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Code Issues Releases Wiki Activity

Updated to 0.14.6

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Fix compatibility issues with newer networkx and pandas versions
This commit is contained in:
J. Fernando Sánchez
2020-03-11 16:17:14 +01:00
parent 6690b6ee5f
commit c8b8149a17
8 changed files with 27 additions and 19 deletions
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2
soil/VERSION
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@@ -1 +1 @@
0.14.4
0.14.6

4
soil/analysis.py
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@@ -20,7 +20,7 @@ def _read_data(pattern, *args, from_csv=False, process_args=None, **kwargs):
process_args = {}
for folder in glob.glob(pattern):
config_file = glob.glob(join(folder, '*.yml'))[0]
config = yaml.load(open(config_file))
config = yaml.load(open(config_file), Loader=yaml.SafeLoader)
df = None
if from_csv:
for trial_data in sorted(glob.glob(join(folder,
@@ -133,7 +133,7 @@ def get_count(df, *keys):
def get_value(df, *keys, aggfunc='sum'):
if keys:
df = df[list(keys)]
return df.groupby(axis=1, level=0).agg(aggfunc, axis=1)
return df.groupby(axis=1, level=0).agg(aggfunc)
def plot_all(*args, **kwargs):

12
soil/environment.py
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@@ -87,7 +87,7 @@ class Environment(nxsim.NetworkEnvironment):
@property
def network_agents(self):
for i in self.G.nodes():
node = self.G.node[i]
node = self.G.nodes[i]
if 'agent' in node:
yield node['agent']
@@ -212,12 +212,12 @@ class Environment(nxsim.NetworkEnvironment):
return self[key] if key in self else default
def get_agent(self, agent_id):
return self.G.node[agent_id]['agent']
return self.G.nodes[agent_id]['agent']
def get_agents(self, nodes=None):
if nodes is None:
return list(self.agents)
return [self.G.node[i]['agent'] for i in nodes]
return [self.G.nodes[i]['agent'] for i in nodes]
def dump_csv(self, f):
with utils.open_or_reuse(f, 'w') as f:
@@ -231,9 +231,9 @@ class Environment(nxsim.NetworkEnvironment):
# Workaround for geometric models
# See soil/soil#4
for node in G.nodes():
if 'pos' in G.node[node]:
G.node[node]['viz'] = {"position": {"x": G.node[node]['pos'][0], "y": G.node[node]['pos'][1], "z": 0.0}}
del (G.node[node]['pos'])
if 'pos' in G.nodes[node]:
G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
del (G.nodes[node]['pos'])
nx.write_gexf(G, f, version="1.2draft")

14
soil/web/__init__.py
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@@ -118,9 +118,9 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
elif msg['type'] == 'download_gexf':
G = self.trials[ int(msg['data']) ].history_to_graph()
for node in G.nodes():
if 'pos' in G.node[node]:
G.node[node]['viz'] = {"position": {"x": G.node[node]['pos'][0], "y": G.node[node]['pos'][1], "z": 0.0}}
del (G.node[node]['pos'])
if 'pos' in G.nodes[node]:
G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
del (G.nodes[node]['pos'])
writer = nx.readwrite.gexf.GEXFWriter(version='1.2draft')
writer.add_graph(G)
self.write_message({'type': 'download_gexf',
@@ -130,9 +130,9 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
elif msg['type'] == 'download_json':
G = self.trials[ int(msg['data']) ].history_to_graph()
for node in G.nodes():
if 'pos' in G.node[node]:
G.node[node]['viz'] = {"position": {"x": G.node[node]['pos'][0], "y": G.node[node]['pos'][1], "z": 0.0}}
del (G.node[node]['pos'])
if 'pos' in G.nodes[node]:
G.nodes[node]['viz'] = {"position": {"x": G.nodes[node]['pos'][0], "y": G.nodes[node]['pos'][1], "z": 0.0}}
del (G.nodes[node]['pos'])
self.write_message({'type': 'download_json',
'filename': self.config['name'] + '_trial_' + str(msg['data']),
'data': nx.node_link_data(G) })
@@ -271,4 +271,4 @@ def main():
parser.add_argument('--verbose', '-v', help='verbose mode', action='store_true')
args = parser.parse_args()
run(name=args.name, port=(args.port[0] if isinstance(args.port, list) else args.port), verbose=args.verbose)
run(name=args.name, port=(args.port[0] if isinstance(args.port, list) else args.port), verbose=args.verbose)