[MRG] rename containment to contained_by

sourmash_lib/_minhash.pyx

@@ -261,7 +261,6 @@ cdef class MinHash(object):
 
     def downsample_scaled(self, new_num):
         max_hash = self.max_hash
-
         if max_hash is None:
             raise ValueError('no max_hash available - cannot downsample')
 
@@ -364,9 +363,9 @@ cdef class MinHash(object):
             distance = 2*math.acos(prod) / math.pi
             return 1.0 - distance
 
-    def containment(self, other):
+    def contained_by(self, other):
         """\
-        Calculate containment of self by other.
+        Calculate how much of self is contained by other.
         """
         return self.count_common(other) / len(self.get_mins())
 

sourmash_lib/commands.py

@@ -625,7 +625,7 @@ def search(args):
     # similarity vs containment
     query_similarity = lambda x: query.similarity(x, downsample=True)
     if args.containment:
-        query_similarity = lambda x: query.containment(x, downsample=True)
+        query_similarity = lambda x: query.contained_by(x, downsample=True)
 
     # set up the search databases
     databases = sourmash_args.load_sbts_and_sigs(args.databases,

sourmash_lib/signature.py

@@ -113,15 +113,15 @@ def jaccard(self, other):
         "Compute Jaccard similarity with the other MinHash signature."
         return self.minhash.similarity(other.minhash, True)
 
-    def containment(self, other, downsample=True):
+    def contained_by(self, other, downsample=False):
         "Compute containment by the other signature. Note: ignores abundance."
         try:
-            return self.minhash.containment(other.minhash)
+            return self.minhash.contained_by(other.minhash)
         except ValueError as e:
             if 'mismatch in max_hash' in str(e) and downsample:
                 xx = self.minhash.downsample_max_hash(other.minhash)
                 yy = other.minhash.downsample_max_hash(self.minhash)
-                return xx.containment(yy)
+                return xx.contained_by(yy)
             else:
                 raise