debian/changelog

-python-biopython (1.71+dfsg-1) UNRELEASED; urgency=medium
+python-biopython (1.71+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * Standards-Version: 4.1.3
@@ -6,8 +6,10 @@ python-biopython (1.71+dfsg-1) UNRELEASED; urgency=medium
   * debhelper 11
   * Add dh-python to Build-Depends since this will be dropped from python3's
     Depends soon
+  * Fix Python version in Suggestes
+  * Make sure Doc dir ends up in python-biopython-doc package
 
- -- Andreas Tille <tille@debian.org>  Thu, 05 Apr 2018 15:14:51 +0200
+ -- Andreas Tille <tille@debian.org>  Fri, 06 Apr 2018 09:03:06 +0200
 
 python-biopython (1.70+dfsg-4) unstable; urgency=medium
 

debian/control

@@ -117,7 +117,6 @@ Depends: ${python3:Depends},
 Recommends: python-biopython-doc (= ${source:Version}),
             ncbi-blast+
 Suggests: python3-tk,
-          python-reportlab,
           bwa [any-amd64],
           clustalo,
           clustalw,
@@ -131,7 +130,7 @@ Suggests: python3-tk,
           phyml [any-amd64 any-i386 arm64 armhf sparc64],
           prank,
           probcons,
-          python-mysqldb,
+          python3-mysqldb,
           python3-matplotlib,
           python3-numpy,
           python3-pil,

debian/patches/fix_encoding.patch

+Author: Klaus Zimmermann <klaus_zimmermann@gmx.de>
+Last-Update: Thu, 5 Apr 2018 16:39:47 +0200
+Origin: https://lists.debian.org/debian-python/2018/04/msg00025.html
+Description: Fix encoding issue in README.rst
+
+--- a/README.rst
++++ b/README.rst
+@@ -168,12 +168,12 @@ deprecated).
+   pacakge).
+ 
+ - Appropriate C compiler for your version of Python, for example GCC on Linux,
+-  MSVC on Windows. For Mac OS X, or as it is now branded, macOS, use Apple’s
++  MSVC on Windows. For Mac OS X, or as it is now branded, macOS, use Apple's
+   command line tools, which can be installed with the terminal command::
+ 
+       xcode-select --install
+ 
+-  This will offer to install Apple’s XCode development suite - you can, but it
++  This will offer to install Apple's XCode development suite - you can, but it
+   is not needed and takes a lot of disk space.
+ 
+ - NumPy, see http://www.numpy.org - this package is used in ``Bio.Cluster``,

debian/patches/more_general_utf-8_reader.patch

+Author: Piotr Ożarowski <piotr@debian.org>
+Last-Update: Thu, 5 Apr 2018 16:35:44 +0200
+Origin: https://lists.debian.org/debian-python/2018/04/msg00023.html
+Description: In case there might be some more encoding issues that
+ are not yet fixed by fix_encoding.patch
+
+--- a/setup.py
++++ b/setup.py
+@@ -431,8 +431,8 @@ for line in open('Bio/__init__.py'):
+ # We now load in our reStructuredText README.rst file to pass
+ # explicitly in the metadata since at time of writing PyPI
+ # did not do this for us:
+-with open("README.rst") as handle:
+-    readme_rst = handle.read()
++with open("README.rst", 'rb') as handle:
++    readme_rst = handle.read().decode('UTF-8')
+ 
+ setup(name='biopython',
+       version=__version__,

debian/patches/series

 remove_mathml-qname.patch
 privacy_breach.patch
+fix_encoding.patch
+more_general_utf-8_reader.patch

debian/python-biopython-doc.docs

-Doc/
+Doc
 debian/README.test
 debian/tests/run-unit-test
 debian/Tests_fixme

debian/rules

@@ -122,12 +122,16 @@ else
 endif
 
 override_dh_installdocs-indep:
-	dh_installdocs
+	dh_installdocs -i
 	find debian -name __pycache__ -type d | xargs rm -rf
 	find debian -name example.fastq.gz
 	# dh_installdocs seems to refuse copying zero length files (for instance Tests/Blast/tab_2226_tblastn_002.txt) but these are needed for the tests as well
 	cp -a debian/tmp_tests/* $(CURDIR)/debian/python-biopython-doc/usr/share/doc/python-biopython-doc/
 	find debian -name .cvsignore -delete
+	# no idea why Doc dir ends up in /usr/share/doc/python-biopython since biopython 1.71 - just move it into right place
+	if [ -d debian/python-biopython-doc/usr/share/doc/python-biopython/Doc ] ; then \
+	    mv debian/python-biopython-doc/usr/share/doc/python-biopython/Doc debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc ; \
+	fi
 	cd debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc && make clean
 	find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -name Makefile -delete
 	find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -name "*.aux" -delete