[med-svn] [Git][med-team/ltrsift][master] 11 commits: Remove hard-coded dependencies on shared libraries
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Apr 4 18:28:59 BST 2024
Andreas Tille pushed to branch master at Debian Med / ltrsift
Commits:
950e0565 by Andreas Tille at 2024-04-04T18:41:44+02:00
Remove hard-coded dependencies on shared libraries
- - - - -
25729c77 by Andreas Tille at 2024-04-04T18:42:14+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
be9a468d by Andreas Tille at 2024-04-04T18:42:14+02:00
routine-update: debhelper-compat 13
- - - - -
e4020a32 by Andreas Tille at 2024-04-04T18:42:19+02:00
routine-update: Rules-Requires-Root: no
- - - - -
2417e0e9 by Andreas Tille at 2024-04-04T16:42:20+00:00
Set field Upstream-Contact in debian/copyright.
Changes-By: lintian-brush
- - - - -
62d75e79 by Andreas Tille at 2024-04-04T16:42:28+00:00
Set upstream metadata fields: Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
5d42ade4 by Andreas Tille at 2024-04-04T16:42:28+00:00
Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
- - - - -
151cdb1c by Andreas Tille at 2024-04-04T16:42:28+00:00
Fix day-of-week for changelog entry 1.0.1-1.
Changes-By: lintian-brush
Fixes: lintian: debian-changelog-has-wrong-day-of-week
See-also: https://lintian.debian.org/tags/debian-changelog-has-wrong-day-of-week.html
- - - - -
d86984af by Andreas Tille at 2024-04-04T18:42:33+02:00
routine-update: watch file standard 4
- - - - -
c75a3334 by Andreas Tille at 2024-04-04T19:22:38+02:00
Add new binary package ltrsift with data that can be used in autopkgtest
- - - - -
da191eac by Andreas Tille at 2024-04-04T19:28:37+02:00
Add TODO
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/ltrsift-examples.examples
- debian/ltrsift.install
- debian/rules
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,28 @@
+ltrsift (1.0.2-10) UNRELEASED; urgency=medium
+
+ * Team upload.
+
+ [ Matthias Klose ]
+ * Remove hard-coded dependencies on shared libraries.
+ Closes: #1068401
+
+ [ Andreas Tille ]
+ * Standards-Version: 4.6.2 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set field Upstream-Contact in debian/copyright.
+ * Set upstream metadata fields: Repository, Repository-Browse.
+ * Remove obsolete fields Contact, Name from debian/upstream/metadata
+ (already present in machine-readable debian/copyright).
+ * Fix day-of-week for changelog entry 1.0.1-1.
+ * watch file standard 4 (routine-update)
+ * Add new binary package ltrsift with data that can be used in
+ autopkgtest
+ TODO: remove ltrsift_encode from examples
+ write autopkgtest
+
+ -- Andreas Tille <tille at debian.org> Thu, 04 Apr 2024 18:40:38 +0200
+
ltrsift (1.0.2-9) unstable; urgency=medium
* Fix EDAM syntax (thanks Andreas Tille).
@@ -82,4 +107,4 @@ ltrsift (1.0.1-1) unstable; urgency=low
* Initial release (Closes: #689961)
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Sun, 06 Oct 2012 15:08:11 +0200
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Sat, 06 Oct 2012 15:08:11 +0200
=====================================
debian/control
=====================================
@@ -3,22 +3,20 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Sascha Steinbiss <satta at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
libgenometools0-dev,
libgtk2.0-dev,
libglib2.0-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/ltrsift
Vcs-Git: https://salsa.debian.org/med-team/ltrsift.git
Homepage: https://www.zbh.uni-hamburg.de/en/forschung/gi/software/ltrsift.html
+Rules-Requires-Root: no
Package: ltrsift
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- libgenometools0,
- libgtk2.0-0,
- libglib2.0-0
Recommends: last-align,
ncbi-blast+
Description: postprocessing and classification of LTR retrotransposons
@@ -29,3 +27,18 @@ Description: postprocessing and classification of LTR retrotransposons
structure in a hierarchical fashion, allowing the user to "sift" through the
sometimes large results of de novo prediction software. It also offers
customizable filtering and classification functionality.
