Better loging; update readme

README.md

@@ -205,7 +205,25 @@ The gui package exposes the command `cadbiom` to the current context.
 
     optional arguments:
     -h, --help     show this help message and exit
-    --make_graphs
+    --graphs
+    --json
+    --output [OUTPUT]
+
+<br>
+
+Usage in scripts:
+
+    >>> from cadbiom_cmd.solution_repr import graph_isomorph_test
+    >>> print(graph_isomorph_test('test.bcx', 'test2.bcx', output_dir='graphs/',
+        make_graphs=False, make_json=False))
+    INFO: 3 transitions loaded
+    INFO: 3 transitions loaded
+    INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0
+    INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0
+    INFO: Topology checking: True
+    INFO: Nodes checking: True
+    INFO: Edges checking: True
+    {u'nodes': True, u'edges': True, u'topology': True}
 
 
 ## Graphical User Interface

command_line/cadbiom_cmd/solution_repr.py

@@ -195,7 +195,8 @@ def get_transitions(file):
     # Return a dict instead of defaultdict to avoid later confusions
     #(masked errors) by searching a transition that was not in the model...
 
-    assert len(transitions) != 0, "No transitions found in the model !"
+    assert len(transitions) != 0, "No transitions found in the model ! " \
+        "Please check the names of events (_h_xxx)"
 
     return dict(transitions)
 
@@ -507,7 +508,7 @@ def build_graph(solution, steps, transitions):
 
 
     # Get & make all needed edges ##############################################
-    LOGGER.info("BUILD GRAPH FOR SOL: " + str(solution))
+    LOGGER.debug("BUILD GRAPH FOR SOL: " + str(solution))
     LOGGER.debug("STEPS: " + str(steps))
 #
 #    print(transitions['_h_2755'])
@@ -801,8 +802,8 @@ def main(output_dir, model_file, solution_file):
     )
 
 
-def graph_isomorph_test(model_file_1, model_file_2,
-                        output_dir, make_graphs=False, make_json=False):
+def graph_isomorph_test(model_file_1, model_file_2, output_dir='graphs/',
+                        make_graphs=False, make_json=False):
     """Entry point for model consistency checking.
 
     This functions checks if the 2 given models have the same topology,

library/README.md

@@ -205,7 +205,25 @@ The gui package exposes the command `cadbiom` to the current context.
 
     optional arguments:
     -h, --help     show this help message and exit
-    --make_graphs
+    --graphs
+    --json
+    --output [OUTPUT]
+
+<br>
+
+Usage in scripts:
+
+    >>> from cadbiom_cmd.solution_repr import graph_isomorph_test
+    >>> print(graph_isomorph_test('test.bcx', 'test2.bcx', output_dir='graphs/',
+        make_graphs=False, make_json=False))
+    INFO: 3 transitions loaded
+    INFO: 3 transitions loaded
+    INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0
+    INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0
+    INFO: Topology checking: True
+    INFO: Nodes checking: True
+    INFO: Edges checking: True
+    {u'nodes': True, u'edges': True, u'topology': True}
 
 
 ## Graphical User Interface