[med-svn] [python-biopython] 03/03: New upstream version

[Andreas Tille]

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

commit 5009bb6ec12ee34098354b062564f838bf564dbc
Author: Andreas Tille <tille at debian.org>
Date:   Mon Aug 29 14:15:34 2016 +0200

    New upstream version
---
 debian/changelog                                   |  6 ++
 debian/patches/fix_detection_of_rpsblast.patch     | 17 ------
 debian/patches/series                              |  2 -
 .../skip_test_needing_network_connection.patch     | 66 ----------------------
 4 files changed, 6 insertions(+), 85 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 78d321c..2938a80 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+python-biopython (1.68+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille <tille at debian.org>  Mon, 29 Aug 2016 13:23:35 +0200
+
 python-biopython (1.67+dfsg-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/patches/fix_detection_of_rpsblast.patch b/debian/patches/fix_detection_of_rpsblast.patch
deleted file mode 100644
index aca596d..0000000
--- a/debian/patches/fix_detection_of_rpsblast.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 08 Jun 2016 21:21:55 +0200
-Origin: https://github.com/biopython/biopython/commit/ccaad103e393a356fb22b98b05772a4c4311fb48
-Description: Fix detection of rpsblast
-
---- a/Tests/test_NCBI_BLAST_tools.py
-+++ b/Tests/test_NCBI_BLAST_tools.py
-@@ -68,7 +68,8 @@ for folder in likely_dirs:
-         del exe_name, name
- 
- # To avoid the name clash with legacy BLAST, Debian introduced rpsblast+ alias
--wanted.remove("rpsblast+")
-+if "rpsblast+" in wanted:
-+    wanted.remove("rpsblast+")
- if "rpsblast+" in exe_names:
-     exe_names["rpsblast"] = exe_names["rpsblast+"]
-     del exe_names["rpsblast+"]
diff --git a/debian/patches/series b/debian/patches/series
index 4ebd9f0..60dbfde 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,3 @@
 remove_mathml-qname.patch
 privacy_breach.patch
 fix_test_phyml_tool.patch
-fix_detection_of_rpsblast.patch
-skip_test_needing_network_connection.patch
diff --git a/debian/patches/skip_test_needing_network_connection.patch b/debian/patches/skip_test_needing_network_connection.patch
deleted file mode 100644
index c89211b..0000000
--- a/debian/patches/skip_test_needing_network_connection.patch
+++ /dev/null
@@ -1,66 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 08 Jun 2016 21:21:55 +0200
-Description: This test requires a working network connection and can not be
- run in a pbuilder chroot
-
---- a/Tests/common_BioSQL.py
-+++ b/Tests/common_BioSQL.py
-@@ -610,58 +610,6 @@ class LoaderTest(unittest.TestCase):
-                                     'M81224.1', 'X55053.1', 'X62281.1'])
- 
- 
--class TaxonomyTest(unittest.TestCase):
--    """Test proper insertion and retrieval of taxonomy data
--    """
--    def setUp(self):
--        from Bio import Entrez
--        Entrez.email = "biopython-dev at biopython.org"
--        # create TESTDB
--        create_database()
--
--        # load the database
--        db_name = "biosql-test"
--        self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
--                                                   user=DBUSER, passwd=DBPASSWD,
--                                                   host=DBHOST, db=TESTDB)
--
--        # remove the database if it already exists
--        try:
--            self.server[db_name]
--            self.server.remove_database(db_name)
--        except KeyError:
--            pass
--
--        self.db = self.server.new_database(db_name)
--
--        # get the GenBank file we are going to put into it
--        self.iterator = SeqIO.parse("GenBank/cor6_6.gb", "gb")
--
--    def tearDown(self):
--        self.server.close()
--        destroy_database()
--        del self.db
--        del self.server
--
--    def test_taxon_left_right_values(self):
--        self.db.load(self.iterator, True)
--        sql = """SELECT DISTINCT include.ncbi_taxon_id FROM taxon
--                  INNER JOIN taxon AS include ON
--                      (include.left_value BETWEEN taxon.left_value
--                                  AND taxon.right_value)
--                  WHERE taxon.taxon_id IN
--                      (SELECT taxon_id FROM taxon_name
--                                  WHERE name = 'Brassicales')
--                      AND include.right_value - include.left_value = 1"""
--
--        rows = self.db.adaptor.execute_and_fetchall(sql)
--        self.assertEqual(4, len(rows))
--        values = set()
--        for row in rows:
--            values.add(row[0])
--        self.assertEqual(set([3704, 3711, 3708, 3702]), set(values))
--
--
- class DeleteTest(unittest.TestCase):
-     """Test proper deletion of entries from a database."""
- 

-- 
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