v0.1.22 fixed max_tips in forest generation

evolbioinfo · Jul 1, 2024 · aded37b · aded37b
1 parent b8969cb
commit aded37b
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -7,7 +7,7 @@ USER root
 RUN apt-get update -y && apt-get install -y bc
 
 # Install treesimulator
-RUN cd /usr/local/ && pip3 install --no-cache-dir treesimulator==0.1.21
+RUN cd /usr/local/ && pip3 install --no-cache-dir treesimulator==0.1.22
 
 # Switch to your new user in the docker image
 USER evolbioinfo

diff --git a/setup.py b/setup.py
@@ -13,7 +13,7 @@
         'Topic :: Software Development',
         'Topic :: Software Development :: Libraries :: Python Modules',
     ],
-    version='0.1.21',
+    version='0.1.22',
     description='Simulation of rooted phylogenetic trees under a given Multitype Birth–Death model.',
     author='Anna Zhukova',
     author_email='anna.zhukova@pasteur.fr',

diff --git a/treesimulator/generator.py b/treesimulator/generator.py
@@ -53,7 +53,8 @@ def simulate_tree_gillespie(model, max_time=np.inf, min_sampled=0, max_sampled=n
 
     logging.debug('Aiming for at most {} sampled cases over time {}'.format(max_sampled, max_time))
 
-    target_sampled = np.round(np.random.uniform(low=min_sampled, high=max_sampled, size=1)[0], 0)
+    target_sampled = np.round(np.random.uniform(low=min_sampled, high=max_sampled, size=1)[0], 0) \
+        if max_sampled < np.inf else np.inf
 
     while infectious_nums.sum() and sampled_nums.sum() < target_sampled and time < max_time:
         # first we need to calculate rate sum