Andreas Tille pushed to branch master at Debian Med / atropos
Commits: a38b5826 by Andreas Tille at 2019-04-12T13:17:49Z Fix runtime test, drop autopkgtest template, fix installation - - - - - 5 changed files: - − debian/README.test - debian/control - debian/rules - − debian/tests/control - − debian/tests/run-unit-test Changes: ===================================== debian/README.test deleted ===================================== @@ -1,8 +0,0 @@ -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/control ===================================== @@ -3,7 +3,14 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 12~) +Build-Depends: debhelper (>= 12~), + dh-python, + cython3, + python3-dev, + python3-setuptools, + python3-pytest <!nocheck>, + python3-jinja2 <!nocheck>, + python3-pysam <!nocheck> Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/atropos Vcs-Git: https://salsa.debian.org/med-team/atropos.git @@ -12,7 +19,10 @@ Homepage: https://github.com/jdidion/atropos Package: atropos Architecture: any Depends: ${shlibs:Depends}, - ${misc:Depends} + ${misc:Depends}, + python3, + python3-pysam +Recommends: python3-jinja2 Description: NGS read trimming tool that is specific, sensitive, and speedy Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of the venerable Cutadapt read trimmer, with the ===================================== debian/rules ===================================== @@ -3,29 +3,17 @@ # 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 +export DEB_BUILD_MAINT_OPTIONS=hardening=+all %: - dh $@ + dh $@ --with python3 --buildsystem=pybuild -### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected -#override_dh_auto_test: -#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) -# do_stuff_for_testing -#endif +override_dh_auto_test: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + \ + dh_auto_test -- --before-test="ln -s $(CURDIR)/tests/cut {build_dir}/tests && ln -s $(CURDIR)/tests/data {build_dir}/tests" +endif -### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script -#get-orig-source: -# . debian/get-orig-source +override_dh_install: + dh_install + find debian -type d -name __pycache__ | xargs rm -rf ===================================== debian/tests/control deleted ===================================== @@ -1,3 +0,0 @@ -Tests: run-unit-test -Depends: @ -Restrictions: allow-stderr ===================================== debian/tests/run-unit-test deleted ===================================== @@ -1,18 +0,0 @@ -#!/bin/bash -set -e - -pkg=#PACKAGENAME# - -if [ "${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# View it on GitLab: https://salsa.debian.org/med-team/atropos/commit/a38b582606695b49806ed1e6a4d02216a2d60db4 -- View it on GitLab: https://salsa.debian.org/med-team/atropos/commit/a38b582606695b49806ed1e6a4d02216a2d60db4 You're receiving this email because of your account on salsa.debian.org.
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