Re: catching 32/64 bit integer mixing

For open source projects, a few online static analyzers are available and usable for free. This kind of integer type mismach will be caught by most of them. Possibly clang-static-analyzer will do the job. Otherwise, an easy one is lgtm for example. See https://lgtm.com/ (I

Re: catching 32/64 bit integer mixing

. > Bug#953116 for 64 bit builds) > > Drew > > > On 2020-05-24 10:02, Drew Parsons wrote: >> Thanks Thomas, I'll pass that on. >> >> Drew >> >> >> On 2020-05-23 21:33, Thomas Schiex wrote: >>> For open source projects, a few o

Just uploaded a new upstream version for toulbar2 on salsa

Dear All, I just uploaded a new upstream version of toulbar2 on salsa. I use git-buildpackage to import the upstream tarball that uscan detected corrected. Is there anything I need to do to see if this compiles correctly? I cloned the repo on a debian:latest docker image and tried a debuild -B.

Re: Just uploaded a new upstream version for toulbar2 on salsa

I think I have put toulbar2 salsa repository in a suitable state, debuild -S works with absolutely no lintian warning and build -B does it job (just missing the signing key of course). So, I would assume it can be uploaded to unstable. Thomas

Should I do something more for toulbar2 package ?

Dear Debian-science maintainers and uploaders, As I mentioned, I have finished uploading a new version of our package (toulbar2) on salsa. I have tried to set everything up so that Debian packages (debuild) build nicely. This kind mail is just to check that I did everything needed/useful on my s

Re: New Mail list debian-ai available

Being an AI scientist, and also the "uploader" of an AI software package (toulbar2, which is not deep learning related but graphical models based), I'm curious whether the toulbar2 package should be referenced in debian-ai (no if it's only Deep Learning there). Reducing AI to Deep learning will pr

Ready to package

Hi everyone, I worked on a new upstream version of the discrete optimization package toulbar2 (currently 1.0 in unstable, testing & stable, upstream is 1.1). The current git salsa repository at https://salsa.debian.org/science-team/toulbar2 is hopefully ready to move to unstable: git clon

Sponsoring before freeze

Dear Anton, I have tried to prepare toulbar2 with a new upstream version. If something is missing I'm happy to inject extra effort in it. Thomas

Re: Sponsoring before freeze

Dear Anton, Thanks a lot for the final commits (just looked into them). I will be looking into autopkgtest. I understand it provides something similar to "travis/ci" which we use on our upstream repo. There is a new upstream version of toulbar2 that popped up in the mean time. I will try to allo

Re: Sponsoring before freeze

Dear Anton, I pushed the new upstream version of toulbar2. I'm now wondering what autopkgtest would be useful for. When you build the package, the dh_auto_test target does launch our ctest target. So the tests are run anyway for all builds. What does autopkgtest would bring then? Also, if someon

Re: Sponsoring before freeze

Thanks Drew. Following a quick exchange with Anton Gladky, it looked that the current ctest tests (already executed at package compilation upon "make test") are sufficient given that toulbar2 is not (debian distributed as) a library. It may become so in the future however, and then we will look i

toulbar2 UNRELEASED

Dear Anton (and dear Debian Scientists), I noticed toulbar2 is "UNRELEASED" (noticed this following the link below):     https://tracker.debian.org/pkg/toulbar2     UNREL: VCS matches the version in the archive, but the VCS changelog is UNRELEASED. The uploader should update the changelog and ta

Re: Quick Poll: Debian to better support hardware acceleration?

I'm a computer scientist working in AI and structural biology. I'm sorry to say that CUDA has slowly invaded a lot of our scientific pipelines, for Deep learning, convex optimization and molecular simulations. I just could not vote for option 2 even if option 1 is tolerable (I'm using it). L

Some help to finish packaging toulbar2

Dear Debian-Science maintainers, I have uploaded a new version of toulbar2 (https://salsa.debian.org/science-team/toulbar2) but I'm facing two issues: 1. when I try a debuild -B (on bookworm) after cloning and installing build dependencies, the toulbar2 binary package builds fine, but not

toulbar2 package: Ready for release?

Dear Debian-science maintainers, Dear Nilesh, I have solved all the errors I had for packaging toulbar2 (https://salsa.debian.org/science-team/toulbar2), now tested on sid. The remaining "privacy-breach-generic" warnings are all false-positive. I would say it's ready for release. Please have

How can I join debian-science ?

