[med-svn] [Git][med-team/q2-vsearch][master] Initial packaging

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / q2-vsearch


Commits:
4d562c48 by Shayan Doust at 2020-07-05T20:26:01+01:00
Initial packaging

- - - - -


10 changed files:

- + debian/changelog
- + debian/control
- + debian/copyright
- + debian/rules
- + debian/salsa-ci.yml
- + debian/source/format
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/upstream/metadata
- + debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -0,0 +1,5 @@
+q2-vsearch (2020.8.0.dev0-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Shayan Doust <hello at shayandoust.me>  Sun, 05 Jul 2020 19:57:45 +0100


=====================================
debian/control
=====================================
@@ -0,0 +1,18 @@
+Source: q2-vsearch
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Shayan Doust <hello at shayandoust.me>
+Section: science
+Priority: optional
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.3.0
+Vcs-Browser: https://salsa.debian.org/med-team/q2-vsearch
+Vcs-Git: https://salsa.debian.org/med-team/q2-vsearch.git
+Homepage: https://github.com/qiime2/q2-vsearch
+
+Package: q2-vsearch
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: QIIME 2 plugin for clustering and dereplicating with vsearch
+ Wraps the vsearch application, and provides methods for clustering and
+ dereplicating features and sequences.


=====================================
debian/copyright
=====================================
@@ -0,0 +1,16 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: q2-vsearch
+Source: <path_to_download>
+Comment: **** Before manually editing this file you should give ****
+           scan-copyrights
+         **** available in cme + lib-config-model-dpkg-perl     ****
+         **** package a try.  For existing copyright files try  ****
+           cme update dpkg-copyright
+
+Files: *
+Copyright: 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: 2020 Shayan Doust <hello at shayandoust.me>
+License: <license>


=====================================
debian/rules
=====================================
@@ -0,0 +1,31 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+include /usr/share/dpkg/default.mk
+# this provides:
+# DEB_SOURCE: the source package name
+# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
+# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
+# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
+# DEB_VERSION_UPSTREAM: the package's upstream version
+# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
+# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
+#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+	dh $@
+
+### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
+#override_dh_auto_test:
+#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+#	do_stuff_for_testing
+#endif
+
+### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
+#get-orig-source:
+#	. debian/get-orig-source


=====================================
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/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+pkg=#PACKAGENAME#
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  # Double quote below to expand the temporary directory variable now versus
+  # later is on purpose.
+  # shellcheck disable=SC2064
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+#do_stuff_to_test_package#


=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,9 @@
+Reference:
+  Author: Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince & Frédéric Mahé
+  Title: "VSEARCH: a versatile open source tool for metagenomics"
+  Journal: PeerJ
+  Year: 2016
+  Volume: 4
+  DOI: 10.7717/peerj.2584
+  URL: https://peerj.com/articles/2584/
+Other-Reference: https://raw.githubusercontent.com/qiime2/q2-vsearch/master/q2_vsearch/citations.bib


=====================================
debian/watch
=====================================
@@ -0,0 +1,4 @@
+version=4
+
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+https://github.com/qiime2/q2-vsearch/releases .*/archive/v?@ANY_VERSION@\.tar\.gz



View it on GitLab: https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944

-- 
View it on GitLab: https://salsa.debian.org/med-team/q2-vsearch/-/commit/4d562c48a3d19006091832f26cdb47703f2ab944
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