)
+            if match:
+                yield entry.group(1)
+
+
 def insert_unique(lst, item):
     if item not in lst:
         lst.append(item)
@@ -207,6 +223,11 @@
                 self.coverage.erase()

         self.coverage.start()
+        if os.path.isdir('src'):
+            roots = sorted(set(get_module_names_under('src')))
+            self.make_import_coverage(roots)
+            print('Covering packages under: {}'.format(roots))
+            self.switch_coverage(self.import_coverage)
         self.code_ran = True
         try:
             if options.module: