Fixing spatiotemporal documentation and tests

modules/spatiotemporal/README.md

@@ -32,7 +32,7 @@ Here, we describe the spatiotemporal modeling package. The goal of this package
 
 ## create_DAG.py
 
-### create_DAG(state_dict)
+### create_DAG(state_dict,input_dir='', scorestr='_scores.log', output_dir='',spatio_temporal_rule=False, subcomplexstr='.config',expected_subcomplexes=[],score_comp=False, exp_comp_map={},out_cdf=True, out_labeled_pdf=True, out_pdf=False, npaths=0,draw_dag=True)
 This functions streamlines the process of creating a graph by performing all the necessary steps and saving relevant input to files. Features of this function are walked through in example/toy/Simple_spatiotemporal_example.ipynb
 
 #### Possible inputs:

modules/spatiotemporal/pyext/src/analysis.py

@@ -1,3 +1,6 @@
+"""@namespace IMP.spatiotemporal.analysis
+   Functions to analyze spatiotemporal models.
+"""
 import numpy as np
 
 

modules/spatiotemporal/pyext/src/composition_scoring.py

@@ -1,3 +1,6 @@
+"""@namespace IMP.spatiotemporal.composition_scoring
+   Functions for weighting graphNode objects based on stoichiometry data.
+"""
 import numpy as np
 import warnings
 import os

modules/spatiotemporal/pyext/src/create_DAG.py

@@ -1,3 +1,6 @@
+"""@namespace IMP.spatiotemporal.create_DAG
+   Simplified function for creating a spatiotemporal model.
+"""
 import os
 import itertools
 import warnings

modules/spatiotemporal/pyext/src/graphNode.py

@@ -1,3 +1,7 @@
+"""@namespace IMP.spatiotemporal.graphNode
+   Defines the graphNode class. Each node corresponds to a snapshot model.
+   Nodes can be connected to create spatiotemporal models.
+"""
 import numpy as np
 import os
 

modules/spatiotemporal/pyext/src/score_graph.py

@@ -1,5 +1,5 @@
 """@namespace IMP.spatiotemporal.score_graph
-   Function to traverse and score the graph.
+   Functions to traverse and score the spatiotemporal graphs.
 """
 
 import numpy as np

modules/spatiotemporal/pyext/src/write_output.py

@@ -1,3 +1,7 @@
+"""@namespace IMP.spatiotemporal.write_output
+   Functions to write spatiotemporal graph information to files.
+"""
+
 import numpy as np
 try:
     from graphviz import Digraph

modules/spatiotemporal/test/test_make_graph.py

@@ -43,8 +43,6 @@ def test_graph_setup(self):
             nodes = []
             # keys correspond to all timepoints
             keys = list(state_dict.keys())
-            # Go to input_dir, if it exists
-            orig_dir = os.getcwd()
             if len(input_dir) > 0:
                 if os.path.exists(input_dir):
                     os.chdir(input_dir)
@@ -74,8 +72,6 @@ def test_graph_setup(self):
             # check that all nodes are graphNode objects
             for node in nodes:
                 self.assertIsInstance(node,graphNode.graphNode)
-            # Restore original working directory
-            os.chdir(orig_dir)
 
     def test_graph_scoring(self):
         """
@@ -152,7 +148,10 @@ def test_writing_output(self):
             line=check_label_pdf.readline()
             line_split=line.split()
             check_label_pdf.close()
-            self.assertEqual(line_split[0], '1_0min|2_5min|2_10min|')
+            # 2 possibilities are acceptable: '1_0min|2_5min|2_10min|','1_0min|2_5min|1_10min|'. Check this output in 3 parts:
+            self.assertEqual(line_split[0][0:14], '1_0min|2_5min|')
+            self.assertAlmostEqual(int(line_split[0][14]), 1.5,delta=0.5000001)
+            self.assertEqual(line_split[0][15:], '_10min|')
 
     def test_writing_dag(self):
         """