Fix openMP issues (#716)

* Set the numpy threading environment variables in every program before anything else is imported.

* PEP8

bin/alignmentSieve

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.alignmentSieve import main
 import sys
 

bin/bamCompare

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.bamCompare import main
 import sys
 

bin/bamCoverage

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.bamCoverage import main
 import sys
 

bin/bamPEFragmentSize

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.bamPEFragmentSize import main
 import sys
 

bin/bigwigCompare

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.bigwigCompare import main
 import sys
 

bin/computeGCBias

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.computeGCBias import main
 import sys
 

bin/computeMatrix

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.computeMatrix import main
 import sys
 

bin/computeMatrixOperations

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.computeMatrixOperations import main
 import sys
 

bin/correctGCBias

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.correctGCBias import main
 import sys
 

bin/deeptools

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.deeptools_list_tools import main
 import sys
 

bin/estimateReadFiltering

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.estimateReadFiltering import main
 import sys
 

bin/estimateScaleFactor

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 import argparse
 import sys
 

bin/multiBamSummary

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.multiBamSummary import main
 import sys
 

bin/multiBigwigSummary

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.multiBigwigSummary import main
 import sys
 

bin/plotCorrelation

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.plotCorrelation import main
 import sys
 

bin/plotCoverage

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.plotCoverage import main
 import sys
 

bin/plotEnrichment

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.plotEnrichment import main
 import sys
 

bin/plotFingerprint

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.plotFingerprint import main
 import sys
 

bin/plotHeatmap

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.plotHeatmap import main
 import sys
 

bin/plotPCA

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.plotPCA import main
 import sys
 

bin/plotProfile

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 #-*- coding: utf-8 -*-
 
+import deeptools.misc
 from deeptools.plotProfile import main
 import sys
 

deeptools/misc.py

@@ -0,0 +1,13 @@
+import os
+
+# This should force numpy to run single threaded. See issue #697
+# This module MUST be imported before numpy
+# Note that these environment variables are internal to deepTools (they won't exist on the shell after the command completes)
+if 'MKL_NUM_THREADS' not in os.environ:
+    os.environ['MKL_NUM_THREADS'] = 'sequential'
+if 'NUMEXPR_NUM_THREADS' not in os.environ:
+    os.environ['NUMEXPR_NUM_THREADS'] = '1'
+if 'OMP_NUM_THREADS' not in os.environ:
+    os.environ['OMP_NUM_THREADS'] = '1'
+if 'VECLIB_MAXIMUM_THREADS' not in os.environ:
+    os.environ['VECLIB_MAXIMUM_THREADS'] = '1'