Makefile

@@ -1,7 +1,4 @@
-quick-test:
+test:
 	docker-compose exec dev python -m pytest -s -v
 
-test:
+.PHONY: test
-	docker run -t -v $$PWD:/usr/src/app -w /usr/src/app python:3.7 python setup.py test
-
-.PHONY: test

requirements.txt

@@ -3,8 +3,8 @@ simpy
 networkx>=2.0
 numpy
 matplotlib
-pyyaml>=5.1
+pyyaml
 pandas>=0.23
-scipy==1.2.1 # scipy 1.3.0rc1 is not compatible with salib
+scipy>=1.2
 SALib>=1.3
 Jinja2

soil/exporters.py

@@ -21,7 +21,6 @@ def for_sim(simulation, names, *args, **kwargs):
         exporters.append(mod(simulation, *args, **kwargs))
     return exporters
 
-
 class DryRunner(BytesIO):
     def __init__(self, fname, *args, copy_to=None, **kwargs):
         super().__init__(*args, **kwargs)

soil/serialization.py

@@ -55,7 +55,7 @@ def load_file(infile):
 
 
 def load_string(string):
-    yield from yaml.load_all(string, Loader=yaml.FullLoader)
+    yield from yaml.load_all(string)
 
 
 def expand_template(config):

tests/test_exporters.py

@@ -1,110 +0,0 @@
-import os
-import io
-import tempfile
-import shutil
-from time import time
-
-from unittest import TestCase
-from soil import exporters
-from soil.utils import safe_open
-from soil import simulation
-
-
-class Dummy(exporters.Exporter):
-    started = False
-    trials = 0
-    ended = False
-    total_time = 0
-
-    def start(self):
-        self.__class__.started = True
-
-    def trial_end(self, env):
-        assert env
-        self.__class__.trials += 1
-        self.__class__.total_time += env.now
-
-    def end(self):
-        self.__class__.ended = True
-
-
-class Exporters(TestCase):
-    def test_basic(self):
-        config = {
-            'name': 'exporter_sim',
-            'network_params': {},
-            'agent_type': 'CounterModel',
-            'max_time': 2,
-            'num_trials': 5,
-            'environment_params': {}
-        }
-        s = simulation.from_config(config)
-        s.run_simulation(exporters=[Dummy], dry_run=True)
-        assert Dummy.started
-        assert Dummy.ended
-        assert Dummy.trials == 5
-        assert Dummy.total_time == 2*5
-
-    def test_distribution(self):
-        '''The distribution exporter should write the number of agents in each state'''
-        config = {
-            'name': 'exporter_sim',
-            'network_params': {
-                'generator': 'complete_graph',
-                'n': 4
-            },
-            'agent_type': 'CounterModel',
-            'max_time': 2,
-            'num_trials': 5,
-            'environment_params': {}
-        }
-        output = io.StringIO()
-        s = simulation.from_config(config)
-        s.run_simulation(exporters=[exporters.Distribution], dry_run=True, exporter_params={'copy_to': output})
-        result = output.getvalue()
-        assert 'count' in result
-        assert 'SEED,Noneexporter_sim_trial_3,1,,1,1,1,1' in result
-
-    def test_writing(self):
-        '''Try to write CSV, GEXF, sqlite and YAML (without dry_run)'''
-        n_trials = 5
-        config = {
-            'name': 'exporter_sim',
-            'network_params': {
-                'generator': 'complete_graph',
-                'n': 4
-            },
-            'agent_type': 'CounterModel',
-            'max_time': 2,
-            'num_trials': n_trials,
-            'environment_params': {}
-        }
-        output = io.StringIO()
-        s = simulation.from_config(config)
-        tmpdir = tempfile.mkdtemp()
-        envs = s.run_simulation(exporters=[
-            exporters.Default,
-            exporters.CSV,
-            exporters.Gexf,
-            exporters.Distribution,
-        ],
-                                outdir=tmpdir,
-                                exporter_params={'copy_to': output})
-        result = output.getvalue()
-
-        simdir = os.path.join(tmpdir, s.group or '', s.name)
-        with open(os.path.join(simdir, '{}.dumped.yml'.format(s.name))) as f:
-            result = f.read()
-            assert result
-
-        try:
-            for e in envs:
-                with open(os.path.join(simdir, '{}.gexf'.format(e.name))) as f:
-                    result = f.read()
-                    assert result
-
-                with open(os.path.join(simdir, '{}.csv'.format(e.name))) as f:
-                    result = f.read()
-                    assert result
-        finally:
-            shutil.rmtree(tmpdir)

tests/test_main.py

@@ -1,7 +1,6 @@
 from unittest import TestCase
 
 import os
-import io
 import yaml
 import pickle
 import networkx as nx
@@ -218,8 +217,7 @@ class TestMain(TestCase):
         """
         G = nx.random_geometric_graph(20, 0.1)
         env = Environment(topology=G)
-        f = io.BytesIO()
+        env.dump_gexf('/tmp/dump-gexf/prueba.gexf')
-        env.dump_gexf(f)
 
     def test_save_graph(self):
         '''