Avoid writing gexf in test

1.3.0rc1 is not compatible with salib

Makefile

@@ -1,4 +1,7 @@
-test:
+quick-test:
 	docker-compose exec dev python -m pytest -s -v
 
-.PHONY: test
+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
+pyyaml>=5.1
 pandas>=0.23
-scipy>=1.2
+scipy==1.2.1 # scipy 1.3.0rc1 is not compatible with salib
 SALib>=1.3
 Jinja2

soil/exporters.py

@@ -21,6 +21,7 @@ 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)
+    yield from yaml.load_all(string, Loader=yaml.FullLoader)
 
 
 def expand_template(config):

tests/test_exporters.py

@@ -0,0 +1,110 @@
+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

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