further changes to comply with diffxpy api

Author: davidsebfischer

batchglm/models/base/input.py

@@ -72,12 +72,14 @@ def feature_isallzero(self):
         return self._feature_allzero
 
     def fetch_x_dense(self, idx):
-        return self.x[idx]
+        assert isinstance(self.x, np.ndarray), "tried to fetch dense from non ndarray"
+
+        return self.x[idx, :]
 
     def fetch_x_sparse(self, idx):
-        assert isinstance(self.x, scipy.sparse.csr_matrix), "tried to fetch sparse from non csr matrix"
+        assert isinstance(self.x, scipy.sparse.csr_matrix), "tried to fetch sparse from non csr_matrix"
 
-        data = self.x[idx]
+        data = self.x[idx, :]
 
         data_idx = np.asarray(np.vstack(data.nonzero()).T, np.int64)
         data_val = np.asarray(data.data, np.float64)

batchglm/models/base_glm/input.py

@@ -133,10 +133,10 @@ def num_scale_params(self):
         return self.constraints_scale.shape[1]
 
     def fetch_design_loc(self, idx):
-        return self.design_loc[idx]
+        return self.design_loc[idx, :]
 
     def fetch_design_scale(self, idx):
-        return self.design_scale[idx]
+        return self.design_scale[idx, :]
 
     def fetch_size_factors(self, idx):
         return self.size_factors[idx]

batchglm/train/tf/base_glm_all/estimator.py

@@ -168,7 +168,7 @@ def fetch_fn(idx):
                 num_design_scale_params=input_data.num_design_scale_params,
                 num_loc_params=input_data.num_loc_params,
                 num_scale_params=input_data.num_scale_params,
-                batch_size=batch_size,
+                batch_size=np.min([batch_size, input_data.x.shape[0]]),
                 graph=graph,
                 init_a=init_a,
                 init_b=init_b,

batchglm/unit_test/test_graph_glm_all.py

@@ -34,7 +34,7 @@ def __init__(
             else:
                 raise ValueError("noise_model not recognized")
 
-        batch_size = 100
+        batch_size = 200
         provide_optimizers = {
             "gd": False, "adam": False, "adagrad": False, "rmsprop": False,
             "nr": False, "nr_tr": False,