From e5ce19599ca759320e665a85706050ee265840d5 Mon Sep 17 00:00:00 2001
From: Daniel Klein <daniel.klein@gatesfoundation.org>
Date: Fri, 26 Jan 2024 14:38:33 -0800
Subject: [PATCH 1/2] Small speed increase in making new cases with multirng.

---
 starsim/diseases/disease.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/starsim/diseases/disease.py b/starsim/diseases/disease.py
index 6c2e890c..cdc17375 100644
--- a/starsim/diseases/disease.py
+++ b/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 [], []
 

From 847f1ecfdc754a8e949f5ea7ba0832e80fffc255 Mon Sep 17 00:00:00 2001
From: Cliff Kerr <questionably@gmail.com>
Date: Sat, 27 Jan 2024 12:17:33 -0500
Subject: [PATCH 2/2] update changelog

---
 CHANGELOG.rst            | 6 ++++++
 starsim/version.py       | 4 ++--
 tests/benchmark.json     | 8 ++++----
 tests/update_baseline.py | 0
 4 files changed, 12 insertions(+), 6 deletions(-)
 mode change 100644 => 100755 tests/update_baseline.py

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 8b71f980..59cfe6ca 100644
--- a/CHANGELOG.rst
+++ b/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
diff --git a/starsim/version.py b/starsim/version.py
index 22e5236f..c0a63bdf 100644
--- a/starsim/version.py
+++ b/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'
diff --git a/tests/benchmark.json b/tests/benchmark.json
index 7693a8fa..6586565f 100644
--- a/tests/benchmark.json
+++ b/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
 }
\ No newline at end of file
diff --git a/tests/update_baseline.py b/tests/update_baseline.py
old mode 100644
new mode 100755