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.

--HG--
rename : test/farm/annotate/gold_anno_dir/a.py,cover => test/farm/annotate/gold_anno_dir/a_a.py,cover
rename : test/farm/annotate/gold_anno_dir/b.py,cover => test/farm/annotate/gold_anno_dir/b_b.py,cover

7 files changed, 45 insertions, 13 deletions

diff --git a/CHANGES.txt b/CHANGES.txt
index 6727d078..2f3d310c 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -9,6 +9,11 @@ Continued refactoring.
 

 - coverage.annotate_file is no longer available.

 

+- Annotation into a directory (-a -d) behaves differently.  The annotated files

+  are named with their hierarchy flattened so that same-named files from

+  different directories no longer collide.  Also, only files in the current

+  tree are included.

+

 - Programs executed with -x now behave more as they should, for example,

   __file__ has the correct value.

 

diff --git a/coverage/annotate.py b/coverage/annotate.py
index 14a7b7c7..c0c69800 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):
diff --git a/coverage/codeunit.py b/coverage/codeunit.py
index 96ed43bb..3c3d30f5 100644
--- a/coverage/codeunit.py
+++ b/coverage/codeunit.py
@@ -47,8 +47,11 @@ def code_unit_factory(morfs, file_locator, omit_prefixes=None):
 class CodeUnit:
     """Code unit: a filename or module.
     
+    Instance attributes:
+    
     `name` is a human-readable name for this code unit.
     `filename` is the os path from which we can read the source.
+    `relative` is a boolean.
     
     """
 
@@ -64,10 +67,26 @@ class CodeUnit:
 
         if hasattr(morf, '__name__'):
             n = morf.__name__
+            self.relative = True
         else:
             n = os.path.splitext(morf)[0]
-            n = file_locator.relative_filename(n)
+            rel = file_locator.relative_filename(n)
+            self.relative = (rel != n)
+            n = rel
         self.name = n
 
     def __cmp__(self, other):
         return cmp(self.name, other.name)
+
+    def flat_rootname(self):
+        """A base for a flat filename to correspond to this code unit.
+        
+        Useful for writing files about the code where you want all the files in
+        the same directory, but need to differentiate same-named files from
+        different directories.
+        
+        For example, the file a/b/c.py might return 'a_b_c'
+        
+        """
+        root = os.path.splitdrive(os.path.splitext(self.name)[0])[1]
+        return root.replace('\\', '_').replace('/', '_')
diff --git a/test/farm/annotate/gold_anno_dir/a___init__.py,cover b/test/farm/annotate/gold_anno_dir/a___init__.py,cover
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/test/farm/annotate/gold_anno_dir/a___init__.py,cover
diff --git a/test/farm/annotate/gold_anno_dir/a.py,cover b/test/farm/annotate/gold_anno_dir/a_a.py,cover
index 0c858f41..0c858f41 100644
--- a/test/farm/annotate/gold_anno_dir/a.py,cover
+++ b/test/farm/annotate/gold_anno_dir/a_a.py,cover
diff --git a/test/farm/annotate/gold_anno_dir/b___init__.py,cover b/test/farm/annotate/gold_anno_dir/b___init__.py,cover
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/test/farm/annotate/gold_anno_dir/b___init__.py,cover
diff --git a/test/farm/annotate/gold_anno_dir/b.py,cover b/test/farm/annotate/gold_anno_dir/b_b.py,cover
index 0bd04dac..0bd04dac 100644
--- a/test/farm/annotate/gold_anno_dir/b.py,cover
+++ b/test/farm/annotate/gold_anno_dir/b_b.py,cover