fix: n_jobs in cluster.cluster() not working

phenograph/cluster.py

@@ -287,11 +287,12 @@ def cluster(
         print("Setting directed=False because prune=True")
         directed = False
 
+    kernelargs = {}
     if n_jobs == 1:
         kernel = jaccard_kernel
     else:
+        kernelargs["n_jobs"] = n_jobs
         kernel = parallel_jaccard_kernel
-    kernelargs = {}
 
     # Start timer
     tic = time.time()

phenograph/core.py

@@ -136,14 +136,30 @@ def calc_jaccard(i, idx):
     return idx[i], coefficients
 
 
-def parallel_jaccard_kernel(idx):
+def parallel_jaccard_kernel(idx, n_jobs=-1):
     """Compute Jaccard coefficient between nearest-neighbor sets in parallel
-    :param idx: n-by-k integer matrix of k-nearest neighbors
 
-    :return (i, j, s): row indices, column indices, and nonzero values for a sparse adjacency matrix
+    Parameters
+    ----------
+    idx
+        n-by-k integer matrix of k-nearest neighbors
+    n_jobs
+        Number of concurrently running workers. If 1 is given, no parallelism is
+        used. If set to -1, all CPUs are used. For n_jobs below -1, `n_cpus + 1 + n_jobs`
+        are used.
+
+    Returns
+    -------
+    i, j, s
+        row indices, column indices, and nonzero values for a sparse adjacency matrix
     """
+    if n_jobs == -1:
+        n_jobs = len(os.sched_getaffinity(0))
+    if n_jobs < -1:
+        n_jobs = len(os.sched_getaffinity(0)) + 1 + n_jobs
+
     n = len(idx)
-    with closing(Pool()) as pool:
+    with closing(Pool(n_jobs)) as pool:
         jaccard_values = pool.starmap(calc_jaccard, zip(range(n), repeat(idx)))
 
     graph = sp.lil_matrix((n, n), dtype=float)
@@ -269,7 +285,6 @@ def get_modularity(msg):
     run = 0
     updated = 0
     while run - updated < 20 and run < max_runs and (time.time() - tic) < time_limit:
-
         # run community
         fout = open(filename + ".tree", "w")
         args = [
@@ -291,7 +306,6 @@ def get_modularity(msg):
 
         # continue only if we've reached a higher modularity than before
         if q[-1] - Q > tol:
-
             Q = q[-1]
             updated = run