debian/changelog

+python-pyvcf (0.6.8+git20170215.476169c-2) unstable; urgency=medium
+
+  * Drop Python2 support
+    Closes: #938106
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Secure URI in copyright format
+  * Remove trailing whitespace in debian/copyright
+  * Remove unused lintian-override
+
+ -- Andreas Tille <tille@debian.org>  Mon, 02 Sep 2019 17:03:56 +0200
+
 python-pyvcf (0.6.8+git20170215.476169c-1) unstable; urgency=medium
 
   * d/watch: use git mode

debian/compat

-11

debian/control

@@ -4,41 +4,16 @@ 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,
-               cython,
-               python-dev,
-               python-setuptools,
                cython3,
                python3-all-dev,
                python3-setuptools
-Standards-Version: 4.1.5
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-pyvcf
 Vcs-Git: https://salsa.debian.org/med-team/python-pyvcf.git
 Homepage: https://pypi.python.org/pypi/PyVCF
 
-Package: python-pyvcf
-Architecture: any
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-         ${python:Depends}
-Description: Variant Call Format (VCF) parser for Python
- The Variant Call Format (VCF) specifies the format of a text file used
- in bioinformatics for storing gene sequence variations. The format has
- been developed with the advent of large-scale genotyping and DNA
- sequencing projects, such as the 1000 Genomes Project.
- .
- The intent of this module is to mimic the ``csv`` module in the Python
- stdlib, as opposed to more flexible serialization formats like JSON or
- YAML. ``vcf`` will attempt to parse the content of each record based on
- the data types specified in the meta-information lines -- specifically
- the ##INFO and
- ##FORMAT lines. If these lines are missing or incomplete, it will check
- against the reserved types mentioned in the spec. Failing that, it will
- just return strings.
- .
- This package provides the Python 2 modules.
-
 Package: python3-pyvcf
 Architecture: any
 Depends: ${shlibs:Depends},
@@ -86,7 +61,7 @@ Description: helper scripts for Variant Call Format (VCF) parser
 Package: python-pyvcf-examples
 Architecture: all
 Depends: ${misc:Depends}
-Suggests: python3-pyvcf | python-pyvcf
+Suggests: python3-pyvcf
 Description: Example data for Variant Call Format (VCF) parser for Python
  The Variant Call Format (VCF) specifies the format of a text file used
  in bioinformatics for storing gene sequence variations. The format has

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: PyVCF
 Upstream-Contact: James Casbon <casbon@gmail.com>
 Source: https://pypi.python.org/pypi/PyVCF
@@ -16,15 +16,15 @@ License: BSD-3-clause
  modification, are permitted provided that the following conditions are met:
  .
  1. Redistributions of source code must retain the above copyright notice, this
-    list of conditions and the following disclaimer.  
+    list of conditions and the following disclaimer.
  .
  2. Redistributions in binary form must reproduce the above copyright notice, this
     list of conditions and the following disclaimer in the documentation and/or
-    other materials provided with the distribution.  
+    other materials provided with the distribution.
  .
  3. Neither the name of the Population Genetics Technologies Ltd nor the names of
     its contributors may be used to endorse or promote products derived from this
-    software without specific prior written permission.  
+    software without specific prior written permission.
  .
  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED

debian/python3-pyvcf.lintian-overrides

-# parser.py is different for Python3 versions - so accept this
-python3-pyvcf: python-module-in-wrong-location usr/lib/python3.7/dist-packages/vcf/ usr/lib/python3/dist-packages/vcf/
-python3-pyvcf: python-module-in-wrong-location usr/lib/python3.7/dist-packages/vcf/parser.py usr/lib/python3/dist-packages/vcf/parser.py
-

debian/rules

@@ -11,22 +11,21 @@ examplesdir=debian/python-$(PYBUILD_NAME)-examples/usr/share/doc/python-$(PYBUIL
 helperdir=debian/$(PYBUILD_NAME)/usr
 
 %:
-	dh $@ --with python2,python3 --buildsystem=pybuild
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_install:
 	dh_install
 	# move testdata to separate dir
 	mkdir -p $(examplesdir)
-	mv `find debian/python-$(PYBUILD_NAME) -type d -name test | head -n 1` $(examplesdir)
+	mv `find debian/python3-$(PYBUILD_NAME) -type d -name test | head -n 1` $(examplesdir)
 	find debian/python3-$(PYBUILD_NAME) -type d -name test | xargs rm -rf
-	find $(examplesdir) -name "*.pyc" -delete
+	find $(examplesdir) -name "__pycache__" | xargs rm -rf
 	mkdir -p $(helperdir)
 	mv debian/python3-$(PYBUILD_NAME)/usr/bin $(helperdir)
 	# strip .py extension
 	for py in $(helperdir)/bin/*.py ; do \
 	    mv $${py} $(helperdir)/bin/`basename $${py} .py` ; \
 	done
-	rm -rf debian/python-$(PYBUILD_NAME)/usr/bin
 
 override_dh_python3:
 	dh_python3 --verbose