Merge remote-tracking branch 'upstream/master' into malloc_hooks

4 files changed, 50 insertions, 16 deletions

diff --git a/numpy/lib/function_base.py b/numpy/lib/function_base.py
index 6d9e65697..f3df3b96b 100644
--- a/numpy/lib/function_base.py
+++ b/numpy/lib/function_base.py
@@ -778,7 +778,7 @@ def select(condlist, choicelist, default=0):
             S = S*ones(asarray(pfac).shape, S.dtype)
     return choose(S, tuple(choicelist))
 
-def copy(a, order='C', maskna=None):
+def copy(a, order='C'):
     """
     Return an array copy of the given object.
 
@@ -791,10 +791,6 @@ def copy(a, order='C', maskna=None):
         'F' means F-order, 'A' means 'F' if `a` is Fortran contiguous,
         'C' otherwise. 'K' means match the layout of `a` as closely
         as possible.
-    maskna : bool, optional
-        If specifies, forces the copy to have or to not have an
-        NA mask. This is a way to remove an NA mask from an array
-        while making a copy.
 
     Returns
     -------
@@ -824,7 +820,7 @@ def copy(a, order='C', maskna=None):
     False
 
     """
-    return array(a, order=order, copy=True, maskna=maskna)
+    return array(a, order=order, copy=True)
 
 # Basic operations
 
@@ -3377,7 +3373,6 @@ def delete(arr, obj, axis=None):
                     "invalid entry")
         newshape[axis]-=1;
         new = empty(newshape, arr.dtype, arr.flags.fnc)
-        new.flags.maskna = arr.flags.maskna
         slobj[axis] = slice(None, obj)
         new[slobj] = arr[slobj]
         slobj[axis] = slice(obj,None)
@@ -3394,7 +3389,6 @@ def delete(arr, obj, axis=None):
                 return arr.copy()
         newshape[axis] -= numtodel
         new = empty(newshape, arr.dtype, arr.flags.fnc)
-        new.flags.maskna = arr.flags.maskna
         # copy initial chunk
         if start == 0:
             pass
@@ -3526,7 +3520,6 @@ def insert(arr, obj, values, axis=None):
                     "in dimension %d" % (obj, N, axis))
         newshape[axis] += 1;
         new = empty(newshape, arr.dtype, arr.flags.fnc)
-        new.flags.maskna = arr.flags.maskna
         slobj[axis] = slice(None, obj)
         new[slobj] = arr[slobj]
         slobj[axis] = obj
@@ -3553,7 +3546,6 @@ def insert(arr, obj, values, axis=None):
     index2 = setdiff1d(arange(numnew+N),index1)
     newshape[axis] += numnew
     new = empty(newshape, arr.dtype, arr.flags.fnc)
-    new.flags.maskna = arr.flags.maskna
     slobj2 = [slice(None)]*ndim
     slobj[axis] = index1
     slobj2[axis] = index2
diff --git a/numpy/lib/npyio.py b/numpy/lib/npyio.py
index 221529929..cb14e4963 100644
--- a/numpy/lib/npyio.py
+++ b/numpy/lib/npyio.py
@@ -359,7 +359,6 @@ def load(file, mmap_mode=None):
         own_fid = True
     elif isinstance(file, gzip.GzipFile):
         fid = seek_gzip_factory(file)
-        own_fid = True
     else:
         fid = file
 
@@ -371,7 +370,7 @@ def load(file, mmap_mode=None):
         fid.seek(-N, 1) # back-up
         if magic.startswith(_ZIP_PREFIX):  # zip-file (assume .npz)
             own_fid = False
-            return NpzFile(fid, own_fid=True)
+            return NpzFile(fid, own_fid=own_fid)
         elif magic == format.MAGIC_PREFIX: # .npy file
             if mmap_mode:
                 return format.open_memmap(file, mode=mmap_mode)
diff --git a/numpy/lib/tests/test_io.py b/numpy/lib/tests/test_io.py
index 8922070df..c539c040a 100644
--- a/numpy/lib/tests/test_io.py
+++ b/numpy/lib/tests/test_io.py
@@ -167,6 +167,51 @@ class TestSavezLoad(RoundtripTest, TestCase):
         if errors:
             raise AssertionError(errors)
 
+    def test_not_closing_opened_fid(self):
+        # Test that issue #2178 is fixed:
+        # verify could seek on 'loaded' file
+
+        fd, tmp = mkstemp(suffix='.npz')
+        os.close(fd)
+        try:
+            fp = open(tmp, 'wb')
+            np.savez(fp, data='LOVELY LOAD')
+            fp.close()
+
+            fp = open(tmp, 'rb', 10000)
+            fp.seek(0)
+            assert_(not fp.closed)
+            _ = np.load(fp)['data']
+            assert_(not fp.closed)        # must not get closed by .load(opened fp)
+            fp.seek(0)
+            assert_(not fp.closed)
+
+        finally:
+            os.remove(tmp)
+
+    def test_closing_fid(self):
+        # Test that issue #1517 (too many opened files) remains closed
+        # It might be a "week" test since failed to get triggered on
+        # e.g. Debian sid of 2012 Jul 05 but was reported to
+        # trigger the failure on Ubuntu 10.04:
+        # http://projects.scipy.org/numpy/ticket/1517#comment:2
+        fd, tmp = mkstemp(suffix='.npz')
+        os.close(fd)
+
+        try:
+            fp = open(tmp, 'wb')
+            np.savez(fp, data='LOVELY LOAD')
+            fp.close()
+
+            for i in range(1, 1025):
+                try:
+                    np.load(tmp)["data"]
+                except Exception, e:
+                    raise AssertionError("Failed to load data from a file: %s" % e)
+        finally:
+            os.remove(tmp)
+
+
 class TestSaveTxt(TestCase):
     def test_array(self):
         a = np.array([[1, 2], [3, 4]], float)
diff --git a/numpy/lib/twodim_base.py b/numpy/lib/twodim_base.py
index eab8f867a..c1f75c630 100644
--- a/numpy/lib/twodim_base.py
+++ b/numpy/lib/twodim_base.py
@@ -166,7 +166,7 @@ def rot90(m, k=1):
         # k == 3
         return fliplr(m.swapaxes(0,1))
 
-def eye(N, M=None, k=0, dtype=float, maskna=False):
+def eye(N, M=None, k=0, dtype=float):
     """
     Return a 2-D array with ones on the diagonal and zeros elsewhere.
 
@@ -182,8 +182,6 @@ def eye(N, M=None, k=0, dtype=float, maskna=False):
       to a lower diagonal.
     dtype : data-type, optional
       Data-type of the returned array.
-    maskna : boolean
-      If this is true, the returned array will have an NA mask.
 
     Returns
     -------
@@ -209,7 +207,7 @@ def eye(N, M=None, k=0, dtype=float, maskna=False):
     """
     if M is None:
         M = N
-    m = zeros((N, M), dtype=dtype, maskna=maskna)
+    m = zeros((N, M), dtype=dtype)
     if k >= M:
         return m
     if k >= 0: