Move graph tools into global

Closes #111

PopPUNK/__main__.py

@@ -7,7 +7,6 @@
 import sys
 # additional
 import numpy as np
-import graph_tool.all as gt
 import subprocess
 from collections import defaultdict
 

PopPUNK/network.py

@@ -12,7 +12,6 @@
 import operator
 import shutil
 import subprocess
-import graph_tool.all as gt
 import numpy as np
 import pandas as pd
 from scipy.stats import rankdata

PopPUNK/reference_pick.py

@@ -7,7 +7,6 @@
 import sys
 # additional
 from shutil import copyfile
-import graph_tool.all as gt
 
 # import poppunk package
 from .__init__ import __version__

PopPUNK/utils.py

@@ -12,7 +12,6 @@
 from collections import defaultdict
 from tempfile import mkstemp
 from functools import partial
-import graph_tool.all as gt
 
 import numpy as np
 import pandas as pd
@@ -21,6 +20,8 @@
 import pp_sketchlib
 
 def setGtThreads(threads):
+    global gt
+    import graph_tool.all as gt
     # Check on parallelisation of graph-tools
     if gt.openmp_enabled():
         gt.openmp_set_num_threads(threads)
@@ -193,24 +194,6 @@ def listDistInts(refSeqs, querySeqs, self=True):
 
     return comparisons
 
-def writeTmpFile(fileList):
-    """Writes a list to a temporary file. Used for turning variable into mash
-    input.
-
-    Args:
-        fileList (list)
-            List of files to write to file
-    Returns:
-        tmpName (str)
-            Name of temp file list written to
-    """
-    tmpName = mkstemp(suffix=".tmp", dir=".")[1]
-    with open(tmpName, 'w') as tmpFile:
-        for fileName in fileList:
-            tmpFile.write(fileName + '\t' + fileName + "\n")
-
-    return tmpName
-
 
 def qcDistMat(distMat, refList, queryList, a_max):
     """Checks distance matrix for outliers. At the moment

PopPUNK/visualise.py

@@ -7,7 +7,6 @@
 import sys
 # additional
 import numpy as np
-import graph_tool.all as gt
 
 # required from v2.1.1 onwards (no mash support)
 import pp_sketchlib

scripts/poppunk_extract_components.py

@@ -3,7 +3,6 @@
 # Copyright 2018 John Lees and Nick Croucher
 
 import sys
-import graph_tool.all as gt
 from scipy.stats import rankdata
 import argparse
 
@@ -27,6 +26,7 @@ def get_options():
     args = get_options()
 
     # open stored graph
+    import graph_tool.all as gt
     G = gt.load_graph(args.graph)
 
     # extract individual components