From 9cdf1cacb82ce7f83a974564a2d59958a3a9cba7 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Fri, 18 Dec 2020 17:42:15 -0500
Subject: [PATCH 01/49] feat(haart): add ability to change haart probability
 given time since dx

Real-world, people are more likely to start treatment soon after diagnosis. This change allows that to be reflected for agents in the model.

BREAKING CHANGE: Need to provide haart initiation based on time
---
 settings/atlanta/demographics.yml   |  4 ++--
 tests/params/simple_integration.yml | 12 ++++++++++--
 titan/features/haart.py             | 13 +++++++++++--
 titan/params/demographics.yml       | 29 ++++++++++++++++++++++++-----
 4 files changed, 47 insertions(+), 11 deletions(-)

diff --git a/settings/atlanta/demographics.yml b/settings/atlanta/demographics.yml
index 9bc31445..5667f1f3 100644
--- a/settings/atlanta/demographics.yml
+++ b/settings/atlanta/demographics.yml
@@ -36,7 +36,7 @@ demographics:
                   init: 0.232
               haart: &black_haart
                 init: 0.625
-                prob: 0.35
+                cap: 0.35
                 adherence:
                   init: 0.885
                   prob: 0.885
@@ -78,7 +78,7 @@ demographics:
               aids: 34.4
             haart: &white_haart
               init: 0.585
-              prob: 0.20
+              cap: 0.20
               adherence:
                 init: 0.817
                 prob: 0.817
diff --git a/tests/params/simple_integration.yml b/tests/params/simple_integration.yml
index 81a550a8..709c7707 100644
--- a/tests/params/simple_integration.yml
+++ b/tests/params/simple_integration.yml
@@ -48,7 +48,11 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                1:
+                  enroll_prob: 0.1
+                  start: 0
+                  stop: 999
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -89,7 +93,11 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                1:
+                  enroll_prob: 0.1
+                  start: 0
+                  stop: 999
               adherence:
                 init: 0.1
                 prob: 0.1
diff --git a/titan/features/haart.py b/titan/features/haart.py
index 5175b24e..690f0c7f 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -94,18 +94,27 @@ def update_agent(self, model: "model.TITAN"):
                 if self.agent.location.params.hiv.haart_cap:
                     # if HAART is based on cap instead of prob, determine number of
                     # HAART agents based on % of diagnosed agents
+                    assert len(haart_params) == 1  # should only have one val for cap TODO check earlier
                     num_dx_agents = self.agent.hiv.dx_counts[self.agent.race][  # type: ignore[attr-defined]
                         self.agent.sex_type
                     ]
                     num_haart_agents = self.counts[self.agent.race][self.agent.sex_type]
 
-                    if num_haart_agents < (haart_params.prob * num_dx_agents):
+                    # take value from dictionary for cap
+                    if num_haart_agents < (haart_params.cap * num_dx_agents):
                         self.initiate(model)
                 else:
+                    # Find enroll probability based on time since diagnosis
+                    for i in haart_params.prob.values():
+                        if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:
+                            enroll_prob = i.enroll_prob
+                            break
+
                     if model.run_random.random() < (
-                        haart_params.prob * model.calibration.haart.coverage
+                        enroll_prob * model.calibration.haart.coverage
                     ):
                         self.initiate(model)
+
             # Go off HAART
             elif self.active and model.run_random.random() < haart_params.discontinue:
                 self.active = False
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index ba680e82..1c6e8677 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -98,7 +98,7 @@ demographics:
             max: 1.0
           duration:
             prob:
-              type: bins
+              type: bin
               description: Binned probabilities of incarceration duration during model run
               fields:
                 prob:
@@ -137,7 +137,7 @@ demographics:
                   min: 130
                   max: 260
             init:
-              type: bins
+              type: bin
               description: Binned probabilities of incarceration duration when initializing population
               fields:
                 prob:
@@ -297,12 +297,31 @@ demographics:
                 type: float
                 min: 0.0
                 max: 1.0
-              prob:
-                default: 0.0
-                description: "Probability that an agent in this class with HIV becomes enrolled in HAART at a given time step"
+              cap:
                 type: float
+                default: 0.0
+                description: "Percent of agents on haart if haart cap is used"
                 min: 0.0
                 max: 1.0
+              prob:
+                type: bin
+                description: "Probability that an agent in this class with HIV becomes enrolled in HAART at a given time step based on time since diagnosis (use 0 for haart cap)"
+                fields:
+                  enroll_prob:
+                    type: float
+                    min: 0.0
+                    max: 1.0
+                  start:
+                    type: int
+                    min: 0
+                  stop:
+                    type: int
+                    min: 1
+                default:
+                  0:
+                    start: 0
+                    stop: 999
+                    enroll_prob: 0.0
               adherence:
                 init:
                   default: 0.0

From 8dd31ceaa8e0bb92fc487e581cbd1d6a0d1faf29 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Mon, 4 Jan 2021 11:23:09 -0500
Subject: [PATCH 02/49] feat(haart): make haart initiation dependent on time
 since dx

For probability-based (not cap-based) haart, allows flexibility to vary probabilities based on time since the agent was diagnosed. This reflects real-world, where people are more likely to initiate treatment soon after diagnosis.

BREAKING CHANGE: Divide haart probability into bins based on time since dx. Use single bin accounting for all times (e.g. start: 0, stop: 9999) if dx-duration basis is unneeded. No change necessary for haart cap.
---
 settings/mississippi/demographics.yml | 14 ++++++-
 settings/nyc-msm/demographics.yml     | 54 +++++++++++++++++++++++++--
 settings/scott/demographics.yml       | 16 ++++----
 tests/features/haart_test.py          | 20 +++++++++-
 tests/params/basic.yml                | 12 +++++-
 tests/params/basic_seeded.yml         | 12 +++++-
 tests/params/basic_seeded_error.yml   | 12 +++++-
 titan/features/haart.py               |  3 +-
 8 files changed, 121 insertions(+), 22 deletions(-)

diff --git a/settings/mississippi/demographics.yml b/settings/mississippi/demographics.yml
index fd0989db..690f4496 100644
--- a/settings/mississippi/demographics.yml
+++ b/settings/mississippi/demographics.yml
@@ -25,7 +25,19 @@ demographics:
                 init: 0.46
             haart:
               init: 0.690
-              prob: 0.057
+              prob:
+                0:
+                  enroll_prob: 0.609
+                  start: 0
+                  stop: 1
+                1:
+                  enroll_prob: 0.074
+                  start: 1
+                  stop: 12
+                2:
+                  enroll_prob: 0.0
+                  start: 12
+                  stop: 9999
               adherence:
                 init: 0.500
                 prob: 0.500
diff --git a/settings/nyc-msm/demographics.yml b/settings/nyc-msm/demographics.yml
index 99096618..5841f726 100644
--- a/settings/nyc-msm/demographics.yml
+++ b/settings/nyc-msm/demographics.yml
@@ -27,7 +27,23 @@ demographics:
                 init: 0.500
             haart:
               init: 0.764
-              prob: 0.212
+              prob:
+                0:
+                  start: 0
+                  stop: 1
+                  enroll_prob: 0.709
+                1:
+                  start: 1
+                  stop: 3
+                  enroll_prob: 0.212
+                2:
+                  start: 3
+                  stop: 12
+                  enroll_prob: 0.051
+                3:
+                  start: 12
+                  stop: 9999
+                  enroll_prob: 0.0
               adherence:
                 init: 0.489
                 prob: 0.489
@@ -81,7 +97,23 @@ demographics:
                 init: 0.487
             haart:
               init: 0.764
-              prob: 0.193
+              prob:
+                0:
+                  enroll_prob: 0.278
+                  start: 0
+                  stop: 1
+                1:
+                  enroll_prob: 0.193
+                  start: 1
+                  stop: 3
+                2:
+                  enroll_prob: 0.037
+                  start: 3
+                  stop: 12
+                3:
+                  start: 12
+                  stop: 9999
+                  enroll_prob: 0.0
               adherence:
                 init: 0.719
                 prob: 0.719
@@ -135,7 +167,23 @@ demographics:
                 init: 0.471
             haart:
               init: 0.791
-              prob: 0.163
+              prob:
+                0:
+                  start: 0
+                  stop: 1
+                  enroll_prob: 0.742
+                1:
+                  start: 1
+                  stop: 3
+                  enroll_prob: 0.163
+                2:
+                  start: 3
+                  stop: 12
+                  enroll_prob: 0.029
+                3:
+                  start: 12
+                  stop: 9999
+                  enroll_prob: 0.0
               adherence:
                 init: 0.707
                 prob: 0.707
diff --git a/settings/scott/demographics.yml b/settings/scott/demographics.yml
index ce8b837c..b25754aa 100644
--- a/settings/scott/demographics.yml
+++ b/settings/scott/demographics.yml
@@ -36,9 +36,13 @@ demographics:
               dx:
                 prob: 0.202
                 init: 1.0
-            haart:
+            haart: &haart_vals
               init: 1.0
-              prob: 0.679
+              prob:
+                0:
+                  enroll_prob: 0.679
+                  start: 0
+                  stop: 999
               adherence:
                 init: 1.0
                 prob: 1.0
@@ -82,13 +86,7 @@ demographics:
               hiv: 3.1
               aids: 10.4
               haart_adherent: 1.0
-            haart:
-              init: 1.0
-              prob: 0.679
-              adherence:
-                init: 1.0
-                prob: 1.0
-              discontinue: 0.000
+            haart: *haart_vals
             num_partners:
               Sex:
                 dist_type: poisson
diff --git a/tests/features/haart_test.py b/tests/features/haart_test.py
index fd535a8e..bc4e8dee 100644
--- a/tests/features/haart_test.py
+++ b/tests/features/haart_test.py
@@ -18,6 +18,7 @@ def test_update_haart_t1(make_model, make_agent):
 
     # t0 agent initialized HAART
     a.hiv.dx = True
+    a.hiv.dx_time = model.time
 
     # go on haart
     model.run_random = FakeRandom(
@@ -48,7 +49,24 @@ def test_update_haart_t1(make_model, make_agent):
     # Increase cap. Agent goes on haart
     a.location.params.demographics[a.race].sex_type[a.sex_type].drug_type[
         a.drug_type
-    ].haart.prob = 2.0
+    ].haart.cap = 2.0
     a.haart.update_agent(model)
     assert a.haart.active
     assert a.haart.adherent is True
+
+
+def test_update_haart_dx_time(make_model, make_agent):
+    model = make_model()
+    model.time = 1
+    a = make_agent(race="white")
+    model.run_random = FakeRandom(0.5)
+
+    a.hiv.active = True
+    a.hiv.dx = True
+    a.hiv.dx_time = 1  # agent dx duration is 0
+    a.haart.update_agent(model)
+    assert not a.haart.active
+
+    a.hiv.dx_time -= 10
+    a.haart.update_agent(model)
+    assert a.haart.active
diff --git a/tests/params/basic.yml b/tests/params/basic.yml
index dfda011e..f7338e99 100644
--- a/tests/params/basic.yml
+++ b/tests/params/basic.yml
@@ -41,7 +41,15 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              prob: &haart_prob
+                0:
+                  enroll_prob: 0.1
+                  start: 0
+                  stop: 10
+                1:
+                  enroll_prob: 1.0
+                  start: 10
+                  stop: 100
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -64,7 +72,7 @@ demographics:
                     value_type: float
             haart:
               init: 0.1
-              prob: 0.1
+              prob: *haart_prob
               adherence:
                 init: 0.1
                 prob: 0.1
diff --git a/tests/params/basic_seeded.yml b/tests/params/basic_seeded.yml
index b5837111..97aedda8 100644
--- a/tests/params/basic_seeded.yml
+++ b/tests/params/basic_seeded.yml
@@ -41,7 +41,11 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                0:
+                  enroll_prob: 0.1
+                  start: 0
+                  stop: 99
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -64,7 +68,11 @@ demographics:
                     value_type: float
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                0:
+                  enroll_prob: 0.1
+                  start: 0
+                  stop: 99
               adherence:
                 init: 0.1
                 prob: 0.1
diff --git a/tests/params/basic_seeded_error.yml b/tests/params/basic_seeded_error.yml
index 83cc3f7e..447b4460 100644
--- a/tests/params/basic_seeded_error.yml
+++ b/tests/params/basic_seeded_error.yml
@@ -41,7 +41,11 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                0:
+                  enroll_prob: 0.1
+                  start: 0
+                  stop: 99
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -64,7 +68,11 @@ demographics:
                     value_type: float
             haart:
               init: 0.1
-              prob: 0.1
+              prob:
+                0:
+                  enroll_prob: 0.1
+                  start: 0
+                  stop: 99
               adherence:
                 init: 0.1
                 prob: 0.1
diff --git a/titan/features/haart.py b/titan/features/haart.py
index 690f0c7f..34971738 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -94,7 +94,6 @@ def update_agent(self, model: "model.TITAN"):
                 if self.agent.location.params.hiv.haart_cap:
                     # if HAART is based on cap instead of prob, determine number of
                     # HAART agents based on % of diagnosed agents
-                    assert len(haart_params) == 1  # should only have one val for cap TODO check earlier
                     num_dx_agents = self.agent.hiv.dx_counts[self.agent.race][  # type: ignore[attr-defined]
                         self.agent.sex_type
                     ]
@@ -106,7 +105,7 @@ def update_agent(self, model: "model.TITAN"):
                 else:
                     # Find enroll probability based on time since diagnosis
                     for i in haart_params.prob.values():
-                        if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:
+                        if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:  # type: ignore[attr-defined]
                             enroll_prob = i.enroll_prob
                             break
 

From 830f401069dd818938f2b1bc2a3c1dbd78cde30c Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Mon, 4 Jan 2021 15:38:45 -0500
Subject: [PATCH 03/49] feat(relationship): allow relationship durations to
 differ by agent race

This change allows relationships to have different relanship durations depending on race of agents. Right now, duration of mixed-race partnerships chooses a random agent from the partnership and uses their params

BREAKING CHANGE: requires subdict-ing duration off of both race and bond type
---
 settings/atlanta/partnership.yml      | 30 +++++-----
 settings/chicago/chicago_baseCase.yml | 45 +++++++-------
 settings/mississippi/model.yml        | 23 ++++----
 settings/nyc-msm/partnership.yml      | 84 +++++++++++++++++++++++----
 settings/scott/model.yml              | 57 +++++++++---------
 tests/params/basic.yml                | 64 +++++++++++---------
 tests/partnering_test.py              |  4 +-
 titan/params/partnership.yml          |  3 +-
 titan/partnering.py                   | 47 ++++++++-------
 titan/population.py                   |  7 ++-
 10 files changed, 224 insertions(+), 140 deletions(-)

diff --git a/settings/atlanta/partnership.yml b/settings/atlanta/partnership.yml
index 21d1d610..5a479b6d 100644
--- a/settings/atlanta/partnership.yml
+++ b/settings/atlanta/partnership.yml
@@ -1,20 +1,22 @@
 partnership:
   duration:
     Sex:
-      type: bins
-      bins:
-        1:
-          prob: 0.456
-          min: 1
-          max: 3
-        2:
-          prob: 0.756
-          min: 3
-          max: 12
-        3:
-          prob: 1.0
-          min: 13
-          max: 24
+      white: &partnership_duration
+        type: bins
+        bins:
+          1:
+            prob: 0.456
+            min: 1
+            max: 3
+          2:
+            prob: 0.756
+            min: 3
+            max: 12
+          3:
+            prob: 1.0
+            min: 13
+            max: 24
+      black: *partnership_duration
   sex:
     frequency:
       Sex:
diff --git a/settings/chicago/chicago_baseCase.yml b/settings/chicago/chicago_baseCase.yml
index 7acd63b1..db136488 100644
--- a/settings/chicago/chicago_baseCase.yml
+++ b/settings/chicago/chicago_baseCase.yml
@@ -144,28 +144,29 @@ demographics:
 partnership:
   duration:
     Social:
-      type: bins
-      bins:
-        1:
-          prob: 0.585
-          min: 1
-          max: 6
-        2:
-          prob: 0.701
-          min: 7
-          max: 12
-        3:
-          prob: 0.822
-          min: 13
-          max: 24
-        4:
-          prob: 0.8819999999999999
-          min: 25
-          max: 36
-        5:
-          prob: 1.0
-          min: 37
-          max: 48
+      black:
+        type: bins
+        bins:
+          1:
+            prob: 0.585
+            min: 1
+            max: 6
+          2:
+            prob: 0.701
+            min: 7
+            max: 12
+          3:
+            prob: 0.822
+            min: 13
+            max: 24
+          4:
+            prob: 0.8819999999999999
+            min: 25
+            max: 36
+          5:
+            prob: 1.0
+            min: 37
+            max: 48
   sex:
     acquisition:
       MSM:
diff --git a/settings/mississippi/model.yml b/settings/mississippi/model.yml
index e3bb5414..4017c65c 100644
--- a/settings/mississippi/model.yml
+++ b/settings/mississippi/model.yml
@@ -57,17 +57,18 @@ partnership:
         versatile: 0.0026625
   duration:
     Sex:
-      type: distribution
-      distribution:
-        dist_type: weibull_modified
-        vars:
-          1:
-            value: 0.586
-            value_type: float
-          2:
-            value: 11.532
-            value_type: float
-        mean: 16
+      black:
+        type: distribution
+        distribution:
+          dist_type: weibull_modified
+          vars:
+            1:
+              value: 0.586
+              value_type: float
+            2:
+              value: 11.532
+              value_type: float
+          mean: 16
 
 prep:
   type:
diff --git a/settings/nyc-msm/partnership.yml b/settings/nyc-msm/partnership.yml
index d76b0a3b..fb566253 100644
--- a/settings/nyc-msm/partnership.yml
+++ b/settings/nyc-msm/partnership.yml
@@ -35,15 +35,77 @@ partnership:
 
   duration:
     Main:
-      type: distribution
-      distribution:
-        dist_type: wald
-        vars:
-          1:
-            value: 52.88
-            value_type: float
-          2:
-            value: 5.248
-            value_type: float
-        mean: 52.88
+      white:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 70.44
+              value_type: float
+            2:
+              value: 6.72
+              value_type: float
+          mean: 70.44
+      black:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 20.88
+              value_type: float
+            2:
+              value: 2.76
+              value_type: float
+          mean: 20.88
+      latino:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 35.52
+              value_type: float
+            2:
+              value: 3.84
+              value_type: float
+          mean: 3.84
+    Casual:
+      white:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 11.76
+              value_type: float
+            2:
+              value: 1.32
+              value_type: float
+          mean: 11.76
+      black:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 17.16
+              value_type: float
+            2:
+              value: 1.56
+              value_type: float
+          mean: 17.16
+      latino:
+        type: distribution
+        distribution:
+          dist_type: wald
+          vars:
+            1:
+              value: 16.32
+              value_type: float
+            2:
+              value: 1.20
+              value_type: float
+          mean: 16.32
 
diff --git a/settings/scott/model.yml b/settings/scott/model.yml
index c21faf8d..a3ddf473 100644
--- a/settings/scott/model.yml
+++ b/settings/scott/model.yml
@@ -180,35 +180,38 @@ partnership:
         adherent: 0.06
   duration:
     Sex:
-      type: distribution
-      distribution:
-        dist_type: set_value
-        vars:
-          1:
-            value: 12100
-            value_type: int
-        mean: 12100
+      white:
+        type: distribution
+        distribution:
+          dist_type: set_value
+          vars:
+            1:
+              value: 12100
+              value_type: int
+          mean: 12100
     SexInj:
-      type: distribution
-      distribution:
-        dist_type: set_value
-        vars:
-          1:
-            value: 121
-            value_type: int
-        mean: 121
+      white:
+        type: distribution
+        distribution:
+          dist_type: set_value
+          vars:
+            1:
+              value: 121
+              value_type: int
+          mean: 121
     Inj:
-      type: distribution
-      distribution:
-        dist_type: gamma
-        vars:
-          1:
-            value: 5.37
-            value_type: float
-          2:
-            value: 23.28
-            value_type: float
-        mean: 125
+      white:
+        type: distribution
+        distribution:
+          dist_type: gamma
+          vars:
+            1:
+              value: 5.37
+              value_type: float
+            2:
+              value: 23.28
+              value_type: float
+          mean: 125
 
 assort_mix:
   assort_pwid:
diff --git a/tests/params/basic.yml b/tests/params/basic.yml
index f7338e99..e21ec975 100644
--- a/tests/params/basic.yml
+++ b/tests/params/basic.yml
@@ -225,35 +225,43 @@ partnership:
         receptive: 0.0138
         versatile: 0.00745
   duration:
-    Sex:
-      type: bins
-      bins:
-        1:
-          prob: 1.0
-          min: 1
-          max: 2
-    Inj:
-      type: distribution
-      distribution:
-        dist_type: randint
-        vars:
-          1:
-            value: 1
-            value_type: int
-          2:
-            value: 3
-            value_type: int
-        mean: 1
-    SexInj: &poisson_one
-      type: distribution
-      distribution:
-        dist_type: poisson
-        vars:
+    Sex: 
+      white: &sex_dur
+        type: bins
+        bins:
           1:
-            value: 1
-            value_type: float
-        mean: 1
-    Social: *poisson_one
+            prob: 1.0
+            min: 1
+            max: 2
+      black: *sex_dur
+    Inj:
+      white: &inj_dur
+        type: distribution
+        distribution:
+          dist_type: randint
+          vars:
+            1:
+              value: 1
+              value_type: int
+            2:
+              value: 3
+              value_type: int
+          mean: 1
+      black: *inj_dur
+    SexInj:
+      white: &poisson_one
+        type: distribution
+        distribution:
+          dist_type: poisson
+          vars:
+            1:
+              value: 1
+              value_type: float
+          mean: 1
+      black: *poisson_one
+    Social:
+      white: *poisson_one
+      black: *poisson_one
 
 prep:
   target: 0.1
diff --git a/tests/partnering_test.py b/tests/partnering_test.py
index 74951f6c..d60500ec 100644
--- a/tests/partnering_test.py
+++ b/tests/partnering_test.py
@@ -11,9 +11,9 @@
 
 def test_partnership_duration(params):
     # test duration with randint
-    assert get_partnership_duration(params, FakeRandom(1.0), "Inj") == 1
+    assert get_partnership_duration(params, FakeRandom(1.0), "Inj", "white") == 1
     # test duration with bins
-    assert get_partnership_duration(params, FakeRandom(0.1), "Sex") == 1
+    assert get_partnership_duration(params, FakeRandom(0.1), "Sex", "white") == 1
 
