v0.2.3.1

- improved decision-making regarding implementation in add_attributes
- enabled multiprocessing in kp-finder, brute-force search
- moved the --threads option in kp-finder only.
- the edge attribute "node_names" was changed to "adjacent_nodes"
- renamed file handles in importer and exporter scripts for graph and attributes methods
- redirected output of importers and exporters to stdout instead of log
- general cleanup of stdout messages
- removed handled TODOs
- restored the 'adjmat' default in 'pyntacle generate'

pyntacle.py

@@ -550,8 +550,7 @@ def generate(self):
                                  "generated.")
 
         parser.add_argument("-u", "--output-format", metavar="",
-                            choices=format_dictionary.keys(),
-                            required=True,
+                            choices=format_dictionary.keys(), default="adjmat",
                             help='Desired output format for the output communities. \'adjmat\' for '
                                  'adjacency matrix, \'edgelist\' for edge list, \'sif\' for '
                                  'Simple Interaction format, \'dot\' for DOT file, \'bin\' for binary file. '