[med-svn] [Git][med-team/paraclu][master] 11 commits: Fix fetch URL - paraclu has moved to gitlab
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Fri Jun 4 21:18:59 BST 2021
Nilesh Patra pushed to branch master at Debian Med / paraclu
Commits:
193aa949 by Nilesh Patra at 2021-06-05T01:27:15+05:30
Fix fetch URL - paraclu has moved to gitlab
- - - - -
a3528cea by Nilesh Patra at 2021-06-05T01:27:25+05:30
New upstream version 10
- - - - -
c9383722 by Nilesh Patra at 2021-06-05T01:27:26+05:30
Update upstream source from tag 'upstream/10'
Update to upstream version '10'
with Debian dir 4da7ad1250958627edff1874fb4c66eb91361a69
- - - - -
1cfdffab by Nilesh Patra at 2021-06-05T01:28:45+05:30
d/control: Fix homepage
- - - - -
0888d948 by Nilesh Patra at 2021-06-05T01:29:16+05:30
Remove override
- - - - -
bcbacf0c by Nilesh Patra at 2021-06-05T01:30:56+05:30
d/copyright: Fix Source URL, migrate to https
- - - - -
385efc16 by Nilesh Patra at 2021-06-05T01:33:53+05:30
Update upstream/metadata
- - - - -
017e0e30 by Nilesh Patra at 2021-06-05T01:40:20+05:30
d/p/do-not-override-cxxflags.patch: Do not override CXXFLAGS
- - - - -
a5dd37df by Nilesh Patra at 2021-06-05T01:40:30+05:30
Remove un-needed patch
- - - - -
d604ba70 by Nilesh Patra at 2021-06-05T01:42:27+05:30
Declare compliance with policy 4.5.1
- - - - -
9dfef4b4 by Nilesh Patra at 2021-06-05T01:48:15+05:30
Interim changelog entry
- - - - -
13 changed files:
- − ChangeLog.txt
- Makefile
- README.txt
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/do-not-override-cxxflags.patch
- − debian/patches/enable_debug.patch
- debian/patches/series
- − debian/source/lintian-overrides
- debian/upstream/metadata
- debian/watch
- + paraclu_sketch.png
Changes:
=====================================
ChangeLog.txt deleted
=====================================
@@ -1,56 +0,0 @@
-2012-12-14 Martin C. Frith <Martin C. Frith>
-
- * README.txt, paraclu-cut.sh:
- ! New version of paraclu-cut: use its -s option to get the old
- behaviour
- [c1086ad752b4] [tip]
-
-2012-09-03 Martin C. Frith <Martin C. Frith>
-
- * README.txt:
- Clarified the minValue parameter in the README
- [77214c740db7]
-
-2012-08-09 Martin C. Frith <Martin C. Frith>
-
- * README.txt:
- Made the README convertible to a manpage by pandoc (thanks: Charles
- Plessy)
- [27f84a76abc0]
-
-2012-08-08 Martin C. Frith <Martin C. Frith>
-
- * Makefile:
- Generalized the Makefile a bit
- [77cfa417a78a]
-
-2011-11-02 Martin C. Frith <Martin C. Frith>
-
- * Makefile:
- Made the Makefile more flexible (thanks: Charles Plessy)
- [4e9b8fb9d6b0]
-
-2011-08-16 Martin C. Frith <Martin C. Frith>
-
- * README.txt, paraclu.cc:
- Try to make the C++ strictly correct and portable
- [cf2ffcee14a7]
-
- * ctss-merge.sh:
- Removed a too-specialized script
- [efcdfe3977b0]
-
- * COPYING.txt, Makefile, README.txt, paraclu-cut.sh:
- Modified the package for public distribution
- [1d012dc9bd10]
-
-2011-02-08 Martin C. Frith <Martin C. Frith>
-
- * README.txt:
- Simplified the README
- [4f75340f8a78]
-
- * Makefile, README.txt, ctss-merge.sh, paraclu-cut.sh, paraclu.cc:
- Start using version control
- [55b4fd7f6316]
-
=====================================
Makefile
=====================================
@@ -1,22 +1,12 @@
-CXX = g++
-CXXFLAGS = -Wall -W -O3
+CXXFLAGS = -Wall -O3
all: paraclu
paraclu: paraclu.cc Makefile
$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ paraclu.cc
-clean: FORCE
+clean:
rm -f paraclu
-log: FORCE
- hg log --style changelog > ChangeLog.txt
-
-distdir = paraclu-`hg id -n`
-
-dist: log
- mkdir ${distdir}
- cp *.cc *.sh *.txt Makefile ${distdir}
- zip -qrm ${distdir} ${distdir}
-
-FORCE:
+tag:
+ git tag -m "" `git rev-list HEAD^ | grep -c .`
=====================================
README.txt
=====================================
@@ -137,9 +137,3 @@ If you use paraclu in your research, please cite:
"A code for transcription initiation in mammalian genomes"
MC Frith, E Valen, A Krogh, Y Hayashizaki, P Carninci, A Sandelin
Genome Research 2008 18(1):1-12.
