added docstrings

Author: judyueshen

pertbio/pertbio/config.py

@@ -1,3 +1,7 @@
+"""
+This module defines the reader for the configuration file
+"""
+
 import json
 
 

pertbio/pertbio/dataset.py

@@ -1,3 +1,9 @@
+"""
+This module defines the data partitioning for different training schemes,
+including single-to-combo (s2c), leave-one-drug-out cross-validations (loo),
+and random partition of the dataset.
+"""
+
 import os
 import numpy as np
 import pandas as pd
@@ -181,6 +187,7 @@ def random_partition(cfg):
 
 
 def npz_to_feedable_arrays(npz):
+    """convert sparse matrix to arrays"""
     coo = npz.tocoo()
     indices = [[i, j] for i, j in zip(coo.row, coo.col)]
     values = coo.data

pertbio/pertbio/kernel.py

@@ -1,3 +1,8 @@
+"""
+This module defines the ODE formulations, including the choices of ODE solvers,
+degree of ODEs, and the envelope forms
+"""
+
 import tensorflow as tf
 
 

pertbio/pertbio/model.py

@@ -1,3 +1,8 @@
+"""
+This module defines the structures for different models, including
+CellBox, linear regression, and co-expression
+"""
+
 import numpy as np
 import tensorflow as tf
 import pertbio.kernel
@@ -20,11 +25,9 @@ def factory(args):
     # elif args.model == 'Bayesian':
     #     return BN(args).build()
     # TODO: baysian model
-
-    else:
-        raise Exception("Illegal model name. Choose from [{}]".format(
-            'CellBox, CoExp, LinReg, NN, CoExp_nonlinear, Bayesian'
-        ))
+    raise Exception("Illegal model name. Choose from [{}]".format(
+        'CellBox, CoExp, LinReg, NN, CoExp_nonlinear, Bayesian'
+    ))
 
 
 class PertBio:
@@ -142,7 +145,7 @@ def build(self):
 
 
 class CoExpNonlinear(CoExp):
-
+    """co-expression model with non-linear envelope"""
     def get_variables(self):
         with tf.compat.v1.variable_scope("initialization", reuse=True):
             Ws = tf.Variable(np.zeros([self.args.n_x, self.args.n_x, self.n_x, self.n_x]), dtype=tf.float32)
@@ -166,6 +169,7 @@ def get_variables(self):
 
 
 class LinReg(PertBio):
+    """linear regression model"""
     def get_variables(self):
         with tf.compat.v1.variable_scope("initialization", reuse=True):
             self.params.update({

pertbio/pertbio/train.py

@@ -1,3 +1,7 @@
+"""
+This module defines the training of the model
+"""
+
 import os
 import glob
 import time
@@ -213,6 +217,7 @@ def __init__(self, args, n_iter_buffer):
         # initialize verbose
         self.summary = {}
         self.summary = {}
+        self.substage_i = []
         try:
             self.export_verbose = args.export_verbose
             # 0: no output, 1: params only, 2: params + prediction, 3: output for each iteration

pertbio/pertbio/utils.py

@@ -1,3 +1,8 @@
+"""
+This module defines utility functions during training, including the loss function,
+the optimizer, the timer, and the md5 key for each configuration
+"""
+
 import time
 import hashlib
 import tensorflow as tf

pertbio/pertbio/version.py

@@ -1,3 +1,7 @@
+"""
+This module defines the version of the package
+"""
+
 __version__ = '0.1.1'
 VERSION = __version__