Merge pull request #212 from pph-collective/develop

v3.0.0 (take 2)

tests/integration_test.py

@@ -531,7 +531,7 @@ def test_treatment_cascade(params_integration, tmpdir):
     path_b = tmpdir.mkdir("b")
     path_b.mkdir("network")
 
-    params_integration.features.enter_and_exit = True
+    params_integration.features.exit_enter = True
     params_integration.model.num_pop = 1000
     params_integration.model.time.num_steps = 20
 

tests/model_test.py

@@ -35,7 +35,7 @@ def test_update_all_agents(make_model, make_agent):
     model = make_model()
     assert model.params.agent_zero.interaction_type == "injection"
     model.time = 1
-    model.params.features.enter_and_exit = False
+    model.params.features.exit_enter = False
     # update all agents passes with agent 0
     model.update_all_agents()
 
@@ -103,7 +103,7 @@ def test_death_all(make_model, params):
 
 @pytest.mark.unit
 def test_dropout_none(make_model, params):
-    params.enter_exit = ObjMap(
+    params.exit_enter = ObjMap(
         {"dropout": {"exit_class": "migrate", "entry_class": "none"}}
     )
     model = make_model(params)
@@ -118,7 +118,7 @@ def test_dropout_none(make_model, params):
 
 @pytest.mark.unit
 def test_dropout_all(make_model, params):
-    params.enter_exit = ObjMap(
+    params.exit_enter = ObjMap(
         {"dropout": {"exit_class": "migrate", "entry_class": "none"}}
     )
     model = make_model(params)
@@ -135,7 +135,7 @@ def test_dropout_all(make_model, params):
 
 @pytest.mark.unit
 def test_ageout(make_model, params):
-    params.enter_exit = ObjMap(
+    params.exit_enter = ObjMap(
         {"dropout": {"exit_class": "age_out", "entry_class": "none"}}
     )
     model = make_model(params)
@@ -160,7 +160,7 @@ def test_ageout(make_model, params):
 
 @pytest.mark.unit
 def test_exit_none(make_model, params):
-    params.enter_exit.death.exit_class = "none"
+    params.exit_enter.death.exit_class = "none"
     params.features.incar = False
     model = make_model(params)
     init_ppl = copy(model.pop.all_agents.members)
@@ -172,8 +172,8 @@ def test_exit_none(make_model, params):
 
 @pytest.mark.unit
 def test_new_agent_no_exit(make_model, params):
-    params.enter_exit.death.exit_class = "none"
-    params.enter_exit.death.entry_class = "new_ag"
+    params.exit_enter.death.exit_class = "none"
+    params.exit_enter.death.entry_class = "new_ag"
     model = make_model(params)
     model.run_random = FakeRandom(0.5)
     init_ppl = copy(model.pop.all_agents.members)
@@ -202,8 +202,8 @@ def test_new_agent_no_exit(make_model, params):
 
 @pytest.mark.unit
 def test_new_agent(make_model, params):
-    params.enter_exit.death.exit_class = "death"
-    params.enter_exit.death.entry_class = "new_ag"
+    params.exit_enter.death.exit_class = "death"
+    params.exit_enter.death.entry_class = "new_ag"
     model = make_model(params)
     model.run_random = FakeRandom(0.0000000001)
     init_ppl = copy(model.pop.all_agents.members)
@@ -248,7 +248,7 @@ def test_replace(make_model, params):
 
 @pytest.mark.unit
 def test_agein(make_model, params):
-    params.enter_exit.death.entry_class = "age_in"
+    params.exit_enter.death.entry_class = "age_in"
     params.features.incar = False
     model = make_model(params)
     init_ppl = copy(model.pop.all_agents.members)

tests/params/basic.yml

@@ -333,7 +333,7 @@ features:
   prep: true
   high_risk: true
   haart: true
-  enter_and_exit: true
+  exit_enter: true
   static_network: false
   agent_zero: true
   assort_mix: false
@@ -359,7 +359,7 @@ location:
 external_exposure:
   convert_prob: 1.0
 
