phylogenie 2.0.9__py3-none-any.whl → 2.0.11__py3-none-any.whl

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Files changed (6) hide show
  1. phylogenie/treesimulator/gillespie.py +3 -2
  2. {phylogenie-2.0.9.dist-info → phylogenie-2.0.11.dist-info}/METADATA +1 -1
  3. {phylogenie-2.0.9.dist-info → phylogenie-2.0.11.dist-info}/RECORD +6 -6
  4. {phylogenie-2.0.9.dist-info → phylogenie-2.0.11.dist-info}/LICENSE.txt +0 -0
  5. {phylogenie-2.0.9.dist-info → phylogenie-2.0.11.dist-info}/WHEEL +0 -0
  6. {phylogenie-2.0.9.dist-info → phylogenie-2.0.11.dist-info}/entry_points.txt +0 -0
phylogenie/treesimulator/gillespie.py CHANGED
@@ -6,7 +6,7 @@ from numpy.random import default_rng
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  from phylogenie.skyline import SkylineParameterLike
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  from phylogenie.tree import Tree
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  from phylogenie.treesimulator.events import Event, get_contact_tracing_events
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- from phylogenie.treesimulator.model import Model, is_CT_state
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+ from phylogenie.treesimulator.model import Model
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  def simulate_tree(
@@ -29,6 +29,8 @@ def simulate_tree(
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  if max_tips is None and max_time == np.inf:
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  raise ValueError("Either max_tips or max_time must be specified.")
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+ root_states = list({e.state for e in events})
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+
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  if notification_probability:
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  events = get_contact_tracing_events(
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  events,
@@ -38,7 +40,6 @@ def simulate_tree(
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  )
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  n_tries = 0
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- root_states = [e.state for e in events if not is_CT_state(e.state)]
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  while max_tries is None or n_tries < max_tries:
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  root_state = init_state if init_state is not None else rng.choice(root_states)
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  model = Model(root_state, max_notified_contacts, notification_probability, rng)
{phylogenie-2.0.9.dist-info → phylogenie-2.0.11.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: phylogenie
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- Version: 2.0.9
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+ Version: 2.0.11
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  Summary: Generate phylogenetic datasets with minimal setup effort
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  Author: Gabriele Marino
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  Author-email: gabmarino.8601@gmail.com
{phylogenie-2.0.9.dist-info → phylogenie-2.0.11.dist-info}/RECORD RENAMED
@@ -17,12 +17,12 @@ phylogenie/skyline/vector.py,sha256=bJP7_FNX_Klt6wXqsyfj0KX3VNj6-dIhzCKSJuQcOV0,
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  phylogenie/tree.py,sha256=dk8Sj1tqyGOunVO2crtIqb0LH-ws-PXqA8SuNcYfVHI,1738
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  phylogenie/treesimulator/__init__.py,sha256=INPU9LrPdUmt3dYGzWDRoRKrPR9xENcHu44pJVUbyNA,525
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  phylogenie/treesimulator/events.py,sha256=X3_0U9qqMpYgh6-7TwQEnlUipANkHz6QTCXlm-qXFQk,9524
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- phylogenie/treesimulator/gillespie.py,sha256=Fn-PyVICx3pWtpHko7rf6omf_kqOkkpebSJy56oPKnQ,3216
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+ phylogenie/treesimulator/gillespie.py,sha256=4uMt_-Rr3cRXWGKC8veBIB-uqtKtN-dLbAHKjAi_5Mo,3182
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  phylogenie/treesimulator/model.py,sha256=XpzAicmg2O6K0Trk5YolH-B_HJZxoSauF2wZOMqp-Iw,5559
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  phylogenie/typeguards.py,sha256=JtqmbEWJZBRHbWgCvcl6nrWm3VcBfzRbklbTBYHItn0,1325
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  phylogenie/typings.py,sha256=O1X6lGKTjJ2YJz3ApQ-rYb_tEJNUIcHdUIeYlSM4s5o,500
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- phylogenie-2.0.9.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
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- phylogenie-2.0.9.dist-info/METADATA,sha256=EHn9nzfQMQCfWXzl1Ddb_dTrowodP7Y4dsDQqsna2xw,5472
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- phylogenie-2.0.9.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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- phylogenie-2.0.9.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
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- phylogenie-2.0.9.dist-info/RECORD,,
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+ phylogenie-2.0.11.dist-info/LICENSE.txt,sha256=NUrDqElK-eD3I0WqC004CJsy6cs0JgsAoebDv_42-pw,1071
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+ phylogenie-2.0.11.dist-info/METADATA,sha256=H9fTgI9BaoI2j7-Od2an5dPivAxl1jk2DACT3m9DCoE,5473
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+ phylogenie-2.0.11.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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+ phylogenie-2.0.11.dist-info/entry_points.txt,sha256=Rt6_usN0FkBX1ZfiqCirjMN9FKOgFLG8rydcQ8kugeE,51
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+ phylogenie-2.0.11.dist-info/RECORD,,