finalized fix of #556 (test failure due os.chdir/tempdir)

- use tempdir.in_tempdir() in test_hole.py
- added Hai Nguyen to AUTHORS and sphinx/source/conf.py
  (for #558)

package/AUTHORS

@@ -63,6 +63,7 @@ Chronological list of authors
   - Max Linke
   - Gorman Stock
   - Jonathan Barnoud
+  - Hai Nguyen
 
 External code
 -------------

package/doc/sphinx/source/conf.py

@@ -84,10 +84,11 @@ def __getattr__(cls, name):
     Xavier Deupi, Jan Domański, David L. Dotson, Lennard van der
     Feltz, Philip Fowler, Joseph Goose, Richard J. Gowers, Lukas
     Grossar, Benjamin Hall, Joe Jordan, Max Linke, Jinju Lu, Robert
-    McGibbon, Alex Nesterenko, Manuel Nuno Melo, Caio S. Souza, Danny
-    Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Sean
-    L. Seyler, Andy Somogyi, Lukas Stelzl, Gorman Stock, Isaac
-    Virshup, Zhuyi Xue, Carlos Yáñez S., and Oliver Beckstein"""
+    McGibbon, Alex Nesterenko, Manuel Nuno Melo, Hai Nguyen,
+    Caio S. Souza, Danny Parton, Joshua L. Phillips, Tyler Reddy,
+    Paul Rigor, Sean L. Seyler, Andy Somogyi, Lukas Stelzl, 
+    Gorman Stock, Isaac Virshup, Zhuyi Xue, Carlos Yáñez S.,
+    and Oliver Beckstein"""
 project = u'MDAnalysis'
 copyright = u'2005-2015, ' + authors
 

testsuite/MDAnalysisTests/analysis/test_hole.py

@@ -17,16 +17,15 @@
 
 import MDAnalysis
 import MDAnalysis.analysis.hole
+from MDAnalysis.analysis.hole import HOLEtraj
 
 from numpy.testing import TestCase, dec
 import numpy as np
 import nose
 from nose.plugins.attrib import attr
 
-import os
 import errno
-import tempfile
-import shutil
+import tempdir
 
 from MDAnalysisTests.datafiles import PDB_HOLE, XTC_HOLE
 from MDAnalysisTests import executable_not_found
@@ -45,11 +44,9 @@ def rlimits_missing():
 class TestHoleModule(TestCase):
     def setUp(self):
         self.universe = MDAnalysis.Universe(PDB_HOLE, XTC_HOLE)
-        self.dir_name = tempfile.mkdtemp()
         try:
             # on Unix we can manipulate our limits: http://docs.python.org/2/library/resource.html
             import resource
-
             self.soft_max_open_files, self.hard_max_open_files = resource.getrlimit(resource.RLIMIT_NOFILE)
         except ImportError:
             pass
@@ -67,41 +64,38 @@ def test_hole_module_fd_closure(self):
         try:
             # Hasten failure by setting "ulimit -n 64" (can't go too low because of open modules etc...)
             import resource
-
             resource.setrlimit(resource.RLIMIT_NOFILE, (64, self.hard_max_open_files))
         except ImportError:
             raise NotImplementedError("Test cannot be run without the resource module.")
-        import errno
-        from MDAnalysis.analysis.hole import HOLEtraj
 
-        os.chdir(self.dir_name)
-        try:
-            # will need to have the 'hole' command available in the path
-            H = HOLEtraj(self.universe, cvect=[0, 1, 0], sample=20.0)
-        except OSError as err:
-            if err.errno == errno.ENOENT:
-                raise OSError(errno.ENOENT, "HOLE binary not found")
-            raise
-        finally:
-            self._restore_rlimits()
-
-        # pretty unlikely that the code will get through 2 rounds if the MDA
-        # issue 129 isn't fixed, although this depends on the file descriptor
-        # open limit for the machine in question
-        try:
-            for i in xrange(2):
-                # will typically get an OSError for too many files being open after
-                # about 2 seconds if issue 129 isn't resolved
-                H.run()
-        except OSError as err:
-            if err.errno == errno.EMFILE:
-                raise AssertionError("HOLEtraj does not close file descriptors (Issue 129)")
-            elif err.errno == errno.ENOENT:
-                raise OSError(errno.ENOENT, "HOLE binary not found")
-            raise
-        finally:
-            # make sure to restore open file limit !!
-            self._restore_rlimits()
+        with tempdir.in_tempdir():
+            try:
+                # will need to have the 'hole' command available in the path
+                H = HOLEtraj(self.universe, cvect=[0, 1, 0], sample=20.0)
+            except OSError as err:
+                if err.errno == errno.ENOENT:
+                    raise OSError(errno.ENOENT, "HOLE binary not found")
+                raise
+            finally:
+                self._restore_rlimits()
+
+            # pretty unlikely that the code will get through 2 rounds if the MDA
+            # issue 129 isn't fixed, although this depends on the file descriptor
+            # open limit for the machine in question
+            try:
+                for i in xrange(2):
+                    # will typically get an OSError for too many files being open after
+                    # about 2 seconds if issue 129 isn't resolved
+                    H.run()
+            except OSError as err:
+                if err.errno == errno.EMFILE:
+                    raise AssertionError("HOLEtraj does not close file descriptors (Issue 129)")
+                elif err.errno == errno.ENOENT:
+                    raise OSError(errno.ENOENT, "HOLE binary not found")
+                raise
+            finally:
+                # make sure to restore open file limit !!
+                self._restore_rlimits()
 
     def _restore_rlimits(self):
         try:
@@ -114,6 +108,5 @@ def _restore_rlimits(self):
     def tearDown(self):
         self._restore_rlimits()
         del self.universe
-        shutil.rmtree(self.dir_name, ignore_errors=True)