+
+Package: ltrsift-examples
+Architecture: all
+Depends: ${misc:Depends},
+Suggests: ltrsift
+Description: postprocessing and classification of LTR retrotransposons (sample data)
+ LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
+ novo predicted LTR retrotransposon annotations, such as the ones generated by
+ LTRharvest and LTRdigest. Its user-friendly interface displays LTR
+ retrotransposon candidates, their putative families and their internal
+ structure in a hierarchical fashion, allowing the user to "sift" through the
+ sometimes large results of de novo prediction software. It also offers
+ customizable filtering and classification functionality.
+ .
+ This package contains sample data to run the autopkgtest.
=====================================
debian/copyright
=====================================
@@ -1,6 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: ltrsift
Source: https://github.com/satta/ltrsift
+Upstream-Contact: Sascha Steinbiss <sascha at steinbiss.name>
Files:
*
=====================================
debian/ltrsift-examples.examples
=====================================
@@ -1,5 +1 @@
-sample_data/clean_encseqs
-sample_data/prepare_encseqs
-sample_data/dmel58.ltrd.gff3
-sample_data/dmel-2L-chromosome-r5.8.fasta.gz
-sample_data/README
+debian/tmp/usr/sample_data/*
=====================================
debian/ltrsift.install
=====================================
@@ -4,3 +4,4 @@ usr/filters usr/share/ltrsift
debian/ltrsift.desktop usr/share/applications
debian/ltrsift.svg usr/share/icons/hicolor/scalable/apps
debian/ltrsift.xpm usr/share/pixmaps
+debian/tmp/usr/style/default.style usr/share/ltrsift
=====================================
debian/rules
=====================================
@@ -40,3 +40,7 @@ override_dh_auto_install:
override_dh_installdocs:
dh_installdocs --exclude=license.template
+
+override_dh_missing:
+ rm -f debian/tmp/usr/sample_data/ltrsift_encode
+ dh_missing
=====================================
debian/upstream/metadata
=====================================
@@ -1,7 +1,5 @@
-Name: LTRsift
Bug-Database: https://github.com/satta/ltrsift/issues
Bug-Submit: https://github.com/satta/ltrsift/issues/new
-Contact: Sascha Steinbiss <sascha at steinbiss.name>
Reference:
Author: Steinbiss, Sascha and Kastens, Sascha and Kurtz, Stefan
Title: >
@@ -16,7 +14,7 @@ Reference:
PMID: 23131050
URL: http://www.mobilednajournal.com/content/3/1/18/abstract
eprint: http://www.mobilednajournal.com/content/pdf/1759-8753-3-18.pdf
-Repository: http://github.com/satta/ltrsift
+Repository: https://github.com/satta/ltrsift.git
Registry:
- Name: OMICtools
Entry: OMICS_11266
@@ -24,3 +22,4 @@ Registry:
Entry: NA
- Name: SciCrunch
Entry: NA
+Repository-Browse: https://github.com/satta/ltrsift
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=3
+version=4
opts=uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha|b|a)\d*)$/$1~$2/,dversionmangle=s/\+(debian|dfsg|ds|deb)\d*$// \
https://github.com/satta/ltrsift/tags .*/v?(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
# Bart Martens <bartm at debian.org> Sat, 22 Dec 2012 13:05:45 +0000
View it on GitLab: https://salsa.debian.org/med-team/ltrsift/-/compare/2a5bc26c4c59519978b75a90214c04668d01b38f...da191eac881fd7b461037f58e8c91b2bd98cdd4a
--
View it on GitLab: https://salsa.debian.org/med-team/ltrsift/-/compare/2a5bc26c4c59519978b75a90214c04668d01b38f...da191eac881fd7b461037f58e8c91b2bd98cdd4a
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