Added utils from broadinstitute/vital-ngs, added simple unit tests to verify Travis CI

.coveragerc

@@ -0,0 +1,14 @@
+# .coveragerc to control test coverage report
+[report]
+
+exclude_lines =
+    pragma: no cover
+
+    raise AssertionError
+    raise NotImplementedError
+
+    def __repr__
+    if self\.debug
+
+    if 0:
+    if __name__ == .__main__.:

.travis.yml

@@ -0,0 +1,29 @@
+language: python
+sudo: false
+
+cache:
+ directories:
+  - $HOME/virtualenv
+
+env:
+  global:
+  - CACHE_DIR="$HOME/virtualenv"
+  - PYTHONIOENCODING=UTF8
+
+python:
+  - 2.7
+  - 3.4
+
+before_install:
+  - travis/before_install.sh
+
+install:
+  - travis/install-pip.sh
+  - travis/install-tools.sh
+
+script:
+  - travis/tests-unit.sh
+  - travis/tests-long.sh
+
+after_success:
+  - coveralls

README.md

@@ -2,6 +2,8 @@
 
 **Composite of Multiple Signals**: tests for selection in meiotically recombinant populations
 
+[![Travis CI Status](https://api.travis-ci.org/broadinstitute/cms.svg)](https://travis-ci.org/broadinstitute/cms)
+[![Coverage Status](https://coveralls.io/repos/broadinstitute/cms/badge.svg)](https://coveralls.io/r/broadinstitute/cms)
 [![Documentation Status](https://readthedocs.org/projects/broad-cms/badge/?version=latest)](https://readthedocs.org/projects/broad-cms/?badge=latest)
 
 More detailed documentation can be found at http://broad-cms.readthedocs.org/

cms/VERSION

@@ -0,0 +1 @@
+7bc1b96-dirty

cms/cms_exceptions.py

@@ -0,0 +1,6 @@
+class CMSException(Exception):
+    '''base class for CMS exceptions. except for built-ins, all should be descendants of this exception so that an except block for this exception will catch all others'''
+    pass
+
+class CMSInputError(CMSException):
+    pass

cms/main.py

@@ -0,0 +1,12 @@
+#!/usr/bin/python
+
+class CMS(object):
+    def __init__(self):
+        pass
+
+    def main(self):
+        return 0
+
+if __name__ == "__main__":
+    cms = CMS()
+    cms.main()

cms/selection.py

@@ -0,0 +1,8 @@
+#!/usr/bin/python
+
+class Selection(object):
+	def __init__(self):
+		pass
+
+	def main(self):
+		return 0

cms/test/__init__.py

@@ -0,0 +1,35 @@
+'''utilities for tests'''
+
+__author__ = "irwin@broadinstitute.org"
+
+import filecmp, os, unittest
+
+import util.file
+
+def assert_equal_contents(testCase, filename1, filename2) :
+    'Assert contents of two files are equal for a unittest.TestCase'
+    testCase.assertTrue(filecmp.cmp(filename1, filename2, shallow=False))
+
+class TestCaseWithTmp(unittest.TestCase) :
+    'Base class for tests that use tempDir'
+    def setUp(self) :
+        util.file.set_tmpDir(type(self).__name__)
+
+    def tearDown(self) :
+        util.file.destroy_tmpDir()
+
+    def assertEqualContents(self, f1, f2) :
+        assert_equal_contents(self, f1, f2)
+
+
+"""
+When "nose" executes python scripts for automated testing, it excludes ones with
+the executable bit set (in case they aren't import safe). To prevent any of the 
+tests in this folder from being silently excluded, assure this bit is not set.
+"""
+def assert_none_executable() :
+    testDir = os.path.dirname(__file__)
+    assert all(not os.access(os.path.join(testDir, filename), os.X_OK)
+               for filename in os.listdir(testDir)
+               if filename.endswith('.py'))
+assert_none_executable()

cms/test/integration/test_main.py

@@ -0,0 +1,18 @@
+#!/usr/bin/python
+
+import unittest
+import main
+
+class TestCMS(unittest.TestCase):
+    # to be executed prior to running tests
+    def setUp(self):
+        self.cms = main.CMS()
+        pass
+
+    # to be executed after running tests, regardless of pass/fail
+    # only called if setUp succeeds
+    def tearDown(self):
+        pass
+
+    def test_main_return_code(self):
+        self.assertEqual( self.cms.main(), 0 )

cms/test/unit/test_selection.py

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+#!/usr/bin/python
+
+import unittest
+from selection import Selection
+
+class TestSelection(unittest.TestCase):
+    # to be executed prior to running tests
+    def setUp(self):
+        self.cms_selection = Selection()
+        pass
+
+    # to be executed after running tests, regardless of pass/fail
+    # only called if setUp succeeds
+    def tearDown(self):
+        pass
+
+    def test_selection_return_code(self):
+        self.assertEqual( self.cms_selection.main(), 0 )

cms/test/unit/test_tools.py

@@ -0,0 +1,33 @@
+# Unit tests for tools/__init__.py
+
+__author__ = "dpark@broadinstitute.org"
+
+import tools
+from tools import *
+import unittest, tempfile, shutil, os, logging
+import util.cmd, util.file
+from test import TestCaseWithTmp
+
+log = logging.getLogger(__name__)
+
+class TestToolsInstallation(TestCaseWithTmp):
+    def setUp(self):
+        super(TestToolsInstallation, self).setUp()
+        util.cmd.setup_logger('INFO')
+    def testAllToolInstallers(self):
+        def iter_leaf_subclasses(aClass) :
+            "Iterate over subclasses at all levels that don't themselves have a subclass"
+            isLeaf = True
+            for subclass in aClass.__subclasses__() :
+                isLeaf = False
+                for leafClass in iter_leaf_subclasses(subclass) :
+                    yield leafClass
+            #if isLeaf :
+            #    yield aClass
+        '''Load every tool's default chain of install methods and try them.'''
+        for tool_class in iter_leaf_subclasses(tools.Tool):
+            t = tool_class()
+            t.install()
+            self.assertTrue(t.is_installed(), "installation of tool %s failed" % tool_class.__name__)
+            log.info(".. installation of %s succeeded with installer %s" % (tool_class.__name__, t.installed_method.__class__.__name__))
+