[med-svn] [python-biopython] 03/03: Preparations for new Upstream versions

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a commit to branch master
in repository python-biopython.

commit 93f39f784e19221cea55ff26530d5d4ec627f692
Author: Steffen Moeller <moeller at debian.org>
Date:   Mon Jul 24 15:32:46 2017 +0200

    Preparations for new Upstream versions
---
 debian/changelog                         | 11 +++++++++++
 debian/control                           |  2 ++
 debian/patches/fix_test_phyml_tool.patch | 18 ------------------
 debian/patches/series                    |  3 +--
 debian/rules                             | 22 ++++++++++++++--------
 debian/upstream/metadata                 |  7 +++++++
 6 files changed, 35 insertions(+), 28 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 90fee5d..5444042 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+python-biopython (1.70+dfsg-1) unstable; urgency=medium
+
+  * Team upload
+
+  * New upstream release.
+  * debian/upstream/metadata: Added references to
+    OMICtools, bio.tools, RRID
+  * debian/rules: Merged two redundant clean overrides
+
+ -- Steffen Moeller <moeller at debian.org>  Sun, 23 Jul 2017 18:08:39 +0200
+  
 python-biopython (1.68+dfsg-3) unstable; urgency=medium
 
   * (Build-)Depend: phyml only on those architectures where it is available
diff --git a/debian/control b/debian/control
index d4ac52e..b0bc428 100644
--- a/debian/control
+++ b/debian/control
@@ -12,6 +12,8 @@ Build-Depends: debhelper (>= 10),
                flex,
                python-reportlab,
                python3-reportlab,
+               python-numpy,
+               python3-numpy,
                hevea,
                texlive-latex-base,
                texlive-latex-extra,
diff --git a/debian/patches/fix_test_phyml_tool.patch b/debian/patches/fix_test_phyml_tool.patch
deleted file mode 100644
index 75014df..0000000
--- a/debian/patches/fix_test_phyml_tool.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Bug-Debian: https://bugs.debian.org/799820
-Forwarded: https://bugs.debian.org/799820#12
-Last-Update: Wed, 23 Sep 2015 10:34:47 +0200
-Description: Fix test_phyml_tool.py
- Remove ".txt" extention that should not be there
-
---- a/Tests/test_phyml_tool.py
-+++ b/Tests/test_phyml_tool.py
-@@ -52,7 +52,7 @@ class AppTests(unittest.TestCase):
-             self.assertTrue(len(out) > 0)
-             self.assertEqual(len(err), 0)
-             # Check the output tree
--            tree = Phylo.read(EX_PHYLIP + '_phyml_tree.txt', 'newick')
-+            tree = Phylo.read(EX_PHYLIP + '_phyml_tree', 'newick')
-             self.assertEqual(tree.count_terminals(), 4)
-         finally:
-             # Clean up generated files
diff --git a/debian/patches/series b/debian/patches/series
index 0336d64..f9f0bf7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
 remove_mathml-qname.patch
 privacy_breach.patch
-fix_test_phyml_tool.patch
-test_phenotype_fit_on_arm64.patch
+#test_phenotype_fit_on_arm64.patch
diff --git a/debian/rules b/debian/rules
index 2578448..138e1e1 100755
--- a/debian/rules
+++ b/debian/rules
@@ -58,6 +58,20 @@ EXCLUDEPACKAGEINFLUX=samtools_tool
 override_dh_auto_clean:
 	dh_auto_clean
 	cd Doc && make distclean
+	rm -f Doc/install/Installation.pdf
+	rm -f Doc/install/Installation.txt
+	rm -f Doc/install/Installation.html
+	rm -f Doc/Tutorial.pdf Doc/biopdb_faq.pdf
+	rm -f Doc/Tutorial/*.aux
+	rm -rf biopython.egg-info
+	
+	dh_auto_clean
+	if [ -d Tests_avoid ] ; then \
+	    mv Tests_avoid/* Tests ; \
+	    rmdir Tests_avoid ; \
+	fi
+	
+	rm -rf debian/tmp_tests
 
 override_dh_auto_build:
 	dh_auto_build
@@ -119,11 +133,3 @@ override_dh_installdocs-indep:
 	find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -name "*.aux" -delete
 	find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -name "*.lyx" -delete
 	find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -type d -empty -delete
-
-override_dh_auto_clean:
-	dh_auto_clean
-	if [ -d Tests_avoid ] ; then \
-	    mv Tests_avoid/* Tests ; \
-	    rmdir Tests_avoid ; \
-	fi
-	rm -rf debian/tmp_tests
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
index 1f7b652..eb737ba 100644
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -10,3 +10,10 @@ Reference:
   DOI: 10.1093/bioinformatics/btp163
   URL: http://bioinformatics.oxfordjournals.org/content/early/2009/03/20/bioinformatics.btp163.abstract
   eprint: http://bioinformatics.oxfordjournals.org/content/early/2009/03/20/bioinformatics.btp163.full.pdf+html
+Registry:
+  - Name: RRID
+    Entry: SCR_007173
+  - Name: bio.tools
+    Entry: Biopython
+  - Name: OMICtools
+    Entry: OMIC_04850

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-biopython.git