[med-svn] [Git][med-team/python-biopython][master] 5 commits: Fix encoding issue
Andreas Tille
gitlab at salsa.debian.org
Wed May 2 14:59:22 BST 2018
Andreas Tille pushed to branch master at Debian Med / python-biopython
Commits:
5e0cc855 by Andreas Tille at 2018-05-02T15:59:16+02:00
Fix encoding issue
- - - - -
1c75d7f8 by Andreas Tille at 2018-05-02T15:59:16+02:00
Fix Python version in Suggestes
- - - - -
036860a5 by Andreas Tille at 2018-05-02T15:59:16+02:00
Make sure Doc dir ends up in python-biopython-doc package
- - - - -
eb139bdb by Andreas Tille at 2018-05-02T15:59:16+02:00
Drop python3-reportlab from Suggests which is also in Depends
- - - - -
a7c393ae by Andreas Tille at 2018-05-02T15:59:16+02:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/fix_encoding.patch
- + debian/patches/more_general_utf-8_reader.patch
- debian/patches/series
- debian/python-biopython-doc.docs
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-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 at debian.org> Thu, 05 Apr 2018 15:14:51 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 06 Apr 2018 09:03:06 +0200
python-biopython (1.70+dfsg-4) unstable; urgency=medium
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/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
=====================================
--- /dev/null
+++ b/debian/patches/fix_encoding.patch
@@ -0,0 +1,22 @@
+Author: Klaus Zimmermann <klaus_zimmermann at 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
=====================================
--- /dev/null
+++ b/debian/patches/more_general_utf-8_reader.patch
@@ -0,0 +1,19 @@
+Author: Piotr Ożarowski <piotr at 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
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,4 @@
remove_mathml-qname.patch
privacy_breach.patch
+fix_encoding.patch
+more_general_utf-8_reader.patch
=====================================
debian/python-biopython-doc.docs
=====================================
--- a/debian/python-biopython-doc.docs
+++ b/debian/python-biopython-doc.docs
@@ -1,4 +1,4 @@
-Doc/
+Doc
debian/README.test
debian/tests/run-unit-test
debian/Tests_fixme
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/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
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/compare/fb1a64085106c49dbf73eddfe9e8066a35c84dcc...a7c393ae3f9361c484fddad795ae1a2039366ada
---
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/compare/fb1a64085106c49dbf73eddfe9e8066a35c84dcc...a7c393ae3f9361c484fddad795ae1a2039366ada
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