[med-svn] [Git][med-team/discosnp][master] 6 commits: Do not tweak Python3 interpreter in d/rules once this was done properly in a patch

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / discosnp


Commits:
45dc3905 by Andreas Tille at 2020-01-27T15:46:18+01:00
Do not tweak Python3 interpreter in d/rules once this was done properly in a patch

- - - - -
38b49ece by Andreas Tille at 2020-01-27T15:52:34+01:00
Fix POSIX shell syntax

- - - - -
d74c1212 by Andreas Tille at 2020-01-27T15:53:16+01:00
discoSnpRAD is a dir with extra scripts

- - - - -
f56c821b by Andreas Tille at 2020-01-27T15:55:26+01:00
Adapt to new names

- - - - -
bbd033a4 by Andreas Tille at 2020-01-27T15:59:17+01:00
Fix autopkgtest

- - - - -
30cd3f3d by Andreas Tille at 2020-01-27T16:02:05+01:00
Upload to unstable

- - - - -


7 changed files:

- debian/changelog
- debian/install
- debian/lintian-overrides
- debian/patches/series
- + debian/patches/shell_syntax.patch
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-discosnp (2.4.3-1) UNRELEASED; urgency=medium
+discosnp (2.4.3-1) unstable; urgency=medium
 
   [ Steffen Moeller ]
   * New upstream version
@@ -13,7 +13,7 @@ discosnp (2.4.3-1) UNRELEASED; urgency=medium
   * Remove trailing whitespace in debian/changelog (routine-update)
   * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
 
- -- Andreas Tille <tille at debian.org>  Mon, 27 Jan 2020 14:14:13 +0100
+ -- Andreas Tille <tille at debian.org>  Mon, 27 Jan 2020 15:59:28 +0100
 
 discosnp (2.3.0-3) unstable; urgency=medium
 


=====================================
debian/install
=====================================
@@ -1,3 +1,3 @@
 scripts			usr/share/discosnp
+discoSnpRAD		usr/share/discosnp
 run_discoSnp*.sh	usr/bin
-discoSnpRAD		usr/bin


=====================================
debian/lintian-overrides
=====================================
@@ -1,5 +1,4 @@
 # see https://lists.debian.org/debian-med/2018/06/msg00043.html
-discosnp: script-with-language-extension usr/bin/run_discoSnp++.sh
-discosnp: script-with-language-extension usr/bin/run_discoSnpRad.sh
+discosnp: script-with-language-extension usr/bin/run_*.sh
 # The doc is where it belongs to
-discosnp: package-contains-documentation-outside-usr-share-doc usr/share/discosnp/scripts_RAD/README.md
+discosnp: package-contains-documentation-outside-usr-share-doc usr/share/discosnp/*/README.md


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ spelling.patch
 #fix_scripts.patch
 adapt_test_scripts.patch
 2to3.patch
+shell_syntax.patch


=====================================
debian/patches/shell_syntax.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 27 Jan 2020 15:51:58 +0100
+Description: Fix POSIX shell syntax
+
+--- a/discoSnpRAD/clustering_scripts/discoRAD_clustering.sh
++++ b/discoSnpRAD/clustering_scripts/discoRAD_clustering.sh
+@@ -13,7 +13,7 @@ bold=`tput bold`
+ reset=`tput sgr0`
+ 
+ 
+-function help {
++help() {
+     echo $reset
+ echo "====================================================="
+ echo "Filtering, clustering per locus and vcf formatting of $rawdiscofile"


=====================================
debian/rules
=====================================
@@ -15,9 +15,6 @@ override_dh_install:
 	mv debian/$(DEB_SOURCE)/usr/bin/read_file_names			debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
 	mv debian/$(DEB_SOURCE)/usr/bin/quick_hierarchical_clustering	debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
 	rm -rf debian/$(DEB_SOURCE)/usr/share/discosnp/scripts/jenkins
-	for pl in `grep -Rl -e '#![[:space:]]*/bin/python' -e '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \
-	    sed -i '1s?^#!.*python?#!/usr/bin/python3?' $${pl} ; \
-	done
 
 override_dh_installman:
 	dh_installman


=====================================
debian/tests/run-unit-test
=====================================
@@ -11,7 +11,7 @@ fi
 cp -a /usr/share/doc/${pkg}/test/* $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
-gunzip ref_discoRes_k_31_c_auto_D_100_P_1_b_0_coherent*.gz
+gunzip ref_*.fa.gz
 chmod +x simple_test.sh
 
 ./simple_test.sh



View it on GitLab: https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6

-- 
View it on GitLab: https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200127/da246e8a/attachment-0001.html>