 
 @pytest.mark.unit
diff --git a/titan/params/partnership.yml b/titan/params/partnership.yml
index b229ca35..53b8d722 100644
--- a/titan/params/partnership.yml
+++ b/titan/params/partnership.yml
@@ -179,7 +179,8 @@ partnership:
     type: sub-dict
     keys:
       - bond_types
-    description: "Duration of relationships given bond type"
+      - races
+    description: "Duration of relationships given agent race and partnership bond type"
     default:
       type:
         type: enum
diff --git a/titan/partnering.py b/titan/partnering.py
index df0436e1..24cd90b3 100644
--- a/titan/partnering.py
+++ b/titan/partnering.py
@@ -124,30 +124,34 @@ def get_mean_rel_duration(params: "parse_params.ObjMap"):
     args:
         params: The current model's parameters
     """
-    mean_rel_duration: Dict[str, int] = {}
+    mean_rel_duration: Dict[str, Dict] = {}
     for bond in params.partnership.duration:
-        if params.partnership.duration[bond].type == "bins":
-            weights = []
-            vals = []
-            dur_bins = params.partnership.duration[bond].bins
-            for bins in dur_bins:
-                if bins > 1:
-                    weights.append(dur_bins[bins].prob - dur_bins[bins - 1].prob)
-                else:
-                    weights.append(dur_bins[bins].prob)
-                vals.append(np.average([dur_bins[bins].min, dur_bins[bins].max]))
-            mean_rel_duration[bond] = np.average(vals, weights=weights)
-        else:
-            mean_rel_duration[bond] = params.partnership.duration[
-                bond
-            ].distribution.mean
-        assert mean_rel_duration[bond] > 0, "All bonds must have a positive duration!"
+        mean_rel_duration[bond] = {}
+        for race in params.classes.races:
+            if params.partnership.duration[bond][race].type == "bins":
+                weights = []
+                vals = []
+                dur_bins = params.partnership.duration[bond][race].bins
+                for bins in dur_bins:
+                    if bins > 1:
+                        weights.append(dur_bins[bins].prob - dur_bins[bins - 1].prob)
+                    else:
+                        weights.append(dur_bins[bins].prob)
+                    vals.append(np.average([dur_bins[bins].min, dur_bins[bins].max]))
+                mean_rel_duration[bond][race] = np.average(vals, weights=weights)
+            else:
+                mean_rel_duration[bond][race] = params.partnership.duration[bond][
+                    race
+                ].distribution.mean
+            assert (
+                mean_rel_duration[bond][race] > 0
+            ), "All bonds must have a positive duration!"
 
     return mean_rel_duration
 
 
 def get_partnership_duration(
-    params: "parse_params.ObjMap", rand_gen, bond_type: str
+    params: "parse_params.ObjMap", rand_gen, bond_type: str, race: Optional[str]
 ) -> int:
     """
     Get duration of a relationship drawn from bins or a distribution per the params [params.partnership.duration]
@@ -161,10 +165,11 @@ def get_partnership_duration(
         number of time steps the partnership should endure
     """
 
-    if params.partnership.duration[bond_type].type == "bins":
-        dur_info = params.partnership.duration[bond_type].bins
+    if params.partnership.duration[bond_type][race].type == "bins":
+        dur_info = params.partnership.duration[bond_type][race].bins
 
         diceroll = rand_gen.random()
+        print(dur_info)
         dur_bin = dur_info[5]
         for i in range(1, 5):
             if diceroll < dur_info[i].prob:
@@ -174,7 +179,7 @@ def get_partnership_duration(
         duration = rand_gen.randint(dur_bin.min, dur_bin.max)
 
     else:
-        dist = params.partnership.duration[bond_type].distribution
+        dist = params.partnership.duration[bond_type][race].distribution
         duration = utils.safe_dist(dist, rand_gen)
 
     return duration
diff --git a/titan/population.py b/titan/population.py
index b9175b6d..64ddaba0 100644
--- a/titan/population.py
+++ b/titan/population.py
@@ -91,7 +91,7 @@ def __init__(self, params: "parse_params.ObjMap", id: Optional[str] = None):
         self.relationships: Set["ag.Relationship"] = set()
 
         # find average partnership durations
-        self.mean_rel_duration: Dict[str, int] = partnering.get_mean_rel_duration(
+        self.mean_rel_duration: Dict[str, Dict] = partnering.get_mean_rel_duration(
             self.params
         )
 
@@ -191,7 +191,7 @@ def create_agent(
                 utils.safe_dist(dist_info, self.np_random)
                 * utils.safe_divide(
                     agent.location.params.calibration.sex.partner,
-                    self.mean_rel_duration[bond],
+                    self.mean_rel_duration[bond][race],
                 )
             )
             # so not zero if added mid-year
@@ -353,8 +353,9 @@ def update_agent_partners(
         no_match = True
 
         if partner:
+            race = utils.safe_random_choice([agent.race, partner.race], self.pop_random)
             duration = partnering.get_partnership_duration(
-                agent.location.params, self.np_random, bond_type
+                agent.location.params, self.np_random, bond_type, race
             )
             relationship = ag.Relationship(
                 agent, partner, duration, bond_type=bond_type

From 58e412490788588c030fe2ec5c908dec22db63b0 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Tue, 5 Jan 2021 11:41:31 -0500
Subject: [PATCH 04/49] feat(sex): allow flexible condom use based on bond type

Bond type influences condom use in real-world relationships. For example, casual relationships may have more consistent condom use than committed, long-term relationships.

BREAKING CHANGE: must sub-dict safe sex off of bond type
---
 settings/atlanta/demographics.yml     |  8 ++++++--
 settings/chicago/chicago_baseCase.yml |  4 ----
 settings/mississippi/demographics.yml |  4 +++-
 settings/nyc-msm/demographics.yml     | 18 ++++++++++++++---
 settings/scott/demographics.yml       | 16 +++++++++++++--
 tests/integration_test.py             | 19 +++++++++++++++---
 tests/params/basic.yml                | 27 +++++++++++++++-----------
 tests/params/basic_seeded.yml         | 28 +++++++++++++++++----------
 tests/params/basic_seeded_error.yml   | 28 +++++++++++++++++----------
 tests/params/simple_integration.yml   | 13 ++++++++++---
 titan/interactions/sex.py             |  3 ++-
 titan/params/demographics.yml         | 15 +++++++++-----
 titan/params/syringe_services.yml     |  2 --
 titan/partnering.py                   |  1 -
 14 files changed, 128 insertions(+), 58 deletions(-)

diff --git a/settings/atlanta/demographics.yml b/settings/atlanta/demographics.yml
index 5667f1f3..76b88d57 100644
--- a/settings/atlanta/demographics.yml
+++ b/settings/atlanta/demographics.yml
@@ -11,7 +11,9 @@ demographics:
             versatile: 0.437
             insertive: 0.242
             receptive: 0.321
-        safe_sex: 0.688
+        safe_sex:
+          Sex: 
+            prob: 0.688
         prep:
           discontinue: 0.0
           adherence: 0.568
@@ -56,7 +58,9 @@ demographics:
             versatile: 0.544
             insertive: 0.228
             receptive: 0.228
-        safe_sex: 0.528
+        safe_sex:
+          Sex:
+            prob: 0.528
         prep:
           adherence: 0.911
           target: 0.415
diff --git a/settings/chicago/chicago_baseCase.yml b/settings/chicago/chicago_baseCase.yml
index db136488..c9a9b71e 100644
--- a/settings/chicago/chicago_baseCase.yml
+++ b/settings/chicago/chicago_baseCase.yml
@@ -102,10 +102,6 @@ demographics:
         incar:
           init: 0.0
           prob: 0.0
-        safe_sex: 0.312
-        injection:
-          unsafe_prob: 0.27
-          num_acts: 5.0
         prep:
           discontinue: 0.0
           adherence: 0.568
diff --git a/settings/mississippi/demographics.yml b/settings/mississippi/demographics.yml
index 690f4496..80b56ce5 100644
--- a/settings/mississippi/demographics.yml
+++ b/settings/mississippi/demographics.yml
@@ -9,7 +9,9 @@ demographics:
             versatile: 0.671
             insertive: 0.169
             receptive: 0.160
-        safe_sex: 0.214
+        safe_sex:
+          Sex:
+            prob: 0.214
         prep:
           discontinue: 0.034
           adherence: 0.860
diff --git a/settings/nyc-msm/demographics.yml b/settings/nyc-msm/demographics.yml
index 5841f726..55f60ff0 100644
--- a/settings/nyc-msm/demographics.yml
+++ b/settings/nyc-msm/demographics.yml
@@ -9,7 +9,11 @@ demographics:
             versatile: 0.200
             insertive: 0.480
             receptive: 0.320
-        safe_sex: 0.275
+        safe_sex:
+          Main:
+            prob: 0.275
+          Casual:
+            prob: 0.409
         prep:
           discontinue: 0.034  # calibration
           adherence: 0.565
@@ -79,7 +83,11 @@ demographics:
             insertive: 0.220
             receptive: 0.195
             versatile: 0.585
-        safe_sex: 0.262
+        safe_sex:
+          Main:
+            prob: 0.183
+          Casual:
+            prob: 0.341
         prep:
           discontinue: 0.025  # calibration
           adherence: 0.719
@@ -144,7 +152,11 @@ demographics:
     sex_type:
       MSM:
         ppl: 1.0
-        safe_sex: 0.126
+        safe_sex:
+          Main:
+            prob: 0.126
+          Casual:
+            prob: 0.277
         sex_role:
           init:
             insertive: 0.439
diff --git a/settings/scott/demographics.yml b/settings/scott/demographics.yml
index b25754aa..205f85fa 100644
--- a/settings/scott/demographics.yml
+++ b/settings/scott/demographics.yml
@@ -24,7 +24,13 @@ demographics:
         sex_role:
           init:
             insertive: 1.0
-        safe_sex: 0.1
+        safe_sex:
+          Sex:
+            prob: 0.1
+          Inj:
+            prob: 0.1
+          SexInj:
+            prob: 0.1
         injection:
           unsafe_prob: 0.321
           num_acts: 5
@@ -99,7 +105,13 @@ demographics:
         sex_role:
           init:
             receptive: 1.0
-        safe_sex: 0.2
+        safe_sex:
+          Sex:
+            prob: 0.2
+          Inj:
+            prob: 0.2
+          SexInj:
+            prob: 0.2
         injection:
           unsafe_prob: 0.321
           num_acts: 5
diff --git a/tests/integration_test.py b/tests/integration_test.py
index 5f9431a4..5bd6fe2f 100644
--- a/tests/integration_test.py
+++ b/tests/integration_test.py
@@ -232,6 +232,7 @@ def test_prep_coverage(make_model_integration, tmpdir):
     t10_hiv_b = res_b["10"]["hiv"]
     t10_diff = t10_hiv_a - t10_hiv_b  # a should be higher
     assert res_a["10"]["prep"] < res_b["10"]["prep"]
+    assert t10_hiv_a > t0_hiv_a
     assert t10_diff > t0_diff
 
 
@@ -243,10 +244,11 @@ def test_syringe_services(params_integration, tmpdir):
     params_integration.demographics.black.sex_type.MSM.drug_type.Inj.ppl = 1.0
     params_integration.demographics.black.sex_type.MSM.drug_type["None"].ppl = 0.0
     model_a = TITAN(params_integration)
-    model_a.params.partnership.sex.frequency.Sex = ObjMap(
-        {"type": "bins", "bins": {1: {"prob": 1.0, "min": 0, "max": 1}}}
+    model_a.params.partnership.sex.frequency.Sex = (
+        ObjMap(  # turn off sex to show only injection effects
+            {"type": "bins", "bins": {1: {"prob": 1.0, "min": 0, "max": 1}}}
+        )
     )
-
     path_a = tmpdir.mkdir("a")
     path_a.mkdir("network")
     path_b = tmpdir.mkdir("b")
@@ -254,6 +256,15 @@ def test_syringe_services(params_integration, tmpdir):
 
     # run with default bins (0-9)
     model_a.run(path_a)
+    num_bonds = 0
+    num_ag = 0
+    for ag in model_a.pop.all_agents:
+        if ag.hiv.active:
+            num_ag += 1
+            for ptnr in ag.get_partners(["Inj", "SexInj"]):
+                if not ptnr.hiv.active:
+                    num_bonds += 1
+    assert num_bonds  # make sure there are serodiscordant partnerships
 
     # change the coverage upward for creating model b, use same seeds
     model_a.params.features.syringe_services = True
@@ -290,6 +301,8 @@ def test_syringe_services(params_integration, tmpdir):
     t10_hiv_a = res_a["10"]
     t10_hiv_b = res_b["10"]
     t10_diff = t10_hiv_a - t10_hiv_b  # a should be higher
+    assert t10_hiv_a > t0_hiv_a
+    assert t10_hiv_b > t0_hiv_b
     assert t10_diff > t0_diff
 
 
diff --git a/tests/params/basic.yml b/tests/params/basic.yml
index e21ec975..f3b6330b 100644
--- a/tests/params/basic.yml
+++ b/tests/params/basic.yml
@@ -81,7 +81,13 @@ demographics:
         incar: &base_incar
           init: 0.02
           prob: 0.02
-        safe_sex: 0.1
+        safe_sex: &safe_sex_default
+          Sex:
+            prob: 0.1
+          Inj:
+            prob: 0.1
+          SexInj:
+            prob: 0.1
         injection: &base_injection
           unsafe_prob: 0.1
           num_acts: 10
@@ -102,7 +108,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep:
           adherence: 0.1
@@ -115,7 +121,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -124,7 +130,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -133,7 +139,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -145,7 +151,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -154,7 +160,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -163,7 +169,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -172,7 +178,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -183,7 +189,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -233,7 +239,6 @@ partnership:
             prob: 1.0
             min: 1
             max: 2
-      black: *sex_dur
     Inj:
       white: &inj_dur
         type: distribution
diff --git a/tests/params/basic_seeded.yml b/tests/params/basic_seeded.yml
index 97aedda8..62e04d91 100644
--- a/tests/params/basic_seeded.yml
+++ b/tests/params/basic_seeded.yml
@@ -81,7 +81,15 @@ demographics:
         incar: &base_incar
           init: 0.02
           prob: 0.02
-        safe_sex: 0.1
+        safe_sex: &safe_sex_default
+          Sex:
+            prob: 0.1
+          Inj:
+            prob: 0.1
+          SexInj:
+            prob: 0.1
+          Social:
+            prob: 0.1
         injection: &base_injection
           unsafe_prob: 0.1
           num_acts: 10
@@ -102,7 +110,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep:
           adherence: 0.1
@@ -115,7 +123,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -124,7 +132,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -133,7 +141,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -145,7 +153,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -154,7 +162,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -163,7 +171,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -172,7 +180,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -183,7 +191,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
diff --git a/tests/params/basic_seeded_error.yml b/tests/params/basic_seeded_error.yml
index 447b4460..cc4fcb88 100644
--- a/tests/params/basic_seeded_error.yml
+++ b/tests/params/basic_seeded_error.yml
@@ -81,7 +81,15 @@ demographics:
         incar: &base_incar
           init: 0.02
           prob: 0.02
-        safe_sex: 0.1
+        safe_sex: &safe_sex_default
+          Sex:
+            prob: 0.1
+          Inj:
+            prob: 0.1
+          SexInj:
+            prob: 0.1
+          Social:
+            prob: 0.1
         injection: &base_injection
           unsafe_prob: 0.1
           num_acts: 10
@@ -102,7 +110,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep:
           adherence: 0.1
@@ -115,7 +123,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -124,7 +132,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -133,7 +141,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -145,7 +153,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -154,7 +162,7 @@ demographics:
         ppl: 0.3
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -163,7 +171,7 @@ demographics:
         ppl: 0.2
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection: *base_injection
         prep: *base_prep
         high_risk: *base_high_risk
@@ -172,7 +180,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
@@ -183,7 +191,7 @@ demographics:
         ppl: 0.1
         drug_type: *base_drug_type
         incar: *base_incar
-        safe_sex: 0.1
+        safe_sex: *safe_sex_default
         injection:
           unsafe_prob: 0.
           num_acts: 10
diff --git a/tests/params/simple_integration.yml b/tests/params/simple_integration.yml
index 709c7707..18582b79 100644
--- a/tests/params/simple_integration.yml
+++ b/tests/params/simple_integration.yml
@@ -20,9 +20,16 @@ demographics:
         ppl: 1.0
         incar:
           prob: 0.5 # default is off, so this only hits when turned on in integration test
-        safe_sex: 0.1
+        safe_sex:
+          Sex:
+            prob: 1.0
+          SexInj:
+            prob: 1.0
+          Inj:
+            prob: 1.0
         injection:
-          unsafe_prob: 0.1
+          unsafe_prob: 0.3
+          num_acts: 10
         prep:
           adherence: 0.9
           discontinue: 0.1
@@ -159,7 +166,7 @@ partnership:
 syringe_services:
   timeline:
     ssp_open:
-      start_time: 2
+      start_time: 0
       stop_time: 12
       num_slots_start: 500
       num_slots_stop: 500
diff --git a/titan/interactions/sex.py b/titan/interactions/sex.py
index 298cec46..fe005c47 100644
--- a/titan/interactions/sex.py
+++ b/titan/interactions/sex.py
@@ -27,7 +27,8 @@ def get_num_acts(cls, model: "model.TITAN", rel: "agent.Relationship") -> int:
         p_safe_sex = (
             rel.agent1.location.params.demographics[rel.agent1.race]
             .sex_type[rel.agent1.sex_type]
-            .safe_sex
+            .safe_sex[rel.bond_type]
+            .prob
         )
 
         # increase condom usage if diagnosed
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index 1c6e8677..eb7dd40f 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -189,11 +189,16 @@ demographics:
             min: 0.0
             max: 1.0
         safe_sex:
-          default: 0.0
-          description: "Probability of safe sex (condom use) per sex act"
-          type: float
-          min: 0.0
-          max: 1.0
+          type: sub-dict
+          description: "Parameters controlling condom use (safe sex) given bond type"
+          keys:
+            - bond_types
+          default:
+            prob:
+              default: 0.0
+              type: float
+              min: 0.0
+              max: 1.0
         prep:
           discontinue:
             default: 0.0
diff --git a/titan/params/syringe_services.yml b/titan/params/syringe_services.yml
index 8f258ff5..32ad2034 100644
--- a/titan/params/syringe_services.yml
+++ b/titan/params/syringe_services.yml
@@ -5,11 +5,9 @@ syringe_services:
       start_time:
         type: int
         description: "What time to start this prevalence of syringe services program"
-        min: 1
       stop_time:
         type: int
         description: "What time to stop this prevalence of syringe services program"
-        min: 1
       num_slots_start:
         type: int
         description: "Cap for number of available slots in SSP at beginning of time period"
diff --git a/titan/partnering.py b/titan/partnering.py
index 24cd90b3..ef130051 100644
--- a/titan/partnering.py
+++ b/titan/partnering.py
@@ -169,7 +169,6 @@ def get_partnership_duration(
         dur_info = params.partnership.duration[bond_type][race].bins
 
         diceroll = rand_gen.random()
-        print(dur_info)
         dur_bin = dur_info[5]
         for i in range(1, 5):
             if diceroll < dur_info[i].prob:

From 25145ad76dd56a935b8220b3eb7de0e5c1b9418f Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Tue, 5 Jan 2021 15:39:42 -0500
Subject: [PATCH 05/49] feat(haart): allow reinitiation of haart

