[Debian-med-packaging] Bug#958840: kmer: autopkgtest regression: No module named 'localAlignerInterface'

[Antoni Villalonga]

Hi,

On Tue, Apr 28, 2020 at 11:44:28AM +0200, Andreas Tille wrote:
> Hi Antoni
> 
> On Sat, Apr 25, 2020 at 09:02:07PM +0200, Paul Gevers wrote:
> > ...
> > python3 /usr/bin/../lib/atac/bin/AtacDriver.py
> > /tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended
> > 
> > Traceback (most recent call last):
> >   File "/usr/bin/../lib/atac/bin/AtacDriver.py", line 26, in <module>
> >     import localAlignerInterface
> > ModuleNotFoundError: No module named 'localAlignerInterface'
> > PYTHONPATH=/usr/bin/../lib/atac/lib
> > Chainer failed.
> > autopkgtest [14:11:24]: test atac-unit-test: -----------------------]
> 
> Since you helped with the Python3 port of kmer I wonder whether you
> might have some idea how to fix this.  The module is available in
> 
>    atac-driver/chainer/localalign/localAlignerInterfacemodule.C
> 
> but for some reason it is not found.
> 
> Any help would be really appreciated.
> 
> Kind regards an thanks a lot for your initial help

I think I've faced that problem and fixed.
Fix should be included into '2to3.patch'

I think the relevant part is:

--- a/atac-driver/chainer/localalign/localAlignerInterfacemodule.C
+++ b/atac-driver/chainer/localalign/localAlignerInterfacemodule.C
@@ -227,8 +227,17 @@
 };
 
 
+static struct PyModuleDef cModMethods =
+{
+    PyModuleDef_HEAD_INIT,
+    "localAlignerInterface",  /* name of module */
+    "",          /* module documentation, may be NULL */
+    -1,          /* size of per-interpreter state of the module, or -1 if the module keeps state in global variables. */
+    registration_table
+};
+
 extern "C"
-void initlocalAlignerInterface() {
-  Py_InitModule("localAlignerInterface", registration_table);
+void PyInit_localAlignerInterface() {
+  PyModule_Create(&cModMethods);
 }



Sorry I can't access salsa due to a maintenance, also can't test autopkgtest
for testing for the same reason.

It worked fine for sid some days ago.

Regards,

-- 
Antoni Villalonga
https://friki.cat/