V22

CHANGELOG.rst

@@ -7,6 +7,18 @@ What's new
 All notable changes to the codebase are documented in this file.
 
 
+Version 1.0.0 (2024-12-11)
+--------------------------
+- Updates to work with Starsim v2.2.1
+- *GitHub info*: PR `63 <https://github.com/starsimhub/stisim/pull/63>`_
+
+
+Version 0.2.0 (2024-11-01)
+--------------------------
+- Updates to work with Starsim v2.0
+- *GitHub info*: PR `62 <https://github.com/starsimhub/stisim/pull/62>`_
+
+
 Version 0.1.0 (2024-10-02)
 --------------------------
 - Collection of updates related to the NG/CT/TV work

setup.py

@@ -39,7 +39,7 @@
     include_package_data=True,
     classifiers=CLASSIFIERS,
     install_requires=[
-        'starsim==1.0.3',
+        'starsim>=2.2.0',
         'optuna',
     ],
 )

stisim/__init__.py

@@ -16,5 +16,5 @@
 print(__license__)
 
 # Double-check key requirements -- should match setup.py
-sc.require(['sciris>=3.1.6', 'pandas>=2.0.0', 'scipy', 'numba', 'networkx'], message=f'The following dependencies for STIsim {__version__} were not met: <MISSING>.')
+sc.require(['starsim>=2.2.0', 'sciris>=3.1.6', 'pandas>=2.0.0', 'scipy', 'numba', 'networkx'], message=f'The following dependencies for STIsim {__version__} were not met: <MISSING>.')
 del sc # Don't keep this in the module

stisim/connectors/gud_syph.py

@@ -5,7 +5,7 @@ class gud_syph(ss.Connector):
 
     def __init__(self, pars=None, **kwargs):
         super().__init__(label='GUD-Syphilis', requires=[sti.GUD, sti.Syphilis])
-        self.default_pars(
+        self.define_pars(
             rel_sus_syph_gud=2,     # People with GUD are 2x more likely to acquire syphilis
             rel_trans_syph_gud=2,   # People with GUD are 2x more likely to transmit syphilis
             rel_sus_gud_syph=2,     # People with syphilis are 2x more likely to acquire GUD
@@ -17,9 +17,7 @@ def __init__(self, pars=None, **kwargs):
 
     def update(self, sim):
         """
-        Specify GUD-syphilis interactions
-        Question, should this be multiplicative?
-        Also, it needs to be reset after infection clears/enters latency
+        GUD-syphilis interactions
         """
         # People with GUD are more likely to acquire syphilis
         sim.diseases.syphilis.rel_sus[sim.people.gud.infected] = self.pars.rel_sus_syph_gud

stisim/connectors/hiv_sti.py

@@ -6,7 +6,7 @@
 from stisim.diseases.syphilis import SyphilisPlaceholder
 
 
-__all__ = ['hiv_syph', 'hiv_tv', 'hiv_ng', 'hiv_ct']
+__all__ = ['hiv_syph', 'hiv_tv', 'hiv_ng', 'hiv_ct', 'hiv_bv']
 
 
 class hiv_syph(ss.Connector):
@@ -16,7 +16,9 @@ def __init__(self, hiv_module, syphilis_module, pars=None, **kwargs):
 
         self.hiv = hiv_module
         self.syphilis = syphilis_module
-        self.default_pars(
+        self.define_pars(
+            unit='month',
+
             # Changes to HIV due to syphilis coinfection
             rel_sus_hiv_syph=2.67,  # Relative increase in susceptibility to HIV due to syphilis
             rel_trans_hiv_syph=1.2,  # Relative increase in transmission due to syphilis
@@ -29,7 +31,7 @@ def __init__(self, hiv_module, syphilis_module, pars=None, **kwargs):
         )
         self.update_pars(pars, **kwargs)
 
-        self.add_states(
+        self.define_states(
             ss.FloatArr('rel_sus_hiv_syph', default=self.pars.rel_sus_hiv_syph),
             ss.FloatArr('rel_trans_hiv_syph', default=self.pars.rel_trans_hiv_syph),
             ss.FloatArr('rel_sus_syph_hiv', default=self.pars.rel_sus_syph_hiv),
@@ -40,7 +42,7 @@ def __init__(self, hiv_module, syphilis_module, pars=None, **kwargs):
 
         return
 
-    def update(self):
+    def step(self):
 
         # HIV changes due to syphilis
         syphilis = self.syphilis.active
@@ -69,7 +71,7 @@ def __init__(self, hiv_module, tv_module, pars=None, **kwargs):
 
         self.hiv = hiv_module
         self.tv = tv_module
-        self.default_pars(
+        self.define_pars(
             # Changes to HIV due to trichonomiasis coinfection
             # Sources:
             #   - https://www.who.int/news-room/fact-sheets/detail/trichomoniasis
@@ -79,7 +81,7 @@ def __init__(self, hiv_module, tv_module, pars=None, **kwargs):
         self.update_pars(pars, **kwargs)
         return
 
-    def update(self):
+    def step(self):
         tv = self.tv.infected
         self.hiv.rel_sus[tv] *= self.pars.rel_sus_hiv_tv
         return
@@ -92,7 +94,7 @@ def __init__(self, hiv_module, ng_module, pars=None, **kwargs):
 
         self.hiv = hiv_module
         self.ng = ng_module
-        self.default_pars(
+        self.define_pars(
             # Changes to HIV due to gonorrhea coinfection
             # Sources:
             #   - TODO
@@ -102,7 +104,7 @@ def __init__(self, hiv_module, ng_module, pars=None, **kwargs):
 
         return
 
-    def update(self):
+    def step(self):
         ng = self.ng.infected
         self.hiv.rel_sus[ng] *= self.pars.rel_sus_hiv_ng
         return
@@ -115,7 +117,7 @@ def __init__(self, hiv_module, ct_module, pars=None, **kwargs):
 
         self.hiv = hiv_module
         self.ct = ct_module
-        self.default_pars(
+        self.define_pars(
             # Changes to HIV due to chlamydia coinfection
             # Sources:
             #   - TODO
@@ -125,8 +127,31 @@ def __init__(self, hiv_module, ct_module, pars=None, **kwargs):
 
         return
 
-    def update(self):
+    def step(self):
         ct = self.ct.infected
         self.hiv.rel_sus[ct] *= self.pars.rel_sus_hiv_ct
         return
 
+
+class hiv_bv(ss.Connector):
+
+    def __init__(self, hiv_module, bv_module, pars=None, **kwargs):
+        super().__init__()
+
+        self.hiv = hiv_module
+        self.bv = bv_module
+        self.define_pars(
+            # Changes to HIV due to BV
+            rel_sus_hiv_bv=2,       # PLACEHOLDER: BV leads to 2x risk of HIV acquisition
+            rel_trans_hiv_bv=2,     # PLACEHOLDER: BV leads to 2x risk of HIV transmission
+        )
+        self.update_pars(pars, **kwargs)
+
+        return
+
+    def step(self):
+        bv = self.bv.infected
+        self.hiv.rel_trans[bv] *= self.pars.rel_trans_hiv_bv
+        self.hiv.rel_sus[bv] *= self.pars.rel_sus_hiv_bv
+        return
+

stisim/diseases/__init__.py

@@ -2,7 +2,7 @@
 
 # Individual diseases
 from .chlamydia     import *
-from .discharging_sti import *
+from .bv            import *
 from .gonorrhea     import *
 from .gud           import *
 from .hiv           import *