[med-svn] [Git][med-team/sift][master] 14 commits: Cleanup changelog
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Jan 9 16:42:49 GMT 2025
Andreas Tille pushed to branch master at Debian Med / sift
Commits:
8a1645c8 by Andreas Tille at 2025-01-09T17:16:01+01:00
Cleanup changelog
- - - - -
48009de0 by Andreas Tille at 2025-01-09T17:18:19+01:00
* Fix watch file
* Fix Vcs fields
- - - - -
fb655322 by Andreas Tille at 2025-01-09T17:19:16+01:00
Standards-Version: 4.7.0 (routine-update)
- - - - -
b7eac8dc by Andreas Tille at 2025-01-09T17:19:16+01:00
debhelper-compat 13 (routine-update)
- - - - -
be6f5ad0 by Andreas Tille at 2025-01-09T17:19:19+01:00
Drop useless get-orig-source target (routine-update)
- - - - -
5cb02e77 by Andreas Tille at 2025-01-09T17:19:19+01:00
Remove trailing whitespace in debian/changelog (routine-update)
- - - - -
14e0ee00 by Andreas Tille at 2025-01-09T17:19:19+01:00
Remove trailing whitespace in debian/rules (routine-update)
- - - - -
79ce50fa by Andreas Tille at 2025-01-09T17:19:19+01:00
No tab in license text (routine-update)
- - - - -
87a97524 by Andreas Tille at 2025-01-09T16:19:20+00:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
9d27e2a3 by Andreas Tille at 2025-01-09T16:19:21+00:00
Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
7224ad69 by Andreas Tille at 2025-01-09T16:19:21+00:00
Update renamed lintian tag names in lintian overrides.
Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html
- - - - -
c0536bf3 by Andreas Tille at 2025-01-09T16:19:22+00:00
Avoid explicitly specifying -Wl,--as-needed linker flag.
Changes-By: lintian-brush
Fixes: lintian: debian-rules-uses-as-needed-linker-flag
See-also: https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html
- - - - -
5478b988 by Andreas Tille at 2025-01-09T17:25:57+01:00
Formatting changelog
- - - - -
52d57b21 by Andreas Tille at 2025-01-09T17:42:26+01:00
Enable Salsa CI to pick packages from non-free
- - - - -
8 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/rules
- debian/salsa-ci.yml
- debian/source/lintian-overrides
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,18 +1,28 @@
-sift (6.2.1-1) unstable; urgency=medium
+sift (6.2.1-1) UNRELEASED; urgency=medium
+ [ Steffen Moeller ]
* Team upload.
* New upstream version.
-
- -- Steffen Moeller <moeller at debian.org> Thu, 12 Jul 2018 12:54:01 +0200
-
-sift (4.0.3b-7) UNRELEASED; urgency=medium
-
* d/u/metadata:
- added RRIDs
- yamllint clean
- -- Steffen Moeller <moeller at debian.org> Thu, 29 Mar 2018 14:27:26 +0200
+ [ Andreas Tille ]
+ * Fix watch file
+ * Fix Vcs fields
+ * Standards-Version: 4.7.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Drop useless get-orig-source target (routine-update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+ * Remove trailing whitespace in debian/rules (routine-update)
+ * No tab in license text (routine-update)
+ * Trim trailing whitespace.
+ * Use secure URI in Homepage field.
+ * Update renamed lintian tag names in lintian overrides.
+ * Avoid explicitly specifying -Wl,--as-needed linker flag.
+
+ -- Andreas Tille <tille at debian.org> Thu, 09 Jan 2025 17:42:02 +0100
sift (4.0.3b-6) unstable; urgency=medium
@@ -47,7 +57,7 @@ sift (4.0.3b-4) unstable; urgency=low
sift (4.0.3b-3ubuntu1) quantal; urgency=low
- * Merge with Debian unstable. Remaining changes:
+ * Merge with Debian unstable. Remaining changes:
- Update patches/debian/ld-as-needed:
Move libs from LDFLAGS to LIBS.
