Annotated files are only created for source files relative to the current directory. When writing to a separate file, annotation file names include the directory hierarchy flattened, so that same-named files won't collide.

1 files changed, 20 insertions, 12 deletions

diff --git a/coverage/annotate.py b/coverage/annotate.py
index 14a7b7c..c0c6980 100644
--- a/coverage/annotate.py
+++ b/coverage/annotate.py
@@ -7,7 +7,6 @@ from coverage.report import Reporter
 class AnnotateReporter(Reporter):
     def __init__(self, coverage, ignore_errors=False):
         super(AnnotateReporter, self).__init__(coverage, ignore_errors)
-        
         self.directory = None
         
     blank_re = re.compile(r"\s*(#|$)")
@@ -17,27 +16,36 @@ class AnnotateReporter(Reporter):
         self.find_code_units(morfs, omit_prefixes)
 
         self.directory = directory
+        if self.directory and not os.path.exists(self.directory):
+            os.makedirs(self.directory)
+
         for cu in self.code_units:
             try:
+                if not cu.relative:
+                    continue
                 statements, excluded, missing, _ = self.coverage.analyze(cu)
-                self.annotate_file(cu.filename, statements, excluded, missing)
+                self.annotate_file(cu, statements, excluded, missing)
             except KeyboardInterrupt:
                 raise
             except:
                 if not self.ignore_errors:
                     raise
                 
-    def annotate_file(self, filename, statements, excluded, missing):
+    def annotate_file(self, cu, statements, excluded, missing):
+        """Annotate a single file.
+        
+        `cu` is the CodeUnit for the file to annotate.
+        
+        """
+        filename = cu.filename
         source = open(filename, 'r')
         if self.directory:
-            if not os.path.exists(self.directory):
-                os.makedirs(self.directory)
-            dest_file = os.path.join(self.directory,
-                                     os.path.basename(filename)
-                                     + ',cover')
+            dest_file = os.path.join(self.directory, cu.flat_rootname()) + ".py"
         else:
-            dest_file = filename + ',cover'
+            dest_file = filename
+        dest_file += ",cover"
         dest = open(dest_file, 'w')
+
         lineno = 0
         i = 0
         j = 0
@@ -46,11 +54,11 @@ class AnnotateReporter(Reporter):
             line = source.readline()
             if line == '':
                 break
-            lineno = lineno + 1
+            lineno += 1
             while i < len(statements) and statements[i] < lineno:
-                i = i + 1
+                i += 1
             while j < len(missing) and missing[j] < lineno:
-                j = j + 1
+                j += 1
             if i < len(statements) and statements[i] == lineno:
                 covered = j >= len(missing) or missing[j] > lineno
             if self.blank_re.match(line):