[med-svn] [Git][med-team/qcat][master] 6 commits: Fix test

Wed Apr 22 13:37:04 BST 2020


Andreas Tille pushed to branch master at Debian Med / qcat


Commits:
f9416489 by Andreas Tille at 2020-04-22T11:40:14+02:00
Fix test

- - - - -
a61b1330 by Andreas Tille at 2020-04-22T13:17:00+02:00
Try hard to get test running as autopkgtest

- - - - -
2701a2f0 by Andreas Tille at 2020-04-22T13:17:39+02:00
Add ITP bug

- - - - -
6a5eb4a5 by Andreas Tille at 2020-04-22T14:30:10+02:00
Finally files should be in place and test should run

- - - - -
9d63accf by Andreas Tille at 2020-04-22T14:31:33+02:00
Upload to new

- - - - -
bec225ab by Andreas Tille at 2020-04-22T14:34:55+02:00
Add ending newline

- - - - -


9 changed files:

- debian/README.test
- debian/changelog
- debian/control
- + debian/qcat-examples.install
- + debian/qcat.docs
- + debian/qcat.install
- debian/manpages → debian/qcat.manpages
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
@@ -1,7 +1,8 @@
 Notes on how this package can be tested.
 ────────────────────────────────────────
 
-This package can be tested by running the provided test:
+This package can be tested by installing qcat-examples and than
+running the provided test:
 
     sh run-unit-test
 


=====================================
debian/changelog
=====================================
@@ -1,6 +1,5 @@
-qcat (1.1.0-1) UNRELEASED; urgency=medium
+qcat (1.1.0-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
-  TODO: https://github.com/jeffdaily/parasail-python
+  * Initial release (Closes: #958458)
 
- -- Andreas Tille <tille at debian.org>  Wed, 22 Apr 2020 09:11:59 +0200
+ -- Andreas Tille <tille at debian.org>  Wed, 22 Apr 2020 14:31:27 +0200


=====================================
debian/control
=====================================
@@ -25,6 +25,7 @@ Depends: ${python3:Depends},
          python3-biopython,
          python3-parasail,
          python3-yaml
+Suggests: qcat-examples
 Description: demultiplexing Oxford Nanopore reads from FASTQ files
  Qcat is a command-line tool for demultiplexing Oxford Nanopore reads
  from FASTQ files. It accepts basecalled FASTQ files and splits the reads
@@ -32,3 +33,20 @@ Description: demultiplexing Oxford Nanopore reads from FASTQ files
  demultiplexing algorithms used in albacore/guppy and EPI2ME available to
  be used locally with FASTQ files. Currently qcat implements the EPI2ME
  algorithm.
+
+Package: qcat-examples
+Architecture: all
+Depends: ${misc:Depends},
+         python3-pytest,
+         python3-pytest-runner,
+         python3-pytest-cov
+Enhances: qcat
+Description: demultiplexing Oxford Nanopore reads from FASTQ files (examples)
+ Qcat is a command-line tool for demultiplexing Oxford Nanopore reads
+ from FASTQ files. It accepts basecalled FASTQ files and splits the reads
+ into separate FASTQ files based on their barcode. Qcat makes the
+ demultiplexing algorithms used in albacore/guppy and EPI2ME available to
+ be used locally with FASTQ files. Currently qcat implements the EPI2ME
+ algorithm.
+ .
+ This package contains examples to test qcat.


=====================================
debian/qcat-examples.install
=====================================
@@ -0,0 +1,2 @@
+pytest.ini				usr/share/doc/qcat/examples
+debian/tests/run-unit-test		usr/share/doc/qcat


=====================================
debian/qcat.docs
=====================================
@@ -0,0 +1 @@
+debian/README.test


=====================================
debian/qcat.install
=====================================
@@ -0,0 +1 @@
+usr


=====================================
debian/manpages → debian/qcat.manpages
=====================================


=====================================
debian/rules
=====================================
@@ -4,28 +4,15 @@
 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 PYBUILD_BEFORE_TEST=cp -r {dir}/$(DEB_SOURCE)/test {build_dir}/$(DEB_SOURCE) ;
 
 %:
 	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
-
-### 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 -name .coverage -delete
+	mkdir -p debian/$(DEB_SOURCE)-examples/usr/share/doc/$(DEB_SOURCE)/examples/$(DEB_SOURCE)
+	mv debian/$(DEB_SOURCE)/usr/lib/python3*/dist-packages/$(DEB_SOURCE)/test debian/$(DEB_SOURCE)-examples/usr/share/doc/$(DEB_SOURCE)/examples/$(DEB_SOURCE)
+	find debian -name __pycache__ -type d | xargs rm -rf


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,19 +1,18 @@
 #!/bin/bash
 set -e
 
-pkg=#PACKAGENAME#
+pkg=qcat
 
 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
 
+mkdir "${AUTOPKGTEST_TMP}"/${pkg}
 cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
 
-#do_stuff_to_test_package#
+pytest-3



View it on GitLab: https://salsa.debian.org/med-team/qcat/-/compare/1b8e86c5aa8e74d0b4096a06eca293edf9bc8c7a...bec225ab35f0765509eb6da9cb80ebdbe4baa7c7

-- 
View it on GitLab: https://salsa.debian.org/med-team/qcat/-/compare/1b8e86c5aa8e74d0b4096a06eca293edf9bc8c7a...bec225ab35f0765509eb6da9cb80ebdbe4baa7c7
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