[med-svn] [Git][med-team/libmuscle][master] 12 commits: update changelog

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Sun Jul 14 16:54:46 BST 2024



Étienne Mollier pushed to branch master at Debian Med / libmuscle


Commits:
de88d4ee by Étienne Mollier at 2024-07-14T16:55:26+02:00
update changelog

Balint Reczey's change notably fixed gcc 14 bug ahead of time.
Thank you!

- - - - -
6b6351a4 by Étienne Mollier at 2024-07-14T17:04:50+02:00
d/libmuscle1.symbols: mark symbols trimmed by LTO builds as optional.

Closes: #1015504

- - - - -
5666b96e by Étienne Mollier at 2024-07-14T17:05:33+02:00
d/rules: force LTO builds.

This is done after ensuring all reverse dependencies are still
operating properly; there were a couple of dubious Muscle symbols
trimmed by LTO builds, but C++ inflation of intricate symbols makes it
hard to make sense whether symbols drop is harmful or not.

- - - - -
d28177f1 by Étienne Mollier at 2024-07-14T17:08:04+02:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
7e1aaf47 by Étienne Mollier at 2024-07-14T17:09:38+02:00
d/control: add myself to uploaders.

- - - - -
4824aa46 by Étienne Mollier at 2024-07-14T17:10:07+02:00
update changelog in prevision of merge of missing revision -7.

- - - - -
ae36de3f by Andreas Tille at 2024-07-14T17:16:03+02:00
Import Debian changes 3.7+4565-7

libmuscle (3.7+4565-7) unstable; urgency=medium
.
  * Standards-Version: 4.5.0 (routine-update)
  * debhelper-compat 13 (routine-update)
  * Secure URI in copyright format (routine-update)
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Trim trailing whitespace.
  * Remove *.la file and usr/bin/muscle to enable dh_missing --fail-missing
  * Fix lintian override

- - - - -
c57affbf by Étienne Mollier at 2024-07-14T17:17:43+02:00
Merge branch 'debian/revision-7'

- - - - -
f13de23b by Étienne Mollier at 2024-07-14T17:21:59+02:00
d/control: migrate from pkg-config to pkgconf.

- - - - -
4866648d by Étienne Mollier at 2024-07-14T17:23:03+02:00
d/libmuscle1.lintian-overrides: delete: unused override.

- - - - -
fb8942c7 by Étienne Mollier at 2024-07-14T17:24:09+02:00
d/libmuscle1.symbols: append missing Build-Depends-Package field.

- - - - -
e0f2a5bd by Étienne Mollier at 2024-07-14T17:53:38+02:00
ready to upload to unstable.

- - - - -


8 changed files:

- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- − debian/libmuscle1.lintian-overrides
- debian/libmuscle1.symbols
- debian/rules
- + debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,41 @@
+libmuscle (3.7+4565-8) unstable; urgency=medium
+
+  [ Steffen Möller ]
+  * Add new file with ref to conda
+
+  [ Balint Reczey ]
+  * debian/libmuscle1.symbols: Mark symbols which were optimized away on
+    s390x as optional (Closes: #1075190)
+
+  [ Étienne Mollier ]
+  * d/libmuscle1.symbols: mark symbols trimmed by LTO builds as optional.
+    (Closes: #1015504)
+  * d/rules: force LTO builds.
+    This is done after ensuring all reverse dependencies are still
+    operating properly; there were a couple of dubious Muscle symbols
+    trimmed by LTO builds, but C++ inflation of intricate symbols makes it
+    hard to make sense whether symbols drop is harmful or not.
+  * d/control: declare compliance to standards version 4.7.0.
+  * d/control: add myself to uploaders.
+  * d/control: migrate from pkg-config to pkgconf.
+  * d/libmuscle1.lintian-overrides: delete: unused override.
+  * d/libmuscle1.symbols: append missing Build-Depends-Package field.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 14 Jul 2024 17:53:17 +0200
+
+libmuscle (3.7+4565-7) unstable; urgency=medium
+
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Secure URI in copyright format (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Trim trailing whitespace.
+  * Remove *.la file and usr/bin/muscle to enable dh_missing --fail-missing
+  * Fix lintian override
+
+ -- Andreas Tille <tille at debian.org>  Mon, 16 Nov 2020 20:06:36 +0100
+
 libmuscle (3.7+4565-6) unstable; urgency=medium
 
   [ Adrian Bunk ]


