[med-svn] [Git][med-team/proteinortho][master] 5 commits: Fix docs and examples

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / proteinortho


Commits:
b1cfba15 by Andreas Tille at 2019-07-15T12:57:06Z
Fix docs and examples

- - - - -
0f915eb8 by Andreas Tille at 2019-07-15T13:04:07Z
Fix permissions

- - - - -
971da6ba by Andreas Tille at 2019-07-15T13:07:52Z
Provide unversioned Link to binary

- - - - -
91cde906 by Andreas Tille at 2019-07-15T14:31:19Z
Fix autopkgtest

- - - - -
1e3a8b8e by Andreas Tille at 2019-07-15T14:33:53Z
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/docs
- debian/examples
- + debian/links
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,7 +1,6 @@
-proteinortho (6.0.6+dfsg-1) UNRELEASED; urgency=medium
+proteinortho (6.0.6+dfsg-1) unstable; urgency=medium
 
   [ Paul Klemm ]
-  * Team upload.
   * New upstream version
 
   [ Andreas Tille ]
@@ -9,8 +8,11 @@ proteinortho (6.0.6+dfsg-1) UNRELEASED; urgency=medium
   * debhelper 12
   * Standards-Version: 4.4.0
   * Build-Depends: s/liblapack3/liblapack-dev|libatlas-base-dev|liblapack.so/
+  * Fix permissions
+  * Provide unversioned Link to binary
+  * Fix autopkgtest
 
- -- Paul Klemm <klemmp at staff.uni-marburg.de>  Mon, 15 Jul 2019 13:17:13 +0200
+ -- Andreas Tille <tille at debian.org>  Mon, 15 Jul 2019 16:31:25 +0200
 
 proteinortho (5.16.b+dfsg-1) unstable; urgency=medium
 


=====================================
debian/docs
=====================================
@@ -1,3 +1,2 @@
 debian/README.test
 debian/tests/run-unit-test
-tools


=====================================
debian/examples
=====================================
@@ -1,3 +1,3 @@
 test/*.faa
 test/*.gff
-chk_test.pl
+src/chk_test.pl


=====================================
debian/links
=====================================
@@ -0,0 +1,2 @@
+usr/bin/proteinortho6			usr/bin/proteinortho
+usr/share/man/man1/proteinortho6.1.gz	usr/share/man/man1/proteinortho.1.gz


=====================================
debian/rules
=====================================
@@ -11,3 +11,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 override_dh_auto_install:
 	dh_auto_install --buildsystem=makefile -- install PREFIX=$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/proteinortho
+
+override_dh_fixperms:
+	dh_fixperms
+	find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \;


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,19 +1,19 @@
 #!/bin/sh -e
 
 pkg=proteinortho
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+
+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 $ADTTMP
+
+cd "${AUTOPKGTEST_TMP}"
+
 mkdir test
 cp -a /usr/share/doc/${pkg}/examples/* test
-find . -type f -name "*.gz" -exec gunzip \{\} \;
-mv test/chk_test.pl .
+gunzip -r *
+
 proteinortho -project=test -synteny -singles test/*.faa
-./src/chk_test.pl test.proteinortho
-./src/chk_test.pl test.poff
+./test/chk_test.pl test.proteinortho.tsv
+./test/chk_test.pl test.poff.tsv
 echo "Test okay"
-
-make test
-
-rm -fr $ADTTMP/*



View it on GitLab: https://salsa.debian.org/med-team/proteinortho/compare/39002aaff3b9a9a3c1da5b08b58065c27d961192...1e3a8b8e4293c01d8302b126fbea38f0c1399f0b

-- 
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/compare/39002aaff3b9a9a3c1da5b08b58065c27d961192...1e3a8b8e4293c01d8302b126fbea38f0c1399f0b
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