@@ -71,4 +81,3 @@ sift (4.0.3b-1) unstable; urgency=low
* Initial release (Closes: #660272)
-- Laszlo Kajan <lkajan at rostlab.org> Thu, 23 Feb 2012 18:55:23 +0100
-
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-10
=====================================
debian/control
=====================================
@@ -4,12 +4,12 @@ Uploaders: Andreas Tille <tille at debian.org>
Section: non-free/science
XS-Autobuild: yes
Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper-compat (= 13),
libblimps3-dev
-Standards-Version: 4.1.1
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/sift
-Vcs-Git: https://salsa.debian.org/git/med-team/sift.git
-Homepage: http://sift.bii.a-star.edu.sg/
+Vcs-Git: https://salsa.debian.org/med-team/sift.git
+Homepage: https://sift.bii.a-star.edu.sg/
Package: sift
Architecture: any
=====================================
debian/copyright
=====================================
@@ -15,7 +15,7 @@ Files-Excluded: bin/choose_seqs_via_psiblastseedmedian
bin/process_alignment
bin/psiblast_res_to_fasta_dbpairwise
bin/seqs_from_psiblast_res
- blimps/obj/*.o
+ blimps/obj/*.o
Files: *
=====================================
debian/rules
=====================================
@@ -4,7 +4,6 @@
export DH_VERBOSE = 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
-export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
PACKAGE:=sift
@@ -63,19 +62,19 @@ override_dh_install:
dh_install -X.svn -X.swp -XIntersectFeatures.jar -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/
#dh_install bin/IntersectFeatures.jar $(pkgdatadir)/
dh_install -X.svn -X.swp blimps/docs $(prefix)/share/sift/blimps/
-
+
#Links are created by debian/links
for f in SIFT_for_submitting_fasta_seq.csh SIFT_for_submitting_NCBI_gi_id.csh; do \
sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \
done;
-
+
for f in seqs_chosen_via_median_info.csh \
SIFT_for_submitting_fasta_seq.csh \
SIFT_for_submitting_NCBI_gi_id.csh; \
do \
sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \
done;
-
+
# look out: DNA_PROT_SUBROUTINES.pl is really a module (should be pm)!
# Update: Not existing at all in 6.2.1
for f in SIFT_subroutines.pm \
@@ -90,14 +89,9 @@ override_dh_install:
chmod +x $$ff; \
fi; \
done;
-
+
for f in IntersectFeatures.jar; do \
if [ -r "$(DESTDIR)$(pkgdatadir)/$$f" ]; then \
chmod -x $(DESTDIR)$(pkgdatadir)/$$f; \
fi; \
done;
-
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
-
=====================================
debian/salsa-ci.yml
=====================================
@@ -1,3 +1,6 @@
---
include:
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
+
+variables:
+ SALSA_CI_COMPONENTS: 'main contrib non-free'
=====================================
debian/source/lintian-overrides
=====================================
@@ -1,7 +1,7 @@
-sift source: source-includes-file-in-files-excluded bin/choose_seqs_via_psiblastseedmedian
-sift source: source-includes-file-in-files-excluded bin/clump_output_alignedseq
-sift source: source-includes-file-in-files-excluded bin/consensus_to_seq
-sift source: source-includes-file-in-files-excluded bin/info_on_seqs
-sift source: source-includes-file-in-files-excluded bin/psiblast_res_to_fasta_dbpairwise
-sift source: source-includes-file-in-files-excluded bin/seqs_from_psiblast_res
+sift source: source-ships-excluded-file bin/choose_seqs_via_psiblastseedmedian
+sift source: source-ships-excluded-file bin/clump_output_alignedseq
+sift source: source-ships-excluded-file bin/consensus_to_seq
+sift source: source-ships-excluded-file bin/info_on_seqs
+sift source: source-ships-excluded-file bin/psiblast_res_to_fasta_dbpairwise
+sift source: source-ships-excluded-file bin/seqs_from_psiblast_res
=====================================
debian/watch
=====================================
@@ -1,5 +1,3 @@
version=4
-http://sift.bii.a-star.edu.sg/www/code.html .*/public/sift at ANY_VERSION@@ARCHIVE_EXT@
-
-# http://sift.bii.a-star.edu.sg/ .*/sift([0-9][0-9a-z.]*)\.tar\.[gzbl2]{2,3}
+http://sift.bii.a-star.edu.sg/www/code.html .*/sift at ANY_VERSION@@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/sift/-/compare/8030396bba462c6053642dddaf729b0eedb2e437...52d57b21eb7d640ae27d91d8bd5622a0dfa983df
--
View it on GitLab: https://salsa.debian.org/med-team/sift/-/compare/8030396bba462c6053642dddaf729b0eedb2e437...52d57b21eb7d640ae27d91d8bd5622a0dfa983df
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