Dear Andreas, On my quest to upload toulbar2 to debian-science, and following the debian science policy document, I have registered on alioth and asked to join the debian-science project but got no feedback. Could it be that I missed some step ? Any guidance will be welcome (alioth seems to be d

Sponsorship request for toulbar2 posted

Dear all, A short note to inform you that, following the kind guidance of Jerome Benoit, a git repository has been created for our exact discrete graphical model optimization software, toulbar2, here: https://anonscm.debian.org/cgit/debian-science/packages/toulbar2.git A request for sponsorshi

Re: Please use Git repository layout as described in Debian Science policy

Dear Andreas When I run the lintian command with a -I to get informational messages and on both the binary and source changes files, I still miss a significant subset of the messages and more precisely these ones: >> I: toulbar2 source: vcs-field-uses-insecure-uri vcs-git >> git://anonscm.debian

toulbar2: another try ?

Dear Andreas, Gianfranco I used some free time to try to kill all issues. There is a brand new toulbar2.git repository on alioth. I list all the things I did below. First Andreas: > $ lintian toulbar2_0.9.8-1_amd64.changes > I: toulbar2 source: vcs-field-uses-insecure-uri vcs-git > git://anons

Re: toulbar2: another try ?

Oops. I had forgotten to include the debian directory. This is now corrected. Thomas

RFS for toulbar2

Dear all, Anything we could do now to facilitate sponsorship for toulbar2 at https://anonscm.debian.org/cgit/debian-science/packages/toulbar2.git/ Kind regards, Thomas

Re: RFS for toulbar2

Thanks again Andreas for filling in the missing steps. Found very decent debian wiki doc on watch files and uscan. Watch file added (and uscan tested: should be Ok, says it's happy). Thomas Le 04/05/16 15:21, Andreas Tille a écrit : > Please provide a watch file for the package. It looks hard

toulbar2: a last try ?

Dear Andreas, Dear Gianfranco, Quick feedback on your comments: > > On Fri, May 06, 2016 at 10:43:08AM +, Gianfranco Costamagna wrote: >> there is an extra space in VCS-fields, triggering a lintian warning Andreas took care of this for me (thanks). W: toulbar2-dbgsym: debug-file-with-

Re: Please categorise your packages for the Debian Science metapackages

Agreed. This is very weird from a Debian user point of view. Astronomy is not Science ? Thomas > I realised that the astronomy task fully vanished from Debian Science > since now there is a Debian Astro Blend. IMHO it makes sense to > consider at least a task that sumarises all Debian Astro met

Re: Please categorise your packages for the Debian Science metapackages (second iteration)

Dear Andreas, I would have been happy to do the job directly but I currently do not have access to a running debian machine I can "control" (have devscripts installed) and I lack time/HD space for a VM install. It perhaps could make sense to have it on alioth? (no troll intended - if it can be cat

Re: Please categorise your packages for the Debian Science metapackages (second iteration)

Andreas, >> I'm sorry,[..] You just need Git to download >> the repository and the repository has 5MB. :-P >> The repositories are on alioth. You can also >> perfectly login to Alioth and clone + commit + push. Sorry, I'm showing off my mediocre knowledge of debian(science) organization. I just

Looking for feedback on a recent upload

Dear All, As a developer and the maintainer of toulbar2 in debian-science (https://salsa.debian.org/science-team/toulbar2), I uploaded a new major release to salsa yesterday. I used a pure "git repo" approach (https://wiki.debian.org/PackagingWithGit#Using_the_upstream_repo) which is easy and feas

Re: Looking for feedback on a recent upload

Dear Lumin, I hope is still do not disturb. I'm coming back to you for one more advice. Here is point by point list of what I did with one question: > I indeed spotted something that doesn't match the debian-science > conventions: > > 1. Git repository layout in question > >File debian/sourc

Re: Looking for feedback on a recent upload

list: Le 03/07/2018 à 11:59, Andreas Tille a écrit : > Hi Thomas, > > On Tue, Jul 03, 2018 at 10:18:19AM +0200, Thomas Schiex wrote: >> Thanks a lot, the uscan worked fine!  Excited with this, I did this: >> >> - I integrated your commit in our upstream git repo (w

Re: Rasmol needs severe contribution to stay in Debian

People used to rasmol interface will likely prefer rasmol over X (pymol, viewmol, I like qutemol too for rendering..). For these users, it will take some time before rasmol becomes obsoleted by pymol or more recent WebGL based molecular viewers such as NGL (MIT licence, http://nglviewer.org/ngl/ga

