Merge pull request #732 from MDAnalysis/issue-669-test-offsets-cleanup

New cleanup plugin that deletes offset files after tests (closes #669)

testsuite/CHANGELOG

@@ -17,6 +17,8 @@ and https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
 
   * 0.14.0
 
+    - Added the cleanup plugin (--with-mda_cleanup) to delete offset files
+      after tests have run (Issue 669)
     - Made memleak testing python 3 compliant (Issue 662). It may be a moot
       point since python 3.4 now cleverly deals with leaks.
 

testsuite/MDAnalysisTests/plugins/__init__.py

@@ -61,7 +61,7 @@
 #  code won't be run again under coverage's watch.
 
 # Don't forget to also add your plugin to the import further ahead
-__all__ = ['memleak', 'capture_err', 'knownfailure']
+__all__ = ['memleak', 'capture_err', 'knownfailure', 'cleanup']
 
 import distutils.version
 try:
@@ -103,7 +103,7 @@ def _check_plugins_loaded():
 loaded_plugins = dict()
 
 # ADD HERE your plugin import
-from . import memleak, capture_err, knownfailure
+from . import memleak, capture_err, knownfailure, cleanup
 
 plugin_classes = []
 for plugin in __all__:

testsuite/MDAnalysisTests/plugins/capture_err.py

@@ -46,13 +46,13 @@ def __init__(self):
         self._buf = None
 
     def options(self, parser, env):
-        """Register commandline options
+        """Registers the commandline option, defaulting to enabled.
         """
         parser.add_option(
             "--no-errorcapture", action="store_false",
             default=not env.get(self.env_opt), dest="capture_error",
             help="Don't capture stderr (any stderr output "
-            "will be printed immediately) [NOSE_NO_ERRORCAPTURE]")
+            "will be printed immediately) [{}]".format(self.env_opt))
 
     def configure(self, options, conf):
         """Configure plugin. Plugin is enabled by default.

testsuite/MDAnalysisTests/plugins/cleanup.py

@@ -0,0 +1,74 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDAnalysis --- http://www.MDAnalysis.org
+# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
+# and contributors (see AUTHORS for the full list)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+"""Plugin that cleans up all .npz created during testing.
+"""
+# We may want to make the glob pattern an option, for extensibility.
+
+import nose
+from nose.plugins.base import Plugin 
+from os import walk, unlink, path
+from pkg_resources import resource_filename
+import warnings
+
+class Cleanup(Plugin):
+    """Removes XDR offset files after all testing is done."""
+    enabled = True
+    name = "mda_cleanup"
+    env_opt = 'NOSE_NO_MDA_CLEANUP'
+    score = 2000
+
+    def options(self, parser, env):
+        """Registers the commandline option, defaulting to enabled.
+        """
+        parser.add_option("--no-%s" % self.name,
+                          action="store_false",
+                          dest="do_mda_cleanup",
+                          default=not env.get(self.env_opt),
+                          help="Disables the cleanup of MDAnalysis offset "
+                          "(*.npz) files. [{}]".format(self.env_opt))
+
+    def configure(self, options, conf):
+        super(Cleanup, self).configure(options, conf)
+        self.config = conf # This will let other tests know about config settings.
+        try:
+            self.enabled = options.do_mda_cleanup
+        except AttributeError:
+            self.enabled = False
+        self.verbosity = options.verbosity
+
+    def report(self, stream):
+        from .. import __name__ as mdatestsname
+        dirname = resource_filename(mdatestsname, 'data')
+        if self.verbosity > 0:
+            stream.write("Cleanup: deleting offset files in "
+                "{}\n".format(dirname))
+        for root, dirs, fnames in walk(dirname):
+            for fname in fnames:
+                if fname.endswith('_offsets.npz'):
+                    fullname = path.join(root, fname)
+                    if self.verbosity > 1:
+                        stream.write("Cleanup: deleting offset file "
+                            "{}\n".format(fullname))
+                    try:
+                        unlink(fullname)
+                    except OSError:
+                        warnings.warn("Cleanup couldn't delete offset file "
+                                "{}".format(fullname))
+
+
+plugin_class = Cleanup
+