Merge pull request #10 from KrishnaswamyLab/dev

Bump version to 0.1.4

graphtools/api.py

@@ -16,10 +16,11 @@ def Graph(data,
           decay=10,
           distance='euclidean',
           thresh=1e-4,
+          kernel_symm='+',
+          gamma=None,
           n_landmark=None,
           n_svd=100,
           beta=1,
-          gamma=0.5,
           n_jobs=-1,
           verbose=False,
           random_state=None,
@@ -71,6 +72,17 @@ def Graph(data,
         All affinities below `thresh` will be set to zero in order to save
         on time and memory constraints.
 
+    kernel_symm : string, optional (default: '+')
+        Defines method of MNN symmetrization.
+        '+'  : additive
+        '*'  : multiplicative
+        'gamma' : min-max
+        'none' : no symmetrization
+
+    gamma: float (default: None)
+        Min-max symmetrization constant or matrix. Only used if kernel_symm='gamma'.
+        K = `gamma * min(K, K.T) + (1 - gamma) * max(K, K.T)`
+
     precomputed : {'distance', 'affinity', 'adjacency', `None`}, optional (default: `None`)
         If the graph is precomputed, this variable denotes which graph
         matrix is provided as `data`.
@@ -79,11 +91,6 @@ def Graph(data,
     beta: float, optional(default: 1)
         Multiply within - batch connections by(1 - beta)
 
-    gamma: float or {'+', '*'} (default: 0.99)
-        Symmetrization method. If '+', use `(K + K.T) / 2`,
-        if '*', use `K * K.T`, if a float, use
-        `gamma * min(K, K.T) + (1 - gamma) * max(K, K.T)`
-
     sample_idx: array-like
         Batch index for MNN kernel
 
@@ -205,44 +212,19 @@ class Graph(parent_classes[0], parent_classes[1]):
         class Graph(parent_classes[0], parent_classes[1], parent_classes[2]):
             pass
     else:
-        raise RuntimeError("unknown graph classes")
+        raise RuntimeError("unknown graph classes {}".format(parent_classes))
+
+    params = kwargs
+    for parent_class in parent_classes:
+        for param in parent_class._get_param_names():
+            try:
+                params[param] = eval(param)
+            except NameError:
+                # keyword argument not specified above - no problem
+                pass
 
     # build graph and return
     log_debug("Initializing {} with arguments {}".format(
         parent_classes,
-        {
-            'n_pca': n_pca,
-            'sample_idx': sample_idx,
-            'adaptive_k': adaptive_k,
-            'precomputed': precomputed,
-            'knn': knn,
-            'decay': decay,
-            'distance': distance,
-            'thresh': thresh,
-            'n_landmark': n_landmark,
-            'n_svd': n_svd,
-            'beta': beta,
-            'gamma': gamma,
-            'n_jobs': n_jobs,
-            'verbose': verbose,
-            'random_state': random_state,
-            'initialize': initialize
-        }))
-    return Graph(data,
-                 n_pca=n_pca,
-                 sample_idx=sample_idx,
-                 adaptive_k=adaptive_k,
-                 precomputed=precomputed,
-                 knn=knn,
-                 decay=decay,
-                 distance=distance,
-                 thresh=thresh,
-                 n_landmark=n_landmark,
-                 n_svd=n_svd,
-                 beta=beta,
-                 gamma=gamma,
-                 n_jobs=n_jobs,
-                 verbose=verbose,
-                 random_state=random_state,
-                 initialize=initialize,
-                 **kwargs)
+        params))
+    return Graph(**params)