Merge pull request #35 from JonathanSeguin/bloody

Add Travis CI

Author: tariqdaouda

.travis.yml

@@ -0,0 +1,25 @@
+sudo: false
+
+notifications:
+    email: false
+
+language: python
+
+python:
+  - "2.7"
+
+before_install:
+    - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+    - bash miniconda.sh -b -p $HOME/miniconda
+    - export PATH="$HOME/miniconda/bin:$PATH"
+    - conda update --yes conda
+
+install:
+    - conda install --yes python=$TRAVIS_PYTHON_VERSION pip numpy scipy
+    - pip install coverage
+    - pip install https://github.com/tariqdaouda/rabaDB/archive/stable.zip
+    - python setup.py install
+
+script: coverage run -m unittest discover pyGeno/tests/
+
+after_success: bash <(curl -s https://codecov.io/bash)

pyGeno/tests/csv_tests.py renamed to pyGeno/tests/test_csv.py

@@ -7,21 +7,30 @@
 class pyGenoSNPTests(unittest.TestCase):
 
 	def setUp(self):
+		try :
+			B.importGenome("Human.GRCh37.75_Y-Only.tar.gz")
+		except KeyError :
+			print "--> Seems to already exist in db"
+     
+		try :
+			B.importSNPs("Human_agnostic.dummySRY.tar.gz")
+		except KeyError :
+			print "--> Seems to already exist in db"
 		self.ref = Genome(name = 'GRCh37.75_Y-Only')
 
 	def tearDown(self):
 		pass
 
-	#@unittest.skip("skipping")	
+	#@unittest.skip("skipping")
 	def test_vanilla(self) :
 		dummy = Genome(name = 'GRCh37.75_Y-Only', SNPs = 'dummySRY_AGN')
 		persProt = dummy.get(Protein, id = 'ENSP00000438917')[0]
 		refProt = self.ref.get(Protein, id = 'ENSP00000438917')[0]
-		
+
 		self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
 		self.assertEqual('HTGCAATCATATGCTTCTGC', persProt.transcript.cDNA[:20])
 
-	#@unittest.skip("skipping")			
+	#@unittest.skip("skipping")
 	def test_noModif(self) :
 		from pyGeno.SNPFiltering import SNPFilter
 
@@ -37,7 +46,7 @@ def filter(self, chromosome, dummySRY_AGN) :
 		refProt = self.ref.get(Protein, id = 'ENSP00000438917')[0]
 
 		self.assertEqual(persProt.transcript.cDNA[:20], refProt.transcript.cDNA[:20])
-	
+
 	def test_insert(self) :
 		from pyGeno.SNPFiltering import SNPFilter
 
@@ -47,7 +56,7 @@ def __init__(self) :
 
 			def filter(self, chromosome, dummySRY_AGN) :
 				from pyGeno.SNPFiltering import  SequenceInsert
-					
+		
 				refAllele = chromosome.refSequence[dummySRY_AGN.start]
 				return SequenceInsert('TCA')
 
@@ -58,7 +67,7 @@ def filter(self, chromosome, dummySRY_AGN) :
 		self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
 		self.assertEqual('TGAATGCAATCATATGCTTC', persProt.transcript.cDNA[:20])
 
-	#@unittest.skip("skipping")		
+	#@unittest.skip("skipping")
 	def test_SNP(self) :
 		from pyGeno.SNPFiltering import SNPFilter
 
@@ -68,17 +77,17 @@ def __init__(self) :
 
 			def filter(self, chromosome, dummySRY_AGN) :
 				from pyGeno.SNPFiltering import SequenceSNP
-				
+	
 				return SequenceSNP(dummySRY_AGN.alt)
-		
+
 		dummy = Genome(name = 'GRCh37.75_Y-Only', SNPs = 'dummySRY_AGN', SNPFilter = MyFilter())
 		persProt = dummy.get(Protein, id = 'ENSP00000438917')[0]
-		
+
 		refProt = self.ref.get(Protein, id = 'ENSP00000438917')[0]
 		self.assertEqual('M', refProt.sequence[0])
 		self.assertEqual('L', persProt.sequence[0])
 
-	#@unittest.skip("skipping")	
+	#@unittest.skip("skipping")
 	def test_deletion(self) :
 		from pyGeno.SNPFiltering import SNPFilter
 
@@ -88,35 +97,35 @@ def __init__(self) :
 
 			def filter(self, chromosome, dummySRY_AGN) :
 				from pyGeno.SNPFiltering import SequenceDel
-					
+		
 				refAllele = chromosome.refSequence[dummySRY_AGN.start]
 				return SequenceDel(1)
-		
+
 		dummy = Genome(name = 'GRCh37.75_Y-Only', SNPs = 'dummySRY_AGN', SNPFilter = MyFilter())
 		persProt = dummy.get(Protein, id = 'ENSP00000438917')[0]
 		refProt = self.ref.get(Protein, id = 'ENSP00000438917')[0]
 
 		self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
 		self.assertEqual('TGCAATCATATGCTTCTGCT', persProt.transcript.cDNA[:20])
 
-	#@unittest.skip("skipping")	
+	#@unittest.skip("skipping")
 	def test_bags(self) :
 		dummy = Genome(name = 'GRCh37.75_Y-Only')
 		self.assertEqual(dummy.wrapped_object, self.ref.wrapped_object)
-	
-	#@unittest.skip("skipping")	
+
+	#@unittest.skip("skipping")
 	def test_prot_find(self) :
 		prot = self.ref.get(Protein, id = 'ENSP00000438917')[0]
 		needle = prot.sequence[:10]
 		self.assertEqual(0, prot.find(needle))
 		needle = prot.sequence[-10:]
 		self.assertEqual(len(prot)-10, prot.find(needle))
 
-	#@unittest.skip("skipping")	
+	#@unittest.skip("skipping")
 	def test_trans_find(self) :
 		trans = self.ref.get(Transcript, name = "SRY-001")[0]
 		self.assertEqual(0, trans.find(trans[:5]))
-	
+
 	# @unittest.skip("remote server down")
 	# def test_import_remote_genome(self) :
 		# self.assertRaises(KeyError, B.importRemoteGenome, "Human.GRCh37.75_Y-Only.tar.gz")
@@ -130,13 +139,13 @@ def runTests() :
 		B.importGenome("Human.GRCh37.75_Y-Only.tar.gz")
 	except KeyError :
 		print "--> Seems to already exist in db"
-		
+
 	try :
 		B.importSNPs("Human_agnostic.dummySRY.tar.gz")
 	except KeyError :
 		print "--> Seems to already exist in db"
 	# import time
-	# time.sleep(10)	
+	# time.sleep(10)
 	unittest.main()
 
 if __name__ == "__main__" :