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -1,15 +1,17 @@
 Source: libmuscle
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
                d-shlibs,
-               pkg-config
-Standards-Version: 4.1.5
+               pkgconf
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/libmuscle
 Vcs-Git: https://salsa.debian.org/med-team/libmuscle.git
 Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/muscle/trunk/
+Rules-Requires-Root: no
 
 Package: libmuscle-dev
 Architecture: any


=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: libMuscle
 Upstream-Contact: Aaron Darling <darling at cs.wisc.edu>
 Source: http://sourceforge.net/p/mauve/code/HEAD/tree/muscle/trunk/


=====================================
debian/libmuscle1.lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# No idea where this error comes from - there is no such symbol in the symbols file neither does any symbol feature a debian revision
-libmuscle1: symbols-file-contains-current-version-with-debian-revision on symbol _ZNSt6vectorIcSaIcEE7reserveEm at Base


=====================================
debian/libmuscle1.symbols
=====================================
@@ -1,11 +1,12 @@
 libMUSCLE.so.1 libmuscle1 #MINVER#
+* Build-Depends-Package: libmuscle-dev
  _ZN6muscle10ALPHAToStrENS_5ALPHAE at Base 3.7+4565
  _ZN6muscle10ALPHA_OptsE at Base 3.7+4565
- _ZN6muscle10ClustSetDF11ComputeDistERKNS_5ClustEjj at Base 3.7+4565
- _ZN6muscle10ClustSetDF11GetLeafNameEj at Base 3.7+4565
- _ZN6muscle10ClustSetDF12GetLeafCountEv at Base 3.7+4565
- _ZN6muscle10ClustSetDF9GetLeafIdEj at Base 3.7+4565
- _ZN6muscle10ClustSetDF9JoinNodesERKNS_5ClustEjjjPdS4_ at Base 3.7+4565
+ (optional)_ZN6muscle10ClustSetDF11ComputeDistERKNS_5ClustEjj at Base 3.7+4565
+ (optional)_ZN6muscle10ClustSetDF11GetLeafNameEj at Base 3.7+4565
+ (optional)_ZN6muscle10ClustSetDF12GetLeafCountEv at Base 3.7+4565
+ (optional)_ZN6muscle10ClustSetDF9GetLeafIdEj at Base 3.7+4565
+ (optional)_ZN6muscle10ClustSetDF9JoinNodesERKNS_5ClustEjjjPdS4_ at Base 3.7+4565
  _ZN6muscle10CountKmersEPKhjPh at Base 3.7+4565
  _ZN6muscle10DiffTreesEERKNS_4TreeES2_Pj at Base 3.7+4565
  _ZN6muscle10DistCalcDF4InitERKNS_8DistFuncE at Base 3.7+4565
@@ -49,11 +50,11 @@ libMUSCLE.so.1 libmuscle1 #MINVER#
  _ZN6muscle11AlignSubFamERNS_7SeqVectERKNS_4TreeEjRNS_3MSAE at Base 3.7+4565
  _ZN6muscle11AssertMSAEqERKNS_3MSAES2_ at Base 3.7+4565
  _ZN6muscle11CheckMemUseEv at Base 3.7+4565
- _ZN6muscle11ClustSetMSA11ComputeDistERKNS_5ClustEjj at Base 3.7+4565
- _ZN6muscle11ClustSetMSA11GetLeafNameEj at Base 3.7+4565
- _ZN6muscle11ClustSetMSA12GetLeafCountEv at Base 3.7+4565
- _ZN6muscle11ClustSetMSA9GetLeafIdEj at Base 3.7+4565
- _ZN6muscle11ClustSetMSA9JoinNodesERKNS_5ClustEjjjPdS4_ at Base 3.7+4565
+ (optional)_ZN6muscle11ClustSetMSA11ComputeDistERKNS_5ClustEjj at Base 3.7+4565
+ (optional)_ZN6muscle11ClustSetMSA11GetLeafNameEj at Base 3.7+4565
+ (optional)_ZN6muscle11ClustSetMSA12GetLeafCountEv at Base 3.7+4565
