debian/changelog

-python-cogent (1.9-12) UNRELEASED; urgency=medium
+python-cogent (1.9-12) unstable; urgency=medium
 
   * Add registry data
   * Testsuite: autopkgtest-pkg-python
@@ -9,8 +9,14 @@ python-cogent (1.9-12) UNRELEASED; urgency=medium
   * Standards-Version: 4.1.4
   * Fix suite fails with latest matplotlib
     Closes: #899205
-
- -- Andreas Tille <tille@debian.org>  Tue, 05 Jun 2018 21:47:29 +0200
+  * Fix privacy issue in doc
+  * Drop obsolete file debian/pyversions
+  * Drop unneeded get-orig-source target
+  * Do not parse d/changelog
+  * Rename debian/tests/control to debian/tests/control.autodep8
+  * Remove useless doctree files
+
+ -- Andreas Tille <tille@debian.org>  Wed, 06 Jun 2018 11:10:01 +0200
 
 python-cogent (1.9-11) unstable; urgency=medium
 

debian/patches/ignore_numpy_test_issue.patch

@@ -7,10 +7,10 @@ Description: Skip test featuring wrong numpy usage
  ...
  TypeError: 'numpy.float64' object cannot be interpreted as an index
  .
- The issue occured after upgrading from Numpy 1.11.2 to 1.12.0~b1 which
+ The issue occurred after upgrading from Numpy 1.11.2 to 1.12.0~b1 which
  has cause also other packages test suites failures.  Since this version
  of Cogent is in low maintenance mode it will probably not be adapted to
- any new Numpy versions so skiping two tests might be the most apropriate
+ any new Numpy versions so skipping two tests might be the most appropriate
  step to deal with this issue
 Bug-Debian: https://bugs.debian.org/848746
 Author: Andreas Tille <tille@debian.org>

debian/patches/privacy.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 05 Jun 2018 21:47:29 +0200
+Description: Avoid insertion of Google phone home code
+
+--- a/doc/templates/layout.html
++++ b/doc/templates/layout.html
+@@ -1,10 +1,5 @@
+ {% extends "!layout.html" %}
+  
+-{% block extrahead %}     
+-<script type="text/javascript" src="http://www.google.com/jsapi?key=ABQIAAAAbW_pA971hrPgosv-Msv7hRQZ4X-jPDmWcshBrz2j7-fJvuUABRTGWmdiw2G89JpgztGlFGG8hDxRAw"></script>\
+-<script type="text/javascript" src="{{ pathto("_static/google_feed.js",1)}}"></script>
+-{% endblock %}
+-
+ {% block sidebartoc %}
+ <div class="news">
+ <table id="feed"><tr><td><h3><a href="http://pycogent.wordpress.com/">PyCogent News and Announcements</a></h3></td>

debian/patches/raxml_unsupported_version.patch

 Author: Andreas Tille <tille@debian.org>
 Last-Update: Thu, 21 May 2015 08:47:01 +0200
-Description: The test is checking for an old verison of raxml
+Description: The test is checking for an old version of raxml
  for no good reason
 
 --- a/tests/test_app/test_raxml_v730.py

debian/patches/series

@@ -11,3 +11,4 @@ ignore_numpy_test_issue.patch
 usr_bin_ls.patch
 numpy_xor.patch
 numpy-doctests.patch
+privacy.patch

debian/patches/usr_bin_ls.patch

 Author: Andreas Tille <tille@debian.org>
 Last-Update: Fri, 16 Jun 2017 13:30:22 +0200
-Desription: ls will be moved from /bin/ls to /usr/bin/ls - lets skip
+Description: ls will be moved from /bin/ls to /usr/bin/ls - lets skip
  this test which does not make real sense anyway.
 
 --- a/tests/test_util/test_misc.py

debian/python-cogent-doc.docs

-tests

debian/python-cogent.install

+tests	usr/share/doc/python-cogent

debian/pyversions

-2.4-

debian/rules

@@ -41,7 +41,8 @@ FAIL_ON_S390X_TESTS := test_maths.test_optimisers \
 FAIL_ON_MIPS_TESTS := test_seqsim.test_sequence_generators
 
 export PYBUILD_NAME=cogent
-PKG := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+
+include /usr/share/dpkg/default.mk
 
 %:
 	dh $@ --with python2 --buildsystem=pybuild
@@ -59,7 +60,7 @@ override_dh_auto_build:
 	dh_auto_build
 	cd doc; $(MAKE) html
 	# remove superfluous files and dirs
-	rm -f doc/_build/doctrees/COGENT_LICENSE.doctree
+	find doc/_build -name "*.doctree*" -delete
 	rm -f doc/_build/html/_sources/COGENT_LICENSE.txt
 	rm -f doc/_build/html/_static/jquery.js
 	rm -f doc/_build/html/_static/underscore.js
@@ -74,7 +75,8 @@ override_dh_compress:
 
 override_dh_installdocs:
 	dh_installdocs
-	rm -rf debian/$(PKG)/usr/share/doc/$(PKG)/html/_sources
+	rm -rf debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/html/_sources
+	find debian -name doctrees -type d | xargs rm -rf
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck, $(DEB_BUILD_OPTIONS)))
@@ -110,8 +112,3 @@ endif
 	mv tests/alltests.py~ tests/alltests.py
 	find tests -name "*.pyc" -delete
 endif
-
-get-orig-source:
-	mkdir -p ../tarballs
-	uscan --verbose --force-download --destdir=../tarballs
-