Merge pull request #2783 abostroem/gzip_fix

Conflicts:

	CHANGES.rst

CHANGES.rst

@@ -18,6 +18,9 @@ Bug Fixes
 
 - ``astropy.io.fits``
 
+  - Fixed crash when reading gzip-compressed FITS tables through the Astropy
+    ``Table`` interface. [#2783]
+
 - ``astropy.io.misc``
 
 - ``astropy.io.registry``

astropy/io/fits/file.py

@@ -2,7 +2,8 @@
 
 from __future__ import division, with_statement
 
-import gzip
+from ...utils.compat import gzip as _astropy_gzip
+import gzip as _system_gzip
 import mmap
 import os
 import tempfile
@@ -70,6 +71,7 @@
 GZIP_MAGIC = b('\x1f\x8b\x08')
 PKZIP_MAGIC = b('\x50\x4b\x03\x04')
 
+_GZIP_FILE_TYPES = (_astropy_gzip, _system_gzip)
 
 class _File(object):
     """
@@ -152,7 +154,7 @@ def __init__(self, fileobj=None, mode=None, memmap=False, clobber=False):
 
         self.fileobj_mode = fileobj_mode(self.__file)
 
-        if isinstance(fileobj, gzip.GzipFile):
+        if isinstance(fileobj, (_astropy_gzip.GzipFile, _system_gzip.GzipFile)):
             self.compression = 'gzip'
         elif isinstance(fileobj, zipfile.ZipFile):
             # Reading from zip files is supported but not writing (yet)
@@ -297,7 +299,7 @@ def seek(self, offset, whence=0):
         # present, we implement our own support for it here
         if not hasattr(self.__file, 'seek'):
             return
-        if isinstance(self.__file, gzip.GzipFile):
+        if isinstance(self.__file, (_astropy_gzip.GzipFile, _system_gzip.GzipFile)):
             if whence:
                 if whence == 1:
                     offset = self.__file.offset + offset
@@ -383,7 +385,7 @@ def _open_fileobj(self, fileobj, mode, clobber):
         elif isfile(fileobj):
             self.__file = fileobj_open(self.name, PYFITS_MODES[mode])
         else:
-            self.__file = gzip.open(self.name, PYFITS_MODES[mode])
+            self.__file = _astropy_gzip.open(self.name, PYFITS_MODES[mode])
 
         if fmode == 'ab+':
             # Return to the beginning of the file--in Python 3 when opening in
@@ -447,7 +449,7 @@ def _open_filename(self, filename, mode, clobber):
 
         if ext == '.gz' or magic.startswith(GZIP_MAGIC):
             # Handle gzip files
-            self.__file = gzip.open(self.name, PYFITS_MODES[mode])
+            self.__file = _astropy_gzip.open(self.name, PYFITS_MODES[mode])
             self.compression = 'gzip'
         elif ext == '.zip' or magic.startswith(PKZIP_MAGIC):
             # Handle zip files
@@ -538,4 +540,4 @@ def _is_random_access_file_backed(fileobj):
     from an already opened `zipfile.ZipFile` object.
     """
 
-    return isfile(fileobj) or isinstance(fileobj, gzip.GzipFile)
+    return isfile(fileobj) or isinstance(fileobj, (_astropy_gzip.GzipFile, _system_gzip.GzipFile))

astropy/io/fits/tests/test_core.py

@@ -644,6 +644,22 @@ def test_open_zipped_writeable(self):
         pytest.raises(IOError, fits.open, zf, 'update')
         pytest.raises(IOError, fits.open, zf, 'append')
 
+    def test_read_open_astropy_gzip_file(self):
+        """
+        Regression test for https://github.com/astropy/astropy/issues/2774
+
+        This tests reading from a ``GzipFile`` object from Astropy's
+        compatibility copy of the ``gzip`` module.
+        """
+
+        from ....utils.compat import gzip
+
+        gf = gzip.GzipFile(self._make_gzip_file())
+        try:
+            assert len(fits.open(gf)) == 5
+        finally:
+            gf.close()
+
     @raises(IOError)
     def test_open_multiple_member_zipfile(self):
         """