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Description: fix SyntaxWarnings in treetime/merger_models.py.
Embedded TeX mathematical snippets are causing the below warnings:
.
/usr/lib/python3/dist-packages/treetime/merger_models.py:187:
SyntaxWarning: invalid escape sequence '\k'
'''
/usr/lib/python3/dist-packages/treetime/merger_models.py:197:
SyntaxWarning: invalid escape sequence '\l'
'''
/usr/lib/python3/dist-packages/treetime/merger_models.py:209:
SyntaxWarning: invalid escape sequence '\l'
'''
.
Switching the affected strings to raw strings with prefix r resolves
the issue first, and second allows getting back our τ characters with
single slash; it is assumed that the duplicate slash was necessary
because Python's regular string would otherwise throw a <Tab>au instead
of a \tau.
Author: Étienne Mollier <emollier@debian.org>
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1086965
Forwarded: https://github.com/neherlab/treetime/pull/285
Last-Update: 2024-11-09
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-treetime.orig/treetime/merger_models.py
+++ python-treetime/treetime/merger_models.py
@@ -184,7 +184,7 @@
np.concatenate(([cost[0]], cost,[cost[-1]])), kind='linear')
def branch_merger_rate(self, t):
- '''
+ r'''
rate at which one particular branch merges with any other branch at time t,
in the Kingman model this is: :math:`\kappa(t) = (k(t)-1)/(2Tc(t))`
'''
@@ -194,7 +194,7 @@
return 0.5*np.maximum(0.5,self.nbranches(t)-1.0)/self.Tc(t)
def total_merger_rate(self, t):
- '''
+ r'''
rate at which any branch merges with any other branch at time t,
in the Kingman model this is: :math:`\lambda(t) = k(t)(k(t)-1)/(2Tc(t))`
'''
@@ -206,12 +206,12 @@
def cost(self, t_node, branch_length, multiplicity=2.0):
- '''
+ r'''
returns the cost associated with a branch starting with divergence time t_node (:math:`t_n`)
- having a branch length :math:`\\tau`.
+ having a branch length :math:`\tau`.
This is equivalent to the probability of there being no merger on that branch and a merger at the end of the branch,
calculated in the negative log
- :math:`-log(\lambda(t_n+ \\tau)^{(m-1)/m}) + \int_{t_n}^{t_n+ \\tau} \kappa(t) dt`, where m is the multiplicity
+ :math:`-log(\lambda(t_n+ \tau)^{(m-1)/m}) + \int_{t_n}^{t_n+ \tau} \kappa(t) dt`, where m is the multiplicity
Parameters
----------
|
