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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
.dockerignore
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@ -1,2 +1,4 @@
**/soil_output
.*
__pycache__
*.pyc

6
CHANGELOG.md
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@ -3,6 +3,12 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [0.14.6]
### Fixed
* Bug with newer versions of networkx (0.24) where the Graph.node attribute has been removed. We have updated our calls, but the code in nxsim is not under our control, so we have pinned the networkx version until that issue is solved.
### Changed
* Explicit yaml.SafeLoader to avoid deprecation warnings when using yaml.load. It should not break any existing setups, but we could move to the FullLoader in the future if needed.
## [0.14.4]
### Fixed
* Bug in `agent.get_agents()` when `state_id` is passed as a string. The tests have been modified accordingly.

2
requirements.txt
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@ -1,6 +1,6 @@
nxsim>=0.1.2
simpy
networkx>=2.0
networkx>=2.0,<2.4
numpy
matplotlib
pyyaml>=5.1

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)

4
tests/test_main.py
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@ -186,7 +186,7 @@ class TestMain(TestCase):
with utils.timer('serializing'):
serial = s.to_yaml()
with utils.timer('recovering'):
recovered = yaml.load(serial)
recovered = yaml.load(serial, Loader=yaml.SafeLoader)
with utils.timer('deleting'):
del recovered['topology']
assert config == recovered
@ -240,7 +240,7 @@ class TestMain(TestCase):
env[0, 0, 'testvalue'] = 'start'
env[0, 10, 'testvalue'] = 'finish'
nG = env.history_to_graph()
values = nG.node[0]['attr_testvalue']
values = nG.nodes[0]['attr_testvalue']
assert ('start', 0, 10) in values
assert ('finish', 10, None) in values