[med-svn] [Git][med-team/circos][master] 9 commits: Fix config path
Andreas Tille
gitlab at salsa.debian.org
Fri Jun 5 09:26:15 BST 2020
Andreas Tille pushed to branch master at Debian Med / circos
Commits:
a98ffa04 by Andreas Tille at 2020-06-05T08:44:25+02:00
Fix config path
- - - - -
9b92b7ff by Andreas Tille at 2020-06-05T08:47:12+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
043ed484 by Andreas Tille at 2020-06-05T08:47:17+02:00
routine-update: debhelper-compat 13
- - - - -
ac9b88bd by Andreas Tille at 2020-06-05T08:47:28+02:00
routine-update: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
- - - - -
8f493bd2 by Andreas Tille at 2020-06-05T08:47:29+02:00
routine-update: Add salsa-ci file
- - - - -
d04a53c0 by Andreas Tille at 2020-06-05T08:47:29+02:00
routine-update: Rules-Requires-Root: no
- - - - -
7a3e2914 by Andreas Tille at 2020-06-05T09:06:14+02:00
Install error message
- - - - -
7d20e603 by Andreas Tille at 2020-06-05T09:48:53+02:00
install example configuration as additional configuration files
- - - - -
9a3a8e43 by Andreas Tille at 2020-06-05T10:20:01+02:00
Do not ship copy of example configuration files but rather symlink to the files that are now provided in /etc/circos
- - - - -
9 changed files:
- debian/changelog
- debian/circos.install
- − debian/compat
- debian/control
- + debian/patches/fix_config_path.patch
- debian/patches/series
- debian/rules
- + debian/salsa-ci.yml
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+circos (0.69.9+dfsg-2) UNRELEASED; urgency=medium
+
+ * Fix config path and install example configuration as additional
+ configuration files
+ Closes: #962247
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Install error message
+ * Do not ship copy of example configuration files but rather symlink to
+ the files that are now provided in /etc/circos
+
+ -- Andreas Tille <tille at debian.org> Fri, 05 Jun 2020 08:43:04 +0200
+
circos (0.69.9+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/circos.install
=====================================
@@ -1,4 +1,6 @@
-bin/circos usr/bin/
-etc/* etc/circos/
-lib/* usr/share/perl5/
-tiles/* usr/share/circos/tiles/
+bin/circos usr/bin
+etc/* etc/circos
+example/etc/* etc/circos
+lib/* usr/share/perl5
+tiles usr/share/circos
+error usr/share/circos
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -4,11 +4,12 @@ Uploaders: Olivier Sallou <osallou at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~)
-Standards-Version: 4.4.0
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/circos
Vcs-Git: https://salsa.debian.org/med-team/circos.git
Homepage: http://circos.ca/
+Rules-Requires-Root: no
Package: circos
Architecture: all
=====================================
debian/patches/fix_config_path.patch
=====================================
@@ -0,0 +1,117 @@
+Description: Fix config path
+Bug-Debian: https://bugs.debian.org/962247
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 05 Jun 2020 08:43:04 +0200
+Comment: May be it would be better to do in d/rules some
+ find debian/circos -type f | xargs sed -i 's:include etc/:include :g'
+
+--- a/bin/circos
++++ b/bin/circos
+@@ -143,10 +143,10 @@ A typical configuration file might look
+ </plots>
+
+ # colors, fonts and fill patterns
+- <<include etc/colors_fonts_patterns.conf>>
++ <<include colors_fonts_patterns.conf>>
+
+ # system parameters
+- <<include etc/housekeeping.conf>>
++ <<include housekeeping.conf>>
+
+ =head2 Modularity
+
+@@ -168,12 +168,12 @@ Parameter definitions that do not freque
+
+ # image size, output file name
+ <image>
+- <<include etc/image.conf>>
++ <<include image.conf>>
+ </image>
+ # color names and lists, location of fonts, fill patterns
+- <<include etc/colors_fonts_patterns.conf>>
++ <<include colors_fonts_patterns.conf>>
+ # low-level system parameters
+- <<include etc/housekeeping.conf>>
++ <<include housekeeping.conf>>
+
+ =head2 Overriding with *
+
+@@ -181,7 +181,7 @@ To override a parameter that has been in
+
+ <image>
+ # included file defines 'radius'
+- <<include etc/image.conf>>
++ <<include image.conf>>
+ # this will override the radius value
+ radius* = 2500p
+ </image>
+@@ -248,7 +248,7 @@ Multiple instances of the following bloc
+ The purpose of this is to allow you to add to canonical definitions.
+
+ # this file defines default <colors>, <fonts> and <patterns>
+- <<include etc/colors_fonts_patterns.conf>>
++ <<include colors_fonts_patterns.conf>>
+
+ # add to the colors block
+ <colors>
+@@ -315,7 +315,7 @@ Users who are unaware of this feature of
+
+ If you want to redefine the search paths, see the C<data_path> parameter in C<etc/housekeeping.conf> in the distribution directory, or overide it in your configuration file
+
+- <<include etc/housekeeping.conf>>
++ <<include housekeeping.conf>>
+ data_path* = ...
