[med-svn] r17696 - in trunk/packages/python-pynast/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-08-12 09:45:05 +0000 (Tue, 12 Aug 2014)
New Revision: 17696

Added:
   trunk/packages/python-pynast/trunk/debian/patches/avoid_python-mpi4py_missing_warning.patch
Modified:
   trunk/packages/python-pynast/trunk/debian/changelog
   trunk/packages/python-pynast/trunk/debian/control
   trunk/packages/python-pynast/trunk/debian/docs
   trunk/packages/python-pynast/trunk/debian/patches/series
Log:
Circumvent missing python-mpi4py at build time


Modified: trunk/packages/python-pynast/trunk/debian/changelog
===================================================================
--- trunk/packages/python-pynast/trunk/debian/changelog	2014-08-12 07:14:25 UTC (rev 17695)
+++ trunk/packages/python-pynast/trunk/debian/changelog	2014-08-12 09:45:05 UTC (rev 17696)
@@ -4,6 +4,12 @@
   * cme fix dpkg-control
   * debian/patches/do_not_install_privacy_breaching_scripts.patch: Do not
     install privacy breaking scripts
+  * debian/rules: run unit tests
+  * debian/control:
+     - Build-Depends + Recommend packages needed in unit tests
+     - Recommends: python-mpi4py
+  * debian/patches/avoid_python-mpi4py_missing_warning.patch: Circumvent
+    missing python-mpi4py at build time
 
  -- Andreas Tille <tille at debian.org>  Mon, 11 Aug 2014 16:33:56 +0200
 

Modified: trunk/packages/python-pynast/trunk/debian/control
===================================================================
--- trunk/packages/python-pynast/trunk/debian/control	2014-08-12 07:14:25 UTC (rev 17695)
+++ trunk/packages/python-pynast/trunk/debian/control	2014-08-12 09:45:05 UTC (rev 17696)
@@ -5,10 +5,15 @@
            Tim Booth <tbooth at ceh.ac.uk>
 Section: python
 Priority: optional
+Testsuite: autopkgtest
 Build-Depends: debhelper (>= 9),
                python,
                python-cogent (>= 1.5.3),
-               python-sphinx
+               python-sphinx,
+               blast2,
+               clustalw,
+               mafft,
+               muscle
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-pynast/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-pynast/trunk/
@@ -21,6 +26,11 @@
          ${python:Depends},
          libjs-jquery,
          libjs-underscore
+Recommends: blast2,
+            clustalw,
+            mafft,
+            muscle,
+            python-mpi4py
 Suggests: uclust
 Conflicts: python-pynast
 Provides: python-pynast

Modified: trunk/packages/python-pynast/trunk/debian/docs
===================================================================
--- trunk/packages/python-pynast/trunk/debian/docs	2014-08-12 07:14:25 UTC (rev 17695)
+++ trunk/packages/python-pynast/trunk/debian/docs	2014-08-12 09:45:05 UTC (rev 17696)
@@ -1,2 +1,3 @@
 README.md
 doc/_build/html
+tests

Added: trunk/packages/python-pynast/trunk/debian/patches/avoid_python-mpi4py_missing_warning.patch
===================================================================
--- trunk/packages/python-pynast/trunk/debian/patches/avoid_python-mpi4py_missing_warning.patch	                        (rev 0)
+++ trunk/packages/python-pynast/trunk/debian/patches/avoid_python-mpi4py_missing_warning.patch	2014-08-12 09:45:05 UTC (rev 17696)
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 11 Aug 2014 16:33:56 +0200
+Description: Since we are not building with python-mpi4py (there is other
+ trouble occuring with this as Build-Depends) we need to strip the warning
+ from script output to make the test successfully passing
+
+--- a/tests/all_tests.py
++++ b/tests/all_tests.py
+@@ -67,6 +67,9 @@ def main():
+         command = '%s %s -h' % (python_name, script_name)
+         result = Popen(command,shell=True,universal_newlines=True,\
+                        stdout=PIPE,stderr=STDOUT).stdout.read()
++        # remove warning cause by missing python-mpi4py
++        result = re.sub(r'(?m)^/usr/lib.*Not using MPI as mpi4py not found\n?', '', result)
++        result = re.sub(r'(?m)^\s*from cogent.util.parallel import MPI\n?', '', result)
+         if not script_good_pattern.search(result):
+             bad_scripts.append(script_name)
+ 

Modified: trunk/packages/python-pynast/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-pynast/trunk/debian/patches/series	2014-08-12 07:14:25 UTC (rev 17695)
+++ trunk/packages/python-pynast/trunk/debian/patches/series	2014-08-12 09:45:05 UTC (rev 17696)
@@ -1,2 +1,3 @@
 do_not_install_privacy_breaching_scripts.patch
 skip_tests_needing_uclust.patch
+avoid_python-mpi4py_missing_warning.patch