On Fri, Aug 02, 2019 at 11:43:01AM +0200, Steffen Möller wrote: > Hi Andreas, > > Thank you for fixing this and for caring in the first place. > > igdiscover is already with us for a llooooonngggg time, just parked in > the new queue, for so long that I just yesterday updated it to remain > compatible with newer versions of cutadapt when I rebuilt it for the > "Debian Med Crash Space" :) - med.functional.domains for those who have > not followed that thread. So I don't feel too bad about IgDiscover. But > I do feel bad for https://salsa.debian.org/med-team/python-alignlib > which I added just a few days ago
I remember Michael has even added code to re-run the script on existing repositories to set all missing hooks. Wanted to try this but master branch does not even have a debian/ dir. > - would you mind to have a pointer to > that script right on top of https://salsa.debian.org/med-team where the > "New project" button is? No, sorry. I do no Salsa hacking. I trust that you will adapt to a more easy and time saving workflow. You managed with routine-update after about one year - so you probably will with inject-into-salsa-git. :-P > I must admit that I used even used the script > once but have not really grasped / ignored the nitty-gritty technical > infrastructure behind it and there was this overhead on getting the > authentication done. There is not really any overhead. It now tells you what needs to be done if not setup properly. > I am busy with other things, which is also why I just do what is under > my fingertips and don't reeducate me on scripts / not even think about > them. It all needs to become simpler. Making things simpler is the actual point of those scripts. Put these in your PATH and just type inject<tab> ... > Just like allowing me to be > sufficiently functional when my mind is not. After all, we do this > Debian bits too often only after the working day has already ended. So, > I propose to start with a more visible pointer to that script right on > top of everything. And then there will more and more patches against > that script to help adopting that in some interactive fashion. A first > patch I would then look into is how to add hooks to projects that are > already on salsa with the same script. That was done by Michael as I said above ... Further enhancements are welcome Andreas. > On 02.08.19 06:58, Andreas Tille wrote: > > Hi, > > > > since I have realised the upload of igdiscover to new and no according > > commit message in our commit mailing list I added the commit hooks > > manually. There would be no need for manual intervention if everybody > > who creates a new repository would use > > > > > > https://salsa.debian.org/med-team/community/helper-scripts/blob/master/inject-into-salsa-git > > > > This script should be called from a new local git repository and will > > create the remote one on salsa.d.o and sets all the hooks we want. I > > would be happy if everybody would prefer this over manual creation of > > repositories since usually this will not include all settings we want > > to have. > > > > Hope this helps > > > > Andreas. > > > > > > ----- Forwarded message from Andreas Tille <[email protected]> ----- > > > > Date: Fri, 02 Aug 2019 03:28:05 +0000 > > From: Andreas Tille <[email protected]> > > To: [email protected] > > Subject: [Git][med-team/igdiscover][master] 2 commits: Adjusting build > > dependencies > > > > > > > > Andreas Tille pushed to branch master at Debian Med / igdiscover > > > > > > Commits: > > 1cc07041 by Steffen Möller at 2019-02-12T09:25:15Z > > Adjusting build dependencies > > > > - - - - - > > df76dec7 by Steffen Möller at 2019-08-01T23:06:59Z > > Fixed FTBFS with new cutadapt (>= 2.3) > > > > - - - - - > > > > > > 4 changed files: > > > > - debian/changelog > > - debian/control > > - + debian/patches/minoverlap.patch > > - + debian/patches/series > > > > > > Changes: > > > > ===================================== > > debian/changelog > > ===================================== > > @@ -1,4 +1,11 @@ > > -igdiscover (0.11-1) UNRELEASED; urgency=medium > > +igdiscover (0.11-2) unstable; urgency=medium > > + > > + * Introduced patch for compatibility with later versions > > + of cutadapt - upstream has it already in their master branch. > > + > > + -- Steffen Moeller <[email protected]> Fri, 02 Aug 2019 00:55:02 +0200 > > + > > +igdiscover (0.11-1) unstable; urgency=medium > > > > * Initial release (Closes: #919718) > > > > > > > > ===================================== > > debian/control > > ===================================== > > @@ -38,9 +38,8 @@ Depends: ${python3:Depends}, > > python3-cutadapt, > > python3-scipy (>=0.16.1), > > python3-xopen (>=0.3.2), > > + python3-seaborn (>=0.9), > > python3-ruamel.yaml > > -Recommends: python3-seaborn (>=0.8.1), > > - python3-matplotlib > > Suggests: snakemake, > > igdiscover-doc > > Description: analyzes antibody repertoires to find new V genes > > > > > > ===================================== > > debian/patches/minoverlap.patch > > ===================================== > > @@ -0,0 +1,14 @@ > > +Index: igdiscover/igdiscover/utils.py > > +=================================================================== > > +--- igdiscover.orig/igdiscover/utils.py > > ++++ igdiscover/igdiscover/utils.py > > +@@ -330,8 +330,7 @@ def find_overlap(s, t, min_overlap=1): > > + >>> find_overlap('ABC', 'X') is None > > + True > > + """ > > +- aligner = Aligner(s, max_error_rate=0) > > +- aligner.min_overlap = min_overlap > > ++ aligner = Aligner(s, max_error_rate=0, min_overlap=min_overlap) > > + result = aligner.locate(t) > > + if result is None: > > + return None > > > > > > ===================================== > > debian/patches/series > > ===================================== > > @@ -0,0 +1 @@ > > +minoverlap.patch > > > > > > > > View it on GitLab: > > https://salsa.debian.org/med-team/igdiscover/compare/dc8ee7231d33b6e526845fcb32a407ead20cb1a1...df76dec71814551cc3d7914005f4a2e15635b7be > > > > -- http://fam-tille.de
