Merge pull request #237 from pph-collective/develop

v3.2.1

.github/workflows/deploy_docs.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Set up Poetry
         run: |

.gitignore

@@ -33,3 +33,5 @@ results/*/*.txt
 
 profile.prof
 site/
+
+.DS_Store

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "titan-model"
-version = "3.2.1"
+version = "3.3.0"
 description = "TITAN Agent Based Model"
 license = "GPL-3.0-only"
 authors = ["Sam Bessey <[email protected]>", "Mary McGrath <[email protected]>"]
@@ -12,11 +12,11 @@ classifiers = ["Operating System :: OS Independent"]
 packages = [{ include = "titan" }]
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.6"
 paraml= "^0.1"
 networkx = "^2.4"
 nanoid = "^2.0"
-numpy = "^1.23"
+numpy = "^1.18"
 black = {version = "^23.1.0", optional = true}
 flake8 = {version = "^3.8", optional = true}
 mypy = {version = "^1.0.0", optional = true}

tests/integration_test.py

@@ -178,7 +178,9 @@ def test_agent_pop_stable_setting(tmpdir):
             os.path.dirname(os.path.abspath(__file__)), "..", "titan", "settings"
         )
     ):
-        if "__" not in item and item != "base":
+        if (
+            "__" not in item and item != "base" and item != "philly-gis"
+        ):  # bypass philly due to constraints
             path = tmpdir.mkdir(item)
             os.mkdir(os.path.join(path, "network"))
             print(f"-----------Starting run for {item}-----------")
@@ -411,6 +413,39 @@ def test_static_network(make_model_integration, tmpdir):
             assert rel in curr_rel_ids
 
 
+@pytest.mark.integration_deterministic
+def test_dissolution(params_integration, tmpdir):
+    model = TITAN(params_integration)
+    inj_r = 0
+    for rel in model.pop.relationships:
+        inj_r += 1
+    assert inj_r > 0
+    model.time = 1
+
+    model.params.partnership.dissolve.time = 1
+    model.params.partnership.dissolve.enabled = True
+
+    model.params.demographics.white.sex_type.MSM.drug_type.Inj.num_partners = (
+        model.params.demographics.black.sex_type.MSM.drug_type.Inj.num_partners
+    )
+    for agent in model.pop.all_agents:
+        agent.mean_num_partners["Inj"] = -1
+        agent.mean_num_partners["Sex"] = -1
+        agent.mean_num_partners["SexInj"] = -1
+        agent.mean_num_partners["Social"] = -1
+    model.pop.update_partner_targets()
+
+    model.step(tmpdir)
+
+    for rel in model.pop.relationships:
+        if rel.bond_type == "Inj":
+            print(rel.agent1.mean_num_partners)
+            print(rel.agent2.mean_num_partners)
+            print(rel.agent1.race, rel.agent1.sex_type, rel.agent1.drug_type)
+            print(rel.agent2.race, rel.agent2.sex_type, rel.agent2.drug_type)
+        assert rel.bond_type != "Inj"
+
+
 @pytest.mark.integration_deterministic
 def test_incar(params_integration, tmpdir):
     # turn on incar - initi is set to 0, so for these purposes, just run time

tests/model_test.py

@@ -30,7 +30,7 @@ def test_model_init(params):
 
 
 @pytest.mark.unit
-def test_update_all_agents(make_model, make_agent):
+def test_update_all_agents(make_model, make_agent, make_relationship):
     # make agent 0
     model = make_model()
     assert model.params.agent_zero.interaction_type == "injection"
@@ -57,6 +57,23 @@ def test_update_all_agents(make_model, make_agent):
 
     assert "No agent zero!" in str(excinfo)
 
+    # check that model dissolves relationships
+    model.params.features.agent_zero = False
+    model.params.partnership.dissolve.enabled = True
+    model.params.partnership.dissolve.time = 1
+    model.time = 1
+    a = make_agent()
+    p = make_agent()
+    r = make_relationship(a, p)
+    model.pop.add_relationship(r)
+    a.target_partners["Sex"] = 0
+    a.target_partners["SexInj"] = 0
+    a.target_partners["Inj"] = 0
+
+    assert a.has_partners() is True
+    model.update_all_agents()
+    assert a.has_partners() is False
+
 
 @pytest.mark.unit
 def test_death_none(make_model):

titan/model.py

@@ -235,7 +235,13 @@ def update_all_agents(self):
         # If static network, ignore relationship progression
         if not self.params.features.static_network:
             for rel in copy(self.pop.relationships):
-                if rel.progress():
+                if (
+                    self.params.partnership.dissolve.enabled
+                    and self.time == self.params.partnership.dissolve.time
+                ):
+                    rel.progress(force=True)
+                    self.pop.remove_relationship(rel)
+                elif rel.progress():
                     self.pop.remove_relationship(rel)
 
         if self.params.features.exit_enter:

titan/params/partnership.yml

@@ -258,3 +258,10 @@ partnership:
         description: Probability that for a given partnering attempt, the agent tries to partner with only other agents in their component. Otherwise, the agent tries to partner with agents from any component.  Network must be enabled.
         min: 0
         max: 1
+  dissolve:
+    time:
+      type: int
+      default: -9999
+    enabled:
+      type: bool
+      default: false

titan/settings/philly-gis/assort_mix.yml

@@ -0,0 +1,17 @@
+assort_mix:
+  assort_disadvantaged:
+    attribute: race
+    agent_value: disadvantaged
+    partner_attribute: location
+    partner_values:
+      __same__: 0.32
+      __neighbor__: 0.15
+      __other__: 0.53
+  assort_notdisadvantaged:
+    attribute: race
+    agent_value: notdisadvantaged
+    partner_attribute: location
+    partner_values:
+      __same__: 0.2
+      __neighbor__: 0.096
+      __other__: 0.704

titan/settings/philly-gis/calibration.yml

@@ -0,0 +1,6 @@
+calibration:
+  sex:
+    act: 1.0
+    partner: 1.0
+  acquisition: 1.0
+  mortality: 1.0