Patch BOC

DEBUG Linux setup

gmatch4py/bag_of_cliques.pyx

@@ -43,9 +43,11 @@ def nx2nk(nxG, weightAttr=None):
 
 def getClique(nx_graph):
     final_cliques=[]
-    if len(nx_graph) ==0:
+    if len(nx_graph) ==0 or not nx_graph:
         return final_cliques
     netkit_graph,idmap=nx2nk(nx_graph)
+    if not netkit_graph:
+        return  final_cliques
     idmap={v:k for k,v in idmap.items()}
     cliques=MaximalCliques(netkit_graph).run().getCliques()
     for cl in cliques:
@@ -63,8 +65,9 @@ class BagOfCliques():
         cdef double[:,:] scores = np.zeros((n,n))
         cdef int i
         for i in range(len(scores)):
-            if not i in selected:
-                continue
+            if selected:
+                if not i in selected:
+                    continue
             for j in range(i,len(scores)):
                 scores[i,j]=(np.dot(bog[i],bog[j]))/(np.sqrt(np.sum(bog[i]**2))*np.sqrt(np.sum(bog[j]**2))) # Can be computed in one line
                 scores[j,i]=scores[i,j]
@@ -163,4 +166,9 @@ class BagOfCliques():
                 if hash in map_str_cliques:
                     vector[map_str_cliques[hash]] = 1
             boc[g] = vector
-        return boc
\ No newline at end of file
+        return boc
+
+    def distance(self,matrix):
+        return 1-np.array(matrix)
+    def similarity(self,matrix):
+        return np.array(matrix)
\ No newline at end of file

setup.py

@@ -10,6 +10,10 @@ except:
     print("copy from www.cython.org and install it")
     sys.exit(1)
 
+is_linux = sys.platform.system() == 'Linux'
+libs=[]
+if is_linux:  # Issue #42
+    libs.append('rt')  # -lrt for clock_gettime
 
 def scandir(dir, files=[]):
     for file in os.listdir(dir):
@@ -22,18 +26,24 @@ def scandir(dir, files=[]):
 
 # generate an Extension object from its dotted name
 def makeExtension(extName):
+    global libs
     extPath = extName.replace(".", os.path.sep)+".pyx"
     return Extension(
         extName,
-        [extPath],include_dirs=[np.get_include()],language='c++'
+        [extPath],include_dirs=[np.get_include()],language='c++',libraries=libs
         )
 
 # get the list of extensions
 extNames = scandir("gmatch4py")
 
 # and build up the set of Extension objects
+
+
 extensions = cythonize([makeExtension(name) for name in extNames])
 
+
+
+
 setup(
     name="GMatch4py",
     description="A module for graph matching",
@@ -45,7 +55,7 @@ setup(
     version="0.1"
 )
 #Clean cpp and compiled file
-f=True
+f=False
 if f:
     if os.path.exists("build"):
         shutil.rmtree("build")