Agents who have previously been on haart can now reinitiate at a separate probability from normal initiation.
---
 settings/mississippi/demographics.yml |  3 +++
 settings/nyc-msm/demographics.yml     |  9 +++++++++
 titan/features/haart.py               | 27 +++++++++++++++++----------
 titan/params/demographics.yml         |  9 +++++++++
 4 files changed, 38 insertions(+), 10 deletions(-)

diff --git a/settings/mississippi/demographics.yml b/settings/mississippi/demographics.yml
index 80b56ce5..931cc51e 100644
--- a/settings/mississippi/demographics.yml
+++ b/settings/mississippi/demographics.yml
@@ -40,6 +40,9 @@ demographics:
                   enroll_prob: 0.0
                   start: 12
                   stop: 9999
+              reinit:
+                allow: true
+                prob: 0.01
               adherence:
                 init: 0.500
                 prob: 0.500
diff --git a/settings/nyc-msm/demographics.yml b/settings/nyc-msm/demographics.yml
index 55f60ff0..d25dbfa5 100644
--- a/settings/nyc-msm/demographics.yml
+++ b/settings/nyc-msm/demographics.yml
@@ -48,6 +48,9 @@ demographics:
                   start: 12
                   stop: 9999
                   enroll_prob: 0.0
+              reinit:
+                allow: true
+                prob: 0.035
               adherence:
                 init: 0.489
                 prob: 0.489
@@ -122,6 +125,9 @@ demographics:
                   start: 12
                   stop: 9999
                   enroll_prob: 0.0
+              reinit:
+                allow: true
+                prob: 0.032
               adherence:
                 init: 0.719
                 prob: 0.719
@@ -196,6 +202,9 @@ demographics:
                   start: 12
                   stop: 9999
                   enroll_prob: 0.0
+              reinit:
+                allow: true
+                prob: 0.041
               adherence:
                 init: 0.707
                 prob: 0.707
diff --git a/titan/features/haart.py b/titan/features/haart.py
index 34971738..b85e059b 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -26,6 +26,7 @@ def __init__(self, agent: "agent.Agent"):
         super().__init__(agent)
 
         self.active = False
+        self.ever = False
         self.adherent = False
 
     @classmethod
@@ -62,6 +63,7 @@ def init_agent(self, pop: "population.Population", time: int):
             and pop.pop_random.random() < agent_params.haart.init
         ):
             self.active = True
+            self.ever = True
             self.add_agent(self.agent)
 
             haart_adh = agent_params.haart.adherence.init
@@ -103,16 +105,20 @@ def update_agent(self, model: "model.TITAN"):
                     if num_haart_agents < (haart_params.cap * num_dx_agents):
                         self.initiate(model)
                 else:
-                    # Find enroll probability based on time since diagnosis
-                    for i in haart_params.prob.values():
-                        if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:  # type: ignore[attr-defined]
-                            enroll_prob = i.enroll_prob
-                            break
-
-                    if model.run_random.random() < (
-                        enroll_prob * model.calibration.haart.coverage
-                    ):
-                        self.initiate(model)
+                    if self.ever and haart_params.reinit.allow:
+                        if model.run_random.random() < haart_params.reinit.prob:
+                            self.initiate(model)
+                    else:
+                        # Find enroll probability based on time since diagnosis
+                        for i in haart_params.prob.values():
+                            if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:  # type: ignore[attr-defined]
+                                enroll_prob = i.enroll_prob
+                                break
+
+                        if model.run_random.random() < (
+                            enroll_prob * model.calibration.haart.coverage
+                        ):
+                            self.initiate(model)
 
             # Go off HAART
             elif self.active and model.run_random.random() < haart_params.discontinue:
@@ -195,4 +201,5 @@ def initiate(self, model: "model.TITAN"):
 
         # Add agent to HAART class set, update agent params
         self.active = True
+        self.ever = True
         self.add_agent(self.agent)
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index eb7dd40f..ebcf5d5f 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -327,6 +327,15 @@ demographics:
                     start: 0
                     stop: 999
                     enroll_prob: 0.0
+              reinit:
+                allow:
+                  type: boolean
+                  description: "Whether or not agents who have previously been on prep have a separate haart probability"
+                  default: false
+                prob:
+                  type: float
+                  description: "Probability of reinitiating haart"
+                  default: 0.0
               adherence:
                 init:
                   default: 0.0

From c1919bd803cee9fb9bc77bdbd5dce84a19a217ea Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Wed, 6 Jan 2021 10:45:57 -0500
Subject: [PATCH 06/49] test(population/partnering): test race-based duration

---
 tests/features/haart_test.py | 12 ++++++++++++
 tests/params/basic.yml       | 13 ++++++++++++-
 tests/partnering_test.py     |  2 ++
 tests/population_test.py     | 13 ++++++++++++-
 4 files changed, 38 insertions(+), 2 deletions(-)

diff --git a/tests/features/haart_test.py b/tests/features/haart_test.py
index bc4e8dee..ac735b4d 100644
--- a/tests/features/haart_test.py
+++ b/tests/features/haart_test.py
@@ -70,3 +70,15 @@ def test_update_haart_dx_time(make_model, make_agent):
     a.hiv.dx_time -= 10
     a.haart.update_agent(model)
     assert a.haart.active
+
+
+def test_update_haart_reinit(make_model, make_agent):
+    model = make_model()
+    a = make_agent(race="white")
+
+    a.hiv.active = True
+    a.hiv.dx = True
+    a.hiv.dx_time = model.time - 1  # make duration 1, would pass if not reinit
+    a.haart.ever = True  # uses reinit prob
+    a.haart.update_agent(model)
+    assert not a.haart.active
diff --git a/tests/params/basic.yml b/tests/params/basic.yml
index f3b6330b..edf9348d 100644
--- a/tests/params/basic.yml
+++ b/tests/params/basic.yml
@@ -50,6 +50,9 @@ demographics:
                   enroll_prob: 1.0
                   start: 10
                   stop: 100
+              reinit: &reinit_prob
+                allow: true
+                prob: 0.0
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -73,6 +76,7 @@ demographics:
             haart:
               init: 0.1
               prob: *haart_prob
+              reinit: *reinit_prob
               adherence:
                 init: 0.1
                 prob: 0.1
@@ -232,13 +236,20 @@ partnership:
         versatile: 0.00745
   duration:
     Sex: 
-      white: &sex_dur
+      white:
         type: bins
         bins:
           1:
             prob: 1.0
             min: 1
             max: 2
+      black:
+        type: bins
+        bins:
+          1:
+            prob: 1.0
+            min: 3
+            max: 4
     Inj:
       white: &inj_dur
         type: distribution
diff --git a/tests/partnering_test.py b/tests/partnering_test.py
index d60500ec..8bee6c36 100644
--- a/tests/partnering_test.py
+++ b/tests/partnering_test.py
@@ -14,6 +14,8 @@ def test_partnership_duration(params):
     assert get_partnership_duration(params, FakeRandom(1.0), "Inj", "white") == 1
     # test duration with bins
     assert get_partnership_duration(params, FakeRandom(0.1), "Sex", "white") == 1
+    # test duration with second race
+    assert get_partnership_duration(params, FakeRandom(0.1), "Sex", "black") == 3
 
 
 @pytest.mark.unit
diff --git a/tests/population_test.py b/tests/population_test.py
index a939a675..c7e1cdaa 100644
--- a/tests/population_test.py
+++ b/tests/population_test.py
@@ -248,7 +248,7 @@ def test_update_agent_partners_MSM_match(make_population, params):
 def test_update_agent_partners_NDU_PWID_match(make_population, params):
     pop = make_population(n=0)
     a = pop.create_agent(pop.geography.locations["world"], "white", 0, "MSM")
-    p = pop.create_agent(pop.geography.locations["world"], "white", 0, "MSM")
+    p = pop.create_agent(pop.geography.locations["world"], "black", 0, "MSM")
     # ensure random sex partner no assorting
     pop.pop_random = FakeRandom(1.1)
     a.drug_type = "None"
@@ -265,6 +265,17 @@ def test_update_agent_partners_NDU_PWID_match(make_population, params):
     assert p in pop.graph.nodes()
     assert a.partners
     assert len(pop.graph.edges()) == 1
+    for (
+        rel
+    ) in (
+        a.relationships
+    ):  # check that duration uses "randomly selected" (first) partner
+        assert rel.duration == partnering.get_partnership_duration(
+            a.location.params, pop.np_random, "Sex", a.race
+        )
+        assert rel.duration != partnering.get_partnership_duration(
+            a.location.params, pop.np_random, "Sex", p.race
+        )
 
 
 @pytest.mark.unit

From 56f56483a590fc7eb259e033d0c0e713ed48a801 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Mon, 11 Jan 2021 10:54:29 -0500
Subject: [PATCH 07/49] build(nyc-msm): establish testing probability by
 "location"

Instead of every agent of a given race having the same testing probability, this creates three categories of test probability.
---
 settings/nyc-msm/location.yml | 55 +++++++++++++++++++++++++++++++++++
 settings/nyc-msm/model.yml    |  8 +++++
 2 files changed, 63 insertions(+)
 create mode 100644 settings/nyc-msm/location.yml

diff --git a/settings/nyc-msm/location.yml b/settings/nyc-msm/location.yml
new file mode 100644
index 00000000..8fc067b0
--- /dev/null
+++ b/settings/nyc-msm/location.yml
@@ -0,0 +1,55 @@
+location:
+  scaling:
+    high_test:
+      demographics|white|ppl:
+        field: override
+        override: 0.384
+      demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &high_test_prob
+        field: override
+        override: 0.333
+      demographics|black|ppl:
+        field: override
+        override: 0.278
+      demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *high_test_prob
+      demographics|latino|ppl:
+        field: override
+        override: 0.338
+      demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *high_test_prob
+
+    mid_test:
+      demographics|white|ppl:
+        field: override
+        override: 0.587
+      demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &mid_test_prob
+        field: override
+        override: 0.167
+      demographics|black|ppl:
+        field: override
+        override: 0.187
+      demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *mid_test_prob
+      demographics|latino|ppl:
+        field: override
+        override: 0.226
+      demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *mid_test_prob
+
+    low_test:
+      demographics|white|ppl:
+        field: override
+        override: 0.605
+      demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &low_test_prob
+        field: override
+        override: 0.042
+      demographics|black|ppl:
+        field: override
+        override: 0.082
+      demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *low_test_prob
+      demographics|latino|ppl:
+        field: override
+        override: 0.313
+      demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *low_test_prob
+
+  edges:
+    edge_default:
+      location_1: high_test
+      location_2: high_test
+      distance: 0
\ No newline at end of file
diff --git a/settings/nyc-msm/model.yml b/settings/nyc-msm/model.yml
index e2c0dd92..517c68f0 100644
--- a/settings/nyc-msm/model.yml
+++ b/settings/nyc-msm/model.yml
@@ -27,6 +27,14 @@ classes:
         - sex
   drug_types:
     - None
+  locations:
+    high_test:
+      ppl: .190
+    mid_test:
+      ppl: .634
+    low_test:
+      ppl: .176
+
   
 features:
   prep: true

From 0b3e3a84137ada3821381972c3e33b18f796af04 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Mon, 11 Jan 2021 14:17:53 -0500
Subject: [PATCH 08/49] feat(haart): allow agents to lose haart adherence

Agents may now become non-adherent while staying on haart.
---
 settings/mississippi/demographics.yml |  1 -
 settings/nyc-msm/demographics.yml     |  6 +++---
 settings/nyc-msm/hiv.yml              |  1 +
 titan/features/haart.py               | 16 +++++++++++-----
 titan/params/demographics.yml         | 10 ++++++----
 titan/params/hiv.yml                  |  4 ++++
 6 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/settings/mississippi/demographics.yml b/settings/mississippi/demographics.yml
index 931cc51e..14e72b75 100644
--- a/settings/mississippi/demographics.yml
+++ b/settings/mississippi/demographics.yml
@@ -41,7 +41,6 @@ demographics:
                   start: 12
                   stop: 9999
               reinit:
-                allow: true
                 prob: 0.01
               adherence:
                 init: 0.500
diff --git a/settings/nyc-msm/demographics.yml b/settings/nyc-msm/demographics.yml
index d25dbfa5..c1cb7166 100644
--- a/settings/nyc-msm/demographics.yml
+++ b/settings/nyc-msm/demographics.yml
@@ -49,11 +49,11 @@ demographics:
                   stop: 9999
                   enroll_prob: 0.0
               reinit:
-                allow: true
                 prob: 0.035
               adherence:
                 init: 0.489
                 prob: 0.489
+                discontinue: 0.0689
               discontinue: 0.0076
             death_rate:
               base: 1.512
@@ -126,11 +126,11 @@ demographics:
                   stop: 9999
                   enroll_prob: 0.0
               reinit:
-                allow: true
                 prob: 0.032
               adherence:
                 init: 0.719
                 prob: 0.719
+                discontinue: 0.0718
               discontinue: 0.0069  # calibration
             death_rate:
               base: 0.792
@@ -203,11 +203,11 @@ demographics:
                   stop: 9999
                   enroll_prob: 0.0
               reinit:
-                allow: true
                 prob: 0.041
               adherence:
                 init: 0.707
                 prob: 0.707
+                discontinue: 0.0745
               discontinue: 0.0059
             death_rate:
               base: 0.0696
diff --git a/settings/nyc-msm/hiv.yml b/settings/nyc-msm/hiv.yml
index 53c0f32a..1cd0eec2 100644
--- a/settings/nyc-msm/hiv.yml
+++ b/settings/nyc-msm/hiv.yml
@@ -5,6 +5,7 @@ hiv:
   aids:
     prob: 0.004
   start_time: -48
+  reinit_haart: true
 
 prep:
   target_model:
diff --git a/titan/features/haart.py b/titan/features/haart.py
index b85e059b..ffcc7c3a 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -105,7 +105,7 @@ def update_agent(self, model: "model.TITAN"):
                     if num_haart_agents < (haart_params.cap * num_dx_agents):
                         self.initiate(model)
                 else:
-                    if self.ever and haart_params.reinit.allow:
+                    if self.ever and self.agent.location.params.hiv.reinit_haart:
                         if model.run_random.random() < haart_params.reinit.prob:
                             self.initiate(model)
                     else:
@@ -121,10 +121,16 @@ def update_agent(self, model: "model.TITAN"):
                             self.initiate(model)
 
             # Go off HAART
-            elif self.active and model.run_random.random() < haart_params.discontinue:
-                self.active = False
-                self.adherent = False
-                self.remove_agent(self.agent)
+            elif self.active:
+                if model.run_random.random() < haart_params.discontinue:
+                    self.active = False
+                    self.adherent = False
+                    self.remove_agent(self.agent)
+                elif (
+                    self.adherent
+                    and model.run_random.random() < haart_params.adherence.discontinue
+                ):
+                    self.adherent = False
 
     @classmethod
     def add_agent(cls, agent: "agent.Agent"):
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index ebcf5d5f..e73aa01d 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -328,10 +328,6 @@ demographics:
                     stop: 999
                     enroll_prob: 0.0
               reinit:
-                allow:
-                  type: boolean
-                  description: "Whether or not agents who have previously been on prep have a separate haart probability"
-                  default: false
                 prob:
                   type: float
                   description: "Probability of reinitiating haart"
@@ -349,6 +345,12 @@ demographics:
                   type: float
                   min: 0.0
                   max: 1.0
+                discontinue:
+                  default: 0.0
+                  description: "Probability that an adherent agent will become nonadherent"
+                  type: float
+                  min: 0.0
+                  max: 1.0
               discontinue:
                 default: 0.0
                 description: "Probability that an agent on HAART discontinues HAART in a given time step"
diff --git a/titan/params/hiv.yml b/titan/params/hiv.yml
index bb6f1a49..5e65a82f 100644
--- a/titan/params/hiv.yml
+++ b/titan/params/hiv.yml
@@ -53,6 +53,10 @@ hiv:
     default: false
     description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
     type: boolean
+  reinit_haart:
+    type: boolean
+    default: false
+    description: Whether a separate probability should be used for haart initiation among agents who have previously discontinued haart
   start_time:
     default: 0
     description: "What timestep to start agent interactions related to hiv transmission"

From 6fdc944f0eb815919f0020a653f8c1860c686a14 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Mon, 11 Jan 2021 16:44:19 -0500
Subject: [PATCH 09/49] test(haart): add test for loss of adherence

---
 settings/nyc-msm/demographics.yml |  6 +++---
 tests/features/haart_test.py      | 10 +++++++++-
 tests/params/basic.yml            |  4 +++-
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/settings/nyc-msm/demographics.yml b/settings/nyc-msm/demographics.yml
index c1cb7166..5a537962 100644
--- a/settings/nyc-msm/demographics.yml
+++ b/settings/nyc-msm/demographics.yml
@@ -54,7 +54,7 @@ demographics:
                 init: 0.489
                 prob: 0.489
                 discontinue: 0.0689
-              discontinue: 0.0076
+              discontinue: 0.014
             death_rate:
               base: 1.512
             num_partners:
@@ -130,7 +130,7 @@ demographics:
               adherence:
                 init: 0.719
                 prob: 0.719
-                discontinue: 0.0718
+                discontinue: 0.0115
               discontinue: 0.0069  # calibration
             death_rate:
               base: 0.792
@@ -208,7 +208,7 @@ demographics:
                 init: 0.707
                 prob: 0.707
                 discontinue: 0.0745
-              discontinue: 0.0059
+              discontinue: 0.00883
             death_rate:
               base: 0.0696
             num_partners:
diff --git a/tests/features/haart_test.py b/tests/features/haart_test.py
index ac735b4d..636b0827 100644
--- a/tests/features/haart_test.py
+++ b/tests/features/haart_test.py
@@ -54,6 +54,15 @@ def test_update_haart_t1(make_model, make_agent):
     assert a.haart.active
     assert a.haart.adherent is True
 
+    # falls off adherence
+    model.run_random = FakeRandom(1.0)
+    a.location.params.demographics[a.race].sex_type[a.sex_type].drug_type[
+        a.drug_type
+    ].haart.adherence.discontinue = 5.0
+    a.haart.update_agent(model)
+    assert a.haart.active
+    assert a.haart.adherent is False
+
 
 def test_update_haart_dx_time(make_model, make_agent):
     model = make_model()
@@ -76,7 +85,6 @@ def test_update_haart_reinit(make_model, make_agent):
     model = make_model()
     a = make_agent(race="white")
 
-    a.hiv.active = True
     a.hiv.dx = True
     a.hiv.dx_time = model.time - 1  # make duration 1, would pass if not reinit
     a.haart.ever = True  # uses reinit prob
diff --git a/tests/params/basic.yml b/tests/params/basic.yml
index edf9348d..3a5beca0 100644
--- a/tests/params/basic.yml
+++ b/tests/params/basic.yml
@@ -51,7 +51,6 @@ demographics:
                   start: 10
                   stop: 100
               reinit: &reinit_prob
-                allow: true
                 prob: 0.0
               adherence:
                 init: 0.1
@@ -314,6 +313,9 @@ exposures:
   hiv: true
   knowledge: true
 
+hiv:
+  reinit_haart: true
+
 features:
   incar: true
   prep: true

From c3ff3c896978cba651cfc3aac55eee81184ef58a Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Wed, 13 Jan 2021 11:15:32 -0500
Subject: [PATCH 10/49] feat(haart): allow agents already on haart to become
 adherent

also includes some edits from PR
---
 settings/chicago/chicago_baseCase.yml |  9 ---------
 settings/scott/demographics.yml       | 16 ++++++----------
 titan/features/haart.py               |  6 ++++++
 titan/params/demographics.yml         | 13 ++++++++++++-
 titan/params/haart.yml                |  9 +++++++++
 titan/params/hiv.yml                  |  8 --------
 6 files changed, 33 insertions(+), 28 deletions(-)
 create mode 100644 titan/params/haart.yml

diff --git a/settings/chicago/chicago_baseCase.yml b/settings/chicago/chicago_baseCase.yml
index c9a9b71e..bd93bd51 100644
--- a/settings/chicago/chicago_baseCase.yml
+++ b/settings/chicago/chicago_baseCase.yml
@@ -37,9 +37,6 @@ features:
 calibration:
   injection:
     act: 1.0
-  sex:
-    partner: 1.0
-    act: 1.0
   acquisition: 1.0
   test_frequency: 1.0
   mortality: 1.0
@@ -163,12 +160,6 @@ partnership:
             prob: 1.0
             min: 37
             max: 48
-  sex:
-    acquisition:
-      MSM:
-        versatile: 0.00745
-        insertive: 0.0011
-        receptive: 0.0138
   pca:
     frequency:
       Social:
diff --git a/settings/scott/demographics.yml b/settings/scott/demographics.yml
index 205f85fa..69c781e6 100644
--- a/settings/scott/demographics.yml
+++ b/settings/scott/demographics.yml
@@ -25,12 +25,10 @@ demographics:
           init:
             insertive: 1.0
         safe_sex:
-          Sex:
-            prob: 0.1
-          Inj:
-            prob: 0.1
-          SexInj:
+          Sex: &condom_use_HM
             prob: 0.1
+          Inj: *condom_use_HM
+          SexInj: *condom_use_HM
         injection:
           unsafe_prob: 0.321
           num_acts: 5
@@ -106,12 +104,10 @@ demographics:
           init:
             receptive: 1.0
         safe_sex:
-          Sex:
-            prob: 0.2
-          Inj:
-            prob: 0.2
-          SexInj:
+          Sex: &condom_use
             prob: 0.2
+          Inj: *condom_use_HF
+          SexInj: *condom_use_HF
         injection:
           unsafe_prob: 0.321
           num_acts: 5
diff --git a/titan/features/haart.py b/titan/features/haart.py
index ffcc7c3a..1912295f 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -109,6 +109,7 @@ def update_agent(self, model: "model.TITAN"):
                         if model.run_random.random() < haart_params.reinit.prob:
                             self.initiate(model)
                     else:
+                        enroll_prob = 0
                         # Find enroll probability based on time since diagnosis
                         for i in haart_params.prob.values():
                             if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:  # type: ignore[attr-defined]
@@ -131,6 +132,11 @@ def update_agent(self, model: "model.TITAN"):
                     and model.run_random.random() < haart_params.adherence.discontinue
                 ):
                     self.adherent = False
+                elif (
+                    not self.adherent
+                    and model.run_random.random() < haart_params.adherence.prob
+                ):
+                    self.adherent = True
 
