Étienne Mollier pushed to branch master at Debian Med / tree-puzzle
Commits: c52f46f4 by Étienne Mollier at 2024-11-09T18:30:41+01:00 preserve-artifacts.patch: new: restore some test artifacts. This is necessary to bring autopkgtest support back into working conditions. - - - - - 2d94e283 by Étienne Mollier at 2024-11-09T18:31:40+01:00 d/control: migrate to mpi-default-*. Closes: #1086907 - - - - - 008c3484 by Étienne Mollier at 2024-11-09T18:36:22+01:00 d/patches/*: normalize Last-Update timestamp. - - - - - 1fd32430 by Étienne Mollier at 2024-11-09T18:37:54+01:00 Patch fix-conftest.c renamed fix-conftest.patch. This unconfuses syntax highlighting, and file name. - - - - - fe3d984c by Étienne Mollier at 2024-11-09T18:48:44+01:00 d/changelog: ready for team upload to unstable. There are transient lintian RPATH errors caused by openmpi at the moment. If necessary, they can be fixed by doing a source only upload once the fixed openmpi version will make it to unstable. In the meantime we may live with them. - - - - - 9 changed files: - debian/changelog - debian/control - debian/patches/fix-conftest.c → debian/patches/fix-conftest.patch - + debian/patches/preserve-artifacts.patch - debian/patches/series - debian/patches/spelling.patch - debian/patches/tests-need-bash.patch - debian/patches/update_test_results.patch - debian/patches/use_debian_packaged_sprng.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +tree-puzzle (5.3~rc16+dfsg-12) unstable; urgency=medium + + * Team upload. + * preserve-artifacts.patch: new: restore some test artifacts. + This is necessary to bring autopkgtest support back into working + conditions. + * d/control: migrate to mpi-default-*. (Closes: #1086907) + * d/patches/*: normalize Last-Update timestamp. + * Patch fix-conftest.c renamed fix-conftest.patch. + This unconfuses syntax highlighting, and file name. + + -- Étienne Mollier <[email protected]> Sat, 09 Nov 2024 18:44:04 +0100 + tree-puzzle (5.3~rc16+dfsg-11) unstable; urgency=medium * Don't install output generated by tests because of nondeterminism. ===================================== debian/control ===================================== @@ -5,7 +5,7 @@ Uploaders: Andreas Tille <[email protected]>, Section: science Priority: optional Build-Depends: debhelper-compat (= 13), - libopenmpi-dev, + mpi-default-dev, libsprng2-dev Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/tree-puzzle @@ -36,7 +36,7 @@ Package: tree-ppuzzle Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends}, - openmpi-bin + mpi-default-bin Recommends: tree-puzzle-doc Suggests: phylip, treetool ===================================== debian/patches/fix-conftest.c → debian/patches/fix-conftest.patch ===================================== ===================================== debian/patches/preserve-artifacts.patch ===================================== @@ -0,0 +1,25 @@ +Description: preserve some of the test artifacts. + These artifacts are necessary to be able to run the test suite outside + the context of tree-puzzle source code, i.e. in autopkgtest context. + These test started to fail when running the clean target of the tests + directory, so this patch is an attempt to keep useful files while + keeping at bay unnecessary bloat, potentially introducing + non-deterministic data in resulting binary packages. + . + This change fixes a Debian specificity and would probably not be + welcome upstream, hence forwarding not needed. +Author: Étienne Mollier <[email protected]> +Forwarded: not-needed +Last-Update: 2024-11-09 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- tree-puzzle.orig/tests/Makefile.am ++++ tree-puzzle/tests/Makefile.am +@@ -85,7 +85,5 @@ + done + + clean: +- rm -f *.param +- rm -f *.nucl *.prot *.bin *.trees *.ctrees + rm -f *.nucl.* *.prot.* *.bin.* *.trees.* *.ctrees.* + ===================================== debian/patches/series ===================================== @@ -6,4 +6,5 @@ update_test_results.patch reproducible-build.patch reduce_decimals_for_testing.patch add-failsafe-for-ut-prottest.patch -fix-conftest.c +fix-conftest.patch +preserve-artifacts.patch ===================================== debian/patches/spelling.patch ===================================== @@ -1,6 +1,6 @@ Description: Fix some spelling issues Author: Andreas Tille <[email protected]> -Last-Update: Tue, 16 Oct 2018 10:51:06 +0200 +Last-Update: 2018-10-16 --- a/src/ml2.c +++ b/src/ml2.c ===================================== debian/patches/tests-need-bash.patch ===================================== @@ -1,5 +1,5 @@ Author: Andreas Tille <[email protected]> -Last-Update: Wed, 25 Nov 2015 13:10:19 +0100 +Last-Update: 2015-11-25 Description: Tests are using bash syntax so declare this on top --- a/tests/build-puzzle ===================================== debian/patches/update_test_results.patch ===================================== @@ -1,5 +1,5 @@ Author: Pranav Ballaney <[email protected]> -Last-Update: 2020-05-14 02:52:25 +0530 +Last-Update: 2020-05-14 Description: Test results to compare with are just wrong as discussed with upstream See https://lists.debian.org/debian-med/2020/05/msg00118.html ===================================== debian/patches/use_debian_packaged_sprng.patch ===================================== @@ -1,6 +1,6 @@ Description: Use Debian packaged libsprng Author: Andreas Tille <[email protected]> -Last-Update: Mon, 08 Jul 2019 16:47:12 +0200 +Last-Update: 2019-07-08 ATTENTION: Please double check the change in src/util.c. The Debian packaged sprng seems to have a different interface for init_sprng (quoting from CHANGES.TEXT): View it on GitLab: https://salsa.debian.org/med-team/tree-puzzle/-/compare/e52253af56d81b733de0c712902cabaaf1b55350...fe3d984cc533005b649ea8deec44292af201157a -- View it on GitLab: https://salsa.debian.org/med-team/tree-puzzle/-/compare/e52253af56d81b733de0c712902cabaaf1b55350...fe3d984cc533005b649ea8deec44292af201157a You're receiving this email because of your account on salsa.debian.org.
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