Re: python3-biopython: incompatible with muscle >= 5

2022-11-24 Thread Étienne Mollier
Hi all, Andreas Tille, on 2022-11-24: > Am Thu, Nov 24, 2022 at 06:58:04PM +0100 schrieb Étienne Mollier: > > Thanks for the upload, I further adjusted the muscle wrapper so > > it would catch the muscle3 binary if it finds it in the path, as > > I see your new package provides the executable

Re: python3-biopython: incompatible with muscle >= 5

2022-11-24 Thread Andreas Tille
Hi Étienne, Am Thu, Nov 24, 2022 at 06:58:04PM +0100 schrieb Étienne Mollier: > > Thanks for the upload, I further adjusted the muscle wrapper so > it would catch the muscle3 binary if it finds it in the path, as > I see your new package provides the executable /usr/bin/muscle3. > If no such

Re: python3-biopython: incompatible with muscle >= 5

2022-11-24 Thread Étienne Mollier
Hi Andreas, Andreas Tille, on 2022-11-24: > Am Thu, Nov 24, 2022 at 10:28:43AM +0900 schrieb Charles Plessy: > > I have read the Muscle5 paper and it is a totally different program than > > Muscle3. > > > > https://pubmed.ncbi.nlm.nih.gov/36379955/ > > > > Reintroducing muscle3 as a

Re: Race condition in uploading libmcfp

2022-11-24 Thread Andreas Tille
Hi Maarten, Am Thu, Nov 24, 2022 at 03:52:16PM +0100 schrieb Maarten L. Hekkelman: > I must learn to get my actions in the correct order, that's clear. Well, this kind of race conditions are *extremely* rare - it was really by pure chance that I stumbled upon the description and felt a need to

Re: Race condition in uploading libmcfp

2022-11-24 Thread Maarten L. Hekkelman
Hi Andreas, Op 24-11-2022 om 15:45 schreef Andreas Tille: it seems there is a race condition in uploading / pushing to git for libmcfp (1.2.2-2). I was by chance stumbling upon the short description that was broken and fixed it besides other routine-update based fixes. I think I've won with

Race condition in uploading libmcfp

2022-11-24 Thread Andreas Tille
Hi Maarten, it seems there is a race condition in uploading / pushing to git for libmcfp (1.2.2-2). I was by chance stumbling upon the short description that was broken and fixed it besides other routine-update based fixes. I think I've won with pushing to Salsa but you won on uploading which is

Re: dssp

2022-11-24 Thread Andrius Merkys
Hi Maarten, On 2022-11-24 14:01, Maarten L. Hekkelman wrote: We're getting closer to finishing all the tools that depend on libcifpp. However, there's one small issue left. I've split dssp into a library and a wrapper. Currently, I create a static library and this is used by the tool

dssp

2022-11-24 Thread Maarten L. Hekkelman
Hi, We're getting closer to finishing all the tools that depend on libcifpp. However, there's one small issue left. I've split dssp into a library and a wrapper. Currently, I create a static library and this is used by the tool tortoize. I can make this a shared library, as it is preferred

Re: Bug#1009118: Bug#1009118: python3-biopython: incompatible with muscle >= 5

2022-11-24 Thread Andreas Tille
Hi Charles, thank you for the hint. Am Thu, Nov 24, 2022 at 10:28:43AM +0900 schrieb Charles Plessy: > I have read the Muscle5 paper and it is a totally different program than > Muscle3. > > https://pubmed.ncbi.nlm.nih.gov/36379955/ > > Reintroducing muscle3 as a separate package might be

Re: [Debian-med-packaging] Bug#1009118: python3-biopython: incompatible with muscle >= 5

2022-11-24 Thread Steffen Moeller
Am 24.11.2022 um 02:28 schrieb Charles Plessy: Hello everybody, I have read the Muscle5 paper and it is a totally different program than Muscle3. https://pubmed.ncbi.nlm.nih.gov/36379955/ Reintroducing muscle3 as a separate package might be useful not only to Biopython, but also to the

Re: Help needed with python-cobra and python-pyani

2022-11-24 Thread Andrius Merkys
Hello, On 2022-11-24 06:31, Nilesh Patra wrote: python-pyani This is because python3-biopython does not vendor shared object libs for python3.11 yet $ apt-file list python3-biopython | grep '_align' ...

Re: Help needed with python-cobra and python-pyani

2022-11-24 Thread Andreas Tille
Hi Nilesh, thanks a lot for having a look. Am Thu, Nov 24, 2022 at 10:01:47AM +0530 schrieb Nilesh Patra: > On Wed, Nov 23, 2022 at 09:01:40PM +0100, Andreas Tille wrote: > > python-cobra > > It seems like that the interpreter is having trouble referencing the > name variable. I tried using