-enter_exit:
+exit_enter:
   death:
     exit_class: death
     entry_class: replace

tests/params/basic_seeded.yml

@@ -303,7 +303,7 @@ features:
   prep: true
   high_risk: true
   haart: true
-  enter_and_exit: true
+  exit_enter: true
   static_network: false
   agent_zero: true
   assort_mix: false

tests/params/basic_seeded_error.yml

@@ -303,7 +303,7 @@ features:
   prep: true
   high_risk: true
   haart: true
-  enter_and_exit: true
+  exit_enter: true
   static_network: false
   agent_zero: true
   assort_mix: false

tests/params/multi_location.yml

@@ -207,7 +207,7 @@ features:
   static_network: false
   incar: false
   partner_tracing: false
-  enter_and_exit: false
+  exit_enter: false
 
 model:
   num_pop: 100

tests/params/simple_integration.yml

@@ -201,7 +201,7 @@ features:
   static_network: false
   incar: false
   partner_tracing: false
-  enter_and_exit: false
+  exit_enter: false
 
 model:
   num_pop: 300

titan/model.py

@@ -238,7 +238,7 @@ def update_all_agents(self):
                 if rel.progress():
                     self.pop.remove_relationship(rel)
 
-        if self.params.features.enter_and_exit:
+        if self.params.features.exit_enter:
             self.exit()
             self.enter()
 
@@ -375,7 +375,7 @@ def exit(self):
             return
 
         for agent in self.pop.all_agents:
-            for strategy in self.params.enter_exit.values():
+            for strategy in self.params.exit_enter.values():
                 # Get parameters of the exit class
                 exit = self.params.classes.exit[strategy.exit_class]
                 if exit.ignore_incar and agent.incar.active:
@@ -426,13 +426,13 @@ def enter(self):
         """
         Create new agents and/or replace exited agents.
 
-        Based on enter/exit pairs [params.enter_exit], create new agents through the following strategies:
+        Based on enter/exit pairs [params.exit_enter], create new agents through the following strategies:
 
             * new_agent: draw agent characteristics from model params
             * replace: use exited agent's characteristics to get new characteristics
 
         """
-        for strategy in self.params.enter_exit.values():
+        for strategy in self.params.exit_enter.values():
             entrance = self.params.classes.enter[strategy.entry_class]
             if entrance.enter_type == "new_agent":
                 # determine new agent locations and characteristics

titan/params/enter_exit.yml

@@ -1,4 +1,4 @@
-enter_exit:
+exit_enter:
   type: definition
   description: pairing of entry information based on exit class. Each exit type can only be represented once.
   fields:

titan/params/features.yml

@@ -19,7 +19,7 @@ features:
     default: false
     description: Whether haart will be used in the model
     type: boolean
-  enter_and_exit:
+  exit_enter:
     default: false
     description: Whether agents can exit and/or enter during model run
     type: boolean

titan/settings/atlanta/model.yml

@@ -15,7 +15,7 @@ features:
   prep: false
   high_risk: false
   haart: true
-  enter_and_exit: true
+  exit_enter: true
   static_network: false
   agent_zero: false
   assort_mix: true

titan/settings/chicago/chicago_baseCase.yml

@@ -29,7 +29,7 @@ features:
   incar: false
   prep: true
   haart: false
-  enter_and_exit: false
+  exit_enter: false
   static_network: true
   random_trial: true
 

titan/settings/mississippi/model.yml

@@ -12,7 +12,7 @@ features:
   prep: true
   high_risk: false
   haart: true
-  enter_and_exit: true
+  exit_enter: true
 
 classes:
   drug_types:

titan/settings/missouri/model.yml

@@ -8,7 +8,7 @@ model:
 features:
   prep: true
   haart: true
-  enter_and_exit: true
+  exit_enter: true
   assort_mix: true
 
 classes:

titan/settings/nyc-msm/model.yml

@@ -54,7 +54,7 @@ classes:
 features:
   prep: true
   haart: true
-  enter_and_exit: true
+  exit_enter: true
   assort_mix: true
 
 outputs:

titan/settings/rhode-island/model.yml

@@ -8,7 +8,7 @@ model:
 features:
   prep: true
   haart: true
-  enter_and_exit: true
+  exit_enter: true
   assort_mix: true
 
 classes:

titan/settings/scott/model.yml

@@ -12,7 +12,7 @@ model:
 
 features:
   haart: true
-  enter_and_exit: true
+  exit_enter: true
   syringe_services: true
   agent_zero: true
   partner_tracing: true