From 09240f594ef6afffe4cd25cbcc264311529c8ce6 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 21 Jul 2020 08:22:23 +0200
Subject: [PATCH] make HHblits tests agnostic of any scicore specific env
variables
Futhermore we only want to run the unit tests if an HHblits 3 installation
is detected.
---
modules/bindings/tests/test_hhblits.py | 23 ++++++++++++++++++-----
1 file changed, 18 insertions(+), 5 deletions(-)
diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index 5a2972919..2c0b2d9c2 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -11,6 +11,7 @@ import datetime
import ost
from ost import seq
+from ost import settings
from ost.bindings import hhblits
class _UnitTestHHblitsLog(ost.LogSink):
@@ -33,7 +34,9 @@ def setUpModule():
class TestHHblitsBindings(unittest.TestCase):
def setUp(self):
- self.hhroot = os.getenv('EBROOTHHMINSUITE')
+ # expects default hhblits installation...
+ hhblits_bin_dir = os.path.dirname(settings.Locate('hhblits'))
+ self.hhroot = os.path.join(hhblits_bin_dir, os.pardir)
def tearDown(self):
if hasattr(self, 'hh'):
@@ -228,6 +231,7 @@ class TestHHblitsBindings(unittest.TestCase):
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
+
csfile = self.hh.A3MToCS("testfiles/testali.a3m",
options={'-alphabet' :
os.path.join(self.hhroot,
@@ -417,10 +421,19 @@ class TestHHblitsBindings(unittest.TestCase):
'a4b2554d... ATPEQAQLVHKEIRKIVKDTC\n')
if __name__ == "__main__":
- hhsuite_root_dir = os.getenv('EBROOTHHMINSUITE')
- if not hhsuite_root_dir:
- print("No environment variable 'EBROOTHHMINSUITE'. To enable the "+\
- "unit test, this needs to point to your HHsuite installation.")
+ try:
+ hhblits_version_string = hhblits.GetHHblitsVersionString()
+ except:
+ print("No HHblits installation found: skip unit tests")
+ sys.exit(0)
+ if hhblits_version_string is None:
+ print("Could not identify HHblits version: skip unit tests")
sys.exit(0)
+ hhblits_version_major = int(hhblits_version_string.split('.')[0])
+ if hhblits_version_major != 3:
+ print("Found hhblits with major version %i. Unit tests only run with "\
+ "version 3: skip unit tests"%(hhblits_version_major))
+ sys.exit(0)
+
from ost import testutils
testutils.RunTests()
--
GitLab