Commit a38b5826 authored by Andreas Tille's avatar Andreas Tille
Browse files

Fix runtime test, drop autopkgtest template, fix installation

parent 18db3a94

debian/README.test

deleted100644 → 0
+0 −8
Original line number Diff line number Diff line 
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

+12 −2
Original line number Diff line number Diff line
@@ -3,7 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian. 
Uploaders: Andreas Tille <tille@debian.org>

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

+10 −22
Original line number Diff line number Diff line
@@ -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

deleted100644 → 0
+0 −3
Original line number Diff line number Diff line 
Tests: run-unit-test

Depends: @

Restrictions: allow-stderr

debian/tests/run-unit-test

deleted100644 → 0
+0 −18
Original line number Diff line number Diff line 
#!/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#