On 14.01.19 17:39, Michael Crusoe wrote: > [Keeping Hannes on the CC in case he isn't subscribed] > > Thanks for the responses, all. >
Thanks for keeping me in the loop, I am not subscribed to debian-med. > În lun., 14 ian. 2019 la 17:48, Sascha Steinbiss <[email protected] > <mailto:[email protected]>> a scris: > > Hi, > > just my 2 cents. I introduced Lambda into Debian some time ago just out > of interest but looking at the uploads, Michael has done more work > recently... > So here are just a few comments from me. > [...] > >> However, there are no references from other Debian packages to > >> lambda-align's binaries, so upgrading to v2 without changing the > package > >> name won't break any packages, but it will break user scripts. > > > > From a plain Debian point of view adding a file debian/NEWS.Debian > > explaining the issue will show the change in the new version. From a > > user perspective it might be interesting to have the old version as > > well. > > I would also advise to create a new package for v2 in order not to > silently break users' pipelines when they upgrade their lambda-align > package to version 2 (or just do an 'apt upgrade' without checking in > detail whether lambda is in the -- potentially tens of packages long -- > list of packages to update). > > > That was my thinking. +1 > > > If you volunteer to maintain the old version as lambda-align1 > > some users might be happy. > > I'd rather use 'lambda-align2' and 'lambda-align'... due to the reasons > above. For me this is not much different than an ABI change that would > require bumping a version number. > > > PS: In any case I'd stick with the lambda-align package name for the > > new version. Otherwise we might need to wait for ftpmaster > > acceptance until after freeze and thus the latest version will > > not make it into Buster. > > IMHO I'd rather not have the newest version in buster (which was > released just a couple of days ago anyway) than breaking user pipelines. > If we're lucky then v2 may even make it through NEW until the freeze > affecting new packages which starts in about a month. > > I can maintain lambda-align 1.x for the time being -- Hannes, do you > still provide updates for the old version (I'm thinking of things like > ensuring compatibility with gcc updates, C++ standards quirks, etc.)? > > > I think this is a good idea, especially if Hannes will be providing > updates for the v1.0.x series. Yes, for the foreseeable future I will make sure that any build failures with newer compilers are addressed and also try to fix severe issues like crashes (should there be any!). > (I consider the v1.9.x series to be release candidates for v2.0) That's what they were! > Pursuant to that I split off the v2.0.0 packaging: > https://salsa.debian.org/med-team/lambda-align2 I have just had a quick look inside and for the 2.x branch I would recommend not setting: -DLAMBDA_MMAPPED_DB=ON or setting it to OFF, because I had problems with high degrees of parallelisation/vectorisation in combination with MMAP leading to very severe slowdowns (some strange contention in the OS somewhere). Also the new cmake script generates man-pages so your packaging doesn't need to do that anymore (I think in the 1.x release you generated this yourself). > Other than the lack of full test suite that we had with v1.0.x [1], I > think this is ready for sponsorship for the NEW queue. > > [1] See https://github.com/seqan/lambda/pull/121 for my (partial) > attempt at fixing that > I will definitely have a look at this this week, I really want the tests back, too. I just pushed the 2.0.0 tag because some people wanted to package it for bioconda and I did not want them to start with the old release. Best regards, Hannes -- Hannes Hauswedell Scientific staff & PhD candidate Freie Universität Berlin / Max Planck Institute for Molecular Genetics address Institut für Informatik Takustraße 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail [email protected]
