[med-svn] [Git][med-team/fieldbioinformatics][master] Step forward with some autopkgtest. Please note: The current test script is...

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / fieldbioinformatics


Commits:
0a85c1b2 by Andreas Tille at 2020-06-22T14:19:15+02:00
Step forward with some autopkgtest.  Please note:  The current test script is requiring downloading data which is not possible at build time.  But as far as I learned it can be done in autopkgtest.  But it should be tested on a local machine first

- - - - -


4 changed files:

- debian/control
- + debian/fieldbioinformatics-examples.install
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/control
=====================================
@@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Malihe Asemani <ml.asemani at gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (=12), python3-all, python3-setuptools, dh-python
+Build-Depends: debhelper-compat (=12), python3, python3-setuptools, dh-python
 Standards-Version: 4.1.3
 Vcs-Browser: https://salsa.debian.org/med-team/fieldbioinformatics
 Vcs-Git: https://salsa.debian.org/med-team/fieldbioinformatics.git
 Homepage: https://github.com/artic-network/fieldbioinformatics
 
 Package: fieldbioinformatics
-Architecture: any
+Architecture: all
 Depends: ${python3:Depends},
          ${misc:Depends}
 Description: pipeline for working with virus sequencing data sequenced with nanopore
@@ -19,3 +19,17 @@ Description: pipeline for working with virus sequencing data sequenced with nano
  protocol to take the output from the sequencing protocol to consensus
  genome sequences. Includes basecalling, de-multiplexing, mapping, polishing
  and consensus generation.
+
+Package: fieldbioinformatics-examples
+Architecture: all
+Depends: ${python3:Depends},
+         ${misc:Depends}
+Enhances: fieldbioinformatics
+Description: pipeline for working with virus sequencing data sequenced with nanopore (examples)
+ This is the ARTIC bioinformatics pipeline for working with virus sequencing
+ data, sequenced with nanopore. Nanopore is a complete bioinformatics
+ protocol to take the output from the sequencing protocol to consensus
+ genome sequences. Includes basecalling, de-multiplexing, mapping, polishing
+ and consensus generation.
+ .
+ This package contains some example data.


=====================================
debian/fieldbioinformatics-examples.install
=====================================
@@ -0,0 +1 @@
+test*	usr/share/doc/fieldbioinformatics/examples


=====================================
debian/rules
=====================================
@@ -21,8 +21,8 @@ export PYBUILD_NAME=fieldbioinformatics
 %:
 	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)))
+	echo "Test is downloading extra data and thus can not be running here"
+	# ./test-runner.sh nanopolish
+endif


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,14 +1,11 @@
 #!/bin/bash
 set -e
 
-pkg=#PACKAGENAME#
+pkg=fieldbioinformatics
 
 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
 
@@ -16,4 +13,6 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
 
-#do_stuff_to_test_package#
+gunzip -r *
+
+bash ./test-runner.sh nanopolish



View it on GitLab: https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/0a85c1b257a6119937875df5c7a5a9a8878d0ee9

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View it on GitLab: https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/0a85c1b257a6119937875df5c7a5a9a8878d0ee9
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