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/