     @classmethod
     def add_agent(cls, agent: "agent.Agent"):
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index e73aa01d..75141940 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -308,6 +308,14 @@ demographics:
                 description: "Percent of agents on haart if haart cap is used"
                 min: 0.0
                 max: 1.0
+              haart_cap:
+                default: false
+                description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
+                type: boolean
+              reinit_haart:
+                type: boolean
+                default: false
+                description: Whether a separate probability should be used for haart initiation among agents who have previously discontinued haart
               prob:
                 type: bin
                 description: "Probability that an agent in this class with HIV becomes enrolled in HAART at a given time step based on time since diagnosis (use 0 for haart cap)"
@@ -347,10 +355,13 @@ demographics:
                   max: 1.0
                 discontinue:
                   default: 0.0
-                  description: "Probability that an adherent agent will become nonadherent"
+                  description: "Probability that an adherent agent will become nonadherent at a given timestep"
                   type: float
                   min: 0.0
                   max: 1.0
+                become:
+                  default: 0.0
+                  description: "Probability that an agent already on haart will become adherent at a given timestep"
               discontinue:
                 default: 0.0
                 description: "Probability that an agent on HAART discontinues HAART in a given time step"
diff --git a/titan/params/haart.yml b/titan/params/haart.yml
new file mode 100644
index 00000000..7df77d11
--- /dev/null
+++ b/titan/params/haart.yml
@@ -0,0 +1,9 @@
+haart:
+  cap:
+    default: false
+    description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
+    type: boolean
+  reinit_haart:
+    type: boolean
+    default: false
+    description: Whether a separate probability should be used for haart initiation among agents who have previously discontinued haart
diff --git a/titan/params/hiv.yml b/titan/params/hiv.yml
index 5e65a82f..11e6321d 100644
--- a/titan/params/hiv.yml
+++ b/titan/params/hiv.yml
@@ -49,14 +49,6 @@ hiv:
     description: On creation, agents are randomly assigned an hiv.time, this is the maximum time
     type: int
     min: 2
-  haart_cap:
-    default: false
-    description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
-    type: boolean
-  reinit_haart:
-    type: boolean
-    default: false
-    description: Whether a separate probability should be used for haart initiation among agents who have previously discontinued haart
   start_time:
     default: 0
     description: "What timestep to start agent interactions related to hiv transmission"

From 8707ebfabf907e8f692e2c9396b4c0f27bef3229 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Wed, 13 Jan 2021 13:09:57 -0500
Subject: [PATCH 11/49] refactor: clarify param names and comment

---
 titan/features/haart.py       |  6 +++---
 titan/params/demographics.yml | 21 ++++++++-------------
 titan/params/haart.yml        |  2 +-
 3 files changed, 12 insertions(+), 17 deletions(-)

diff --git a/titan/features/haart.py b/titan/features/haart.py
index 1912295f..e459c0c1 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -93,7 +93,7 @@ def update_agent(self, model: "model.TITAN"):
             )
             # Go on HAART
             if not self.active:
-                if self.agent.location.params.hiv.haart_cap:
+                if self.agent.location.params.haart.use_cap:
                     # if HAART is based on cap instead of prob, determine number of
                     # HAART agents based on % of diagnosed agents
                     num_dx_agents = self.agent.hiv.dx_counts[self.agent.race][  # type: ignore[attr-defined]
@@ -111,9 +111,9 @@ def update_agent(self, model: "model.TITAN"):
                     else:
                         enroll_prob = 0
                         # Find enroll probability based on time since diagnosis
-                        for i in haart_params.prob.values():
+                        for i in haart_params.enroll_prob.values():
                             if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:  # type: ignore[attr-defined]
-                                enroll_prob = i.enroll_prob
+                                enroll_prob = i.prob
                                 break
 
                         if model.run_random.random() < (
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index 75141940..f8f09de1 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -190,7 +190,7 @@ demographics:
             max: 1.0
         safe_sex:
           type: sub-dict
-          description: "Parameters controlling condom use (safe sex) given bond type"
+          description: "Parameters controlling condom use/safe sex per sex act given bond type"
           keys:
             - bond_types
           default:
@@ -305,22 +305,14 @@ demographics:
               cap:
                 type: float
                 default: 0.0
-                description: "Percent of agents on haart if haart cap is used"
+                description: "Percent of diagnosed agents on haart if haart cap is used"
                 min: 0.0
                 max: 1.0
-              haart_cap:
-                default: false
-                description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
-                type: boolean
-              reinit_haart:
-                type: boolean
-                default: false
-                description: Whether a separate probability should be used for haart initiation among agents who have previously discontinued haart
-              prob:
+              enroll_prob:
                 type: bin
                 description: "Probability that an agent in this class with HIV becomes enrolled in HAART at a given time step based on time since diagnosis (use 0 for haart cap)"
                 fields:
-                  enroll_prob:
+                  prob:
                     type: float
                     min: 0.0
                     max: 1.0
@@ -334,7 +326,7 @@ demographics:
                   0:
                     start: 0
                     stop: 999
-                    enroll_prob: 0.0
+                    prob: 0.0
               reinit:
                 prob:
                   type: float
@@ -362,6 +354,9 @@ demographics:
                 become:
                   default: 0.0
                   description: "Probability that an agent already on haart will become adherent at a given timestep"
+                  type: float
+                  min: 0.0
+                  max: 1.0
               discontinue:
                 default: 0.0
                 description: "Probability that an agent on HAART discontinues HAART in a given time step"
diff --git a/titan/params/haart.yml b/titan/params/haart.yml
index 7df77d11..b48a3673 100644
--- a/titan/params/haart.yml
+++ b/titan/params/haart.yml
@@ -1,5 +1,5 @@
 haart:
-  cap:
+  use_cap:
     default: false
     description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
     type: boolean

From b81ac4b32cd3fc33b3d4d4124cea9650b873e296 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Wed, 13 Jan 2021 14:27:54 -0500
Subject: [PATCH 12/49] refactor: change param names for consistency and
 correct param names in tests

---
 settings/mississippi/demographics.yml |  8 +++----
 settings/nyc-msm/demographics.yml     | 30 +++++++++++++--------------
 settings/nyc-msm/hiv.yml              |  4 +++-
 settings/scott/demographics.yml       |  6 +++---
 settings/scott/model.yml              |  4 +++-
 tests/features/haart_test.py          |  2 +-
 tests/params/basic.yml                | 12 +++++------
 tests/params/basic_seeded.yml         |  4 ++--
 tests/params/basic_seeded_error.yml   |  4 ++--
 tests/params/simple_integration.yml   |  4 ++--
 titan/features/haart.py               |  6 +++---
 titan/params/demographics.yml         |  2 +-
 titan/params/haart.yml                |  2 +-
 13 files changed, 46 insertions(+), 42 deletions(-)

diff --git a/settings/mississippi/demographics.yml b/settings/mississippi/demographics.yml
index 14e72b75..d603935f 100644
--- a/settings/mississippi/demographics.yml
+++ b/settings/mississippi/demographics.yml
@@ -27,17 +27,17 @@ demographics:
                 init: 0.46
             haart:
               init: 0.690
-              prob:
+              enroll:
                 0:
-                  enroll_prob: 0.609
+                  prob: 0.609
                   start: 0
                   stop: 1
                 1:
-                  enroll_prob: 0.074
+                  prob: 0.074
                   start: 1
                   stop: 12
                 2:
-                  enroll_prob: 0.0
+                  prob: 0.0
                   start: 12
                   stop: 9999
               reinit:
diff --git a/settings/nyc-msm/demographics.yml b/settings/nyc-msm/demographics.yml
index 5a537962..b41fe626 100644
--- a/settings/nyc-msm/demographics.yml
+++ b/settings/nyc-msm/demographics.yml
@@ -31,23 +31,23 @@ demographics:
                 init: 0.500
             haart:
               init: 0.764
-              prob:
+              enroll:
                 0:
                   start: 0
                   stop: 1
-                  enroll_prob: 0.709
+                  prob: 0.709
                 1:
                   start: 1
                   stop: 3
-                  enroll_prob: 0.212
+                  prob: 0.212
                 2:
                   start: 3
                   stop: 12
-                  enroll_prob: 0.051
+                  prob: 0.051
                 3:
                   start: 12
                   stop: 9999
-                  enroll_prob: 0.0
+                  prob: 0.0
               reinit:
                 prob: 0.035
               adherence:
@@ -108,23 +108,23 @@ demographics:
                 init: 0.487
             haart:
               init: 0.764
-              prob:
+              enroll:
                 0:
-                  enroll_prob: 0.278
+                  prob: 0.278
                   start: 0
                   stop: 1
                 1:
-                  enroll_prob: 0.193
+                  prob: 0.193
                   start: 1
                   stop: 3
                 2:
-                  enroll_prob: 0.037
+                  prob: 0.037
                   start: 3
                   stop: 12
                 3:
                   start: 12
                   stop: 9999
-                  enroll_prob: 0.0
+                  prob: 0.0
               reinit:
                 prob: 0.032
               adherence:
@@ -185,23 +185,23 @@ demographics:
                 init: 0.471
             haart:
               init: 0.791
-              prob:
+              enroll:
                 0:
                   start: 0
                   stop: 1
-                  enroll_prob: 0.742
+                  prob: 0.742
                 1:
                   start: 1
                   stop: 3
-                  enroll_prob: 0.163
+                  prob: 0.163
                 2:
                   start: 3
                   stop: 12
-                  enroll_prob: 0.029
+                  prob: 0.029
                 3:
                   start: 12
                   stop: 9999
-                  enroll_prob: 0.0
+                  prob: 0.0
               reinit:
                 prob: 0.041
               adherence:
diff --git a/settings/nyc-msm/hiv.yml b/settings/nyc-msm/hiv.yml
index 1cd0eec2..42212def 100644
--- a/settings/nyc-msm/hiv.yml
+++ b/settings/nyc-msm/hiv.yml
@@ -5,7 +5,6 @@ hiv:
   aids:
     prob: 0.004
   start_time: -48
-  reinit_haart: true
 
 prep:
   target_model:
@@ -15,3 +14,6 @@ prep:
   efficacy:
     adherent: 0.96
     non_adherent: 0.76
+
+haart:
+  reinit: true
diff --git a/settings/scott/demographics.yml b/settings/scott/demographics.yml
index 69c781e6..06aa124a 100644
--- a/settings/scott/demographics.yml
+++ b/settings/scott/demographics.yml
@@ -42,9 +42,9 @@ demographics:
                 init: 1.0
             haart: &haart_vals
               init: 1.0
-              prob:
+              enroll:
                 0:
-                  enroll_prob: 0.679
+                  prob: 0.679
                   start: 0
                   stop: 999
               adherence:
@@ -104,7 +104,7 @@ demographics:
           init:
             receptive: 1.0
         safe_sex:
-          Sex: &condom_use
+          Sex: &condom_use_HF
             prob: 0.2
           Inj: *condom_use_HF
           SexInj: *condom_use_HF
diff --git a/settings/scott/model.yml b/settings/scott/model.yml
index a3ddf473..45ca3646 100644
--- a/settings/scott/model.yml
+++ b/settings/scott/model.yml
@@ -43,12 +43,14 @@ hiv:
   dx:
     risk_reduction:
       sex: 0.19
-  haart_cap: true
   start_time: -48
   init: -48
   aids:
     prob: 0.0029
 
+haart:
+  use_cap: true
+
 timeline_scaling:
   timeline:
     burn_scale:
diff --git a/tests/features/haart_test.py b/tests/features/haart_test.py
index 636b0827..f9febf98 100644
--- a/tests/features/haart_test.py
+++ b/tests/features/haart_test.py
@@ -36,7 +36,7 @@ def test_update_haart_t1(make_model, make_agent):
     assert a.haart.active is False
 
     # Try haart cap with low cap, one agent on haart and one diagnosed agent. Nothing happens
-    a.location.params.hiv.haart_cap = True
+    a.location.params.haart.use_cap = True
     a.haart.counts[a.race][a.sex_type] = 1
     a.hiv.dx_counts[a.race][a.sex_type] = 5
     a.location.params.demographics[a.race].sex_type[a.sex_type].drug_type[
diff --git a/tests/params/basic.yml b/tests/params/basic.yml
index 3a5beca0..a6b876a6 100644
--- a/tests/params/basic.yml
+++ b/tests/params/basic.yml
@@ -41,13 +41,13 @@ demographics:
                 init: 0.1
             haart:
               init: 0.1
-              prob: &haart_prob
+              enroll: &haart_prob
                 0:
-                  enroll_prob: 0.1
+                  prob: 0.1
                   start: 0
                   stop: 10
                 1:
-                  enroll_prob: 1.0
+                  prob: 1.0
                   start: 10
                   stop: 100
               reinit: &reinit_prob
@@ -74,7 +74,7 @@ demographics:
                     value_type: float
             haart:
               init: 0.1
-              prob: *haart_prob
+              enroll: *haart_prob
               reinit: *reinit_prob
               adherence:
                 init: 0.1
@@ -313,8 +313,8 @@ exposures:
   hiv: true
   knowledge: true
 
-hiv:
-  reinit_haart: true
+haart:
+  reinit: true
 
 features:
   incar: true
diff --git a/tests/params/basic_seeded.yml b/tests/params/basic_seeded.yml
index 62e04d91..cc8577f3 100644
--- a/tests/params/basic_seeded.yml
+++ b/tests/params/basic_seeded.yml
@@ -43,7 +43,7 @@ demographics:
               init: 0.1
               prob:
                 0:
-                  enroll_prob: 0.1
+                  enroll: 0.1
                   start: 0
                   stop: 99
               adherence:
@@ -70,7 +70,7 @@ demographics:
               init: 0.1
               prob:
                 0:
-                  enroll_prob: 0.1
+                  enroll: 0.1
                   start: 0
                   stop: 99
               adherence:
diff --git a/tests/params/basic_seeded_error.yml b/tests/params/basic_seeded_error.yml
index cc4fcb88..0a78f81b 100644
--- a/tests/params/basic_seeded_error.yml
+++ b/tests/params/basic_seeded_error.yml
@@ -43,7 +43,7 @@ demographics:
               init: 0.1
               prob:
                 0:
-                  enroll_prob: 0.1
+                  enroll: 0.1
                   start: 0
                   stop: 99
               adherence:
@@ -70,7 +70,7 @@ demographics:
               init: 0.1
               prob:
                 0:
-                  enroll_prob: 0.1
+                  enroll: 0.1
                   start: 0
                   stop: 99
               adherence:
diff --git a/tests/params/simple_integration.yml b/tests/params/simple_integration.yml
index 18582b79..4bc57b3b 100644
--- a/tests/params/simple_integration.yml
+++ b/tests/params/simple_integration.yml
@@ -57,7 +57,7 @@ demographics:
               init: 0.1
               prob:
                 1:
-                  enroll_prob: 0.1
+                  enroll: 0.1
                   start: 0
                   stop: 999
               adherence:
@@ -102,7 +102,7 @@ demographics:
               init: 0.1
               prob:
                 1:
-                  enroll_prob: 0.1
+                  enroll: 0.1
                   start: 0
                   stop: 999
               adherence:
diff --git a/titan/features/haart.py b/titan/features/haart.py
index e459c0c1..c3626eb5 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -105,13 +105,13 @@ def update_agent(self, model: "model.TITAN"):
                     if num_haart_agents < (haart_params.cap * num_dx_agents):
                         self.initiate(model)
                 else:
-                    if self.ever and self.agent.location.params.hiv.reinit_haart:
+                    if self.ever and self.agent.location.params.haart.reinit:
                         if model.run_random.random() < haart_params.reinit.prob:
                             self.initiate(model)
                     else:
-                        enroll_prob = 0
+                        enroll = 0
                         # Find enroll probability based on time since diagnosis
-                        for i in haart_params.enroll_prob.values():
+                        for i in haart_params.enroll.values():
                             if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:  # type: ignore[attr-defined]
                                 enroll_prob = i.prob
                                 break
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index f8f09de1..3a42ad4e 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -308,7 +308,7 @@ demographics:
                 description: "Percent of diagnosed agents on haart if haart cap is used"
                 min: 0.0
                 max: 1.0
-              enroll_prob:
+              enroll:
                 type: bin
                 description: "Probability that an agent in this class with HIV becomes enrolled in HAART at a given time step based on time since diagnosis (use 0 for haart cap)"
                 fields:
diff --git a/titan/params/haart.yml b/titan/params/haart.yml
index b48a3673..d6c9589b 100644
--- a/titan/params/haart.yml
+++ b/titan/params/haart.yml
@@ -3,7 +3,7 @@ haart:
     default: false
     description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
     type: boolean
-  reinit_haart:
+  reinit:
     type: boolean
     default: false
     description: Whether a separate probability should be used for haart initiation among agents who have previously discontinued haart

From 8115c5991ccb63a6aa6c81cfc0ad9dd51f7fdb7f Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Wed, 13 Jan 2021 15:40:16 -0500
Subject: [PATCH 13/49] refactor(output): add degree centrality to component
 report

---
 titan/output.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/titan/output.py b/titan/output.py
index c86e9855..4d391e65 100644
--- a/titan/output.py
+++ b/titan/output.py
@@ -6,6 +6,7 @@
 import os
 
 import networkx as nx  # type: ignore
+from numpy import mean  # type: ignore
 
 from .parse_params import ObjMap
 from . import utils
@@ -284,8 +285,8 @@ def print_components(
     if f.tell() == 0:
         f.write(
             "run_id\trunseed\tpopseed\tt\tcompID\ttotalN\tNhiv\tNprep\tNtrtHIV"
-            "\tComp_Status\tPCA\tOral\tInjectable\tAware\tnidu\tcentrality\tDensity"
-            "\tEffectiveSize" + header + "\n"
+            "\tComp_Status\tPCA\tOral\tInjectable\tAware\tnidu\tcentrality\tdensity"
+            "\tEffectiveSize" + header + "\tdeg_cent\n"
         )
 
     comp_id = 0
@@ -341,6 +342,7 @@ def print_components(
             else:
                 component_status = "treatment_no_eligible"
 
+        deg_cent = mean(list(nx.degree_centrality(comp).values()))
         race_str = ""
         for race in race_list:
             race_str += "\t" + str(race_count[race])
@@ -350,7 +352,7 @@ def print_components(
             f"{nhiv}\t"
             f"{nprep}\t{ntrthiv}\t{component_status}\t{pca}\t{oral}\t{injectable_prep}"
             f"\t{aware}\t{nidu}\t{comp_centrality:.4f}\t{comp_density:.4f}"
-            f"\t{average_size:.4f}{race_str}\n"
+            f"\t{average_size:.4f}{race_str}\t{deg_cent}\n"
         )
 
         comp_id += 1

From 64c6776d836fa1ae370ce4f93aeb3b6565c7ed5d Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Thu, 14 Jan 2021 12:45:17 -0500
Subject: [PATCH 14/49] test(haart): correct test for haart reinit

---
 tests/features/haart_test.py | 6 ++++++
 titan/features/haart.py      | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/tests/features/haart_test.py b/tests/features/haart_test.py
index f9febf98..d728b1f1 100644
--- a/tests/features/haart_test.py
+++ b/tests/features/haart_test.py
@@ -83,10 +83,16 @@ def test_update_haart_dx_time(make_model, make_agent):
 
 def test_update_haart_reinit(make_model, make_agent):
     model = make_model()
+    model.time = 1
     a = make_agent(race="white")
 
+    a.hiv.active = True
     a.hiv.dx = True
     a.hiv.dx_time = model.time - 1  # make duration 1, would pass if not reinit
     a.haart.ever = True  # uses reinit prob
     a.haart.update_agent(model)
     assert not a.haart.active
+
+    model.run_random = FakeRandom(-1.1)
+    a.haart.update_agent(model)
+    assert a.haart.active
diff --git a/titan/features/haart.py b/titan/features/haart.py
index c3626eb5..de47bf79 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -109,7 +109,7 @@ def update_agent(self, model: "model.TITAN"):
                         if model.run_random.random() < haart_params.reinit.prob:
                             self.initiate(model)
                     else:
-                        enroll = 0
+                        enroll_prob = 0
                         # Find enroll probability based on time since diagnosis
                         for i in haart_params.enroll.values():
                             if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:  # type: ignore[attr-defined]