+
+ =head1 OPTIONS
+--- a/etc/colors_fonts_patterns.conf
++++ b/etc/colors_fonts_patterns.conf
+@@ -1,12 +1,12 @@
+
+ <colors>
+-<<include etc/colors.conf>>
++<<include colors.conf>>
+ </colors>
+
+ <fonts>
+-<<include etc/fonts.conf>>
++<<include fonts.conf>>
+ </fonts>
+
+ <patterns>
+-<<include etc/patterns.conf>>
+-</patterns>
+\ No newline at end of file
++<<include patterns.conf>>
++</patterns>
+--- a/etc/gddiag.conf
++++ b/etc/gddiag.conf
+@@ -18,6 +18,6 @@ marginy = 10
+
+ output_file_root = gddiag
+
+-<<include etc/colors_fonts_patterns.conf>>
+-<<include etc/housekeeping.conf>>
++<<include colors_fonts_patterns.conf>>
++<<include housekeeping.conf>>
+
+--- a/etc/brewer.conf
++++ b/etc/brewer.conf
+@@ -4,6 +4,6 @@
+ # Your color blocks should now be
+ #
+ # <colors>
+-# <<include etc/colors.conf>>
++# <<include colors.conf>>
+ # # any custom colors here
+ # </colors>
+--- a/lib/Circos/Error.pm
++++ b/lib/Circos/Error.pm
+@@ -129,7 +129,7 @@ $ERROR{configuration} =
+ no_debug_group=>"You asked for debug group [%s] using -debug_group. This group is not defined. Please use one of\n\n[%s]\n\nTo request all groups, use -debug_group _all.",
+ deprecated =>"The configuration syntax [%s] is deprecated and no longer supported. Instead, use [%s].",
+ no_such_conf_item => "You attempted to reference a configuration parameter using %s, but no parameter was found at the configuration file position %s.\n\nTo reference a parameter in another block, provide the full block path, such as conf(ideogram,spacing,default). In general, conf(block1,block2,...,blockn,parameter).\n\nTo reference the first defined parameter above the block in which conf() is called, use conf(.,parameter).",
+- no_housekeeping => "You did not include the etc/housekeeping.conf file in your configuration file. This file contains many important system parameters and must be included in each Circos configuration.\n\nTo do so, use\n\n <<include etc/housekeeping.conf>>\n\nin your main configuration file. For an example, see\n\n http://www.circos.ca/documentation/tutorials/quick_guide/hello_world/configuration\n\nIf you have made other provisions to include these parameters, make sure you have\n\n housekeeping = yes\n\ndefined to skip this check.",
++ no_housekeeping => "You did not include the etc/housekeeping.conf file in your configuration file. This file contains many important system parameters and must be included in each Circos configuration.\n\nTo do so, use\n\n <<include housekeeping.conf>>\n\nin your main configuration file. For an example, see\n\n http://www.circos.ca/documentation/tutorials/quick_guide/hello_world/configuration\n\nIf you have made other provisions to include these parameters, make sure you have\n\n housekeeping = yes\n\ndefined to skip this check.",
+ multi_word_key => "Your parameter [%s] contains a white space. This is not allowed. You either forgot a '=' in assignment (e.g. 'red 255,0,0' vs 'red = 255,0,0') or used a multi-word parameter name\n (e.g. 'my red = 255,0,0' vs 'my_red = 255,0,0'",
+ missing => "file(error/configuration.missing.txt)",
+ bad_parameter_type => "You attempted to reference a configuration parameter group with name [%s], but it is not defined",
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ configpath_add_etc
fix_examples
fix_manpage
fix_pod_syntax.patch
+fix_config_path.patch
=====================================
debian/rules
=====================================
@@ -1,6 +1,7 @@
#!/usr/bin/make -f
# -*- makefile -*-
-# debian/rules file for circos
+
+include /usr/share/dpkg/default.mk
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
@@ -8,16 +9,23 @@
%:
dh $@
-
override_dh_install:
dh_install
- # Update circos relative path to absolute debian paths
- find debian/circos -type f | xargs sed -i 's/include etc/include \/usr\/share\/circos\/etc/g'
- find debian/circos -type f | xargs sed -i 's/include fonts/include \/usr\/share\/circos\/fonts/g'
- find debian/circos -type f | xargs sed -i 's/include tiles/include \/usr\/share\/circos\/tiles/g'
+ # Update $(DEB_SOURCE) relative path to absolute debian paths
+ find debian/$(DEB_SOURCE) -type f | xargs sed -i 's/include etc/include \/usr\/share\/$(DEB_SOURCE)\/etc/g'
+ find debian/$(DEB_SOURCE) -type f | xargs sed -i 's/include fonts/include \/usr\/share\/$(DEB_SOURCE)\/fonts/g'
+ find debian/$(DEB_SOURCE) -type f | xargs sed -i 's/include tiles/include \/usr\/share\/$(DEB_SOURCE)\/tiles/g'
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/*` ; do \
sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
done
override_dh_installman:
- pod2man bin/circos > $(CURDIR)/debian/circos/usr/share/man/man1/circos.1
+ pod2man bin/$(DEB_SOURCE) > $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/$(DEB_SOURCE).1
+
+override_dh_link:
+ dh_link
+ for cfgfile in debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/etc/*.conf ; do \
+ rm $${cfgfile} ; \
+ dh_link etc/$(DEB_SOURCE)/`basename $${cfgfile}` usr/share/doc/$(DEB_SOURCE)/examples/etc/`basename $${cfgfile}` ; \
+ done
+
=====================================
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
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,12 +1,12 @@
#!/bin/sh -e
pkg=circos
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
- trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
-cd $ADTTMP
-cp -a /usr/share/doc/$pkg/examples/* $ADTTMP
+cd $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/$pkg/examples/* $AUTOPKGTEST_TMP
ln -s /etc/circos/tracks etc
find . -name "*.gz" -exec gunzip \{\} \;
cp -a circos.svg circos-orig.svg
View it on GitLab: https://salsa.debian.org/med-team/circos/-/compare/83be615103743566efe5398763176890dac10b5f...9a3a8e439697f8a17f977e76570ecfcc07bdfeb4
--
View it on GitLab: https://salsa.debian.org/med-team/circos/-/compare/83be615103743566efe5398763176890dac10b5f...9a3a8e439697f8a17f977e76570ecfcc07bdfeb4
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