+ (optional)_ZN6muscle11ClustSetMSA9GetLeafIdEj at Base 3.7+4565
+ (optional)_ZN6muscle11ClustSetMSA9JoinNodesERKNS_5ClustEjjjPdS4_ at Base 3.7+4565
  _ZN6muscle11ClusterTree14AddToDisjointsEPNS_11ClusterNodeE at Base 3.7+4565
  _ZN6muscle11ClusterTree19DeleteFromDisjointsEPNS_11ClusterNodeE at Base 3.7+4565
  _ZN6muscle11ClusterTree6CreateERKNS_8DistFuncE at Base 3.7+4565
@@ -402,9 +403,9 @@ libMUSCLE.so.1 libmuscle1 #MINVER#
  _ZN6muscle3Seq7ToUpperEv at Base 3.7+4565
  _ZN6muscle3Seq8FixAlphaEv at Base 3.7+4565
  _ZN6muscle3Seq9StripGapsEv at Base 3.7+4565
- _ZN6muscle3SeqD0Ev at Base 3.7+4565
- _ZN6muscle3SeqD1Ev at Base 3.7+4565
- _ZN6muscle3SeqD2Ev at Base 3.7+4565
+ (optional)_ZN6muscle3SeqD0Ev at Base 3.7+4565
+ (optional)_ZN6muscle3SeqD1Ev at Base 3.7+4565
+ (optional)_ZN6muscle3SeqD2Ev at Base 3.7+4565
  _ZN6muscle3lp2Ed at Base 3.7+4565
  _ZN6muscle4BTEqEdd at Base 3.7+4565
  _ZN6muscle4DoSPEv at Base 3.7+4565
@@ -424,16 +425,16 @@ libMUSCLE.so.1 libmuscle1 #MINVER#
  _ZN6muscle4Tree16RootUnrootedTreeENS_4ROOTE at Base 3.7+4565
  _ZN6muscle4Tree20UnrootByDeletingRootEv at Base 3.7+4565
  _ZN6muscle4Tree4CopyERKS0_ at Base 3.7+4565
- _ZN6muscle4Tree5ClearEv at Base 3.7+4565
+ (optional)_ZN6muscle4Tree5ClearEv at Base 3.7+4565
  _ZN6muscle4Tree6CreateEjjPKjS2_PKfS4_S2_PPc at Base 3.7+4565
  _ZN6muscle4Tree8FromFileERNS_8TextFileE at Base 3.7+4565
  _ZN6muscle4Tree9FromClustERNS_5ClustE at Base 3.7+4565
  _ZN6muscle4Tree9InitCacheEj at Base 3.7+4565
  _ZN6muscle4Tree9PruneTreeERKS0_Pjj at Base 3.7+4565
  _ZN6muscle4Tree9SetLeafIdEjj at Base 3.7+4565
- _ZN6muscle4TreeD0Ev at Base 3.7+4565
- _ZN6muscle4TreeD1Ev at Base 3.7+4565
- _ZN6muscle4TreeD2Ev at Base 3.7+4565
+ (optional)_ZN6muscle4TreeD0Ev at Base 3.7+4565
+ (optional)_ZN6muscle4TreeD1Ev at Base 3.7+4565
+ (optional)_ZN6muscle4TreeD2Ev at Base 3.7+4565
  _ZN6muscle4log2Ed at Base 3.7+4565
  _ZN6muscle4pow2Ed at Base 3.7+4565
  _ZN6muscle5BreakEv at Base 3.7+4565
@@ -683,10 +684,10 @@ libMUSCLE.so.1 libmuscle1 #MINVER#
  _ZNK6muscle11DistCalcMSA8GetCountEv at Base 3.7+4565
  _ZNK6muscle12DPRegionList5LogMeEv at Base 3.7+4565
  _ZNK6muscle12DPRegionList9GetDPAreaEv at Base 3.7+4565
- _ZNK6muscle12DistCalcTest13CalcDistRangeEjPf at Base 3.7+4565
- _ZNK6muscle12DistCalcTest5GetIdEj at Base 3.7+4565
- _ZNK6muscle12DistCalcTest7GetNameEj at Base 3.7+4565
- _ZNK6muscle12DistCalcTest8GetCountEv at Base 3.7+4565
+ (optional)_ZNK6muscle12DistCalcTest13CalcDistRangeEjPf at Base 3.7+4565
+ (optional)_ZNK6muscle12DistCalcTest5GetIdEj at Base 3.7+4565
+ (optional)_ZNK6muscle12DistCalcTest7GetNameEj at Base 3.7+4565
+ (optional)_ZNK6muscle12DistCalcTest8GetCountEv at Base 3.7+4565
  _ZNK6muscle12ScoreHistory5LogMeEv at Base 3.7+4565
  _ZNK6muscle12ScoreHistory8GetScoreEjjbb at Base 3.7+4565
  _ZNK6muscle3MSA10GetAvgConsEv at Base 3.7+4565
@@ -843,15 +844,15 @@ libMUSCLE.so.1 libmuscle1 #MINVER#
  (optional)_ZNSt6vectorIcSaIcEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPcS1_EE at Base 3.7+4565
