[med-svn] r19217 - in trunk/packages/python-biopython/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Tue May 12 09:30:16 UTC 2015
Author: tille
Date: 2015-05-12 09:30:16 +0000 (Tue, 12 May 2015)
New Revision: 19217
Added:
trunk/packages/python-biopython/trunk/debian/patches/privacy_breach.patch
Modified:
trunk/packages/python-biopython/trunk/debian/README.source
trunk/packages/python-biopython/trunk/debian/changelog
trunk/packages/python-biopython/trunk/debian/control
trunk/packages/python-biopython/trunk/debian/patches/series
trunk/packages/python-biopython/trunk/debian/rules
Log:
Versioned (Build-)Depends: python-rdflib (>= 4), Prevent privacy-breach-logo, Upload to unstable
Modified: trunk/packages/python-biopython/trunk/debian/README.source
===================================================================
--- trunk/packages/python-biopython/trunk/debian/README.source 2015-05-12 08:22:42 UTC (rev 19216)
+++ trunk/packages/python-biopython/trunk/debian/README.source 2015-05-12 09:30:16 UTC (rev 19217)
@@ -69,9 +69,4 @@
So the Build-Depends from bwa is only on these architectures and the
test is consequently only run there.
-
-The test test_Phylo_CDAO for Python3 also needs python3-rdflib, but this is
-currently only avialable in experimental, so this will be ignored for the
-moment.
-
-- Andreas Tille <tille at debian.org> Tue, 04 Mar 2014 11:16:02 +0100
Modified: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog 2015-05-12 08:22:42 UTC (rev 19216)
+++ trunk/packages/python-biopython/trunk/debian/changelog 2015-05-12 09:30:16 UTC (rev 19217)
@@ -1,9 +1,11 @@
-python-biopython (1.65+dfsg-1) UNRELEASED; urgency=medium
+python-biopython (1.65+dfsg-1) unstable; urgency=medium
* New upstream version
* Apply fix for broken test from Upstream Git
+ * Versioned (Build-)Depends: python-rdflib (>= 4)
+ * Prevent privacy-breach-logo
- -- Andreas Tille <tille at debian.org> Sat, 09 May 2015 07:13:03 +0200
+ -- Andreas Tille <tille at debian.org> Tue, 12 May 2015 11:08:43 +0200
python-biopython (1.64+dfsg-5) unstable; urgency=medium
Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control 2015-05-12 08:22:42 UTC (rev 19216)
+++ trunk/packages/python-biopython/trunk/debian/control 2015-05-12 09:30:16 UTC (rev 19217)
@@ -3,7 +3,6 @@
Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
Section: python
-Testsuite: autopkgtest
Priority: optional
Build-Depends: debhelper (>= 9),
dpkg-dev (>= 1.16.1~),
@@ -32,8 +31,8 @@
python3-matplotlib,
python-pil,
python3-pil,
- python-rdflib,
- python3-rdflib,
+ python-rdflib (>= 4),
+ python3-rdflib (>= 4),
python-renderpm,
python3-renderpm,
python-psycopg2,
@@ -73,7 +72,7 @@
python-matplotlib,
python-numpy,
python-pil,
- python-rdflib,
+ python-rdflib (>= 4),
python-renderpm,
python-psycopg2,
raxml,
@@ -122,7 +121,7 @@
python3-matplotlib,
python3-numpy,
python3-pil,
- python3-rdflib,
+ python3-rdflib (>= 4),
python3-renderpm,
python3-psycopg2,
raxml,
Added: trunk/packages/python-biopython/trunk/debian/patches/privacy_breach.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/privacy_breach.patch (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/patches/privacy_breach.patch 2015-05-12 09:30:16 UTC (rev 19217)
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 12 May 2015 11:08:43 +0200
+Description: Do not use privacy-breach-logo
+
+--- a/Tests/Blast/html_msgid_29_blastx_001.html
++++ b/Tests/Blast/html_msgid_29_blastx_001.html
+@@ -42,8 +42,7 @@
+ <script language="JavaScript" type="text/javascript"><!--
+ // --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td
