diff -Nru squizz-0.99d+dfsg/debian/changelog squizz-0.99d+dfsg/debian/changelog --- squizz-0.99d+dfsg/debian/changelog 2018-10-30 11:01:25.000000000 +0000 +++ squizz-0.99d+dfsg/debian/changelog 2020-08-15 13:21:14.000000000 +0000 @@ -1,3 +1,18 @@ +squizz (0.99d+dfsg-3) unstable; urgency=medium + + * Team Upload. + [ Steffen Möller ] + * Update metadata with ref to conda + + [ Nilesh Patra ] + * Add autopkgtests + * compat version: 13, standards version: 4.5.0 + * Add "Rules-Requires-Root:no" + * Fix whatis entry + * Remove un-needed html and la files + + -- Nilesh Patra Sat, 15 Aug 2020 18:51:14 +0530 + squizz (0.99d+dfsg-2) unstable; urgency=medium * debhelper 11 (+ dh_auto_test --no-parallel) diff -Nru squizz-0.99d+dfsg/debian/compat squizz-0.99d+dfsg/debian/compat --- squizz-0.99d+dfsg/debian/compat 2018-10-30 11:01:25.000000000 +0000 +++ squizz-0.99d+dfsg/debian/compat 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -11 diff -Nru squizz-0.99d+dfsg/debian/control squizz-0.99d+dfsg/debian/control --- squizz-0.99d+dfsg/debian/control 2018-10-30 11:01:25.000000000 +0000 +++ squizz-0.99d+dfsg/debian/control 2020-08-15 13:04:35.000000000 +0000 @@ -4,11 +4,12 @@ Andreas Tille Section: science Priority: optional -Build-Depends: debhelper (>= 11~) -Standards-Version: 4.2.1 +Build-Depends: debhelper-compat (= 13) +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/squizz Vcs-Git: https://salsa.debian.org/med-team/squizz.git Homepage: ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/ +Rules-Requires-Root: no Package: squizz Architecture: any diff -Nru squizz-0.99d+dfsg/debian/patches/correct-manpages-section.patch squizz-0.99d+dfsg/debian/patches/correct-manpages-section.patch --- squizz-0.99d+dfsg/debian/patches/correct-manpages-section.patch 2018-10-30 11:01:25.000000000 +0000 +++ squizz-0.99d+dfsg/debian/patches/correct-manpages-section.patch 2020-08-15 13:15:01.000000000 +0000 @@ -1,11 +1,11 @@ Subject: Fix man page section Description: wrong section used -Author: Olivier Sallou -Last-Updated: 2013-02-18 +Author: Olivier Sallou , Nilesh Patra +Last-Updated: 2020-08-15 Forwarded: Yes --- a/doc/alifmt.man +++ b/doc/alifmt.man -@@ -123,8 +123,8 @@ +@@ -123,14 +123,14 @@ .rm #[ #] #H #V #F C .\" ======================================================================== .\" @@ -16,9 +16,16 @@ .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l + .nh + .SH "NAME" +-.IP "\fBalifmt\fR \- Aligned sequences formats" 4 ++alifmt \- Aligned sequences formats" 4 + .IX Item "alifmt - Aligned sequences formats" + .SH "DESCRIPTION" + .IX Header "DESCRIPTION" --- a/doc/seqfmt.man +++ b/doc/seqfmt.man -@@ -123,8 +123,8 @@ +@@ -123,14 +123,14 @@ .rm #[ #] #H #V #F C .\" ======================================================================== .\" @@ -29,3 +36,21 @@ .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l + .nh + .SH "NAME" +-.IP "\fBseqfmt\fR \- Sequences formats" 4 ++seqfmt \- Sequences formats" 4 + .IX Item "seqfmt - Sequences formats" + .SH "DESCRIPTION" + .IX Header "DESCRIPTION" +--- a/doc/squizz.man ++++ b/doc/squizz.man +@@ -139,7 +139,7 @@ + .if n .ad l + .nh + .SH "NAME" +-.IP "\fBsquizz\fR \- Sequence format checker" 4 ++squizz \- Sequence format checker" 4 + .IX Item "squizz - Sequence format checker" + .SH "SYNOPSIS" + .IX Header "SYNOPSIS" diff -Nru squizz-0.99d+dfsg/debian/rules squizz-0.99d+dfsg/debian/rules --- squizz-0.99d+dfsg/debian/rules 2018-10-30 11:01:25.000000000 +0000 +++ squizz-0.99d+dfsg/debian/rules 2020-08-15 13:20:47.000000000 +0000 @@ -15,3 +15,9 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) dh_auto_test --no-parallel endif + +override_dh_missing: + # Remove un-needed html and la files + find debian/tmp -name '*.la' | xargs rm -rf + find debian/tmp -name '*.html' | xargs rm -rf + dh_missing diff -Nru squizz-0.99d+dfsg/debian/tests/control squizz-0.99d+dfsg/debian/tests/control --- squizz-0.99d+dfsg/debian/tests/control 1970-01-01 00:00:00.000000000 +0000 +++ squizz-0.99d+dfsg/debian/tests/control 2020-06-12 16:55:10.000000000 +0000 @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr + diff -Nru squizz-0.99d+dfsg/debian/tests/run-unit-test squizz-0.99d+dfsg/debian/tests/run-unit-test --- squizz-0.99d+dfsg/debian/tests/run-unit-test 1970-01-01 00:00:00.000000000 +0000 +++ squizz-0.99d+dfsg/debian/tests/run-unit-test 2020-06-26 14:46:55.000000000 +0000 @@ -0,0 +1,33 @@ +#!/bin/bash +set -e + +pkg=squizz +TEST_DIR=`pwd` + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp ${TEST_DIR}/test/* -a "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +gunzip -r * +export srcdir=. + +testnum=1 +for f in *.sh +do + if [ "$f" = "sprot.sh" ]; + then + continue + fi + echo "Test $testnum" + echo "Executing $f" + sed -i 's/\.\.\/src\/squizz/squizz/' $f + /bin/bash $f + echo "PASS" + ((testnum++)) + echo +done + diff -Nru squizz-0.99d+dfsg/debian/upstream/metadata squizz-0.99d+dfsg/debian/upstream/metadata --- squizz-0.99d+dfsg/debian/upstream/metadata 2018-10-30 11:01:25.000000000 +0000 +++ squizz-0.99d+dfsg/debian/upstream/metadata 2020-06-12 16:40:29.000000000 +0000 @@ -3,5 +3,7 @@ Entry: OMICS_28981 - Name: bio.tools Entry: NA + - Name: conda:bioconda + Entry: squizz - Name: SciCrunch Entry: NA