v0.1.21 fixed max_tips in forest generation

evolbioinfo · Jul 1, 2024 · b8969cb · b8969cb
1 parent 00ea487
commit b8969cb
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Showing 3 changed files with 6 additions and 6 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==0.1.20
+RUN cd /usr/local/ && pip3 install --no-cache-dir treesimulator==0.1.21
 
 # 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='0.1.20',
+    version='0.1.21',
     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
@@ -51,7 +51,7 @@ def simulate_tree_gillespie(model, max_time=np.inf, min_sampled=0, max_sampled=n
     id2current_id = {0: 0}
     id2state = {0: root_state}
 
-    # logging.info('Aiming for at most {} sampled cases over time {}'.format(max_sampled, max_time))
+    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)
 
@@ -279,7 +279,7 @@ def generate_forest(model, max_time=np.inf, min_tips=1000, max_sampled=np.inf, k
     res_ltt = None
     while total_n_tips < min_tips:
         if ltt:
-            tree, cur_ltt, _ = simulate_tree_gillespie(model, max_time=max_time, max_sampled=max_sampled, ltt=True,
+            tree, cur_ltt, _ = simulate_tree_gillespie(model, max_time=max_time, ltt=True,
                                                        state_feature=state_feature, state_frequencies=state_frequencies,
                                                        max_notified_partners=max_notified_partners)
             if res_ltt is None:
@@ -296,7 +296,7 @@ def generate_forest(model, max_time=np.inf, min_tips=1000, max_sampled=np.inf, k
                         prev_res = res_ltt[time]
                     res_ltt[time] = total
         else:
-            tree, _ = simulate_tree_gillespie(model, max_time=max_time, max_sampled=max_sampled,
+            tree, _ = simulate_tree_gillespie(model, max_time=max_time,
                                               state_feature=state_feature, state_frequencies=state_frequencies,
                                               max_notified_partners=max_notified_partners)
         total_trees += 1
@@ -347,7 +347,7 @@ def generate(model, min_tips, max_tips, T=np.inf, state_frequencies=None, max_no
 
     if T < np.inf:
         while True:
-            forest, ltt = generate_forest(model, max_time=T, min_tips=min_tips,
+            forest, ltt = generate_forest(model, max_time=T, min_tips=min_tips, max_sampled=max_tips,
                                           keep_nones=True, state_frequencies=state_frequencies, ltt=True,
                                           max_notified_partners=max_notified_partners)
             total_trees = len(forest)