[med-svn] [Git][med-team/ghmm][master] 5 commits: fix-test-mcmc.patch: new: fix missing imports.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Tue Mar 12 22:05:34 GMT 2024
Étienne Mollier pushed to branch master at Debian Med / ghmm
Commits:
0087650a by Étienne Mollier at 2024-03-12T22:39:54+01:00
fix-test-mcmc.patch: new: fix missing imports.
Closes: #1065974
- - - - -
162fe929 by Étienne Mollier at 2024-03-12T22:54:08+01:00
python3.12.patch: new: fix remaining failures.
There were a couple of occurrences of calls to obsolet APIs causing
build failures.
- - - - -
38daae13 by Étienne Mollier at 2024-03-12T23:02:07+01:00
d/control: move to pkgconf.
- - - - -
607814d2 by Étienne Mollier at 2024-03-12T23:02:18+01:00
d/s/lintian-overrides: new: hide new error.
The lintian error looks to be a side effect of necessary changes for
the 64-bit time_t transition.
- - - - -
a33a7e10 by Étienne Mollier at 2024-03-12T23:04:57+01:00
ready to upload to unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/fix-test-mcmc.patch
- + debian/patches/python3.12.patch
- debian/patches/series
- + debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+ghmm (0.9~rc3-6) unstable; urgency=medium
+
+ * Team upload.
+ * fix-test-mcmc.patch: new: fix missing imports. (Closes: #1065974)
+ * python3.12.patch: new: fix remaining failures.
+ There were a couple of occurrences of calls to obsolet APIs causing
+ build failures.
+ * d/control: move to pkgconf.
+ * d/s/lintian-overrides: new: hide new error.
+ The lintian error looks to be a side effect of necessary changes for
+ the 64-bit time_t transition.
+
+ -- Étienne Mollier <emollier at debian.org> Tue, 12 Mar 2024 23:02:56 +0100
+
ghmm (0.9~rc3-5.1) unstable; urgency=medium
* Non-maintainer upload.
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
dh-sequence-python3,
d-shlibs (>= 0.106~),
python3-dev,
- pkg-config,
+ pkgconf,
libxml2-dev,
libgsl-dev,
liblapacke-dev,
=====================================
debian/patches/fix-test-mcmc.patch
=====================================
@@ -0,0 +1,62 @@
+--- ghmm.orig/tests/mcmc.c
++++ ghmm/tests/mcmc.c
+@@ -14,6 +14,8 @@
+ #include <ghmm/foba.h>
+ #include <ghmm/reestimate.h>
+ #include <ghmm/obsolete.h>
++#include <ghmm/fbgibbs.h>
++#include <ghmm/cfbgibbs.h>
+
+ #include <time.h>//time
+ int* getList(char* fileName, int count){
+--- ghmm.orig/ghmmwrapper/sclass_change.c
++++ ghmm/ghmmwrapper/sclass_change.c
+@@ -95,7 +95,7 @@
+ if (pModule == NULL) {
+ printf("C: Importing Python module ... ");
+
+- pName = PyString_FromString(ModuleName);
++ pName = PyUnicode_FromString(ModuleName);
+
+ pModule = PyImport_Import(pName); /* Import module */
+ if(!pModule) {
+@@ -130,16 +130,16 @@
+ }
+ PyTuple_SetItem(pArgs, 0, pList);
+
+- pValue = PyInt_FromLong((long)k);
++ pValue = PyLong_FromLong((long)k);
+ PyTuple_SetItem(pArgs, 1, pValue);
+
+- pValue = PyInt_FromLong((long)t);
++ pValue = PyLong_FromLong((long)t);
+ PyTuple_SetItem(pArgs, 2, pValue);
+
+ pValue = PyObject_CallObject(pFunc, pArgs); // Calling Python
+
+ /* parsing the result from Python to C data type */
+- class = PyInt_AsLong(pValue);
