[med-svn] [python-freecontact] 08/10: Imported Upstream version 1.1

[Laszlo Kajan]

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lkajan pushed a commit to branch master
in repository python-freecontact.

commit 7df0af84a4be6a81ca339f7b1116a63f330e756a
Author: Laszlo Kajan <lkajan at debian.org>
Date:   Thu Sep 19 19:23:16 2013 +0200

    Imported Upstream version 1.1
---
 Changes             |    4 ++++
 PKG-INFO            |    2 +-
 setup.py            |    2 +-
 src/freecontact.cpp |    2 +-
 test/test01.py      |   19 ++++++++++---------
 5 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/Changes b/Changes
index 5e0b69b..2f88911 100644
--- a/Changes
+++ b/Changes
@@ -1,4 +1,8 @@
 Revision history for Python module freecontact.
 
+1.1   Thu Sep 19 18:49:41 CEST 2013
+	- Increased test precision threshold to match Perl module.
+	- Made test fail (instead of be skipped) when module is not found.
+
 1.0   Wed Jul 17 18:27:02 CEST 2013
 	- original version
diff --git a/PKG-INFO b/PKG-INFO
index d08c238..2704aba 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: python-freecontact
-Version: 1.0
+Version: 1.1
 Summary: fast protein contact predictor
 Home-page: http://rostlab.org/
 Author: Laszlo Kajan
diff --git a/setup.py b/setup.py
index 6bf26b9..7781985 100755
--- a/setup.py
+++ b/setup.py
@@ -19,7 +19,7 @@ from distutils.core import setup, Extension
 from glob import glob
 
 setup(	name = 'python-freecontact',
-    	version = '1.0',
+    	version = '1.1',
     	author = 'Laszlo Kajan',
     	author_email = 'lkajan at rostlab.org',
     	description = 'fast protein contact predictor',
diff --git a/src/freecontact.cpp b/src/freecontact.cpp
index 6a517f5..8486a49 100644
--- a/src/freecontact.cpp
+++ b/src/freecontact.cpp
@@ -344,7 +344,7 @@ BOOST_PYTHON_MODULE(freecontact)
 "========\n"
 "import freecontact\n"
 "\n"
-"EXAMPLE = open('/mnt/home/lkajan/project/rostlab/python-freecontact/examples/demo_1000.aln', 'r')\n"
+"EXAMPLE = open('/usr/share/doc/python-freecontact/examples/demo_1000.aln', 'r')\n"
 "aln = EXAMPLE.readlines(); aln = map(lambda s: s.rstrip(), aln)\n"
 "EXAMPLE.close()\n"
 "\n"
diff --git a/test/test01.py b/test/test01.py
index 9dad5a7..8c7519d 100755
--- a/test/test01.py
+++ b/test/test01.py
@@ -15,6 +15,7 @@
 #   You should have received a copy of the GNU General Public License
 #   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 # 
+import freecontact
 import unittest
 from test import test_support
 
@@ -23,22 +24,22 @@ class MyTestCase1(unittest.TestCase):
     # Only use setUp() and tearDown() if necessary
 
     def setUp(self):
-        self.fc = test_support.import_module('freecontact')
+        pass
 
     def tearDown(self):
         pass # ... code to execute to clean up after tests ...
 
     def test1(self):
-        ps = self.fc.get_ps_evfold()
+        ps = freecontact.get_ps_evfold()
         assert ps['clustpc'] == 0.7
-        ps = self.fc.get_ps_psicov()
+        ps = freecontact.get_ps_psicov()
         assert ps['clustpc'] == 0.62
-        self.fc.get_ps_psicov_sd()
+        freecontact.get_ps_psicov_sd()
 
     def test2(self):
-        fcp = self.fc.Predictor()
+        fcp = freecontact.Predictor()
         assert fcp.dbg == False
-        fcp = self.fc.Predictor(dbg = True)
+        fcp = freecontact.Predictor(dbg = True)
         assert fcp.dbg == True
 
     def test3(self):
@@ -48,10 +49,10 @@ class MyTestCase1(unittest.TestCase):
 
         num_threads = 1
         evfold_24_42 = 0.0129471030086279 # 0-based indices
-        prec_threshold = 5e-5
+        prec_threshold = 3e-4
         timing = {}
 
-        fcp = self.fc.Predictor(dbg = True)
+        fcp = freecontact.Predictor(dbg = True)
 
         # run with timing test
         res = fcp.run(ali = aln, num_threads = num_threads, timing = timing)
@@ -60,7 +61,7 @@ class MyTestCase1(unittest.TestCase):
 
         # run psicov with icme_timeout exception test
         try:
-            args = self.fc.get_ps_psicov(); args.update({'ali': aln, 'num_threads': num_threads, 'icme_timeout': 2, 'timing': None})
+            args = freecontact.get_ps_psicov(); args.update({'ali': aln, 'num_threads': num_threads, 'icme_timeout': 2, 'timing': None})
             fcp.run(**args) # this is expected to fail
             assert False    # fail if fell through
         except RuntimeError as e:

-- 
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