[med-svn] [Git][med-team/circlator][master] 2 commits: Rewrite test

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / circlator


Commits:
d744eeca by Andreas Tille at 2020-11-30T14:55:12+01:00
Rewrite test

- - - - -
5855b2c4 by Andreas Tille at 2020-11-30T15:21:18+01:00
Fix tests

- - - - -


8 changed files:

- + debian/README.test
- debian/changelog
- debian/control
- debian/docs
- + debian/examples
- debian/rules
- debian/tests/control
- + debian/tests/run-unit-test


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 +1,12 @@
+circlator (1.5.6-2) UNRELEASED; urgency=medium
+
+  * Rewrite autopkgtest
+    Closes: #976100
+  * Depends: canu (instead of Suggests)
+  * Skip some failing tests in autopkgtest
+
+ -- Andreas Tille <tille at debian.org>  Mon, 30 Nov 2020 14:37:58 +0100
+
 circlator (1.5.6-1) unstable; urgency=medium
 
   * Afif removed himself from Uploaders (thanks for your work on this)


=====================================
debian/control
=====================================
@@ -31,8 +31,8 @@ Depends: ${misc:Depends},
          bwa (>= 0.7.12),
          mummer,
          samtools,
-         spades
-Suggests: canu
+         spades,
+         canu
 Description: circularize genome assemblies
  Circlator is a tool to automate assembly circularization for bacterial and
  small eukaryotic genomes and produce accurate linear representations of


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


=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+circlator/tests/*.py
+circlator/tests/data


=====================================
debian/rules
=====================================
@@ -1,7 +1,7 @@
 #!/usr/bin/make -f
 
 #DH_VERBOSE = 1
-#include /usr/share/dpkg/default.mk
+include /usr/share/dpkg/default.mk
 
 export LC_ALL=C.UTF-8
 
@@ -12,3 +12,7 @@ override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	PYTHONPATH=$(CURDIR) nosetests3 -v --where=circlator/tests
 endif
+
+override_dh_installexamples:
+	dh_installexamples
+	cd debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples && tar caf data.tar.xz data && rm -rf data


=====================================
debian/tests/control
=====================================
@@ -1,2 +1,3 @@
-Test-Command: cd $ADTTMP && circlator test test-dir
+Tests: run-unit-test
+Depends: @, python3-nose
 Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+set -x
+
+pkg=circlator
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+tar xaf data.tar.xz
+sed -i "s/data_dir = os.path.join(modules_dir, 'tests', 'data')/data_dir = os.path.join(os.getcwd(), 'data')/" *.py
+
+nosetests3 -v .



View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/85828934d7a403a329ffb56c4a1630c7d19ca1ca...5855b2c40b24a1e65d2b33d4ee72911cf3a9433d

-- 
View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/85828934d7a403a329ffb56c4a1630c7d19ca1ca...5855b2c40b24a1e65d2b33d4ee72911cf3a9433d
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