[med-svn] [Git][med-team/atropos][master] Fix runtime test, drop autopkgtest template, fix installation

[Andreas Tille]

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 <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at 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
=====================================
@@ -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
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