From ef5f0a62be63b745a1e8f0b026d8d22cd0a44100 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Thu, 14 Jan 2021 13:02:15 -0500
Subject: [PATCH 15/49] refactor: fix typo in assertion

---
 titan/population_io.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/titan/population_io.py b/titan/population_io.py
index 4a66d71a..c8a095c2 100644
--- a/titan/population_io.py
+++ b/titan/population_io.py
@@ -54,7 +54,7 @@ def write(pop: Population, dir: str, compress: bool = True) -> str:
     returns:
         path, or archive name if compress is true
     """
-    assert len(pop.relationships) > 0, "can't write empty population"
+    assert len(pop.relationships) > 0, "Can't write empty population"
 
     # open agent file
     agent_file = os.path.join(dir, f"{pop.id}_agents.csv")

From 09ad1ad9c57451f2215662204a3f94f4d847691c Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 12:12:24 -0500
Subject: [PATCH 16/49] build: add setup.py so titan can be installed with pip

---
 setup.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 setup.py

diff --git a/setup.py b/setup.py
new file mode 100644
index 00000000..0f2b67fa
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,21 @@
+import setuptools
+
+with open("README.md", "r", encoding="utf-8") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="titan", # Replace with your own username
+    version="2.0.0",
+    # author="Example Author",
+    # author_email="author@example.com",
+    description="TITAN Agent Based Model",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/marshall-lab/TITAN",
+    packages=setuptools.find_packages(),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Operating System :: OS Independent",
+    ],
+    python_requires='>=3.6',
+)

From dec1f22091864b689e48331fccf670bdbf383edf Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 12:26:36 -0500
Subject: [PATCH 17/49] fix: add params files to buil

---
 setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.py b/setup.py
index 0f2b67fa..8503159b 100644
--- a/setup.py
+++ b/setup.py
@@ -18,4 +18,5 @@
         "Operating System :: OS Independent",
     ],
     python_requires='>=3.6',
+    package_data={'titan': 'params/*.yml'},
 )

From 82e04d70fc2480b0054ceb9a6ee99bb9cd0e1877 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 12:30:35 -0500
Subject: [PATCH 18/49] build: add settings

---
 setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 8503159b..91aa98fb 100644
--- a/setup.py
+++ b/setup.py
@@ -18,5 +18,6 @@
         "Operating System :: OS Independent",
     ],
     python_requires='>=3.6',
-    package_data={'titan': 'params/*.yml'},
+    package_data={'titan': ['params/*.yml']},
+    data_files=[('settings', ['settings/*/*.yml', 'settings/*/*.yaml'])]
 )

From 0af42f1ab003bd4916ef84931eddea8e2ff0cdf2 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 12:35:49 -0500
Subject: [PATCH 19/49] refactor: move settings into titan

---
 run_titan.py                                              | 5 -----
 setup.py                                                  | 3 +--
 titan/parse_params.py                                     | 4 ++--
 {settings => titan/settings}/atlanta/assort_mix.yml       | 0
 {settings => titan/settings}/atlanta/calibration.yml      | 0
 {settings => titan/settings}/atlanta/demographics.yml     | 0
 {settings => titan/settings}/atlanta/model.yml            | 0
 {settings => titan/settings}/atlanta/outputs.yml          | 0
 {settings => titan/settings}/atlanta/partnership.yml      | 0
 {settings => titan/settings}/chicago/chicago_baseCase.yml | 0
 {settings => titan/settings}/mississippi/demographics.yml | 0
 {settings => titan/settings}/mississippi/model.yml        | 0
 {settings => titan/settings}/nyc-msm/demographics.yml     | 0
 {settings => titan/settings}/nyc-msm/hiv.yml              | 0
 {settings => titan/settings}/nyc-msm/model.yml            | 0
 {settings => titan/settings}/nyc-msm/partnership.yml      | 0
 {settings => titan/settings}/scott/demographics.yml       | 0
 {settings => titan/settings}/scott/model.yml              | 0
 18 files changed, 3 insertions(+), 9 deletions(-)
 rename {settings => titan/settings}/atlanta/assort_mix.yml (100%)
 rename {settings => titan/settings}/atlanta/calibration.yml (100%)
 rename {settings => titan/settings}/atlanta/demographics.yml (100%)
 rename {settings => titan/settings}/atlanta/model.yml (100%)
 rename {settings => titan/settings}/atlanta/outputs.yml (100%)
 rename {settings => titan/settings}/atlanta/partnership.yml (100%)
 rename {settings => titan/settings}/chicago/chicago_baseCase.yml (100%)
 rename {settings => titan/settings}/mississippi/demographics.yml (100%)
 rename {settings => titan/settings}/mississippi/model.yml (100%)
 rename {settings => titan/settings}/nyc-msm/demographics.yml (100%)
 rename {settings => titan/settings}/nyc-msm/hiv.yml (100%)
 rename {settings => titan/settings}/nyc-msm/model.yml (100%)
 rename {settings => titan/settings}/nyc-msm/partnership.yml (100%)
 rename {settings => titan/settings}/scott/demographics.yml (100%)
 rename {settings => titan/settings}/scott/model.yml (100%)

diff --git a/run_titan.py b/run_titan.py
index 8950c45d..999d0d09 100755
--- a/run_titan.py
+++ b/run_titan.py
@@ -341,11 +341,6 @@ def main(
     setting = setting.lower()
     if setting == "custom":
         setting = None
-    else:
-        setting = os.path.join(
-            os.path.dirname(os.path.abspath(__file__)), "settings", setting
-        )
-        assert os.path.isdir(setting), f"{setting} is not a directory"
 
     params = create_params(
         setting,
diff --git a/setup.py b/setup.py
index 91aa98fb..1fee8cfd 100644
--- a/setup.py
+++ b/setup.py
@@ -18,6 +18,5 @@
         "Operating System :: OS Independent",
     ],
     python_requires='>=3.6',
-    package_data={'titan': ['params/*.yml']},
-    data_files=[('settings', ['settings/*/*.yml', 'settings/*/*.yaml'])]
+    package_data={'titan': ['params/*.yml', 'settings/*/*.yml']}
 )
diff --git a/titan/parse_params.py b/titan/parse_params.py
index 6a7dfc2a..119edaeb 100644
--- a/titan/parse_params.py
+++ b/titan/parse_params.py
@@ -86,7 +86,7 @@ def check_params(params: ObjMap):
 
 
 def create_params(
-    setting_path: Optional[str],
+    setting_name: Optional[str],
     param_path: str,
     outdir: str,
     error_on_unused: bool = False,
@@ -117,7 +117,7 @@ def create_params(
 
     # merge setting and params
     if setting_path is not None:
-        param_paths.append(setting_path)
+        param_paths.append(os.path.join(parent, "settings", setting_name))
 
     param_paths.append(param_path)
 
diff --git a/settings/atlanta/assort_mix.yml b/titan/settings/atlanta/assort_mix.yml
similarity index 100%
rename from settings/atlanta/assort_mix.yml
rename to titan/settings/atlanta/assort_mix.yml
diff --git a/settings/atlanta/calibration.yml b/titan/settings/atlanta/calibration.yml
similarity index 100%
rename from settings/atlanta/calibration.yml
rename to titan/settings/atlanta/calibration.yml
diff --git a/settings/atlanta/demographics.yml b/titan/settings/atlanta/demographics.yml
similarity index 100%
rename from settings/atlanta/demographics.yml
rename to titan/settings/atlanta/demographics.yml
diff --git a/settings/atlanta/model.yml b/titan/settings/atlanta/model.yml
similarity index 100%
rename from settings/atlanta/model.yml
rename to titan/settings/atlanta/model.yml
diff --git a/settings/atlanta/outputs.yml b/titan/settings/atlanta/outputs.yml
similarity index 100%
rename from settings/atlanta/outputs.yml
rename to titan/settings/atlanta/outputs.yml
diff --git a/settings/atlanta/partnership.yml b/titan/settings/atlanta/partnership.yml
similarity index 100%
rename from settings/atlanta/partnership.yml
rename to titan/settings/atlanta/partnership.yml
diff --git a/settings/chicago/chicago_baseCase.yml b/titan/settings/chicago/chicago_baseCase.yml
similarity index 100%
rename from settings/chicago/chicago_baseCase.yml
rename to titan/settings/chicago/chicago_baseCase.yml
diff --git a/settings/mississippi/demographics.yml b/titan/settings/mississippi/demographics.yml
similarity index 100%
rename from settings/mississippi/demographics.yml
rename to titan/settings/mississippi/demographics.yml
diff --git a/settings/mississippi/model.yml b/titan/settings/mississippi/model.yml
similarity index 100%
rename from settings/mississippi/model.yml
rename to titan/settings/mississippi/model.yml
diff --git a/settings/nyc-msm/demographics.yml b/titan/settings/nyc-msm/demographics.yml
similarity index 100%
rename from settings/nyc-msm/demographics.yml
rename to titan/settings/nyc-msm/demographics.yml
diff --git a/settings/nyc-msm/hiv.yml b/titan/settings/nyc-msm/hiv.yml
similarity index 100%
rename from settings/nyc-msm/hiv.yml
rename to titan/settings/nyc-msm/hiv.yml
diff --git a/settings/nyc-msm/model.yml b/titan/settings/nyc-msm/model.yml
similarity index 100%
rename from settings/nyc-msm/model.yml
rename to titan/settings/nyc-msm/model.yml
diff --git a/settings/nyc-msm/partnership.yml b/titan/settings/nyc-msm/partnership.yml
similarity index 100%
rename from settings/nyc-msm/partnership.yml
rename to titan/settings/nyc-msm/partnership.yml
diff --git a/settings/scott/demographics.yml b/titan/settings/scott/demographics.yml
similarity index 100%
rename from settings/scott/demographics.yml
rename to titan/settings/scott/demographics.yml
diff --git a/settings/scott/model.yml b/titan/settings/scott/model.yml
similarity index 100%
rename from settings/scott/model.yml
rename to titan/settings/scott/model.yml

From 471df757f1c8f1294de18de4945841776b531927 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 12:37:15 -0500
Subject: [PATCH 20/49] fix: change all var references

---
 titan/parse_params.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/titan/parse_params.py b/titan/parse_params.py
index 119edaeb..fdbdd3cd 100644
--- a/titan/parse_params.py
+++ b/titan/parse_params.py
@@ -96,7 +96,7 @@ def create_params(
     or not to use the base setting. Parse and create a params (ObjMap) object.
 
     args:
-        setting_path: path to a settings file or directory or `None`
+        setting_name: path to a settings file or directory or `None`
         param_path: path to parameter file or directory
         outdir: path to directory where computed params will be saved
         error_on_unused: throw a hard error if there are unused parameters, otherwise warnings are only printed
@@ -116,7 +116,7 @@ def create_params(
     param_paths = []
 
     # merge setting and params
-    if setting_path is not None:
+    if setting_name is not None:
         param_paths.append(os.path.join(parent, "settings", setting_name))
 
     param_paths.append(param_path)

From 210a4172b45a5cc7e335974b6491975fed5bd433 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 12:55:52 -0500
Subject: [PATCH 21/49] build: make run_titan installed executable

---
 setup.py                           | 5 ++++-
 run_titan.py => titan/run_titan.py | 6 ++++--
 2 files changed, 8 insertions(+), 3 deletions(-)
 rename run_titan.py => titan/run_titan.py (99%)

diff --git a/setup.py b/setup.py
index 1fee8cfd..1c783c6a 100644
--- a/setup.py
+++ b/setup.py
@@ -18,5 +18,8 @@
         "Operating System :: OS Independent",
     ],
     python_requires='>=3.6',
-    package_data={'titan': ['params/*.yml', 'settings/*/*.yml']}
+    package_data={'titan': ['params/*.yml', 'settings/*/*.yml']},
+    entry_scripts={
+        'console_scripts': ['run_titan'='titan:run_titan:main']
+    }
 )
diff --git a/run_titan.py b/titan/run_titan.py
similarity index 99%
rename from run_titan.py
rename to titan/run_titan.py
index 999d0d09..a6d18641 100755
--- a/run_titan.py
+++ b/titan/run_titan.py
@@ -405,8 +405,7 @@ def mean(seq):
     print(("all tasks - sum:  %8.4f seconds" % sum(wct)))
     print(f"all tasks - total: {toc} seconds")
 
-
-if __name__ == "__main__":
+def main():
     args = parser.parse_args()
     rows = args.rows.strip() if args.rows is not None else None
     sweepfile = args.sweepfile.strip() if args.sweepfile is not None else None
@@ -424,3 +423,6 @@ def mean(seq):
         save_pop=args.savepop,
         pop_path=poppath,
     )
+
+if __name__ == "__main__":
+    main()

From 636f1af453499c9d907a212d18cde37062ec5157 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 12:56:59 -0500
Subject: [PATCH 22/49] fix: quotes

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 1c783c6a..d7b0c6f5 100644
--- a/setup.py
+++ b/setup.py
@@ -20,6 +20,6 @@
     python_requires='>=3.6',
     package_data={'titan': ['params/*.yml', 'settings/*/*.yml']},
     entry_scripts={
-        'console_scripts': ['run_titan'='titan:run_titan:main']
+        'console_scripts': ['run_titan=titan:run_titan:main']
     }
 )

From 1c615655ff4c02ebe635d8c4fb114c9f4b7d0ffd Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 12:58:41 -0500
Subject: [PATCH 23/49] fix: no plural

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index d7b0c6f5..4bbf3493 100644
--- a/setup.py
+++ b/setup.py
@@ -20,6 +20,6 @@
     python_requires='>=3.6',
     package_data={'titan': ['params/*.yml', 'settings/*/*.yml']},
     entry_scripts={
-        'console_scripts': ['run_titan=titan:run_titan:main']
+        'console_script': ['run_titan=titan:run_titan:main']
     }
 )

From eb9e7a25bcb151766bfd27982505f4c4d838ef33 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 12:59:53 -0500
Subject: [PATCH 24/49] fix: use a real kwarg

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 4bbf3493..74578e63 100644
--- a/setup.py
+++ b/setup.py
@@ -19,7 +19,7 @@
     ],
     python_requires='>=3.6',
     package_data={'titan': ['params/*.yml', 'settings/*/*.yml']},
-    entry_scripts={
+    entry_points={
         'console_script': ['run_titan=titan:run_titan:main']
     }
 )

From b96107e6e2b714c35b9bff6f5ad4810216ab5098 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 13:03:47 -0500
Subject: [PATCH 25/49] build: make main top level

---
 setup.py          | 2 +-
 titan/__init__.py | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 74578e63..646b6eab 100644
--- a/setup.py
+++ b/setup.py
@@ -20,6 +20,6 @@
     python_requires='>=3.6',
     package_data={'titan': ['params/*.yml', 'settings/*/*.yml']},
     entry_points={
-        'console_script': ['run_titan=titan:run_titan:main']
+        'console_script': ['run_titan=titan:main']
     }
 )
diff --git a/titan/__init__.py b/titan/__init__.py
index 00adb5e6..e712b2f4 100644
--- a/titan/__init__.py
+++ b/titan/__init__.py
@@ -1 +1,2 @@
 # makes src a package
+from .run_titan import main

From a15a83a462d177554b76b871760f778d7d1c34cf Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 13:05:41 -0500
Subject: [PATCH 26/49] fix: plural again

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 646b6eab..65469241 100644
--- a/setup.py
+++ b/setup.py
@@ -20,6 +20,6 @@
     python_requires='>=3.6',
     package_data={'titan': ['params/*.yml', 'settings/*/*.yml']},
     entry_points={
-        'console_script': ['run_titan=titan:main']
+        'console_scripts': ['run_titan=titan:main']
     }
 )

From ac2f2d257d944d88d47c7c45f9d29259f6a65ee0 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Fri, 15 Jan 2021 13:09:09 -0500
Subject: [PATCH 27/49] fix: only one main

---
 setup.py           | 2 +-
 titan/__init__.py  | 2 +-
 titan/run_titan.py | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/setup.py b/setup.py
index 65469241..e5ef9e0a 100644
--- a/setup.py
+++ b/setup.py
@@ -20,6 +20,6 @@
     python_requires='>=3.6',
     package_data={'titan': ['params/*.yml', 'settings/*/*.yml']},
     entry_points={
-        'console_scripts': ['run_titan=titan:main']
+        'console_scripts': ['run_titan=titan:script_init']
     }
 )
diff --git a/titan/__init__.py b/titan/__init__.py
index e712b2f4..6e01ee0c 100644
--- a/titan/__init__.py
+++ b/titan/__init__.py
@@ -1,2 +1,2 @@
 # makes src a package
-from .run_titan import main
+from .run_titan import script_init
diff --git a/titan/run_titan.py b/titan/run_titan.py
index a6d18641..2261a4d3 100755
--- a/titan/run_titan.py
+++ b/titan/run_titan.py
@@ -405,7 +405,7 @@ def mean(seq):
     print(("all tasks - sum:  %8.4f seconds" % sum(wct)))
     print(f"all tasks - total: {toc} seconds")
 
-def main():
+def script_init():
     args = parser.parse_args()
     rows = args.rows.strip() if args.rows is not None else None
     sweepfile = args.sweepfile.strip() if args.sweepfile is not None else None
@@ -425,4 +425,4 @@ def main():
     )
 
 if __name__ == "__main__":
-    main()
+    init()

From 754b0f976c29d6b204beb3152c2e5b2e503b346d Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 09:13:00 -0500
Subject: [PATCH 28/49] fix: add dependencies to setup.py

---
 setup.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/setup.py b/setup.py
index e5ef9e0a..bc9d79a6 100644
--- a/setup.py
+++ b/setup.py
@@ -3,6 +3,9 @@
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
+with open('requirements.txt') as f:
+    required = f.read().splitlines()
+
 setuptools.setup(
     name="titan", # Replace with your own username
     version="2.0.0",
@@ -13,6 +16,7 @@
     long_description_content_type="text/markdown",
     url="https://github.com/marshall-lab/TITAN",
     packages=setuptools.find_packages(),
+    install_requires=required,
     classifiers=[
         "Programming Language :: Python :: 3",
         "Operating System :: OS Independent",

From 55ff6a5a7cc2d6bbfec825b2cd36936c84fc26c9 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 09:27:53 -0500
Subject: [PATCH 29/49] build: use git branch/ref as setup version

---
 setup.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index bc9d79a6..0e04ce03 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,13 @@
 import setuptools
+from pathlib import Path
+
+def get_active_branch_name():
+    head_dir = Path(".") / ".git" / "HEAD"
+    with head_dir.open("r") as f: content = f.read().splitlines()
+
+    for line in content:
+        if line[0:4] == "ref:":
+            return line.partition("refs/heads/")[2]
 
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
@@ -8,7 +17,7 @@
 
 setuptools.setup(
     name="titan", # Replace with your own username
-    version="2.0.0",
+    version=get_active_branch_name(),
     # author="Example Author",
     # author_email="author@example.com",
     description="TITAN Agent Based Model",

From 32e5c390a42b79f7fd4990a2bea470efa92beab7 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 09:30:11 -0500
Subject: [PATCH 30/49] build: try prefixing version with 0.0.0

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 0e04ce03..a6a97c5a 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@ def get_active_branch_name():
 
 setuptools.setup(
     name="titan", # Replace with your own username
-    version=get_active_branch_name(),
+    version=f"0.0.0-{get_active_branch_name()}",
     # author="Example Author",
     # author_email="author@example.com",
     description="TITAN Agent Based Model",

From cd204ca04f8e70713009cb25b0d94b8bcc12b806 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 09:53:08 -0500
Subject: [PATCH 31/49] build: debugging print

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index a6a97c5a..ab7a65bb 100644
--- a/setup.py
+++ b/setup.py
@@ -4,8 +4,8 @@
 def get_active_branch_name():
     head_dir = Path(".") / ".git" / "HEAD"
     with head_dir.open("r") as f: content = f.read().splitlines()
-
     for line in content:
+        print(line)
         if line[0:4] == "ref:":
             return line.partition("refs/heads/")[2]
 

From 1da03139aedf6c25ac21c19e53ee21624e088812 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 10:00:27 -0500
Subject: [PATCH 32/49] build: more printing

---
 setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.py b/setup.py
index ab7a65bb..70dd1702 100644
--- a/setup.py
+++ b/setup.py
@@ -2,6 +2,7 @@
 from pathlib import Path
 
 def get_active_branch_name():
+    print("getting active branch name...")
     head_dir = Path(".") / ".git" / "HEAD"
     with head_dir.open("r") as f: content = f.read().splitlines()
     for line in content:

From 0b60c1737f451ab82c507e6f0181f70bd1cdb219 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 10:06:31 -0500
Subject: [PATCH 33/49] build: force error