-
-CONTACT
-=======
-
-Website: http://www.cbrc.jp/paraclu/
-E-mail: paraclu (ATmark) cbrc (dot) jp
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+paraclu (10-1) UNRELEASED; urgency=medium
+
+ * Team Upload.
+ * Fix fetch URL - paraclu has moved to gitlab
+ * New upstream version 10
+ * d/control: Fix homepage
+ * Remove lintian override
+ * d/copyright: Fix Source URL, migrate to https
+ * Update upstream/metadata
+ * d/p/do-not-override-cxxflags.patch: Do not override CXXFLAGS
+ * Declare compliance with policy 4.5.1
+
+ -- Nilesh Patra <nilesh at debian.org> Sat, 05 Jun 2021 01:40:35 +0530
+
paraclu (9-3) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -4,10 +4,10 @@ Uploaders: Charles Plessy <plessy at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/paraclu
Vcs-Git: https://salsa.debian.org/med-team/paraclu.git
-Homepage: http://cbrc3.cbrc.jp/~martin/paraclu/
+Homepage: https://gitlab.com/mcfrith/paraclu
Rules-Requires-Root: no
Package: paraclu
=====================================
debian/copyright
=====================================
@@ -1,7 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: paraclu
-Upstream-Contact: paraclu at cbrc.jp
-Source: http://cbrc3.cbrc.jp/~martin/paraclu/paraclu-9.zip
+Upstream-Contact: Martin C. Frith
+Source: https://gitlab.com/mcfrith/paraclu/-/tags
License: GPL-3+
Files: *
@@ -24,6 +24,6 @@ License: GPL-3+
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
Comment: On Debian systems, a copy of the GNU General Public License
version 3 is placed in “/usr/share/common-licenses/GPL-3”..
=====================================
debian/patches/do-not-override-cxxflags.patch
=====================================
@@ -0,0 +1,14 @@
+Description: CXXFLAGS would be passed by debhelper, do not override
+Author: Nilesh Patra <nilesh at debian.org>
+Forwarded: not-needed
+Last-Update: 2021-06-05
+diff --git a/Makefile b/Makefile
+index b2aebc5..5819d7b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,3 @@
+-CXXFLAGS = -Wall -O3
+-
+ all: paraclu
+
+ paraclu: paraclu.cc Makefile
=====================================
debian/patches/enable_debug.patch deleted
=====================================
@@ -1,13 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 03 Jul 2018 14:54:48 +0200
-Description: Enable debug symbols
-
---- a/Makefile
-+++ b/Makefile
-@@ -1,5 +1,5 @@
- CXX = g++
--CXXFLAGS = -Wall -W -O3
-+CXXFLAGS += -Wall -W -O3 -g
-
- all: paraclu
-
=====================================
debian/patches/series
=====================================
@@ -1 +1 @@
-enable_debug.patch
+do-not-override-cxxflags.patch
=====================================
debian/source/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# upstream seems to be dead so we can not do much about this
-paraclu source: debian-watch-uses-insecure-uri http://cbrc3.cbrc.jp/~martin/paraclu/
\ No newline at end of file
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,8 @@
+---
+Bug-Database: https://gitlab.com/mcfrith/paraclu/issues
+Changelog: https://gitlab.com/mcfrith/paraclu/tags
+Repository: https://gitlab.com/mcfrith/paraclu.git
+Repository-Browse: https://gitlab.com/mcfrith/paraclu
Reference:
- author: >
Frith, Martin C. and Valen, Eivind and Krogh, Anders and Hayashizaki,
@@ -8,8 +13,8 @@ Reference:
pages: 1-12
year: 2008
doi: 10.1101/gr.6831208
- URL: http://genome.cshlp.org/content/18/1/1.abstract
- eprint: http://genome.cshlp.org/content/18/1/1.full.pdf+html
+ URL: https://genome.cshlp.org/content/18/1/1.abstract
+ eprint: https://genome.cshlp.org/content/18/1/1.full.pdf+html
journal: Genome Research
Registry:
- Name: OMICtools
=====================================
debian/watch
=====================================
@@ -1,3 +1,2 @@
version=4
-
-http://cbrc3.cbrc.jp/~martin/paraclu/ paraclu-(.*).zip
+https://gitlab.com/mcfrith/paraclu/-/tags?sort=updated_desc .*/archive/(\d\S+)/.*\.tar\.gz
=====================================
paraclu_sketch.png
=====================================
Binary files /dev/null and b/paraclu_sketch.png differ
View it on GitLab: https://salsa.debian.org/med-team/paraclu/-/compare/d99888162bdf6836fa05f415f058d86d106b1491...9dfef4b428ee4d3688b286f2acfb776635a75812
--
View it on GitLab: https://salsa.debian.org/med-team/paraclu/-/compare/d99888162bdf6836fa05f415f058d86d106b1491...9dfef4b428ee4d3688b286f2acfb776635a75812
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