[med-svn] [Git][med-team/roary][master] 11 commits: Use common naming scheme for autopkgtest scripts

Wed Nov 16 07:05:59 GMT 2022


Andreas Tille pushed to branch master at Debian Med / roary


Commits:
e0ef4f1f by Andreas Tille at 2022-11-16T07:42:58+01:00
Use common naming scheme for autopkgtest scripts

- - - - -
0a6ae859 by Andreas Tille at 2022-11-16T07:45:07+01:00
Provide autopkgtest as user example

- - - - -
3fd2f269 by Andreas Tille at 2022-11-16T07:45:51+01:00
routine-update: Standards-Version: 4.6.1

- - - - -
9bb174d4 by Andreas Tille at 2022-11-16T07:45:51+01:00
routine-update: debhelper-compat 13

- - - - -
c614145b by Andreas Tille at 2022-11-16T07:45:55+01:00
routine-update: Add salsa-ci file

- - - - -
223d9c62 by Andreas Tille at 2022-11-16T07:45:55+01:00
routine-update: Rules-Requires-Root: no

- - - - -
88957ffe by Andreas Tille at 2022-11-16T07:45:57+01:00
Use secure URI in Homepage field.

Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html

- - - - -
fea93d46 by Andreas Tille at 2022-11-16T07:45:57+01:00
Update renamed lintian tag names in lintian overrides.

Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html

- - - - -
539bfb0d by Andreas Tille at 2022-11-16T07:45:59+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
6b8f98a4 by Andreas Tille at 2022-11-16T08:02:37+01:00
Drop unneeded lintian-overrides

- - - - -
9be376f7 by Andreas Tille at 2022-11-16T08:05:30+01:00
Add debug for "Cannot find the mcxdeblast executable, please ensure its in your PATH"

- - - - -


11 changed files:

- + debian/README.test
- debian/changelog
- − debian/compat
- debian/control
- + debian/docs
- − debian/lintian-overrides
- + debian/salsa-ci.yml
- debian/source/lintian-overrides
- debian/tests/control
- debian/tests/test-installed → debian/tests/run-unit-test
- debian/upstream/metadata


Changes:

=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+roary (3.13.0+dfsg-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Use common naming scheme for autopkgtest scripts
+  * Provide autopkgtest as user example
+  * Standards-Version: 4.6.1 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Use secure URI in Homepage field.
+  * Drop unneeded lintian-overrides
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org>  Wed, 16 Nov 2022 07:40:26 +0100
+
 roary (3.13.0+dfsg-1) unstable; urgency=medium
 
   * New upstream release.


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Sascha Steinbiss <satta at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 13),
                dh-dist-zilla,
                libdist-zilla-plugin-podweaver-perl,
                bioperl (>= 1.7.4),
@@ -35,10 +35,11 @@ Build-Depends: debhelper (>= 12~),
                mafft,
                fasttree
 Build-Depends-Indep: perl
-Standards-Version: 4.4.1
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/roary
 Vcs-Git: https://salsa.debian.org/med-team/roary.git
-Homepage: http://sanger-pathogens.github.io/Roary/
+Homepage: https://sanger-pathogens.github.io/Roary/
+Rules-Requires-Root: no
 
 Package: roary
 Architecture: all


=====================================
debian/docs
=====================================
@@ -0,0 +1,3 @@
+debian/tests/expected_files.out
+debian/tests/run-unit-test
+debian/README.test


=====================================
debian/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# Upstream does not provide a changelog.
-roary: no-upstream-changelog


=====================================
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/source/lintian-overrides
=====================================
@@ -1,2 +1,2 @@
 # Upstream does not provide signed tarballs.
-roary source: debian-watch-does-not-check-gpg-signature
+roary source: debian-watch-does-not-check-openpgp-signature


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
-Tests: test-installed
+Tests: run-unit-test
 Depends: @
 Restrictions: allow-stderr


=====================================
debian/tests/test-installed → debian/tests/run-unit-test
=====================================
@@ -5,12 +5,20 @@ set -e
 
 ORIGDIR=$(pwd)
 DATADIR=$ORIGDIR/t/data/genbank_gbff
-WORKDIR=$(mktemp -d)
 
-trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
-cd $WORKDIR
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd $AUTOPKGTEST_TMP
 
 cp $DATADIR/*.gff .
+
+# DEBUG: roary issues "Cannot find the mcxdeblast executable, please ensure its in your PATH" thus checking ...
+which mcxdeblast
+
 roary -f out *.gff
 
 [ -d out ]


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/sanger-pathogens/Roary/issues
+Bug-Submit: https://github.com/sanger-pathogens/Roary/issues/new
 Reference:
  - Author: >
     Andrew J. Page and Carla A. Cummins and Martin Hunt and Vanessa
@@ -23,3 +25,5 @@ Registry:
    Entry: NA
  - Name: conda:bioconda
    Entry: roary
+Repository: https://github.com/sanger-pathogens/Roary.git
+Repository-Browse: https://github.com/sanger-pathogens/Roary



View it on GitLab: https://salsa.debian.org/med-team/roary/-/compare/3703d0adc86a07d2983f4d65f8c5fcb40c0e006e...9be376f71397018377c71067e822398b76e605a0

-- 
View it on GitLab: https://salsa.debian.org/med-team/roary/-/compare/3703d0adc86a07d2983f4d65f8c5fcb40c0e006e...9be376f71397018377c71067e822398b76e605a0
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