---
 setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.py b/setup.py
index 70dd1702..ae8a264f 100644
--- a/setup.py
+++ b/setup.py
@@ -8,6 +8,7 @@ def get_active_branch_name():
     for line in content:
         print(line)
         if line[0:4] == "ref:":
+            assert False
             return line.partition("refs/heads/")[2]
 
 with open("README.md", "r", encoding="utf-8") as fh:

From f4af0ce27868ec0a8289715f45b4066fe464be7c Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 10:11:15 -0500
Subject: [PATCH 34/49] build: try using setuptools-git-version

---
 setup.py | 19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

diff --git a/setup.py b/setup.py
index ae8a264f..0b9ec82e 100644
--- a/setup.py
+++ b/setup.py
@@ -1,15 +1,4 @@
 import setuptools
-from pathlib import Path
-
-def get_active_branch_name():
-    print("getting active branch name...")
-    head_dir = Path(".") / ".git" / "HEAD"
-    with head_dir.open("r") as f: content = f.read().splitlines()
-    for line in content:
-        print(line)
-        if line[0:4] == "ref:":
-            assert False
-            return line.partition("refs/heads/")[2]
 
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
@@ -18,8 +7,12 @@ def get_active_branch_name():
     required = f.read().splitlines()
 
 setuptools.setup(
-    name="titan", # Replace with your own username
-    version=f"0.0.0-{get_active_branch_name()}",
+    name="titan", # Replace with your own username,
+    version_config={
+        "version_format": "{tag}.dev{sha}",
+        "starting_version": "0.1.0"
+    },
+    setup_requires=['better-setuptools-git-version'],
     # author="Example Author",
     # author_email="author@example.com",
     description="TITAN Agent Based Model",

From b7261ce941e6bd5812ed4e86c6c220508dc42eb3 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 10:30:49 -0500
Subject: [PATCH 35/49] build: lift/edit get-git-vesion

---
 setup.py | 43 ++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 38 insertions(+), 5 deletions(-)

diff --git a/setup.py b/setup.py
index 0b9ec82e..83adb717 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,41 @@
 import setuptools
+import subprocess
+
+# ========= FROM https://github.com/vivin/better-setuptools-git-version/blob/master/better_setuptools_git_version.py with edits =========
+def get_latest_tag():
+    subprocess.getoutput("git describe --tags `git rev-list --tags --max-count=1`")
+
+def get_tag_commit_sha(tag):
+    """Return the commit that the tag is pointing to."""
+    return subprocess.getoutput("git rev-list -n 1 {tag}".format(tag=tag))
+
+def get_head_sha():
+    """Return the sha key of HEAD."""
+    return subprocess.getoutput('git rev-parse HEAD')
+
+def is_head_at_tag(tag):
+    """Return True or False depending on whether the given tag is pointing to HEAD"""
+    return get_head_sha() == get_tag_commit_sha(tag)
+
+def get_version():
+    """
+    Return the full git version using the given template. If there are no annotated tags, the version specified by
+    starting_version will be used. If HEAD is at the tag, the version will be the tag itself. If there are commits ahead
+    of the tag, the first 8 characters of the sha of the HEAD commit will be included.
+    In all of the above cases, if the working tree is also dirty or contains untracked files, a "+dirty" suffix will be
+    appended to the version.
+    Returns:
+        the formatted version based on tags in the git repository.
+    """
+    template="{tag}.dev{sha}"
+    tag = get_latest_tag()
+    if is_head_at_tag(tag):
+        version = tag
+    else:
+        sha = get_head_sha()[:8]
+        version = template.format(tag=tag, sha=sha)
+
+    return version
 
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
@@ -8,11 +45,7 @@
 
 setuptools.setup(
     name="titan", # Replace with your own username,
-    version_config={
-        "version_format": "{tag}.dev{sha}",
-        "starting_version": "0.1.0"
-    },
-    setup_requires=['better-setuptools-git-version'],
+    version=get_version(),
     # author="Example Author",
     # author_email="author@example.com",
     description="TITAN Agent Based Model",

From 3d80b63599c89a600a1313f7a26e9b65b31b1597 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 10:32:02 -0500
Subject: [PATCH 36/49] build: return the tag

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 83adb717..c7792306 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 
 # ========= FROM https://github.com/vivin/better-setuptools-git-version/blob/master/better_setuptools_git_version.py with edits =========
 def get_latest_tag():
-    subprocess.getoutput("git describe --tags `git rev-list --tags --max-count=1`")
+    return subprocess.getoutput("git describe --tags `git rev-list --tags --max-count=1`")
 
 def get_tag_commit_sha(tag):
     """Return the commit that the tag is pointing to."""

From ab5df07247f315d676676fb83eb9ca3ec4a10b8b Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 11:04:36 -0500
Subject: [PATCH 37/49] test: fix tests

---
 scripts/bs_Core.sh        |  54 -----------
 setup.py                  |  29 +++---
 subTitan.sh               | 189 --------------------------------------
 tests/integration_test.py |  20 +++-
 titan/parse_params.py     |   6 +-
 titan/run_titan.py        |  14 +--
 6 files changed, 45 insertions(+), 267 deletions(-)
 delete mode 100755 scripts/bs_Core.sh
 delete mode 100755 subTitan.sh

diff --git a/scripts/bs_Core.sh b/scripts/bs_Core.sh
deleted file mode 100755
index fd156520..00000000
--- a/scripts/bs_Core.sh
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/bin/bash
-#SBATCH -J MODEL_NAME
-#SBATCH -c NCORES
-#SBATCH --time=WALL_TIME
-#SBATCH --mail-type=FAIL
-#SBATCH --mail-type=END
-#SBATCH --mail-user=NoMail
-#SBATCH --mem=MEMORYGB
-
-if [ -z "$SLURM_NPROCS" ] ; then
-  if [ -z "$SLURM_NTASKS_PER_NODE" ] ; then
-    SLURM_NTASKS_PER_NODE=1
-  fi
-  SLURM_NPROCS=$(( $SLURM_JOB_NUM_NODES * $SLURM_NTASKS_PER_NODE ))
-fi
-
-#!/bin/bash
-module load graphviz
-
-setting=""
-paramPath=""
-nMC=""
-forceFlag=""
-sweepDefs=""
-sweepfile=""
-rows=""
-
-while getopts S:n:w:W:r:Fa:p:P: option
-do
-    case "${option}"
-        in
-	S) setting=${OPTARG};;
-	n) nMC=${OPTARG};;
-	w) sweepDefs+="-w ${OPTARG} ";;
-	W) sweepfile="-W ${OPTARG}";;
-	r) rows="-r ${OPTARG}";;
-	F) forceFlag="-F";;
-	a) paramPath=${OPTARG};;
-	p) savePop="--savepop";;
-	P) popPath="--poppath ${OPTARG}";;
-    esac
-done
-
-cd $PWD
-
-echo Master process running on `hostname`
-echo Directory is `pwd`
-echo PBS has allocated the following nodes:
-echo `cat $PBS_NODEFILE`
-echo Starting execution at `date`
-NCPU=`wc -l < $PBS_NODEFILE`
-echo This job has allocated $NCPU CPUs
-
-./run_titan.py -S $setting -n $nMC -p $paramPath $forceFlag $sweepDefs $sweepfile $rows $savePop $popPath
diff --git a/setup.py b/setup.py
index c7792306..c237da2e 100644
--- a/setup.py
+++ b/setup.py
@@ -3,20 +3,26 @@
 
 # ========= FROM https://github.com/vivin/better-setuptools-git-version/blob/master/better_setuptools_git_version.py with edits =========
 def get_latest_tag():
-    return subprocess.getoutput("git describe --tags `git rev-list --tags --max-count=1`")
+    return subprocess.getoutput(
+        "git describe --tags `git rev-list --tags --max-count=1`"
+    )
+
 
 def get_tag_commit_sha(tag):
     """Return the commit that the tag is pointing to."""
     return subprocess.getoutput("git rev-list -n 1 {tag}".format(tag=tag))
 
+
 def get_head_sha():
     """Return the sha key of HEAD."""
-    return subprocess.getoutput('git rev-parse HEAD')
+    return subprocess.getoutput("git rev-parse HEAD")
+
 
 def is_head_at_tag(tag):
     """Return True or False depending on whether the given tag is pointing to HEAD"""
     return get_head_sha() == get_tag_commit_sha(tag)
 
+
 def get_version():
     """
     Return the full git version using the given template. If there are no annotated tags, the version specified by
@@ -27,7 +33,7 @@ def get_version():
     Returns:
         the formatted version based on tags in the git repository.
     """
-    template="{tag}.dev{sha}"
+    template = "{tag}.dev{sha}"
     tag = get_latest_tag()
     if is_head_at_tag(tag):
         version = tag
@@ -35,16 +41,19 @@ def get_version():
         sha = get_head_sha()[:8]
         version = template.format(tag=tag, sha=sha)
 
-    return version
+    return versio
+
 
+# add the readme as the description
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
-with open('requirements.txt') as f:
+# make the requirements.txt be installed (not good practice for general packaging, good for current oscar set up)
+with open("requirements.txt") as f:
     required = f.read().splitlines()
 
 setuptools.setup(
-    name="titan", # Replace with your own username,
+    name="titan",  # Replace with your own username,
     version=get_version(),
     # author="Example Author",
     # author_email="author@example.com",
@@ -58,9 +67,7 @@ def get_version():
         "Programming Language :: Python :: 3",
         "Operating System :: OS Independent",
     ],
-    python_requires='>=3.6',
-    package_data={'titan': ['params/*.yml', 'settings/*/*.yml']},
-    entry_points={
-        'console_scripts': ['run_titan=titan:script_init']
-    }
+    python_requires=">=3.6",
+    package_data={"titan": ["params/*.yml", "settings/*/*.yml"]},
+    entry_points={"console_scripts": ["run_titan=titan:script_init"]},
 )
diff --git a/subTitan.sh b/subTitan.sh
deleted file mode 100755
index e49eb126..00000000
--- a/subTitan.sh
+++ /dev/null
@@ -1,189 +0,0 @@
-#!/bin/bash
-
-#Read in source code path, then shift for optargs
-titanPath=$PWD
-paramPath="$1"
-shift
-
-setting="custom"
-date=`date +%Y-%m-%d-T%H-%M-%S`
-user=${USER}
-walltime=12:00:00
-memory=12g
-outfile="Jobname.o"
-repeats=1
-nMC=1
-model=${PWD##*/}
-basePath=$PWD
-jobname=""
-folderName=""
-sweepDefs=""
-sweepfile=""
-rows=""
-num_cores=1
-forceFlag=""
-savePop=""
-popPath=""
-
-while getopts m:j:T:S:r:n:f:w:W:R:Fc:t:p:P: option
-do
-    case "${option}"
-        in
-	m) memory=${OPTARG};;
-	j) jobname=${OPTARG};;
-	T) walltime=${OPTARG};;
-	S) setting=${OPTARG};;
-	r) repeats=${OPTARG};;
-	n) nMC=${OPTARG};;
-	f) folderName=${OPTARG};;
-	w) sweepDefs+="-w ${OPTARG} ";;
-	W) sweepfile="-W ${OPTARG}";;
-	R) rows="-r ${OPTARG}";;
-	F) forceFlag="-F";;
-	c) num_cores=${OPTARG};;
-	t) titanPath=${OPTARG};;
-	p) savePop="-p";;
-	P) popPath="-P ${OPTARG}";;
-    esac
-done
-
-if [[ $jobname == "" ]]; then
-	jobname="Analysis_$setting_$date"
-fi
-
-if [[ $folderName == "" ]]; then
-	folderName="$setting/"
-fi
-
-srcCode="${titanPath}/titan/"
-outPath="$HOME/scratch/$folderName"
-
-usage() {
-echo "
-usage: subtitan {Parameter file or directory}[-T walltime] [-m memory] [-S setting] [-j jobname] [-r repeats] [-n iterations] [-b use_base] [-f folder_name] [-w sweep_defs] [-F force] [-c num_cores ] [-t titanPath ]
-
-Starts a TITAN simulation in ~/scratch/{SourceFolder}/{jobname}
-
-options:
-  -j jobname	  name of analysis for organization (default: {SourceFolder}_date)
-  -T walltime     as hh:mm:ss, max compute time (default: $walltime)
-  -m memory       per node, as #[k|m|g] (default: $memory)
-  -S setting      name of setting for this model
-  -r repeats      number of times to repeat the analysis (default: $repeats)
-  -n iterations   number of mode iterations per job (default: $nMC)
-  -f folder_name  What the parent folder for the model run outputs should be called (default: <setting>)
-  -w sweep_defs   Optionally, definitions of sweep parameters in the format param:start:stop[:step]
-  -W sweepfile    Optionally, a csv file with sweep definitions (if used, -w flag is ignored)
-  -R rows         Optionally, which data rows of the sweep file to use in format start:stop
-  -F force	  If the number of sweep combinations exceeds 100, run anyway
-  -c num_cores	  How many cores to request and run the job on (default: $num_cores)
-  -t titanPath	  where the code is
-	-p savePop			save population, either 'all' or 'core' (default none)
-	-P popPath			load population from the provide path (by default, creates a new population)
-"
-exit 0
-}
-
-updateParams() {
-echo "
-
-    Updating params:
-	savePath	$PWD
-	sourceCode	$srcCode
-	jobname 	$jobname
-	walltime	$walltime
-	memory		$memory
-	num_cores	$num_cores
-"
-
-#Submit script params
-sed -i "s/MODEL_NAME/$jobname/g" scripts/bs_Core.sh
-sed -i "s/WALL_TIME/$walltime/g" scripts/bs_Core.sh
-sed -i "s/MEMORY/$memory/g" scripts/bs_Core.sh
-sed -i "s/NCORES/$num_cores/g" scripts/bs_Core.sh
-
-}
-
-prepSubmit() {
-    #Copy source code into parent path
-    echo -e "\n\tCopying $srcCode to $finalPath"
-    mkdir -p $finalPath
-    cp $titanPath/run_titan.py $finalPath
-    cp -rT $titanPath/titan $finalPath/titan
-    cp -rT $titanPath/scripts $finalPath/scripts
-	  cp -rT $titanPath/settings $finalPath/settings
-    #Move into new source code folder
-    echo -e "\n\tMoving to model folder directory"
-    cd $finalPath
-    echo -e "\t$PWD"
-    updateParams;
-
-    #Submit job to cluster
-    sbatch scripts/bs_Core.sh -S $setting -a $paramPath -n $nMC $forceFlag $sweepDefs $sweepfile $rows $savePop $popPath
-
-    #Move back to base directory
-    cd $basePath
-}
-
-
-# User and Date will be ignored if job ID is specified
-
-if [ ! $paramPath ]; then
-    usage;
-fi
-
-if [[ ${paramPath:0:1} != "/" ]] || [[ ${paramPath:0:1} == "~" ]]; then
-	paramPath="${pwd}/$paramPath"
-fi
-
-if [ ! -d $srcCode ]; then
-    echo -e "\n\n$srcCode is not a directory! Source code must be provided as a directory\n"
-    exit 0
-fi
-
-if [ -d $outPath$jobname ]; then
-    echo -e "\n\n!! WARNING !!\nThe folder $jobname already exists and will be OVERWRITTEN!\n"
-    read -p "Continue (y/n)?" choice
-    case "$choice" in
-      y|Y ) echo "Proceeding";;
-      n|N|* ) echo "Aborting"
-	    exit 0;;
-    esac
-fi
-
-if [ $srcCode ]; then
-
-    echo "
-        jobname     $jobname
-        outPath	    $outPath
-        paramPath   $paramPath
-        user        $user
-        date        $date
-        walltime    $walltime
-        memory      $memory
-        outfile     $outfile
-        model       $model"
-    echo -e "\n"
-
-    echo -e "\tMaking parent directory in scratch"
-    mkdir -p $outPath
-    echo -e "\t $outPath"
-
-    if [ $repeats -gt 1 ]; then
-        # mkdir -p $outPath$jobname
-        basejobname=$jobname
-        for ((i=1; i<=repeats; i++)); do
-            echo -e "\n\nWorking on repeat $i"
-            jobname=$basejobname"_"$i
-            finalPath=$outPath"/"$basejobname"/"$jobname
-            prepSubmit;
-        done
-    else
-        finalPath=$outPath"/"$jobname
-        prepSubmit;
-    fi
-
-else
-    echo -e "\nSOMETHING WENT WRONG!!! Abort"
-    exit 1;
-fi
diff --git a/tests/integration_test.py b/tests/integration_test.py
index 5f9431a4..9b54e2f1 100644
--- a/tests/integration_test.py
+++ b/tests/integration_test.py
@@ -30,7 +30,9 @@ def _make_model_integration():
 
 @pytest.mark.integration_deterministic
 def test_model_runs():
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "basic.yml"
     )
@@ -43,7 +45,9 @@ def test_model_runs():
 def test_model_reproducible(tmpdir):
     path_a = tmpdir.mkdir("result_a")
     path_b = tmpdir.mkdir("result_b")
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "basic_seeded.yml"
     )
@@ -80,7 +84,9 @@ def test_model_reproducible(tmpdir):
 @pytest.mark.integration_deterministic
 def test_model_pop_write_read(tmpdir):
     path_a = tmpdir.mkdir("a")
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "basic.yml"
     )
@@ -99,13 +105,17 @@ def test_model_pop_write_read(tmpdir):
 
 @pytest.mark.integration_deterministic
 def test_model_settings_run(tmpdir):
-    f = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "run_titan.py")
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
     param_file = os.path.join(
         os.path.dirname(os.path.abspath(__file__)), "params", "integration_base.yml"
     )
 
     for item in os.listdir(
-        os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "settings")
+        os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), "..", "titan", "settings"
+        )
     ):
         if "__" not in item and item != "base":
             path = tmpdir.mkdir(item)
diff --git a/titan/parse_params.py b/titan/parse_params.py
index fdbdd3cd..9b7de6ab 100644
--- a/titan/parse_params.py
+++ b/titan/parse_params.py
@@ -117,7 +117,11 @@ def create_params(
 
     # merge setting and params
     if setting_name is not None:
-        param_paths.append(os.path.join(parent, "settings", setting_name))
+        # check if it's a known setting or pass it through as a path
+        if setting_name in os.listdir(os.path.join(parent, "settings")):
+            param_paths.append(os.path.join(parent, "settings", setting_name))
+        else:
+            param_paths.append(setting_name)
 
     param_paths.append(param_path)
 
diff --git a/titan/run_titan.py b/titan/run_titan.py
index 2261a4d3..5926cda1 100755
--- a/titan/run_titan.py
+++ b/titan/run_titan.py
@@ -21,9 +21,8 @@
 from titan.parse_params import create_params
 from titan import utils
 
-# how many cores can we use
-NCORES = os.environ.get("SLURM_CPUS_PER_TASK", cpu_count())
-NCORES = int(NCORES)  # environment variable returns string
+# how many cores can we use, environment variable returns string
+NCORES = int(os.environ.get("SLURM_CPUS_PER_TASK", cpu_count()))
 
 # set up args parsing
 parser = argparse.ArgumentParser(description="Run TITAN model")
@@ -339,11 +338,10 @@ def main(
 
     # generate params - if no setting, set to none
     setting = setting.lower()
-    if setting == "custom":
-        setting = None
+    setting_parsed = None if setting == "custom" else setting
 
     params = create_params(
-        setting,
+        setting_parsed,
         params_path,
         outfile_dir,
         error_on_unused=error_on_unused,
@@ -405,6 +403,7 @@ def mean(seq):
     print(("all tasks - sum:  %8.4f seconds" % sum(wct)))
     print(f"all tasks - total: {toc} seconds")
 
+
 def script_init():
     args = parser.parse_args()
     rows = args.rows.strip() if args.rows is not None else None
@@ -424,5 +423,6 @@ def script_init():
         pop_path=poppath,
     )
 
+
 if __name__ == "__main__":
-    init()
+    script_init()

From ec35b39ea40faac095106361ce9bed6f398942e2 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 11:47:16 -0500
Subject: [PATCH 38/49] test: allow run_titan to work as local script still

---
 titan/run_titan.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/titan/run_titan.py b/titan/run_titan.py
index 5926cda1..62a4fadd 100755
--- a/titan/run_titan.py
+++ b/titan/run_titan.py
@@ -5,6 +5,7 @@
 from copy import copy
 import sys
 import os
+from inspect import getsourcefile
 import shutil
 import argparse
 import itertools
@@ -15,6 +16,14 @@
 from typing import List, Optional
 import subprocess
 
+# allow imports to work if running it as a script for development locally
+if __name__ == "__main__":
+    PACKAGE_PARENT = ".."
+    SCRIPT_DIR = os.path.dirname(
+        os.path.realpath(os.path.join(os.getcwd(), os.path.expanduser(__file__)))
+    )
+    sys.path.append(os.path.normpath(os.path.join(SCRIPT_DIR, PACKAGE_PARENT)))
+
 from titan.model import TITAN
 from titan.population import Population
 import titan.population_io as pop_io

From b9738c8ee5052c9701a545e0adedb483e00d8e55 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 11:48:18 -0500
Subject: [PATCH 39/49] fix: typo versio => version

