Description: Fix Python3.12 string syntax
Bug-Debian: https://bugs.debian.org/1085608
Author: Andreas Tille <tille@debian.org>
Last-Update: 2024-06-07

--- a/ghmmwrapper/ghmm.py
+++ b/ghmmwrapper/ghmm.py
@@ -287,7 +287,7 @@ class EmissionDomain(object):
 
 
     def isAdmissable(self, emission):
-        """ Check whether \p emission is admissable (contained in) the domain
+        """ Check whether p emission is admissable (contained in) the domain
         raises GHMMOutOfDomain else
         """
         return None
@@ -1507,7 +1507,7 @@ class HMMOpenFactory(HMMFactory):
         f = open(fileName,"r")
 
         res = re.compile("^//")
-        stat = re.compile("^ACC\s+(\w+)")
+        stat = re.compile(r"^ACC\s+(\w+)")
         for line in f.readlines():
             string = string + line
             m = stat.match(line)
@@ -1533,11 +1533,11 @@ class HMMOpenFactory(HMMFactory):
         #
         file = open(fileName,'r')
 
-        hmmRe = re.compile("^HMM\s*=")
-        shmmRe = re.compile("^SHMM\s*=")
-        mvalueRe = re.compile("M\s*=\s*([0-9]+)")
-        densityvalueRe = re.compile("density\s*=\s*([0-9]+)")
-        cosvalueRe = re.compile("cos\s*=\s*([0-9]+)")
+        hmmRe = re.compile(r"^HMM\s*=")
+        shmmRe = re.compile(r"^SHMM\s*=")
+        mvalueRe = re.compile(r"M\s*=\s*([0-9]+)")
+        densityvalueRe = re.compile(r"density\s*=\s*([0-9]+)")
+        cosvalueRe = re.compile(r"cos\s*=\s*([0-9]+)")
         emission_domain = None
 
         while 1:
@@ -2099,7 +2099,7 @@ class HMM(object):
         @param emissionSequences can either be a SequenceSet or a EmissionSequence
 
         @returns log( P[emissionSequences| model]) of type float which is
-        computed as \f$\sum_{s} log( P[s| model])\f$ when emissionSequences
+        computed as $sum_{s} log( P[s| model])$ when emissionSequences
         is a SequenceSet
 
         @note The implementation does not compute the full forward matrix since
@@ -2375,7 +2375,7 @@ class HMM(object):
 
         @param eseqs can either be a SequenceSet or an EmissionSequence
 
-        @returns [q_0, ..., q_T] the viterbi-path of \p eseqs is an
+        @returns [q_0, ..., q_T] the viterbi-path of p eseqs is an
         EmmissionSequence object,
         [[q_0^0, ..., q_T^0], ..., [q_0^k, ..., q_T^k]} for a k-sequence
         SequenceSet
@@ -2470,14 +2470,14 @@ class HMM(object):
         return self.name2id[stateLabel]
 
     def getInitial(self, i):
-        """ Accessor function for the initial probability \f$\pi_i\f$ """
+        """ Accessor function for the initial probability $pi_i$ """
         state = self.cmodel.getState(i)
         return state.pi
 
     def setInitial(self, i, prob, fixProb=False):
-        """ Accessor function for the initial probability \f$\pi_i\f$.
+        """ Accessor function for the initial probability $pi_i$.
 
-        If 'fixProb' = True \f$\pi\f$ will be rescaled to 1 with 'pi[i]'
+        If 'fixProb' = True $pi$ will be rescaled to 1 with 'pi[i]'
         fixed to the arguement value of 'prob'.
 
         """
@@ -3321,7 +3321,7 @@ class StateLabelHMM(DiscreteEmissionHMM)
 
     def labeledlogikelihoods(self, emissionSequences):
         """ Compute a vector ( log( P[s,l| model]) )_{s} of log-likelihoods of the
-        individual \p emissionSequences using the forward algorithm
+        individual p emissionSequences using the forward algorithm
 
         @param emissionSequences SequenceSet
 
--- a/ghmmwrapper/modhmmer.py
+++ b/ghmmwrapper/modhmmer.py
@@ -189,10 +189,10 @@ class hmmer:
                 self.acc = self.acc[:-1]
                     	
             #get number of match states
-            n = int(gotoLine(f,re.compile("^LENG\s*(\d+)")).group(1))
+            n = int(gotoLine(f,re.compile(r"^LENG\s*(\d+)")).group(1))
             self.n = n
             #get type of profile hmm: amino/nucleotide
-            m = self.dicType[gotoLine(f,re.compile("^ALPH\s*(\S+)")).group(1)];
+            m = self.dicType[gotoLine(f,re.compile(r"^ALPH\s*(\S+)")).group(1)];
             self.m = m
 
             #build matrix for transition: N B E J C T M1 I1 D1 M2 I2 D2 ... Mn In Dn
@@ -202,13 +202,13 @@ class hmmer:
             self.maems = [build_matrix(n,m),build_matrix(n,m),build_matrix(1,m)]
 
 			#get line "XT" transitions
-            trans = string.split(gotoLine(f,re.compile("^XT([\s\d\S]*)")).group(1))
+            trans = string.split(gotoLine(f,re.compile(r"^XT([\s\d\S]*)")).group(1))
             self.set_matrix("XT",trans)
 
             #null model
-            trans = string.split(gotoLine(f,re.compile("^NULT([\s\d\S]*)")).group(1))
+            trans = string.split(gotoLine(f,re.compile(r"^NULT([\s\d\S]*)")).group(1))
             self.manull = [self.H2P(trans[0],1.0),self.H2P(trans[1],1.0)] #[G->G,G->F]
-            trans = string.split(gotoLine(f,re.compile("^NULE([\s\d\S]*)")).group(1))
+            trans = string.split(gotoLine(f,re.compile(r"^NULE([\s\d\S]*)")).group(1))
             for k in range(len(trans)):
                 self.maems[2][0][k] = self.H2P(trans[k],1/float(m))