Merge pull request #199 from rwest/fixtests

Progress towards fixing unit tests.  

There are some fixes to the makefile, instructions, and default database location.
Also, a work_in_progress decorator, that we should use to annotate any Unit Tests that we currently expect to fail. You just add @work_in_progress to the line before the unit test definition. 
If someone could do that for all the currently failing tests, as a half-way house to actually making them work, we will at least be able to detect changes and extra errors.

Author: connie

Makefile

@@ -14,12 +14,16 @@ minimal:
 	python setup.py build_ext minimal --build-lib . --build-temp build --pyrex-c-in-temp
 
 main:
+	echo "Checking you have PyDQED..."
+	@ python -c 'import pydqed; print pydqed.__file__'
 	python setup.py build_ext main --build-lib . --build-temp build --pyrex-c-in-temp
 
 measure:
 	python setup.py build_ext measure --build-lib . --build-temp build --pyrex-c-in-temp
 
 solver:
+	echo "Checking you have PyDAS..."
+	@ python -c 'import pydas; print pydas.__file__'
 	python setup.py build_ext solver --build-lib . --build-temp build --pyrex-c-in-temp
 
 cantherm:

documentation/source/users/rmg/installation/linux.rst

@@ -26,10 +26,10 @@ The instructions listed below have been confirmed on a fresh Ubuntu 12.04 instal
 	sudo pip install scipy cython nose matplotlib quantities guppy sphinx psutil xlwt freetype2 libpng-dev
 	
 	cd ~
-	git clone git@github.com:jwallen/PyDAS.git
-	git clone git@github.com:jwallen/PyDQED.git
-	cd PyDAS; make F77=gfortran; sudo make install
-	cd ../PyDQED; make F77=gfortran; sudo make install
+	git clone https://github.com/GreenGroup/PyDAS.git
+	git clone https://github.com/GreenGroup/PyDQED.git
+	cd PyDAS; make F77=gfortran; sudo make install; cd ..
+	cd PyDQED; make F77=gfortran; sudo make install; cd ..
 
 * Install RDKit
 
@@ -61,10 +61,11 @@ The instructions listed below have been confirmed on a fresh Ubuntu 12.04 instal
 * Install RMG-Py: ::
 
 	cd ~
-	git clone git@github.com:GreenGroup/RMG-database.git
-	git clone git@github.com:GreenGroup/RMG-Py.git
+	git clone https://github.com/GreenGroup/RMG-database.git
+	git clone https://github.com/GreenGroup/RMG-Py.git
 	sudo pip install -r RMG-Py/requirements.txt
-	cd RMG-Py; make
+	cd RMG-Py
+    make
 
 * Run an example: ::
 
@@ -74,6 +75,6 @@ The instructions listed below have been confirmed on a fresh Ubuntu 12.04 instal
 
   You can also use the Makefile targets to test and run examples: ::
   
-  make test
-  make eg1
-  make eg2
+	make test
+	make eg1
+	make eg2

external/wip.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+# encoding: utf-8
+#
+# Decorator to mark a unit test as a "work_in_progress"
+# From http://www.natpryce.com/articles/000788.html
+# Copyright 2011 Nat Pryce. Posted 2011-05-30
+from functools import wraps
+from nose.plugins.attrib import attr
+from nose.plugins.skip import SkipTest
+
+def fail(message):
+    raise AssertionError(message)
+
+def work_in_progress(f):
+    @wraps(f)
+    def run_test(*args, **kwargs):
+        try:
+            f(*args, **kwargs)
+        except Exception as e:
+            raise SkipTest("WIP test failed: " + str(e))
+        fail("test passed but marked as work in progress")
+
+    return attr('work_in_progress')(run_test)

rmgpy/__init__.py

@@ -139,8 +139,8 @@ def reset(self):
         Reset all settings to their default values.
         """
         self.filename = None
-        working_dir = os.path.abspath(os.path.dirname(__file__))
-        self['database.directory'] = os.path.realpath(os.path.join(working_dir, '..', '..', 'RMG-database', 'input'))
+        rmgpy_module_dir = os.path.abspath(os.path.dirname(__file__))
+        self['database.directory'] = os.path.realpath(os.path.join(rmgpy_module_dir, '..', '..', 'RMG-database', 'input'))
         self.sources['database.directory'] = 'Default, relative to RMG-Py source code'
 
 # The global settings object

rmgpy/cantherm/gaussianTest.py

@@ -8,15 +8,15 @@
 from rmgpy.cantherm.gaussian import GaussianLog
 from rmgpy.statmech import Conformer, IdealGasTranslation, LinearRotor, NonlinearRotor, HarmonicOscillator, HinderedRotor
 import rmgpy.constants as constants
-
+from external.wip import work_in_progress
 ################################################################################
 
 class GaussianTest(unittest.TestCase):
     """
     Contains unit tests for the chempy.io.gaussian module, used for reading
     and writing Gaussian files.
     """
-    
+    @work_in_progress
     def testLoadEthyleneFromGaussianLog_CBSQB3(self):
         """
         Uses a Gaussian03 log file for ethylene (C2H4) to test that its
@@ -71,6 +71,7 @@ def testLoadOxygenFromGaussianLog(self):
         self.assertEqual(conformer.spinMultiplicity, 3)
         self.assertEqual(conformer.opticalIsomers, 1)
 
+    @work_in_progress
     def testLoadEthyleneFromGaussianLog_G3(self):
         """
         Uses a Gaussian03 log file for ethylene (C2H4) to test that its

rmgpy/data/solvationTest.py

@@ -3,6 +3,7 @@
 
 import os
 from unittest import TestCase
+from external.wip import work_in_progress
 
 from rmgpy import settings
 from rmgpy.species import Species
@@ -55,6 +56,7 @@ def testSoluteGeneration(self):
             print self.assertAlmostEqual(soluteData.L, L)
             print self.assertAlmostEqual(soluteData.A, A)
 
+    @work_in_progress
     def testCorrectionGeneration(self):
         "Test we can estimate solvation thermochemistry."
         self.database = SolvationDatabase()