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index c237da2e..972740e0 100644
--- a/setup.py
+++ b/setup.py
@@ -41,7 +41,7 @@ def get_version():
         sha = get_head_sha()[:8]
         version = template.format(tag=tag, sha=sha)
 
-    return versio
+    return version
 
 
 # add the readme as the description

From b40b9d915dd7a6e9d564414322e60bbb3a216640 Mon Sep 17 00:00:00 2001
From: mcmcgrath13 <m.c.mcgrath13@gmail.com>
Date: Tue, 19 Jan 2021 12:31:28 -0500
Subject: [PATCH 40/49] test: add run_titan tests

---
 tests/integration_test.py | 13 ++++++++
 tests/run_titan_test.py   | 65 +++++++++++++++++++++++++++++++++++++++
 titan/run_titan.py        |  2 +-
 3 files changed, 79 insertions(+), 1 deletion(-)
 create mode 100644 tests/run_titan_test.py

diff --git a/tests/integration_test.py b/tests/integration_test.py
index 9b54e2f1..1bf99f93 100644
--- a/tests/integration_test.py
+++ b/tests/integration_test.py
@@ -41,6 +41,19 @@ def test_model_runs():
     assert True
 
 
+@pytest.mark.integration_deterministic
+def test_model_runs_sweep():
+    f = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "..", "titan", "run_titan.py"
+    )
+    param_file = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "params", "basic.yml"
+    )
+
+    subprocess.check_call([f, f"-p {param_file}", "-w model.seed.run:1:3"])
+    assert True
+
+
 @pytest.mark.integration_deterministic
 def test_model_reproducible(tmpdir):
     path_a = tmpdir.mkdir("result_a")
diff --git a/tests/run_titan_test.py b/tests/run_titan_test.py
new file mode 100644
index 00000000..2445e589
--- /dev/null
+++ b/tests/run_titan_test.py
@@ -0,0 +1,65 @@
+import pytest
+
+from titan.run_titan import *
+
+
+@pytest.mark.unit
+def test_sweep_range():
+    assert sweep_range("param:1:2") == {
+        "start": 1,
+        "stop": 2,
+        "step": 1,
+        "param": "param",
+    }
+    assert sweep_range("param:1.5:2:0.5") == {
+        "start": 1.5,
+        "stop": 2.0,
+        "step": 0.5,
+        "param": "param",
+    }
+
+    with pytest.raises(ValueError):
+        sweep_range("param:a:b:c")
+
+
+@pytest.mark.unit
+def test_drange():
+    start = 1
+    step = 0.1
+    stop = 2
+    i = 0
+    for val in drange(start, stop, step):
+        i += 1
+        assert val >= start and val < stop
+
+    assert i == 10
+
+
+@pytest.mark.unit
+def test_setup_sweeps():
+    sweeps = [
+        {"start": 1.5, "stop": 2.3, "step": 0.5, "param": "param1"},
+        {"start": 1, "stop": 4, "step": 1, "param": "param2"},
+    ]
+
+    defs = setup_sweeps(sweeps)
+
+    assert len(defs) == 6
+
+
+@pytest.mark.unit
+def test_setup_seepfile():
+    sweepfile = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "params", "sweepfile.csv"
+    )
+    rows = None
+    defs = setup_sweeps_file(sweepfile, rows)
+
+    assert len(defs) == 7
+    assert defs[0] == {"model.seed.run": 0, "model.seed.ppl": 0}
+
+    rows = "2:3"
+    defs = setup_sweeps_file(sweepfile, rows)
+
+    assert len(defs) == 2
+    assert defs[0] == {"model.seed.run": 1, "model.seed.ppl": 1}
diff --git a/titan/run_titan.py b/titan/run_titan.py
index 62a4fadd..e5575f6c 100755
--- a/titan/run_titan.py
+++ b/titan/run_titan.py
@@ -98,7 +98,7 @@ def sweep_range(string):
         except ValueError:
             raise ValueError("start, stop, and step must have same type (int or float)")
 
-    return {"param": parts[0], "start": start, "stop": stop, "step": step}
+    return {"param": parts[0].strip(), "start": start, "stop": stop, "step": step}
 
 
 parser.add_argument(

From 2141428c0935696adba6be2660320e0ed453ac8b Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Tue, 19 Jan 2021 13:05:22 -0500
Subject: [PATCH 41/49] refactor(aids): move haart scale on aids progression to
 haart.py

HAART is a feature, so all related methods should live in it (and all related params in haart.yml)

BREAKING CHANGE: hiv.aids.haart_scale is now haart.aids_scale
---
 titan/exposures/hiv.py  |  6 +-----
 titan/features/haart.py |  9 +++++++++
 titan/params/haart.yml  | 13 +++++++++++++
 titan/params/hiv.yml    | 13 -------------
 4 files changed, 23 insertions(+), 18 deletions(-)

diff --git a/titan/exposures/hiv.py b/titan/exposures/hiv.py
index 82004c77..40dc2240 100644
--- a/titan/exposures/hiv.py
+++ b/titan/exposures/hiv.py
@@ -326,11 +326,7 @@ def progress_to_aids(self, model: "model.TITAN"):
         """
         aids_params = self.agent.location.params.hiv.aids
         p = 1.0
-        if self.agent.haart.active:  # type: ignore[attr-defined]
-            if self.agent.haart.adherent:  # type: ignore[attr-defined]
-                p = aids_params.haart_scale.adherent
-            else:
-                p = aids_params.haart_scale.non_adherent
+        self.agent.haart.aids_scale()
 
         if model.run_random.random() < p * aids_params.prob:
             self.aids = True
diff --git a/titan/features/haart.py b/titan/features/haart.py
index de47bf79..fad961d7 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -194,6 +194,15 @@ def get_transmission_risk_multiplier(self, time: int, interaction_type: str):
 
         return prob
 
+    def aids_scale(self):
+        prob = 1.0
+        if self.active:
+            params = self.agent.location.params
+            adherence = "adherent" if self.adherent else "non_adherent"
+            prob = params.haart.aids_scale[adherence]
+
+        return prob
+
     # =========== HELPER METHODS ============
 
     def initiate(self, model: "model.TITAN"):
diff --git a/titan/params/haart.yml b/titan/params/haart.yml
index d6c9589b..e62883f8 100644
--- a/titan/params/haart.yml
+++ b/titan/params/haart.yml
@@ -7,3 +7,16 @@ haart:
     type: boolean
     default: false
     description: Whether a separate probability should be used for haart initiation among agents who have previously discontinued haart
+  aids_scale:
+    non_adherent:
+      description: Scalar for aids progression for agents on haart but non-adherent
+      default: 0.00368
+      type: float
+      min: 0.
+      max: 1.
+    adherent:
+      description: Scalar for aids progression for agents adherent to haart
+      default: 0.0008
+      type: float
+      min: 0.
+      max: 1.
diff --git a/titan/params/hiv.yml b/titan/params/hiv.yml
index 11e6321d..108ef18b 100644
--- a/titan/params/hiv.yml
+++ b/titan/params/hiv.yml
@@ -31,19 +31,6 @@ hiv:
       type: float
       min: 0
       max: 1
-    haart_scale:
-      non_adherent:
-        description: Scalar for aids progression for agents on haart but non-adherent
-        default: 0.00368
-        type: float
-        min: 0.
-        max: 1.
-      adherent:
-        description: Scalar for aids progression for agents adherent to haart
-        default: 0.0008
-        type: float
-        min: 0.
-        max: 1.
   max_init_time:
     default: 42
     description: On creation, agents are randomly assigned an hiv.time, this is the maximum time

From e6187b610b95ea62db3b616ee094bad77874ade3 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Tue, 19 Jan 2021 13:12:43 -0500
Subject: [PATCH 42/49] refactor(prep): change prep enrollment to def instead
 of bin

---
 settings/mississippi/demographics.yml | 6 +++---
 settings/nyc-msm/demographics.yml     | 8 ++++----
 settings/scott/demographics.yml       | 2 +-
 titan/params/demographics.yml         | 4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/settings/mississippi/demographics.yml b/settings/mississippi/demographics.yml
index d603935f..4d478e44 100644
--- a/settings/mississippi/demographics.yml
+++ b/settings/mississippi/demographics.yml
@@ -28,15 +28,15 @@ demographics:
             haart:
               init: 0.690
               enroll:
-                0:
+                enroll_0:
                   prob: 0.609
                   start: 0
                   stop: 1
-                1:
+                enroll_1:
                   prob: 0.074
                   start: 1
                   stop: 12
-                2:
+                enroll_2:
                   prob: 0.0
                   start: 12
                   stop: 9999
diff --git a/settings/nyc-msm/demographics.yml b/settings/nyc-msm/demographics.yml
index b41fe626..0f5528cd 100644
--- a/settings/nyc-msm/demographics.yml
+++ b/settings/nyc-msm/demographics.yml
@@ -32,19 +32,19 @@ demographics:
             haart:
               init: 0.764
               enroll:
-                0:
+                enroll_0:
                   start: 0
                   stop: 1
                   prob: 0.709
-                1:
+                enroll_1:
                   start: 1
                   stop: 3
                   prob: 0.212
-                2:
+                enroll_2:
                   start: 3
                   stop: 12
                   prob: 0.051
-                3:
+                enroll_3:
                   start: 12
                   stop: 9999
                   prob: 0.0
diff --git a/settings/scott/demographics.yml b/settings/scott/demographics.yml
index 06aa124a..045142a7 100644
--- a/settings/scott/demographics.yml
+++ b/settings/scott/demographics.yml
@@ -43,7 +43,7 @@ demographics:
             haart: &haart_vals
               init: 1.0
               enroll:
-                0:
+                enroll_0:
                   prob: 0.679
                   start: 0
                   stop: 999
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index 3a42ad4e..6bd1d15b 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -309,7 +309,7 @@ demographics:
                 min: 0.0
                 max: 1.0
               enroll:
-                type: bin
+                type: definition
                 description: "Probability that an agent in this class with HIV becomes enrolled in HAART at a given time step based on time since diagnosis (use 0 for haart cap)"
                 fields:
                   prob:
@@ -323,7 +323,7 @@ demographics:
                     type: int
                     min: 1
                 default:
-                  0:
+                  enroll_0:
                     start: 0
                     stop: 999
                     prob: 0.0

From 5ca9c58288772a968a6ded8bc7cae14a0b5e23f5 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Tue, 19 Jan 2021 13:26:43 -0500
Subject: [PATCH 43/49] refactor(prep): change target to cap

Use of "target" and "cap" were inconsistent between haart and prep. "Cap" is more accurate, as number of agents on prep/haart cannot go over this threshold

BREAKING CHANGE: params naming change
---
 settings/atlanta/demographics.yml     |  4 ++--
 settings/chicago/chicago_baseCase.yml |  4 ++--
 settings/mississippi/model.yml        |  4 ++--
 settings/nyc-msm/demographics.yml     |  6 +++---
 settings/nyc-msm/hiv.yml              |  2 +-
 tests/features/prep_test.py           |  8 ++++----
 tests/features/random_trial_test.py   |  6 +++---
 tests/integration_test.py             |  4 ++--
 tests/model_test.py                   | 12 ++++++------
 tests/params/basic.yml                |  8 ++++----
 tests/params/basic_seeded.yml         |  8 ++++----
 tests/params/basic_seeded_error.yml   |  8 ++++----
 tests/params/simple_integration.yml   |  4 ++--
 tests/population_io_test.py           |  2 +-
 titan/features/prep.py                | 10 +++++-----
 titan/features/random_trial.py        |  2 +-
 titan/params/demographics.yml         |  4 ++--
 titan/params/location.yml             |  2 +-
 titan/params/prep.yml                 |  8 ++++----
 titan/utils.py                        |  4 ++--
 20 files changed, 55 insertions(+), 55 deletions(-)

diff --git a/settings/atlanta/demographics.yml b/settings/atlanta/demographics.yml
index 76b88d57..84238956 100644
--- a/settings/atlanta/demographics.yml
+++ b/settings/atlanta/demographics.yml
@@ -17,7 +17,7 @@ demographics:
         prep:
           discontinue: 0.0
           adherence: 0.568
-          target: 0.258
+          cap: 0.258
           init: 0.258
         drug_type:
             NonInj:
@@ -63,7 +63,7 @@ demographics:
             prob: 0.528
         prep:
           adherence: 0.911
-          target: 0.415
+          cap: 0.415
           discontinue: 0.0
           init: 0.415
         drug_type:
diff --git a/settings/chicago/chicago_baseCase.yml b/settings/chicago/chicago_baseCase.yml
index bd93bd51..dc37cf19 100644
--- a/settings/chicago/chicago_baseCase.yml
+++ b/settings/chicago/chicago_baseCase.yml
@@ -81,7 +81,7 @@ prep:
   type:
   - Oral
   - Inj
-  target: 0.088
+  cap: 0.088
   init: 0.088
   start_time: 0
   efficacy:
@@ -102,7 +102,7 @@ demographics:
         prep:
           discontinue: 0.0
           adherence: 0.568
-          target: 0.5
+          cap: 0.5
           init: 0.5
         high_risk:
           init: 0.0
diff --git a/settings/mississippi/model.yml b/settings/mississippi/model.yml
index 4017c65c..9a9f2201 100644
--- a/settings/mississippi/model.yml
+++ b/settings/mississippi/model.yml
@@ -73,9 +73,9 @@ partnership:
 prep:
   type:
     - Oral
-  target: 0.049
+  cap: 0.049
   init: 0.25
-  target_as_prob: true
+  cap_as_prob: true
   efficacy:
     adherent: 0.96
     non_adherent: 0.83
diff --git a/settings/nyc-msm/demographics.yml b/settings/nyc-msm/demographics.yml
index 0f5528cd..b866c00b 100644
--- a/settings/nyc-msm/demographics.yml
+++ b/settings/nyc-msm/demographics.yml
@@ -17,7 +17,7 @@ demographics:
         prep:
           discontinue: 0.034  # calibration
           adherence: 0.565
-          target: 0.028
+          cap: 0.028
           init: 0.252
         drug_type:
           None:
@@ -94,7 +94,7 @@ demographics:
         prep:
           discontinue: 0.025  # calibration
           adherence: 0.719
-          target: 0.026
+          cap: 0.026
           init: 0.234
         drug_type:
           None:
@@ -171,7 +171,7 @@ demographics:
         prep:
           discontinue: 0.014
           adherence: 0.738
-          target: 0.031
+          cap: 0.031
           init: 0.279
         drug_type:
           None:
diff --git a/settings/nyc-msm/hiv.yml b/settings/nyc-msm/hiv.yml
index 42212def..89cfd555 100644
--- a/settings/nyc-msm/hiv.yml
+++ b/settings/nyc-msm/hiv.yml
@@ -9,7 +9,7 @@ hiv:
 prep:
   target_model:
     - Racial
-  target_as_prob: true
+  cap_as_prob: true
   start_time: -48
   efficacy:
     adherent: 0.96
diff --git a/tests/features/prep_test.py b/tests/features/prep_test.py
index aa1e632e..034b4bfb 100644
--- a/tests/features/prep_test.py
+++ b/tests/features/prep_test.py
@@ -199,7 +199,7 @@ def test_initiate_prep_eligible(make_model, make_agent):
     p.hiv.dx = True
     p.external_exposure.active = True
     model.time = 10
-    a.location.params.prep.target = 1.0
+    a.location.params.prep.cap = 1.0
     a.location.params.prep.target_model = ["cdc_women"]
     rel = Relationship(a, p, 10, bond_type="Sex")
     # non-forcing, adherant, inj
@@ -223,7 +223,7 @@ def test_initiate_prep_eligible_racial(make_model, make_agent):
     p.hiv.dx = True
     p.external_exposure.active = True
     model.time = 10
-    a.location.params.prep.target = 1.0
+    a.location.params.prep.cap = 1.0
     a.location.params.prep.target_model = ["Racial"]
     rel = Relationship(a, p, 10, bond_type="Sex")
     # non-forcing, adherant, inj
@@ -383,10 +383,10 @@ def test_progress_inj_prep(make_agent, params, make_model):
 
 
 @pytest.mark.unit
-def test_target_as_prob(make_agent, make_model, params):
+def test_cap_as_prob(make_agent, make_model, params):
     model = make_model(params)
     a = make_agent()
-    a.location.params.prep.target_as_prob = True
+    a.location.params.prep.cap_as_prob = True
 
     model.run_random = FakeRandom(0.2)
     a.prep.initiate(model)
diff --git a/tests/features/random_trial_test.py b/tests/features/random_trial_test.py
index 28a41e81..0bc2ffe5 100644
--- a/tests/features/random_trial_test.py
+++ b/tests/features/random_trial_test.py
@@ -10,7 +10,7 @@
 def test_initialize_random_trial_prep_all(make_model, params):
     params.features.prep = True
     params.vaccine.on_init = False
-    params.prep.target = 0
+    params.prep.cap = 0
     params.random_trial.choice = "all"
     model = make_model(params)
     model.run_random = FakeRandom(-0.1)
@@ -27,7 +27,7 @@ def test_initialize_random_trial_prep_all(make_model, params):
 def test_initialize_random_trial_prep_eigenvector(make_model, params):
     params.features.prep = True
     params.vaccine.on_init = False
-    params.prep.target = 0
+    params.prep.cap = 0
     params.hiv.start_time = 5
     params.random_trial.choice = "eigenvector"
     model = make_model(params)
@@ -53,7 +53,7 @@ def test_initialize_random_trial_prep_eigenvector(make_model, params):
 def test_initialize_random_trial_prep_random(make_model, params):
     params.features.prep = True
     params.vaccine.on_init = False
-    params.prep.target = 0
+    params.prep.cap = 0
     params.hiv.start_time = 5
     params.random_trial.choice = "random"
     model = make_model(params)
diff --git a/tests/integration_test.py b/tests/integration_test.py
index 5bd6fe2f..9a857d0a 100644
--- a/tests/integration_test.py
+++ b/tests/integration_test.py
@@ -189,7 +189,7 @@ def test_prep_coverage(make_model_integration, tmpdir):
     model_a.run(path_a)
 
     # change the coverage upward for creating model b, use same seeds
-    model_a.params.prep.target = 0.9
+    model_a.params.prep.cap = 0.9
     model_a.params.prep.init = 0.9
     model_a.params.model.seed.run = model_a.run_seed
     model_a.params.model.seed.ppl = model_a.pop.pop_seed
@@ -197,7 +197,7 @@ def test_prep_coverage(make_model_integration, tmpdir):
     model_b = TITAN(model_a.params)
     model_b.run(path_b)
     print(
-        f"model b prep world target: {model_b.pop.geography.locations['world'].params.prep.target}"
+        f"model b prep world target: {model_b.pop.geography.locations['world'].params.prep.cap}"
     )
 
     result_file_a = os.path.join(path_a, "basicReport.txt")
diff --git a/tests/model_test.py b/tests/model_test.py
index 36b4bbf7..e9ba2e52 100644
--- a/tests/model_test.py
+++ b/tests/model_test.py
@@ -141,21 +141,21 @@ def test_timeline_scaling_prep_def(make_model):
     model.params.timeline_scaling.timeline = ObjMap(
         {
             "scale": {
-                "parameter": "prep|target",
+                "parameter": "prep|cap",
                 "start_time": 1,
                 "stop_time": 3,
                 "scalar": scalar,
             }
         }
     )
-    original_prep_target = model.params.prep.target
+    original_prep_target = model.params.prep.cap
 
     # scale the param
     model.time = 1
     model.timeline_scaling()
 
     assert math.isclose(
-        original_prep_target * scalar, model.params.prep.target, abs_tol=0.001
+        original_prep_target * scalar, model.params.prep.cap, abs_tol=0.001
     )
 
     # param still scaled
@@ -163,17 +163,17 @@ def test_timeline_scaling_prep_def(make_model):
     model.timeline_scaling()
 
     assert math.isclose(
-        original_prep_target * scalar, model.params.prep.target, abs_tol=0.001
+        original_prep_target * scalar, model.params.prep.cap, abs_tol=0.001
     )
 
     # revert to original
     model.time = 3
     model.timeline_scaling()
 
-    assert math.isclose(original_prep_target, model.params.prep.target, abs_tol=0.001)
+    assert math.isclose(original_prep_target, model.params.prep.cap, abs_tol=0.001)
 
