debian/changelog

+python-ruffus (2.8.1-5) unstable; urgency=medium
+
+  * Remove Python2 module
+    Closes: #938152
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * rename debian/tests/control.autodep8 to debian/tests/control
+  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
+  * Set upstream metadata fields: Bug-Database, Repository, Repository-
+    Browse.
+
+ -- Andreas Tille <tille@debian.org>  Sun, 22 Dec 2019 20:04:05 +0100
+
 python-ruffus (2.8.1-4) unstable; urgency=medium
 
   * Enable reproducible build by removing non-deterministic temporary temp

debian/compat

-11

debian/control

@@ -4,40 +4,19 @@ Uploaders: Andreas Tille <tille@debian.org>
 Section: python
 Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-all,
-               python-setuptools,
-               python-pytest,
                python3-all,
                python3-setuptools,
                python3-sphinx,
                python3-sphinx-rtd-theme,
                python3-pytest,
                graphviz
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-ruffus
 Vcs-Git: https://salsa.debian.org/med-team/python-ruffus.git
 Homepage: http://www.ruffus.org.uk/
 
-Package: python-ruffus
-Architecture: all
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-         ${python:Depends},
-         graphviz
-Suggests: python-drmaa
-Description: Python computation pipeline library widely used in bioinformatics
- Ruffus is designed to allow scientific and other analyses to be automated
- with the minimum of fuss and the least effort.
- .
-  * Lightweight: Suitable for the simplest of tasks
-  * Scalable: Handles even fiendishly complicated pipelines which would cause
-    make or scons to go cross-eyed and recursive.
-  * Standard Python: No "clever magic", no pre-processing.
-  * Unintrusive: Unambitious, lightweight syntax which tries to do this one
-    small thing well.
-
 Package: python3-ruffus
 Architecture: all
 Depends: ${shlibs:Depends},

debian/python-ruffus-doc.doc-base.html

@@ -14,5 +14,5 @@ Abstract: Python computation pipeline library widely used in bioinformatics
 Section: Science/Biology
 
 Format: html
-Files: /usr/share/doc/python-ruffus/html
-Index: /usr/share/doc/python-ruffus/html/index.html
+Files: /usr/share/doc/python-ruffus-doc/html
+Index: /usr/share/doc/python-ruffus-doc/html/index.html

debian/python-ruffus-doc.doc-base.pdf

@@ -14,4 +14,4 @@ Abstract: Python computation pipeline library widely used in bioinformatics
 Section: Science/Biology
 
 Format: pdf
-Files: /usr/share/doc/python-ruffus/ruffus.pdf.gz
+Files: /usr/share/doc/python-ruffus-doc/ruffus.pdf.gz

debian/rules

@@ -9,7 +9,7 @@ docpkg:=$(DEB_SOURCE)-doc
 export PYBUILD_NAME=ruffus
 
 %:
-	dh $@ --with python2,python3,sphinxdoc --buildsystem=pybuild
+	dh $@ --with python3,sphinxdoc --buildsystem=pybuild
 
 override_dh_auto_build:
 	dh_auto_build
@@ -18,6 +18,7 @@ override_dh_auto_build:
 override_dh_installdocs:
 	dh_installdocs -ppython-ruffus-doc doc/_build/html
 	dh_installdocs -A
+	find debian -name run_all_unit_tests.cmd -delete
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
@@ -60,7 +61,6 @@ override_dh_install:
 	find debian/python3-$(PYBUILD_NAME)/usr/lib/python3*/dist-packages/ruffus/test -name "*.py" -exec sed -i 's+^\(#!/usr/bin/.*python\)[[:space:]]*$$+\13+' \{\} \;
 	# leave only the test starter that fits Python version
 	find debian/python3-$(PYBUILD_NAME) -name run_all_unit_tests.cmd -delete
-	find debian/python-$(PYBUILD_NAME) -name run_all_unit_tests3.cmd -delete
 	sed -i '1s?^#! */usr/bin/env *python *$$?#!/usr/bin/python3?' `grep -Rl '^#! */usr/bin/env *python *$$' debian/python3-$(PYBUILD_NAME)`
 
 override_dh_fixperms:

debian/tests/run-unit-test

 #!/bin/sh -e
 
 pkg=python-ruffus
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
 mkdir ruffus
 cd ruffus
 cp -a /usr/share/doc/python-ruffus-doc/test .
 cd test
 find . -type f -name "*.gz" -exec gunzip \{\} \;
-# mod +x [a-z]*.py
 
 export LC_ALL=C.UTF-8
-export HOME=$ADTTMP
-for testscript in run_all_unit_tests*.cmd ; do
-    # exclude tests with known issues ... should not be needed any more since fix_test.patch
-#    sed -i -e 's/\(unittest test_file_name_parameters.*\)\\/\1 true/' \
-#           -e 's/\(unittest test_ruffus_utility.*\)\\/\1 true/' \
-#        $testscript
-    bash $testscript
-done
+export HOME=$AUTOPKGTEST_TMP
+bash run_all_unit_tests3.cmd

debian/upstream/metadata

 Reference:
   Author: Leo Goodstadt
- Title: "Ruffus: A Lightweight Python Library for Computational Pipelines"
+  Title: 'Ruffus: A Lightweight Python Library for Computational Pipelines'
   Journal: Bioinformatics
   Year: 2010
   Volume: 26
@@ -8,10 +8,8 @@ Reference:
   Pages: 2778-9
   DOI: 10.1093/bioinformatics/btq524
   PMID: 20847218
- URL: "http://bioinformatics.oxfordjournals.org/content/early/\
-  2010/09/16/bioinformatics.btq524"
- ePrint: "http://bioinformatics.oxfordjournals.org/content/early/\
-  2010/09/16/bioinformatics.btq524.full.pdf+html"
+  URL: http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524
+  ePrint: http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524.full.pdf+html
 Registry:
 - Name: OMICtools
   Entry: OMICS_07398
@@ -21,3 +19,6 @@ Registry:
   Entry: NA
 - Name: conda:bioconda
   Entry: ruffus
+Bug-Database: https://github.com/bunbun/ruffus/issues
+Repository: https://github.com/bunbun/ruffus.git
+Repository-Browse: https://github.com/bunbun/ruffus