But i think, this watchdog is not watchdog package, it's python-watchdog. I'll try this parameter and push changes in tomorrow.
2017-02-22 21:51 GMT+03:00 Çağrı ULAŞ <[email protected]>: > > Hi Andreas, > > In README.md file they said: > > If you want to watch a directory for new files, first install: >> >> - watchdog==0.8.3 >> >> And then use (the output parameter has no effect, we output separate >> fasta files for each fast5 file): >> OMP_NUM_THREADS=1 python basecall_no_metrichor.py --watch <directory name> > > watchdog version is fixed there but didn't test this feature with watchdog > package in sid > > or version 0.8.3 though. > > Regards. > > 2017-02-22 11:45 GMT+03:00 Andreas Tille <[email protected]>: > >> Hi Çağrı, >> >> On Wed, Feb 22, 2017 at 01:45:56AM +0300, Çağrı ULAŞ wrote: >> > I made some changes and will push them soon. Add manpages for scripts, >> > changes in testsuite etc. >> >> Sounds good. >> >> I checked this and noticed you added "Suggests: watchdog". Do you have >> any specific reason for this suggestion? I do not think that the fact >> that calls to deepnano might take some time makes this suggestion >> necessary specifically since some status update is given as output. >> >> One hint for your debug code in run-test.sh: The sequence !! will be >> interpreted by bash by he history function. I wrapped your debug line >> into '' to prevent this. >> >> > But when writing manpages, I realize that >> > deepnano uses some files under nets_data/ in default arguments. >> > >> > in source code: >> > >> > parser.add_argument('--template_net', type=str, >> default="nets_data/map6temp. >> > npz") >> > parser.add_argument('--complement_net', type=str, default= >> > "nets_data/map6comp.npz") >> > parser.add_argument('--big_net', type=str, default="nets_data/map6-2d- >> > big.npz") >> > >> > these .npz files is python numpy saves. And I think, they use different >> > reads >> > according to this issue[1]. What can we do for this defaults? (Quilt >> patch?) >> >> If upstream has a solution for [1] a quilt patch drawn from their >> repository would be an apropriate solution. As far as I can see there >> is no solution for the issue yet so what we can do is giving a hint >> for the users of the Debian package in README.Debian. >> >> In case you feel able to find a patch to solve this issue, yes, a quilt >> patch would be an excelent solution and you should forward this patch to >> the upstream tracker. This will be recieved as a very welcome >> distribution from Debian to upstream and might give a good motivation >> for upstream in case of further issues. Otherwise I do not think that >> an open issue of upstream code should prevent us from releasing the >> package since the test suite is running and seems to do something >> sensible. >> >> BTW, when checking for fresh commits I realised that my versioning which >> should have matched the last commit data was wrong. I've fixed this. >> >> > Are there anything else I can do for this program until we get a >> response >> > from developer? >> >> I do not think so. Usually new packages need to wait in the Debian new >> queue for some time - if we are lucky upstream has fixed the issue >> meanwhile and we can come up with a fix. So I'm tempted to upload the >> package (after commenting out the debug code in run-test.sh) and if you >> clarified your motivation for watchdog suggestion. >> >> Please also inspect the latest changes I did: >> >> 1. Upstream does not provide a proper makefile and thus you added >> the compilation lines in d/rules which is fine. I just added >> $(CFLAGS) which was missing. >> 2. There was a lintian info about duplicated short description - >> thus I've added (data) to the data package. Its a pretty minor >> issue but simple to fix. >> 3. You ITPed the package (#844010) >> >> Kind regards and thanks for your work on this >> >> Andreas. >> >> > [1] https://bitbucket.org/vboza/deepnano/issues/4/deepnano-with- >> metrichor-bad-input-argument >> >> -- >> http://fam-tille.de >> >> > > > -- > *Çağrı ULAŞ* > about.me/cagriulas > -- *Çağrı ULAŞ* about.me/cagriulas