  (arch-bits=32)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 3.7+4565
  (optional)_ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 3.7+4565
- _ZTIN6muscle10ClustSetDFE at Base 3.7+4565
+ (optional)_ZTIN6muscle10ClustSetDFE at Base 3.7+4565
  _ZTIN6muscle10DistCalcDFE at Base 3.7+4565
- _ZTIN6muscle11ClustSetMSAE at Base 3.7+4565
+ (optional)_ZTIN6muscle11ClustSetMSAE at Base 3.7+4565
  _ZTIN6muscle11ClusterTreeE at Base 3.7+4565
  _ZTIN6muscle11DistCalcMSAE at Base 3.7+4565
- _ZTIN6muscle12DistCalcTestE at Base 3.7+4565
+ (optional)_ZTIN6muscle12DistCalcTestE at Base 3.7+4565
  _ZTIN6muscle3MSAE at Base 3.7+4565
- _ZTIN6muscle3SeqE at Base 3.7+4565
- _ZTIN6muscle4TreeE at Base 3.7+4565
+ (optional)_ZTIN6muscle3SeqE at Base 3.7+4565
+ (optional)_ZTIN6muscle4TreeE at Base 3.7+4565
  _ZTIN6muscle5ClustE at Base 3.7+4565
  _ZTIN6muscle6PWPathE at Base 3.7+4565
  _ZTIN6muscle7SeqVectE at Base 3.7+4565
@@ -885,15 +886,15 @@ libMUSCLE.so.1 libmuscle1 #MINVER#
  _ZTSSt12_Vector_baseIcSaIcEE at Base 3.7+4565
  _ZTSSt6vectorIPN6muscle3SeqESaIS2_EE at Base 3.7+4565
  _ZTSSt6vectorIcSaIcEE at Base 3.7+4565
- _ZTVN6muscle10ClustSetDFE at Base 3.7+4565
+ (optional)_ZTVN6muscle10ClustSetDFE at Base 3.7+4565
  _ZTVN6muscle10DistCalcDFE at Base 3.7+4565
- _ZTVN6muscle11ClustSetMSAE at Base 3.7+4565
+ (optional)_ZTVN6muscle11ClustSetMSAE at Base 3.7+4565
  _ZTVN6muscle11ClusterTreeE at Base 3.7+4565
  _ZTVN6muscle11DistCalcMSAE at Base 3.7+4565
- _ZTVN6muscle12DistCalcTestE at Base 3.7+4565
+ (optional)_ZTVN6muscle12DistCalcTestE at Base 3.7+4565
  _ZTVN6muscle3MSAE at Base 3.7+4565
- _ZTVN6muscle3SeqE at Base 3.7+4565
- _ZTVN6muscle4TreeE at Base 3.7+4565
+ (optional)_ZTVN6muscle3SeqE at Base 3.7+4565
+ (optional)_ZTVN6muscle4TreeE at Base 3.7+4565
  _ZTVN6muscle5ClustE at Base 3.7+4565
  _ZTVN6muscle6PWPathE at Base 3.7+4565
  _ZTVN6muscle7SeqVectE at Base 3.7+4565


=====================================
debian/rules
=====================================
@@ -1,6 +1,6 @@
 #!/usr/bin/make -f
 
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all optimize=+lto
 
 %:
 	dh $@
@@ -15,10 +15,12 @@ override_dh_install:
 		    --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
 		    debian/tmp/usr/lib/*/*.so
 	dh_link	-plibmuscle1 usr/lib/$(DEB_HOST_MULTIARCH)/libMUSCLE.so.1 usr/lib/$(DEB_HOST_MULTIARCH)/libMUSCLE-3.7.so.1
+	find debian -name "lib*.la" -delete
+	# The binary is taken rather from the package muscle
+	rm -rf debian/tmp/usr/bin/muscle
 
 #override_dh_auto_test:
 #	echo 'Disable test since some header (gnDNXSource.h) seems to be missing.'
 
 get-orig-source:
 	. debian/get-orig-source
-


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml



View it on GitLab: https://salsa.debian.org/med-team/libmuscle/-/compare/397dd4bc3f583a1a149e9dc169d128eeaa7497ed...e0f2a5bd1c0281f769bccfb5cdea3c6e80efa313

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