Merge pull request scipy#8633 from rgommers/netcdf-append-issue

BUG: io: fix regression in `io.netcdf_file` with append mode.
haidark · Apr 1, 2018 · fadc841 · fadc841
2 parents 47c0a24 + 5d0e3b0
commit fadc841
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Showing 2 changed files with 20 additions and 3 deletions.
diff --git a/scipy/io/netcdf.py b/scipy/io/netcdf.py
@@ -701,7 +701,8 @@ def _read_var_array(self):
                 else:
                     pos = self.fp.tell()
                     self.fp.seek(begin_)
-                    data = frombuffer(self.fp.read(a_size), dtype=dtype_)
+                    data = frombuffer(self.fp.read(a_size), dtype=dtype_
+                                     ).copy()
                     data.shape = shape
                     self.fp.seek(pos)
 
@@ -723,7 +724,8 @@ def _read_var_array(self):
             else:
                 pos = self.fp.tell()
                 self.fp.seek(begin)
-                rec_array = frombuffer(self.fp.read(self._recs*self._recsize), dtype=dtypes)
+                rec_array = frombuffer(self.fp.read(self._recs*self._recsize),
+                                       dtype=dtypes).copy()
                 rec_array.shape = (self._recs,)
                 self.fp.seek(pos)
 
@@ -766,7 +768,7 @@ def _read_att_values(self):
         self.fp.read(-count % 4)  # read padding
 
         if typecode is not 'c':
-            values = frombuffer(values, dtype='>%s' % typecode)
+            values = frombuffer(values, dtype='>%s' % typecode).copy()
             if values.shape == (1,):
                 values = values[0]
         else:

diff --git a/scipy/io/tests/test_netcdf.py b/scipy/io/tests/test_netcdf.py
@@ -254,6 +254,21 @@ def test_itemset_no_segfault_on_readonly():
     assert_raises(RuntimeError, time_var.assignValue, 42)
 
 
+def test_appending_issue_gh_8625():
+    stream = BytesIO()
+
+    with make_simple(stream, mode='w') as f:
+        f.createDimension('x', 2)
+        f.createVariable('x', float, ('x',))
+        f.variables['x'][...] = 1
+        f.flush()
+        contents = stream.getvalue()
+
+    stream = BytesIO(contents)
+    with netcdf_file(stream, mode='a') as f:
+        f.variables['x'][...] = 2
+
+
 def test_write_invalid_dtype():
     dtypes = ['int64', 'uint64']
     if np.dtype('int').itemsize == 8:   # 64-bit machines