ghmm/xmlwriter.c | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 fix implicit declaration of function issue

ghmm/xmlwriter.c | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---

HMMEd/Makefile.am | 2 1 + 1 - 0 !
ghmmwrapper/Makefile.am | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

---

configure.in | 9 0 + 9 - 0 !
1 file changed, 9 deletions(-)

 skip non-working check for libxml2 version which is
 granted by Build-Depends anyway

HMMEd/EditingContext.py | 26 13 + 13 - 0 !
HMMEd/HMMEd | 2 1 + 1 - 0 !
HMMEd/HMMEditingContext.py | 16 8 + 8 - 0 !
HMMEd/HMMEditor.py | 126 63 + 63 - 0 !
HMMEd/ObjectHMM.py | 100 50 + 50 - 0 !
HMMEd/setup.py | 2 1 + 1 - 0 !
ghmmwrapper/class_change.py | 8 4 + 4 - 0 !
ghmmwrapper/ghmm.py | 74 37 + 37 - 0 !
ghmmwrapper/ghmmhelper.py | 2 1 + 1 - 0 !
ghmmwrapper/ghmmunittests.py | 50 25 + 25 - 0 !
ghmmwrapper/mixture.py | 30 15 + 15 - 0 !
ghmmwrapper/modhmmer.py | 24 12 + 12 - 0 !
ghmmwrapper/setup.py | 2 1 + 1 - 0 !
13 files changed, 231 insertions(+), 231 deletions(-)

 use 2to3 to port to python3
Bug-Debian: https://bugs.debian.org/936609

configure.in | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 make sure python3 is used
Bug-Debian: https://bugs.debian.org/936609

configure.in | 65 13 + 52 - 0 !
ghmm/matrixop.c | 14 7 + 7 - 0 !
2 files changed, 20 insertions(+), 59 deletions(-)

 use lapacke instead of atlas
Bug-Debian: https://bugs.debian.org/1056673

HMMEd/HMMEditingContext.py | 4 2 + 2 - 0 !
HMMEd/HMMEditor.py | 4 2 + 2 - 0 !
HMMEd/ObjectHMM.py | 12 6 + 6 - 0 !
ghmmwrapper/ghmm.py | 4 2 + 2 - 0 !
4 files changed, 12 insertions(+), 12 deletions(-)

 fix: syntaxwarning: "is" with a literal. did you mean "=="?

ghmmwrapper/sclass_change.c | 14 7 + 7 - 0 !
tests/mcmc.c | 2 2 + 0 - 0 !
2 files changed, 9 insertions(+), 7 deletions(-)

---

ghmm/smodel.c | 4 2 + 2 - 0 !
ghmmwrapper/wrapper_arrays.i | 12 6 + 6 - 0 !
2 files changed, 8 insertions(+), 8 deletions(-)

---

tests/mcmc.c | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix pointer indirection level in tests/mcmc.c.
 Attempts to build ghmm with gcc 14 end up with the following error:
 .
  mcmc.c: In function main:
  mcmc.c:148:15: error: initialization of int * from incompatible pointer type int ** [-Wincompatible-pointer-types]
    148 |   int * Q =   ghmm_dmodel_cfbgibbs(mo, my_output,
        |               ^~~~~~~~~~~~~~~~~~~~
  mcmc.c:150:108: error: passing argument 4 of ghmm_dmodel_viterbi_logp makes pointer from integer without a cast [-Wint-conversion]
    150 |   printf("viterbi prob mcmc%f \n", ghmm_dmodel_viterbi_logp(mo, my_output->seq[0], my_output->seq_len[0], Q[0]));
        |                                                                                                           ~^~~
        |                                                                                                            |
        |                                                                                                            int
 .
 This looks to be caused by a missing '*' in Q declaration.

ghmmwrapper/ghmm.py | 26 13 + 13 - 0 !
ghmmwrapper/modhmmer.py | 10 5 + 5 - 0 !
2 files changed, 18 insertions(+), 18 deletions(-)

 fix python3.12 string syntax
Bug-Debian: https://bugs.debian.org/1085608

ghmmwrapper/ghmmwrapper.i | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 replace pyeval_callobject with pyobject_callobject deprecated in python 3.9 and removed in python 3.13