Merge 27f9c7f into 72f3db5

requirements.txt

@@ -5,7 +5,7 @@ pandas>=0.15.2
 ordered-set==1.2
 inspyred==1.0
 cobra==0.4.0b6
-optlang==0.2.17
+optlang==0.2.18
 escher==1.0.0
 numexpr==2.4
 networkx==1.9.1

setup.py

@@ -33,7 +33,7 @@
                 'pandas>=0.15.2',
                 'ordered-set>=1.2',
                 'cobra==0.4.0b6',
-                'optlang>=0.2.17',
+                'optlang>=0.2.18',
                 'requests>=2.5.0',
                 'numexpr>=2.4',
                 'networkx>=1.9.1',

tests/test_parallel.py

@@ -41,6 +41,11 @@ def interactive(f):
 TRAVIS = os.getenv('TRAVIS', False)
 SKIP_PARALLEL = TRAVIS
 
+if os.getenv('REDIS_PORT_6379_TCP_ADDR'):
+    REDIS_HOST = os.getenv('REDIS_PORT_6379_TCP_ADDR')  # wercker
+else:
+    REDIS_HOST = 'localhost'
+
 @interactive
 def to_the_power_of_2_interactive(arg):
     return arg ** 2
@@ -94,11 +99,13 @@ def test_length(self):
 
     class TestRedisQueue(unittest.TestCase):
         def test_queue_size(self):
-            queue = RedisQueue("test-queue-size-1", maxsize=1)
+            print(REDIS_HOST)
+            print(os.getenv('REDIS_PORT_6379_TCP_ADDR'))
+            queue = RedisQueue("test-queue-size-1", maxsize=1, host=REDIS_HOST)
             queue.put(1)
             self.assertRaises(six.moves.queue.Full, queue.put, 1)
 
-            queue = RedisQueue("test-queue-size-2", maxsize=2)
+            queue = RedisQueue("test-queue-size-2", maxsize=2, host=REDIS_HOST)
             queue.put(1)
             queue.put(1)
             self.assertRaises(six.moves.queue.Full, queue.put, 1)
@@ -107,7 +114,7 @@ def test_queue_size(self):
             self.assertRaises(six.moves.queue.Empty, queue.get_nowait)
 
         def test_queue_objects(self):
-            queue = RedisQueue("test-queue", maxsize=100)
+            queue = RedisQueue("test-queue", maxsize=100, host=REDIS_HOST)
             # put int
             queue.put(1)
             v = queue.get_nowait()
@@ -140,7 +147,7 @@ def test_queue_objects(self):
             self.assertIsInstance(v, dict)
 
         def test_queue_len(self):
-            queue = RedisQueue("test-queue-len", maxsize=100)
+            queue = RedisQueue("test-queue-len", maxsize=100, host=REDIS_HOST)
             self.assertEqual(queue.length, 0)
             queue.put(1)
             self.assertEqual(queue.length, 1)

tests/test_strain_design_heuristics.py

@@ -50,6 +50,11 @@
 
 TRAVIS = os.getenv('TRAVIS', False)
 
+if os.getenv('REDIS_PORT_6379_TCP_ADDR'):
+    REDIS_HOST = os.getenv('REDIS_PORT_6379_TCP_ADDR')  # wercker
+else:
+    REDIS_HOST = 'localhost'
+
 SEED = 1234
 
 CURRENT_PATH = os.path.dirname(__file__)
@@ -592,21 +597,23 @@ def setUp(self):
         self.population = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
         self.random = Random(SEED)
 
+    # unittest.skipIf(os.getenv('WERCKER', False), 'Currently not working on wercker as redis is not running on localhost')
     def test_migrator_constructor(self):
-        migrator = MultiprocessingMigrator(max_migrants=1)
+        migrator = MultiprocessingMigrator(max_migrants=1, host=REDIS_HOST)
         self.assertIsInstance(migrator.migrants, RedisQueue)
         self.assertEqual(migrator.max_migrants, 1)
 
-        migrator = MultiprocessingMigrator(max_migrants=2)
+        migrator = MultiprocessingMigrator(max_migrants=2, host=REDIS_HOST)
         self.assertIsInstance(migrator.migrants, RedisQueue)
         self.assertEqual(migrator.max_migrants, 2)
 
-        migrator = MultiprocessingMigrator(max_migrants=3)
+        migrator = MultiprocessingMigrator(max_migrants=3, host=REDIS_HOST)
         self.assertIsInstance(migrator.migrants, RedisQueue)
         self.assertEqual(migrator.max_migrants, 3)
 
+    # unittest.skipIf(os.getenv('WERCKER', False), 'Currently not working on wercker as redis is not running on localhost')
     def test_migrate_individuals_without_evaluation(self):
-        migrator = MultiprocessingMigrator(max_migrants=1)
+        migrator = MultiprocessingMigrator(max_migrants=1, host=REDIS_HOST)
         self.assertIsInstance(migrator.migrants, RedisQueue)
         self.assertEqual(migrator.max_migrants, 1)
 

wercker.yml

@@ -0,0 +1,42 @@
+box:
+  id: biosustain/cameo-wercker-box
+  username: $USERNAME
+  password: $PASSWORD
+  tag: latest
+
+services:
+     - redis
+build:
+
+  steps:
+
+    - script:
+        name: env
+        code: |
+          env
+
+    - script:
+        name: run tests for Python 3.4
+        code: |
+          source activate cameo3.4
+          nosetests
+          codecov --token=$CODECOV_TOKEN
+
+    - script:
+        name: run tests for Python 2.7
+        code: |
+          source activate cameo2.7
+          nosetests
+          codecov --token=$CODECOV_TOKEN
+
+deploy:
+
+  PyPI:  # this is triggered if master branch
+
+    - script:
+        name: deploy to PyPI
+        code: |
+          source activate cameo3.4
+          pip install twine
+          python setup.py sdist
+          twine upload -u $PYPI_USERNAME -p $PYPI_PASSWD dist/*