     # still original
     model.time = 4
     model.timeline_scaling()
 
-    assert math.isclose(original_prep_target, model.params.prep.target, abs_tol=0.001)
+    assert math.isclose(original_prep_target, model.params.prep.cap, abs_tol=0.001)
diff --git a/tests/params/basic.yml b/tests/params/basic.yml
index a6b876a6..b13719fe 100644
--- a/tests/params/basic.yml
+++ b/tests/params/basic.yml
@@ -97,7 +97,7 @@ demographics:
         prep: &base_prep
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.3
         high_risk: &base_high_risk
           init: 0.1
@@ -116,7 +116,7 @@ demographics:
         prep:
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.5
         high_risk: *base_high_risk
         vaccine: *base_vaccine
@@ -279,9 +279,9 @@ partnership:
       black: *poisson_one
 
 prep:
-  target: 0.1
+  cap: 0.1
   init: 0.7
-  target_as_prob: false
+  cap_as_prob: false
 
 knowledge:
   prob: 0.3
diff --git a/tests/params/basic_seeded.yml b/tests/params/basic_seeded.yml
index cc8577f3..a6dc0cea 100644
--- a/tests/params/basic_seeded.yml
+++ b/tests/params/basic_seeded.yml
@@ -96,7 +96,7 @@ demographics:
         prep: &base_prep
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.3
         high_risk: &base_high_risk
           init: 0.1
@@ -115,7 +115,7 @@ demographics:
         prep:
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.5
         high_risk: *base_high_risk
         vaccine: *base_vaccine
@@ -264,9 +264,9 @@ partnership:
     Social: *poisson_one
 
 prep:
-  target: 0.1
+  cap: 0.1
   init: 0.7
-  target_as_prob: false
+  cap_as_prob: false
 
 knowledge:
   prob: 0.3
diff --git a/tests/params/basic_seeded_error.yml b/tests/params/basic_seeded_error.yml
index 0a78f81b..373ec902 100644
--- a/tests/params/basic_seeded_error.yml
+++ b/tests/params/basic_seeded_error.yml
@@ -96,7 +96,7 @@ demographics:
         prep: &base_prep
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.3
         high_risk: &base_high_risk
           init: 0.1
@@ -115,7 +115,7 @@ demographics:
         prep:
           adherence: 0.1
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.5
         high_risk: *base_high_risk
         vaccine: *base_vaccine
@@ -264,9 +264,9 @@ partnership:
     Social: *poisson_one
 
 prep:
-  target: 0.1
+  cap: 0.1
   init: 0.7
-  target_as_prob: false
+  cap_as_prob: false
 
 knowledge:
   prob: 0.3
diff --git a/tests/params/simple_integration.yml b/tests/params/simple_integration.yml
index 4bc57b3b..508af68f 100644
--- a/tests/params/simple_integration.yml
+++ b/tests/params/simple_integration.yml
@@ -33,7 +33,7 @@ demographics:
         prep:
           adherence: 0.9
           discontinue: 0.1
-          target: 0.3
+          cap: 0.3
           init: 0.3
         high_risk:
           init: 0.1
@@ -176,7 +176,7 @@ partner_tracing:
   prob: 1
 
 prep:
-  target: 0.1
+  cap: 0.1
   init: 0.1
   start_time: -6
 
diff --git a/tests/population_io_test.py b/tests/population_io_test.py
index 3c60b4b4..38a20894 100644
--- a/tests/population_io_test.py
+++ b/tests/population_io_test.py
@@ -96,7 +96,7 @@ def test_read_pop(tmpdir, make_population, params):
 
 @pytest.mark.unit
 def test_write_read_pop_compressed(tmpdir, make_population, params):
-    params.prep.target = 0.5
+    params.prep.cap = 0.5
     pop = make_population(n=10)
     prep_counts = deepcopy(Prep.counts)
 
diff --git a/titan/features/prep.py b/titan/features/prep.py
index 1e30e48e..6ff569c7 100644
--- a/titan/features/prep.py
+++ b/titan/features/prep.py
@@ -168,17 +168,17 @@ def initiate(self, model: "model.TITAN", force: bool = False):
 
         if force:
             self.enroll(model.run_random, model.time)
-        elif params.prep.target_as_prob:
+        elif params.prep.cap_as_prob:
             if "Racial" in params.prep.target_model:
                 if (
                     model.run_random.random()
                     <= params.demographics[self.agent.race]
                     .sex_type[self.agent.sex_type]
-                    .prep.target
+                    .prep.cap
                 ):
                     self.enroll(model.run_random, model.time)
             else:
-                if model.run_random.random() <= params.prep.target:
+                if model.run_random.random() <= params.prep.cap:
                     self.enroll(model.run_random, model.time)
         else:
             if "Racial" in params.prep.target_model:
@@ -191,12 +191,12 @@ def initiate(self, model: "model.TITAN", force: bool = False):
                 num_hiv_agents = len(all_hiv_agents & all_race)
                 target_prep = (len(all_race) - num_hiv_agents) * params.demographics[
                     self.agent.race
-                ].sex_type[self.agent.sex_type].prep.target
+                ].sex_type[self.agent.sex_type].prep.cap
             else:
                 num_prep_agents = sum(self.counts.values())
                 target_prep = int(
                     (model.pop.all_agents.num_members() - len(exposures.HIV.agents))
-                    * params.prep.target
+                    * params.prep.cap
                 )
 
             if num_prep_agents < target_prep:
diff --git a/titan/features/random_trial.py b/titan/features/random_trial.py
index 8ea8985a..72f420b6 100644
--- a/titan/features/random_trial.py
+++ b/titan/features/random_trial.py
@@ -152,7 +152,7 @@ def suitable_prep(agent, model) -> bool:
     if (
         not agent.hiv.active
         and not agent.prep.active
-        and model.run_random.random() < agent.location.params.prep.target
+        and model.run_random.random() < agent.location.params.prep.cap
         and not agent.vaccine.active
     ):
         return True
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index 6bd1d15b..4e3cab8e 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -212,9 +212,9 @@ demographics:
             type: float
             min: 0.0
             max: 1.0
-          target:
+          cap:
             default: 0.0
-            description: "Target percentage of PrEP coverage for this population class, or probability of going on PrEP if target_as_prob is true"
+            description: "Ceiling/target percentage of PrEP coverage for this population class, or probability of going on PrEP if cap_as_prob is true"
             type: float
             min: 0.0
             max: 1.0
diff --git a/titan/params/location.yml b/titan/params/location.yml
index cfb920e1..036675c2 100644
--- a/titan/params/location.yml
+++ b/titan/params/location.yml
@@ -6,7 +6,7 @@ location:
       - locations
     default:
       type: definition
-      description: "Definition of applying a scalar to a parameter.  The parameter should be the definition name with pipes instead of dots (e.g. `prep.target` would be `prep|target`). Some parameter categories can't be scaled, these include: model, classes, features, calibration, outputs, agent_zero, syringe_services, location.  Additionally, some fields within otherwise scalable categories cannot be changed by location if their use is not tied to a specific agent (e.g. prep.pca.choice, prep.random_trial). When a parameter is related to the interaction of an agent and a partner, the params of the location where the agent lives is typically used unless the parameter use clearly relates to the partner."
+      description: "Definition of applying a scalar to a parameter.  The parameter should be the definition name with pipes instead of dots (e.g. `prep.cap` would be `prep|cap`). Some parameter categories can't be scaled, these include: model, classes, features, calibration, outputs, agent_zero, syringe_services, location.  Additionally, some fields within otherwise scalable categories cannot be changed by location if their use is not tied to a specific agent (e.g. prep.pca.choice, prep.random_trial). When a parameter is related to the interaction of an agent and a partner, the params of the location where the agent lives is typically used unless the parameter use clearly relates to the partner."
       fields:
         field:
           type: enum
diff --git a/titan/params/prep.yml b/titan/params/prep.yml
index c1fc26d6..609a5f0d 100644
--- a/titan/params/prep.yml
+++ b/titan/params/prep.yml
@@ -7,9 +7,9 @@ prep:
       - Inj
     description: Type of PrEP used in model
     type: array
-  target:
+  cap:
     default: 0.0
-    description: Target coverage for PrEP coverage, or probability of initiating prep at a timestep if target_as_prob is true
+    description: Ceiling/target coverage for PrEP coverage, or probability of initiating prep at a timestep if cap_as_prob is true
     type: float
     min: 0
     max: 1
@@ -19,9 +19,9 @@ prep:
     type: float
     min: 0.
     max: 1.
-  target_as_prob:
+  cap_as_prob:
     default: false
-    description: If prep.target should be treated as a probability instead of a target
+    description: If prep.cap should be treated as a probability instead of a cap
     type: boolean
   start_time:
     default: 0
diff --git a/titan/utils.py b/titan/utils.py
index 6de0d151..b218df56 100644
--- a/titan/utils.py
+++ b/titan/utils.py
@@ -176,7 +176,7 @@ def get_param_from_path(params, param_path, delimiter):
 
 def scale_param(params, param_path, scalar, delimiter="|"):
     """
-    Given the params and a parameter path in the format prep|target, scale the
+    Given the params and a parameter path in the format prep|cap, scale the
     current value by the scalar
     """
     scaling_item, last_key = get_param_from_path(params, param_path, delimiter)
@@ -188,7 +188,7 @@ def scale_param(params, param_path, scalar, delimiter="|"):
 
 def override_param(params, param_path, value, delimiter="|"):
     """
-    Given the params and a parameter path in the format prep|target, change the
+    Given the params and a parameter path in the format prep|cap, change the
     current value to new value
     """
     override_item, last_key = get_param_from_path(params, param_path, delimiter)

From 5d8b7ada50523baca268d1236430daa6ceb1aa7b Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Tue, 19 Jan 2021 14:19:37 -0500
Subject: [PATCH 44/49] fix: type ignore in hiv

---
 titan/exposures/hiv.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/titan/exposures/hiv.py b/titan/exposures/hiv.py
index 40dc2240..8f5a13e8 100644
--- a/titan/exposures/hiv.py
+++ b/titan/exposures/hiv.py
@@ -326,7 +326,7 @@ def progress_to_aids(self, model: "model.TITAN"):
         """
         aids_params = self.agent.location.params.hiv.aids
         p = 1.0
-        self.agent.haart.aids_scale()
+        self.agent.haart.aids_scale()  # type: ignore[attr-defined]
 
         if model.run_random.random() < p * aids_params.prob:
             self.aids = True

From f25a285ebb49a4294a21497a7ad9566b76800458 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Tue, 19 Jan 2021 16:29:40 -0500
Subject: [PATCH 45/49] refactor: change names/descriptions and remove
 unnecessary intermediate variable

---
 settings/nyc-msm/hiv.yml      |  2 +-
 tests/features/haart_test.py  |  6 ++++--
 tests/integration_test.py     |  3 ++-
 tests/params/basic.yml        |  2 +-
 titan/exposures/hiv.py        |  2 +-
 titan/features/haart.py       | 19 ++++++++++---------
 titan/params/demographics.yml |  2 +-
 titan/params/haart.yml        |  2 +-
 8 files changed, 21 insertions(+), 17 deletions(-)

diff --git a/settings/nyc-msm/hiv.yml b/settings/nyc-msm/hiv.yml
index 89cfd555..73445206 100644
--- a/settings/nyc-msm/hiv.yml
+++ b/settings/nyc-msm/hiv.yml
@@ -16,4 +16,4 @@ prep:
     non_adherent: 0.76
 
 haart:
-  reinit: true
+  use_reinit: true
diff --git a/tests/features/haart_test.py b/tests/features/haart_test.py
index d728b1f1..a9694dfd 100644
--- a/tests/features/haart_test.py
+++ b/tests/features/haart_test.py
@@ -72,7 +72,7 @@ def test_update_haart_dx_time(make_model, make_agent):
 
     a.hiv.active = True
     a.hiv.dx = True
-    a.hiv.dx_time = 1  # agent dx duration is 0
+    a.hiv.dx_time = model.time  # agent dx duration is 0
     a.haart.update_agent(model)
     assert not a.haart.active
 
@@ -93,6 +93,8 @@ def test_update_haart_reinit(make_model, make_agent):
     a.haart.update_agent(model)
     assert not a.haart.active
 
-    model.run_random = FakeRandom(-1.1)
+    a.location.params.demographics[a.race].sex_type[a.sex_type].drug_type[
+        a.drug_type
+    ].haart.reinit.prob = 1.0
     a.haart.update_agent(model)
     assert a.haart.active
diff --git a/tests/integration_test.py b/tests/integration_test.py
index 9a857d0a..4c1f6b02 100644
--- a/tests/integration_test.py
+++ b/tests/integration_test.py
@@ -197,7 +197,7 @@ def test_prep_coverage(make_model_integration, tmpdir):
     model_b = TITAN(model_a.params)
     model_b.run(path_b)
     print(
-        f"model b prep world target: {model_b.pop.geography.locations['world'].params.prep.cap}"
+        f"model b prep world cap: {model_b.pop.geography.locations['world'].params.prep.cap}"
     )
 
     result_file_a = os.path.join(path_a, "basicReport.txt")
@@ -243,6 +243,7 @@ def test_syringe_services(params_integration, tmpdir):
     """
     params_integration.demographics.black.sex_type.MSM.drug_type.Inj.ppl = 1.0
     params_integration.demographics.black.sex_type.MSM.drug_type["None"].ppl = 0.0
+    params_integration.model.num_pop = 500
     model_a = TITAN(params_integration)
     model_a.params.partnership.sex.frequency.Sex = (
         ObjMap(  # turn off sex to show only injection effects
diff --git a/tests/params/basic.yml b/tests/params/basic.yml
index b13719fe..de5970c0 100644
--- a/tests/params/basic.yml
+++ b/tests/params/basic.yml
@@ -314,7 +314,7 @@ exposures:
   knowledge: true
 
 haart:
-  reinit: true
+  use_reinit: true
 
 features:
   incar: true
diff --git a/titan/exposures/hiv.py b/titan/exposures/hiv.py
index 8f5a13e8..db125cd5 100644
--- a/titan/exposures/hiv.py
+++ b/titan/exposures/hiv.py
@@ -326,7 +326,7 @@ def progress_to_aids(self, model: "model.TITAN"):
         """
         aids_params = self.agent.location.params.hiv.aids
         p = 1.0
-        self.agent.haart.aids_scale()  # type: ignore[attr-defined]
+        p = self.agent.haart.aids_scale()  # type: ignore[attr-defined]
 
         if model.run_random.random() < p * aids_params.prob:
             self.aids = True
diff --git a/titan/features/haart.py b/titan/features/haart.py
index fad961d7..22191854 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -105,14 +105,15 @@ def update_agent(self, model: "model.TITAN"):
                     if num_haart_agents < (haart_params.cap * num_dx_agents):
                         self.initiate(model)
                 else:
-                    if self.ever and self.agent.location.params.haart.reinit:
+                    if self.ever and self.agent.location.params.haart.use_reinit:
                         if model.run_random.random() < haart_params.reinit.prob:
                             self.initiate(model)
                     else:
                         enroll_prob = 0
                         # Find enroll probability based on time since diagnosis
+                        haart_duration = model.time - self.agent.hiv.dx_time  # type: ignore[attr-defined]
                         for i in haart_params.enroll.values():
-                            if i.start <= (model.time - self.agent.hiv.dx_time) < i.stop:  # type: ignore[attr-defined]
+                            if i.start <= haart_duration < i.stop:  # type: ignore[attr-defined]
                                 enroll_prob = i.prob
                                 break
 
@@ -121,20 +122,21 @@ def update_agent(self, model: "model.TITAN"):
                         ):
                             self.initiate(model)
 
-            # Go off HAART
-            elif self.active:
+            # Update agents on HAART
+            else:
+                # Go off HAART
                 if model.run_random.random() < haart_params.discontinue:
                     self.active = False
                     self.adherent = False
                     self.remove_agent(self.agent)
-                elif (
+                elif (  # Become non-adherent
                     self.adherent
                     and model.run_random.random() < haart_params.adherence.discontinue
                 ):
                     self.adherent = False
-                elif (
+                elif (  # Become adherent
                     not self.adherent
-                    and model.run_random.random() < haart_params.adherence.prob
+                    and model.run_random.random() < haart_params.adherence.become
                 ):
                     self.adherent = True
 
@@ -197,9 +199,8 @@ def get_transmission_risk_multiplier(self, time: int, interaction_type: str):
     def aids_scale(self):
         prob = 1.0
         if self.active:
-            params = self.agent.location.params
             adherence = "adherent" if self.adherent else "non_adherent"
-            prob = params.haart.aids_scale[adherence]
+            prob = self.agent.location.params.haart.aids_scale[adherence]
 
         return prob
 
diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index 4e3cab8e..3e564d28 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -310,7 +310,7 @@ demographics:
                 max: 1.0
               enroll:
                 type: definition
-                description: "Probability that an agent in this class with HIV becomes enrolled in HAART at a given time step based on time since diagnosis (use 0 for haart cap)"
+                description: "Probability that an agent in this class with HIV becomes enrolled in HAART given the agent's time since diagnosis (unused if use_cap is true)"
                 fields:
                   prob:
                     type: float
diff --git a/titan/params/haart.yml b/titan/params/haart.yml
index e62883f8..036719ee 100644
--- a/titan/params/haart.yml
+++ b/titan/params/haart.yml
@@ -3,7 +3,7 @@ haart:
     default: false
     description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
     type: boolean
-  reinit:
+  use_reinit:
     type: boolean
     default: false
     description: Whether a separate probability should be used for haart initiation among agents who have previously discontinued haart

From 74a947b2377e6a93613bcdfd13d4d9feeef9d510 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Wed, 20 Jan 2021 10:06:17 -0500
Subject: [PATCH 46/49] style: fix comments and remove unnecessary type ignore

---
 titan/exposures/hiv.py  | 1 -
 titan/features/haart.py | 8 +++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/titan/exposures/hiv.py b/titan/exposures/hiv.py
index db125cd5..19097c93 100644
--- a/titan/exposures/hiv.py
+++ b/titan/exposures/hiv.py
@@ -325,7 +325,6 @@ def progress_to_aids(self, model: "model.TITAN"):
              model: the running model
         """
         aids_params = self.agent.location.params.hiv.aids
-        p = 1.0
         p = self.agent.haart.aids_scale()  # type: ignore[attr-defined]
 
         if model.run_random.random() < p * aids_params.prob:
diff --git a/titan/features/haart.py b/titan/features/haart.py
index 22191854..a1a7acc7 100644
--- a/titan/features/haart.py
+++ b/titan/features/haart.py
@@ -113,7 +113,7 @@ def update_agent(self, model: "model.TITAN"):
                         # Find enroll probability based on time since diagnosis
                         haart_duration = model.time - self.agent.hiv.dx_time  # type: ignore[attr-defined]
                         for i in haart_params.enroll.values():
-                            if i.start <= haart_duration < i.stop:  # type: ignore[attr-defined]
+                            if i.start <= haart_duration < i.stop:
                                 enroll_prob = i.prob
                                 break
 
@@ -129,12 +129,14 @@ def update_agent(self, model: "model.TITAN"):
                     self.active = False
                     self.adherent = False
                     self.remove_agent(self.agent)
-                elif (  # Become non-adherent
+                # Become non-adherent
+                elif (
                     self.adherent
                     and model.run_random.random() < haart_params.adherence.discontinue
                 ):
                     self.adherent = False
-                elif (  # Become adherent
+                # Become adherent
+                elif (
                     not self.adherent
                     and model.run_random.random() < haart_params.adherence.become
                 ):

From 825b5d947ff28a9e8c097d27b7430918c756391c Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Wed, 20 Jan 2021 10:13:07 -0500
Subject: [PATCH 47/49] docs(demographics): correct description for
 haart.adherence.become

---
 titan/params/demographics.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/titan/params/demographics.yml b/titan/params/demographics.yml
index 3e564d28..30300723 100644
--- a/titan/params/demographics.yml
+++ b/titan/params/demographics.yml
@@ -353,7 +353,7 @@ demographics:
                   max: 1.0
                 become:
                   default: 0.0
-                  description: "Probability that an agent already on haart will become adherent at a given timestep"
+                  description: "Probability that a non-adherent agent will become adherent at a given timestep"
                   type: float
                   min: 0.0
                   max: 1.0

From f821d8553111f23789b63bc60ebb68469d6bf585 Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Wed, 20 Jan 2021 10:20:38 -0500
Subject: [PATCH 48/49] docs: correct description of haart.use_cap

---
 titan/params/haart.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/titan/params/haart.yml b/titan/params/haart.yml
index 036719ee..02a4c8c3 100644
--- a/titan/params/haart.yml
+++ b/titan/params/haart.yml
@@ -1,7 +1,7 @@
 haart:
   use_cap:
     default: false
-    description: Whether "prob" defined in demographics.race.sex_type.haart is a percent of diagnosed, HIV+ agents instead of a per-time-step probability for HAART coverage
+    description: Whether "cap" defined in demographics.race.sex_type.haart is used. Otherwise, haart probability is based on time since diagnosis.
     type: boolean
   use_reinit:
     type: boolean

From 5f53044b92e24a7dedcbec49549920eb945a733e Mon Sep 17 00:00:00 2001
From: sbessey <sarah_bessey@brown.edu>
Date: Wed, 20 Jan 2021 10:26:16 -0500
Subject: [PATCH 49/49] docs: further clarify haart.use_cap desc

---
 titan/params/haart.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/titan/params/haart.yml b/titan/params/haart.yml
index 02a4c8c3..4aec7ba3 100644
--- a/titan/params/haart.yml
+++ b/titan/params/haart.yml
@@ -1,7 +1,7 @@
 haart:
   use_cap:
     default: false
-    description: Whether "cap" defined in demographics.race.sex_type.haart is used. Otherwise, haart probability is based on time since diagnosis.
+    description: Whether "cap" defined in demographics.race.sex_type.haart.cap is used. Otherwise, haart probability is based on time since diagnosis (demographics.race.sex_type.haart.enroll).
     type: boolean
   use_reinit:
     type: boolean