dvc: properly build DAG for dependency directories

Fixes #1338

Signed-off-by: Ruslan Kuprieiev <[email protected]>

dvc/project.py

@@ -1058,7 +1058,8 @@ class Project(object):
             for dep in stage.deps:
                 for out in outs:
                     if out.path != dep.path \
-                       and not dep.path.startswith(out.path + out.sep):
+                       and not dep.path.startswith(out.path + out.sep) \
+                       and not out.path.startswith(dep.path + dep.sep):
                         continue
 
                     dep_stage = out.stage

tests/test_repro.py

@@ -79,6 +79,47 @@ class TestReproDepUnderDir(TestDvc):
         self.assertTrue(filecmp.cmp(self.file1, self.FOO, shallow=False))
 
 
+class TestReproDepDirWithOutputsUnderIt(TestDvc):
+    def test(self):
+        stages = self.dvc.add(self.DATA)
+        self.assertEqual(len(stages), 1)
+        self.assertTrue(stages[0] is not None)
+
+        sleep()
+
+        stages = self.dvc.add(self.DATA_SUB)
+        self.assertEqual(len(stages), 1)
+        self.assertTrue(stages[0] is not None)
+
+        sleep()
+
+        stage = self.dvc.run(fname='Dvcfile',
+                             deps=[self.DATA, self.DATA_SUB])
+        self.assertTrue(stage is not None)
+
+        sleep()
+
+        file1 = 'file1'
+        file1_stage = file1 + '.dvc'
+        stage = self.dvc.run(fname=file1_stage,
+                             deps=[self.DATA_DIR],
+                             outs=[file1],
+                             cmd='python {} {} {}'.format(self.CODE,
+                                                          self.DATA,
+                                                          file1))
+        self.assertTrue(stage is not None)
+
+        sleep()
+
+        os.unlink(self.DATA)
+        shutil.copyfile(self.FOO, self.DATA)
+
+        sleep()
+
+        stages = self.dvc.reproduce(file1_stage)
+        self.assertEqual(len(stages), 2)
+
+
 class TestReproNoDeps(TestRepro):
     def test(self):
         out = 'out'