+ bgcolor="#336699" align="left"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td
+-bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img border="0"
+-src="http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif" alt="My NCBI help" /></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a
++bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help">My NCBI help</a></td></tr><tr><td colspan="2" nowrap="nowrap"><a
+ href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FCMD%3DPut%26DATABASE%3Dnr%26ERROR%3DMessage%2BID%252329%2BError%253A%2BQuery%2Bstring%2Bnot%2Bfound%2Bin%2Bthe%2BCGI%2Bcontext%26EXPECT%3D1e%2D07%26HITLIST%5FSIZE%3D10%26MYNCBI%5FUSER%3D%2D1%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblastx%26QUERY%3D%26USER%5FTYPE%3D0%26USER%5FTYPE%3D0" title="Click to sign in"
+ onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FCMD%3DPut%26DATABASE%3Dnr%26ERROR%3DMessage%2BID%252329%2BError%253A%2BQuery%2Bstring%2Bnot%2Bfound%2Bin%2Bthe%2BCGI%2Bcontext%26EXPECT%3D1e%2D07%26HITLIST%5FSIZE%3D10%26MYNCBI%5FUSER%3D%2D1%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblastx%26QUERY%3D%26USER%5FTYPE%3D0%26USER%5FTYPE%3D0');return false;">[Sign In]</a> <a
+ href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FCMD%3DPut%26DATABASE%3Dnr%26ERROR%3DMessage%2BID%252329%2BError%253A%2BQuery%2Bstring%2Bnot%2Bfound%2Bin%2Bthe%2BCGI%2Bcontext%26EXPECT%3D1e%2D07%26HITLIST%5FSIZE%3D10%26MYNCBI%5FUSER%3D%2D1%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblastx%26QUERY%3D%26USER%5FTYPE%3D0%26USER%5FTYPE%3D0" title="Click to register for an account"
+@@ -565,4 +564,4 @@ QBlastInfoEnd
+ <script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js"></script>
+ </body>
+
+-</html>
+\ No newline at end of file
++</html>
Modified: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series 2015-05-12 08:22:42 UTC (rev 19216)
+++ trunk/packages/python-biopython/trunk/debian/patches/series 2015-05-12 09:30:16 UTC (rev 19217)
@@ -1,2 +1,3 @@
remove_mathml-qname.patch
fix_broken_test.patch
+privacy_breach.patch
Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules 2015-05-12 08:22:42 UTC (rev 19216)
+++ trunk/packages/python-biopython/trunk/debian/rules 2015-05-12 09:30:16 UTC (rev 19217)
@@ -34,10 +34,6 @@
# This would not trigger a failure but bloats the build log with irrelevant noise
EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2
-# The following test works only with python-rdflib (>= 4)
-# If python-rdflib (>= 4) then do not exclude it - otherwise we exclude this test
-EXCLUDERDFLIB=$(shell if dpkg --compare-versions `dpkg -l python-rdflib | grep ^ii | sed 's/ii *python-rdflib *\([-.0-9]\+\) *.*/\1/'` gt 4 ; then echo ""; else echo "Phylo_CDAO" ; fi)
-
# FIXME: These tests are failing for unknown reasons and this needs to be investigated
# specifically since test_ColorSpiral and test_trie are running when called manually
# .
@@ -69,8 +65,7 @@
echo "***************************************************************************"
else
mkdir -p Tests_avoid
- if [ "$(EXCLUDERDFLIB)" != "" ] ; then echo "You might like to install python-rdflib from experimental to run Phylo_CDAO test" ; else echo "Phylo_CDAO will be done"; fi
- for avoid in $(EXCLUDEONLINE) $(EXCLUDENONFREE) $(EXCLUDENOTPACKAGED) $(EXCLUDEARCHamd64) $(EXCLUDEDATABASE) $(EXCLUDERDFLIB) $(EXCLUDEFAILINGTESTS) $(EXCLUDEPACKAGEINFLUX) \
+ for avoid in $(EXCLUDEONLINE) $(EXCLUDENONFREE) $(EXCLUDENOTPACKAGED) $(EXCLUDEARCHamd64) $(EXCLUDEDATABASE) $(EXCLUDEFAILINGTESTS) $(EXCLUDEPACKAGEINFLUX) \
; do \
mv Tests/test_$${avoid}.py Tests_avoid ; \
done
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