How to handle a change in "Files-Excluded:" with gbp

Hello everyone, I'm trying to polish the packaging for toulbar2 on salsa and I would like to remove a file from upstream (a doc that is included there and regenerated from source during compilation).This is to avoid a lintian "source-contains-prebuilt-doxygen-documentation". Some files are alread

Re: How to handle a change in "Files-Excluded:" with gbp

Thanks Aaron, I should have thought about this :-) I did and I now have 3 less lintian warnings, and I will push to salsa. However now that I have improved documentation installation, I have a new lintian flag that pops up: I: toulbar2: arch-dep-package-has-big-usr-share 4967kB 67% Is it tolera

Re: How to handle a change in "Files-Excluded:" with gbp

Thanks Aaron, I did as advised and everything seems to be working properly. I now have 2 packages, with proper contents (well, I still need to compress examples). Will come back when everything looks fine to me. Thomas >> I: toulbar2: arch-dep-package-has-big-usr-share 4967kB 67% >> Is it tolera

Re: How to handle a change in "Files-Excluded:" with gbp

Hello Aaron, hello everyone ! I have reached a state for the toulbar2 repo that is close to satisfy me. It generates two deb files (a binary and a doc package), the documentation is now decent and the examples are compressed in .txz. I'm still surprised by one lintian -EviI --pedantic message:  

Re: How to handle a change in "Files-Excluded:" with gbp

> Good question; I'm surprised -v doesn't say. Does adding --debug help? It just gives a directory: doc/ but it contains several doc files and I thought I had removed the culprit (the doxygen doc of toulbar2). The --debug variant does help however. N: Running check: cruft on source:toulbar2/1.0.

toulbar2 packaging

Hello Aaron, hello everyone, The doc installation for toulbar2  is now managed by dh_installdocs.gbp buildpackage builds the 2 packages (toulbar2 and toulbar2-doc). They seem to have proper contents (debc checked). I just pushed everything to salsa and would be happy if someone could give it a lo

Re: toulbar2 packaging

of advice and the guidance. Thomas Le 10/08/2018 à 17:02, Aaron M. Ucko a écrit : > Thomas Schiex writes: > >> I just pushed everything to salsa and would be happy if someone could >> give it a look and possibly bless it :-) > The master branch looks to be in good shape no

Re: toulbar2 packaging

Hello Aaron, Andreas, everyone, Aaron M. Ucko wrote: > - There is a file named clean in the top-level directory, throwing make > off. You can unconfuse it by adding the following lines (at minimum) > to debian/rules: > > .PHONY: clean > clean: > dh clean Yep. Done. > - The build process

Re: toulbar2 packaging

Thanks Aaron ! Thomas Le 13/08/2018 à 05:42, Aaron M. Ucko a écrit : > Anyway, sponsored and pushed. (I merely added a formal changelog update > and a Debian release tag.)

Re: toulbar2 packaging

Dear Aaron, After reading https://manpages.debian.org/unstable/dpkg-dev/deb-changelog.5.en.html, it appears I used an improper syntax for "bug closing" in the debian/changelog. I edited the the debian/changelog on salsa and pushed (https://salsa.debian.org/science-team/toulbar2). This was appare

Re: toulbar2 packaging

Thanks Aaron ! It's so good when issues end up being simpler to solve than expected :-) Le 24/09/2018 à 22:01, Aaron M. Ucko a écrit : > Thomas Schiex writes: >> it appears I used an improper syntax for "bug closing" in the >> debian/changelog. > The syntax yo

Re: Nonlinear integer optimization in python?

Dear Kingsley, The description of your optimization problem is probably too flexible to answer definitely but I'm the maintainer of a package (toulbar2) that is targeted at solving optimization problems over discrete variables with a decomposable criteria (the criteria is a sum of functions, each

Re: Nonlinear integer optimization in python?

I forgot to mention that toulbar2 has a python interface through "numberjack" (https://github.com/eomahony/Numberjack) but is also usable directly from python as a C++ library using ctypes python interface (an example of use bu cimputer vision persons being available here https://github.com/vislear

Package not compiling anymore because of a likely texlive issue

Dear all, the package toulbar2 has problem compiling. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=920459 It took some time to pin down the issue precisely but this seems to be an issue in the last texlive release. The release 2018.20190131 seems to break the latex package "tabu" which is u