++ class = PyLong_AsLong(pValue);
+ /*printf("C: The returned class is %d\n",class);*/
+
+ /* cleaning up */
+@@ -211,16 +211,16 @@
+ }
+ PyTuple_SetItem(pArgs, 0, pList);
+
+- pValue = PyInt_FromLong((long)k);
++ pValue = PyLong_FromLong((long)k);
+ PyTuple_SetItem(pArgs, 1, pValue);
+
+- pValue = PyInt_FromLong((long)t);
++ pValue = PyLong_FromLong((long)t);
+ PyTuple_SetItem(pArgs, 2, pValue);
+
+ pValue = PyObject_CallObject(pyCallback, pArgs); // Calling Python
+
+ /* parsing the result from Python to C data type */
+- class = PyInt_AsLong(pValue);
++ class = PyLong_AsLong(pValue);
+ /*printf("C: The returned class is %d\n",class);*/
+
+ if (class == -1) {
=====================================
debian/patches/python3.12.patch
=====================================
@@ -0,0 +1,63 @@
+--- ghmm.orig/ghmm/smodel.c
++++ ghmm/ghmm/smodel.c
+@@ -2069,13 +2069,13 @@
+ pFunc = PyDict_GetItemString(pDict, FunctionName);
+
+ pArgs = PyTuple_New(1);
+- pValue = PyInt_FromLong(pos);
++ pValue = PyLong_FromLong(pos);
+
+ PyTuple_SetItem(pArgs, 0, pValue);
+ pValue = PyObject_CallObject(pFunc, pArgs); /* Calling Python */
+
+ /* parsing the result from Python to C data type
+- class = PyInt_AsLong(pValue);
++ class = PyLong_AsLong(pValue);
+ printf("C: The returned class is %d\n",class); */
+
+ /*Py_Finalize(); */
+--- ghmm.orig/ghmmwrapper/wrapper_arrays.i
++++ ghmm/ghmmwrapper/wrapper_arrays.i
+@@ -14,13 +14,13 @@
+ }
+ for (i = 0; i < $2; i++) {
+ PyObject *o = PySequence_GetItem($input,i);
+- if (!PyInt_Check(o)) {
++ if (!PyLong_Check(o)) {
+ Py_XDECREF(o);
+ PyErr_SetString(PyExc_ValueError,"Expecting a sequence of integers");
+ free($1);
+ return NULL;
+ }
+- $1[i] = (int)PyInt_AsLong(o);
++ $1[i] = (int)PyLong_AsLong(o);
+ Py_DECREF(o);
+ }
+ }
+@@ -41,7 +41,7 @@
+ if (result) {
+ $result = PyList_New(*$1);
+ for (i=0; i<*$1; i++) {
+- PyList_SetItem($result, i, PyInt_FromLong(result[i]));
++ PyList_SetItem($result, i, PyLong_FromLong(result[i]));
+ }
+ }
+ else {
+@@ -67,8 +67,8 @@
+ Py_DECREF(o);
+ }
+ // conversion from int to double is without loss
+- else if (PyInt_Check(o)) {
+- $1[i] = (double)PyInt_AsLong(o);
++ else if (PyLong_Check(o)) {
++ $1[i] = (double)PyLong_AsLong(o);
+ Py_DECREF(o);
+ }
+ else {
+@@ -161,4 +161,4 @@
+ %}
+ %enddef
+ MATRIX(int)
+-MATRIX(double)
+\ No newline at end of file
++MATRIX(double)
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,5 @@ python3_build_system.patch
lapacke.patch
python3_syntax.patch
# setuptools.patch
+fix-test-mcmc.patch
+python3.12.patch
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# libghmm1 is the package name prior 64-bit time_t transition.
+ghmm source: version-substvar-for-external-package Conflicts ${source:Version} libghmm1t64 -> libghmm1 [debian/control:56]
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/c9de8903821fd7baab39295d8a5b566336319994...a33a7e103e7aa53d8df4c6aea9fe09aefb594e7b
--
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/c9de8903821fd7baab39295d8a5b566336319994...a33a7e103e7aa53d8df4c6aea9fe09aefb594e7b
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