debian/changelog

+python-pybedtools (0.8.0-3) unstable; urgency=medium
+
+  * Mark the -doc package Multi-Arch: foreign
+  * debhelper-compat 12
+  * Testsuite: autopkgtest-pkg-python
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/control
+  * Set upstream metadata fields: Repository.
+  * Remove obsolete fields Name from debian/upstream/metadata.
+  * -doc: add ${sphinxdoc:Built-Using}
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 14 Nov 2019 13:16:33 +0100
+
 python-pybedtools (0.8.0-2) unstable; urgency=medium
 
   * Improved parsing of version of bedtool binary

debian/compat

-10

debian/control

@@ -3,8 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>,
            Steffen Moeller <moeller@debian.org>
 Section: python
+Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
                bedtools,
                cython3,
@@ -16,6 +17,8 @@ Build-Depends: debhelper (>= 10),
                python3-numpy,
                python3-numpydoc,
                python3-pandas,
+               python3-psutil,
+               python3-pytest,
                python3-yaml,
                python3-tk,
                python3-sphinx,
@@ -55,6 +58,8 @@ Description: Python 3 wrapper around BEDTools for bioinformatics work
 Package: python-pybedtools-doc
 Architecture: all
 Section: doc
+Multi-Arch: foreign
+Built-Using: ${sphinxdoc:Built-Using}
 Depends: ${misc:Depends},
          ${sphinxdoc:Depends}
 Suggests: python3-pybedtools|python-pybedtools

debian/manpages

-debian/*.1

debian/patches/parseDebianVersions.patch

+Author: Steffen Moeller <moeller@debian.org>
+Description: Fixed incompatibility with latest bedtools package
 Index: python-pybedtools/pybedtools/helpers.py
 ===================================================================
 --- python-pybedtools.orig/pybedtools/helpers.py

debian/rules

@@ -5,10 +5,13 @@ DH_VERBOSE := 1
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 export PYBUILD_NAME=pybedtools
 export MATPLOTLIBRC=$(CURDIR)/debian/
-# Add back test_issue_178 after upstream provided a patch https://github.com/daler/pybedtools/pull/228
-export PYBUILD_TEST_ARGS=--attr '!url' # --exclude='(test_issue_178)'
-export PYBUILD_BEFORE_TEST=cp {dir}/debian/mpl-expected.png {build_dir}/pybedtools/test/
-export HOME=$(shell echo $$PWD"/fakehome")
+#export PYBUILD_TEST_ARGS=--attr '!url' 
+export PYBUILD_BEFORE_TEST=cp {dir}/debian/mpl-expected.png {build_dir}/pybedtools/test/ ; python3 {dir}/setup.py install --user ; export HOME=$(CURDIR)/fakehome
+export PYBUILD_TEST_ARGS=-v --doctest-modules
+export PYBUILD_AFTER_TEST=cd {dir}/docs ; make clean doctest
+export PYBUILD_DISABLE=test  # tests aren't passing upstream
+export HOME=$(CURDIR)/fakehome
+export PATH:=$(PATH):$(HOME)/.local/bin
 
 %:
 	dh $@ --with python3,sphinxdoc --buildsystem=pybuild
@@ -27,11 +30,6 @@ override_dh_auto_install:
 	rm -fr debian/python-pybedtools/usr/bin
 	rm -fr debian/python3-pybedtools/usr/bin
 
-override_dh_auto_test:
-	@echo
-	@echo *** NOT TESTING ***
-	@echo
-
 override_dh_auto_clean:
 	/bin/rm -rf fakehome .eggs .pybuild
 	/bin/rm -rf debian/python3-pybedtools debian/files

debian/upstream/metadata

-Name: pybedtools
 Reference:
 - Author: R. K. Dale and B. S. Pedersen and A. R. Quinlan
-   Title: >
-    Pybedtools: a flexible Python library for manipulating genomic
-    datasets and annotations"
+  Title: "Pybedtools: a flexible Python library for manipulating genomic datasets\
+    \ and annotations\"\n"
   Journal: Bioinformatics
   Publisher: Oxford University Press (OUP)
   Volume: 27
@@ -23,3 +21,4 @@ Registry:
   Entry: OMICS_09508
 - Name: conda:bioconda
   Entry: pybedtools
+Repository: https://github.com/daler/pybedtools