[med-svn] [Git][med-team/tree-puzzle][master] 5 commits: preserve-artifacts.patch: new: restore some test artifacts.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Nov 9 17:50:26 GMT 2024
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 <emollier at debian.org> 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 <tille at debian.org>,
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 <emollier at debian.org>
+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 <tille at debian.org>
-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 <tille at debian.org>
-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 <ballaneypranav at gmail.com>
-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 <tille at debian.org>
-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
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