Small speed increase in making new cases with multirng

CHANGELOG.rst

@@ -9,6 +9,12 @@ All notable changes to the codebase are documented in this file. Changes that ma
    :depth: 1
 
 
+Version 0.1.7 (2024-01-27)
+--------------------------
+- Performance enhancement for disease transmission, leading to a 10% decrease in runtime.
+- *GitHub info*: PR `217 <https://github.com/amath-idm/stisim/pull/217>`_
+
+
 Version 0.1.6 (2024-01-23)
 --------------------------
 - Adds template interventions and products for diagnostics and treatment

starsim/diseases/disease.py

@@ -344,7 +344,9 @@ def _make_new_cases_multirng(self, people):
         n = len(people.uid)  # TODO: possibly could be shortened to just the people who are alive
         p_acq_node = np.zeros(n)
 
-        dfs = []
+        avec = []
+        bvec = []
+        pvec = []
         for lkey, layer in people.networks.items():
             if lkey in self.pars['beta']:
                 contacts = layer.contacts
@@ -358,12 +360,12 @@ def _make_new_cases_multirng(self, people):
                         continue
 
                     a, b = contacts[lbl_src], contacts[lbl_tgt]
-                    df = pd.DataFrame({'p1': a, 'p2': b})
-                    df['p'] = (rel_trans[a] * rel_sus[b] * contacts.beta * beta * people.dt).values
-                    df = df.loc[df['p'] > 0]
-                    dfs.append(df)
+                    nzi = (rel_trans[a]>0) & (rel_sus[b]>0) & (contacts.beta>0)
+                    avec.append(a[nzi])
+                    bvec.append(b[nzi])
+                    pvec.append(rel_trans[a[nzi]].__array__() * rel_sus[b[nzi]].__array__() * contacts.beta[nzi] * beta * people.dt)
 
-        df = pd.concat(dfs)
+        df = pd.DataFrame({'p1': np.concatenate(avec), 'p2': np.concatenate(bvec), 'p': np.concatenate(pvec)})
         if len(df) == 0:
             return [], []
 

starsim/version.py

@@ -4,6 +4,6 @@
 
 __all__ = ['__version__', '__versiondate__', '__license__']
 
-__version__ = '0.1.6'
-__versiondate__ = '2024-01-23'
+__version__ = '0.1.7'
+__versiondate__ = '2024-01-27'
 __license__ = f'STIsim {__version__} ({__versiondate__}) — © 2024 by IDM'

tests/benchmark.json

@@ -1,13 +1,13 @@
 {
   "time": {
-    "people": 0.019,
-    "initialize": 0.046,
-    "run": 0.275
+    "people": 0.018,
+    "initialize": 0.041,
+    "run": 0.251
   },
   "parameters": {
     "n_agents": 10000,
     "n_years": 20,
     "dt": 0.2
   },
-  "cpu_performance": 0.30820661368745095
+  "cpu_performance": 0.9938153654580599
 }