Python console file shouldn't be treated as physical.

python/src/com/jetbrains/python/psi/impl/PyFileImpl.java

@@ -24,6 +24,7 @@ import com.intellij.openapi.fileTypes.FileType;
 import com.intellij.openapi.roots.ProjectFileIndex;
 import com.intellij.openapi.util.Key;
 import com.intellij.openapi.util.io.FileUtil;
+import com.intellij.openapi.vfs.NonPhysicalFileSystem;
 import com.intellij.openapi.vfs.VfsUtilCore;
 import com.intellij.openapi.vfs.VirtualFile;
 import com.intellij.psi.*;
@@ -729,7 +730,8 @@ public class PyFileImpl extends PsiFileBase implements PyFile, PyExpression {
   public String extractDeprecationMessage() {
     if (canHaveDeprecationMessage(getText())) {
       return PyFunctionImpl.extractDeprecationMessage(getStatements());
-    } else {
+    }
+    else {
       return null;
     }
   }
@@ -894,4 +896,13 @@ public class PyFileImpl extends PsiFileBase implements PyFile, PyExpression {
       }
     };
   }
+
+  @Override
+  public boolean isPhysical() {
+    VirtualFile virtualFile = getVirtualFile();
+    if (virtualFile != null && virtualFile.getFileSystem() instanceof NonPhysicalFileSystem) {
+      return false;
+    }
+    return super.isPhysical();
+  }
 }