v1.0.a1

.travis.yml

@@ -1,6 +1,5 @@
 language: python
 python:
-  - "2.7"
   - "3.4"
   - "3.5"
   - "3.6"

README.md

@@ -146,7 +146,7 @@ Colexification analyses are named by three components as `g-t-f.gml`, with g poi
 The communities in the paper have been calculated with the following parameters:
 
 ```shell
-$ clics -t 3 -f families -n communities
+$ clics -t 3 -f families communities
 ```
 
 

setup.py

@@ -3,7 +3,7 @@
 
 setup(
     name='pyclics',
-    version='0.1',
+    version='1.0',
     author='Johann-Mattis List and Robert Forkel',
     url='https://github.com/clics/clics2',
     classifiers=[
@@ -18,12 +18,11 @@
     packages=find_packages(where='src'),
     package_dir={'': 'src'},
     install_requires=[
-        'lingpy',
-        'pycldf~=1.0',
         'pylexibank>=0.7',
         'clldutils~=2.0',
         'geojson',
         'python-igraph',
+        'networkx',
         'unidecode'
     ],
     extras_require={

src/pyclics/__main__.py

@@ -1,8 +1,9 @@
 # coding: utf8
-from __future__ import unicode_literals, print_function, division
 import sys
 import argparse
+import random
 
+import numpy
 from clldutils.clilib import ArgumentParserWithLogging
 from clldutils.path import Path
 
@@ -12,16 +13,17 @@
 
 assert pyclics.commands
 
+random.seed(123456)
+numpy.random.seed(123456)
+
 
 def main():  # pragma: no cover
     parser = ArgumentParserWithLogging(pyclics.__name__)
     parser.add_argument('-t', '--threshold', type=int, default=None)
     parser.add_argument('-f', '--edgefilter', default='families')
     parser.add_argument('-n', '--normalize', action='store_true')
     parser.add_argument('-g', '--graphname', default=None)
-    parser.add_argument('-s', '--subgraph', default='infomap')
     parser.add_argument('-w', '--weight', default='FamilyWeight')
-    parser.add_argument('-a', '--aspect', default=None)
     parser.add_argument('--unloaded', action='store_true', default=False)
     parser.add_argument('-v', '--verbose', default=False, action='store_true')
     parser.add_argument(

src/pyclics/api.py

@@ -1,5 +1,4 @@
 # coding: utf8
-from __future__ import unicode_literals, print_function, division
 import json
 
 from clldutils.apilib import API
@@ -11,6 +10,8 @@
 from pyclics.db import Database
 from pyclics.models import Network
 
+__all__ = ['Clics']
+
 
 class Clics(API):
     _log = None
@@ -32,6 +33,7 @@ def db(self):
     def file_written(self, p):
         if self._log:
             self._log.info('{0} written'.format(p))
+        return p
 
     def csv_writer(self, comp, name, delimiter=',', suffix='csv'):
         p = self.existing_dir(comp).joinpath('{0}.{1}'.format(name, suffix))
@@ -51,8 +53,9 @@ def write_js_var(self, var_name, var, *path):
     def save_graph(self, graph, network, threshold=None, edgefilter=None):
         if not isinstance(network, Network):
             assert threshold is not None and edgefilter is not None
-            network = Network(network, threshold, edgefilter)
-        self.file_written(network.save(graph))
+            network = Network(
+                network, threshold, edgefilter, graphdir=self.path('output', 'graphs'))
+        return self.file_written(network.save(graph))
 
     def load_graph(self, network, threshold=None, edgefilter=None):
         if not isinstance(network, Network):