Merge pull request #1570 from effigies/readlink_bug

FIX: Fix symlink test in copyfile

Author: satra

CHANGES

@@ -3,6 +3,7 @@ Upcoming release 0.13
 
 * TST: reduce the size of docker images & use tags for images (https://github.com/nipy/nipype/pull/1564)
 * ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563)
+* FIX: Fix symlink test in copyfile (https://github.com/nipy/nipype/pull/1570)
 
 
 Release 0.12.1 (August 3, 2016)

nipype/utils/filemanip.py

@@ -234,8 +234,8 @@ def copyfile(originalfile, newfile, copy=False, create_new=False,
     keep = False
     if os.path.lexists(newfile):
         if os.path.islink(newfile):
-            if all(os.path.readlink(newfile) == originalfile, not use_hardlink,
-                   not copy):
+            if all((os.readlink(newfile) == originalfile, not use_hardlink,
+                    not copy)):
                 keep = True
         elif posixpath.samefile(newfile, originalfile):
             keep = True

nipype/utils/tests/test_filemanip.py

@@ -157,6 +157,21 @@ def test_linkchain():
     yield assert_false, os.path.islink(new_hdr3)
     yield assert_true, os.path.samefile(orig_img, new_img3)
     yield assert_true, os.path.samefile(orig_hdr, new_hdr3)
+
+    # Test that re-copying leaves files
+    stat1 = os.stat(new_img1)
+    stat2 = os.stat(new_img2)
+    stat3 = os.stat(new_img3)
+    # Same symlink
+    copyfile(orig_img, new_img1)
+    # Hash matches
+    copyfile(new_img1, new_img2, copy=True)
+    # Hardlinks
+    copyfile(new_img1, new_img3, copy=True, use_hardlink=True)
+    yield assert_equal, stat1, os.stat(new_img1)
+    yield assert_equal, stat2, os.stat(new_img2)
+    yield assert_equal, stat3, os.stat(new_img3)
+
     os.unlink(new_img1)
     os.unlink(new_hdr1)
     os.unlink(new_img2)