removed import of geom,io,mol,seq,gfx and img from ost base __init__.py

changed python unit tests to run with python instead of ost

Remarks
-------

Python unit tests using blast, clustalw or the compound lib where
skipped on my system. There might be still some missing imports in
these tests.

cmake_support/OST.cmake

@@ -423,6 +423,7 @@ macro(script)
     if (NOT _ARG_INPUT)
       message(FATAL_ERROR "script() can only substitute when INPUT is present.")    
     endif()
+
     substitute(IN_FILE "${CMAKE_CURRENT_SOURCE_DIR}/${_INPUT}" OUT_FILE ${_ARG_NAME} 
                DICT ${_ARG_SUBSTITUTE})
   endif()
@@ -687,15 +688,21 @@ macro(ost_unittest)
         set_target_properties("${_test_name}_run" PROPERTIES EXCLUDE_FROM_ALL "1")
       endif()
     endif()
+
     foreach(py_test ${PY_TESTS})
       if(WIN32)
-        set (PY_TESTS_CMD "${EXECUTABLE_OUTPUT_PATH}/ost.bat")
+        set (PY_TESTS_CMD "${PYTHON_BINARY}")
         add_custom_target("${py_test}_run"
                   CALL "${PY_TESTS_CMD} ${CMAKE_CURRENT_SOURCE_DIR}/${py_test} || echo"
                   WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
                   COMMENT "running checks ${py_test}" VERBATIM)
       else()
-        set (PY_TESTS_CMD "${EXECUTABLE_OUTPUT_PATH}/ost")
+        set(python_path $ENV{PYTHONPATH})
+        if(python_path)
+          set(python_path "${python_path}:")
+        endif(python_path)
+        set(python_path "${python_path}${LIB_STAGE_PATH}/python${PYTHON_VERSION}/site-packages")
+        set (PY_TESTS_CMD "PYTHONPATH=${python_path}  ${PYTHON_BINARY}")
         add_custom_target("${py_test}_run"
                   sh -c "${PY_TESTS_CMD} ${CMAKE_CURRENT_SOURCE_DIR}/${py_test} || echo"
                   WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}

modules/base/pymod/CMakeLists.txt

@@ -7,5 +7,28 @@ set(OST_BASE_PYMOD_SOURCES
 if (NOT ENABLE_STATIC)
   pymod(NAME base OUTPUT_DIR ost 
         CPP ${OST_BASE_PYMOD_SOURCES} 
-        PY __init__.py settings.py stutil.py table.py xmlrunner.py testutils.py)
+        PY settings.py stutil.py table.py xmlrunner.py testutils.py)
 endif() 
+
+set(SQ "\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'")
+set(SUBST_DICT "ALL_ADDITIONAL_MODULES=")
+if(ENABLE_GUI)
+  set(SUBST_DICT "${SUBST_DICT},${SQ}gui${SQ}")
+endif(ENABLE_GUI)
+if(ENABLE_GFX)
+  set(SUBST_DICT "${SUBST_DICT},${SQ}gfx${SQ}")
+endif(ENABLE_GFX)
+if(ENABLE_IMG)
+  set(SUBST_DICT "${SUBST_DICT},${SQ}img${SQ}")
+endif(ENABLE_IMG)
+if(ENABLE_INFO)
+  set(SUBST_DICT ${SUBST_DICT},${SQ}info${SQ})
+endif(ENABLE_INFO)
+
+
+script(NAME __init__.py
+       INPUT __init__.py.in
+       SUBSTITUTE "${SUBST_DICT}"
+       TARGET ost_base_pymod
+       OUTPUT_DIR "${LIB_DIR}/python${PYTHON_VERSION}/site-packages/ost")
+

modules/base/pymod/__init__.py → modules/base/pymod/__init__.py.in

@@ -16,27 +16,12 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_base import *
-from stutil import *
 
-from ost import geom
-from ost import io
-from ost import mol
-from ost import seq
 
-try:
-  from ost import gfx
-  scene = gfx.Scene()
-  scene.Stereo=gfx.Stereo
-except ImportError:
-  pass
-  
-  
-try:
-  from ost import img
-except ImportError:
-  pass
+__all__=['Correl', 'FileLogSink', 'FloatList', 'GetCurrentLogSink', 'GetPrefixPath', 'GetSharedDataPath', 'GetVerbosityLevel', 'Histogram', 'IntList', 'LogDebug', 'LogError', 'LogInfo', 'LogScript', 'LogSink', 'LogTrace', 'LogVerbose', 'LogWarning', 'Max', 'Mean', 'Median', 'Min', 'MultiLogSink', 'PopLogSink', 'PopVerbosityLevel', 'PushLogSink', 'PushVerbosityLevel', 'Range', 'SetPrefixPath', 'StdDev', 'StreamLogSink', 'StringList', 'StringLogSink', 'Units', 'VERSION', 'VERSION_MAJOR', 'VERSION_MINOR', 'VERSION_PATCH', 'WITH_NUMPY', 'conop', 'geom', 'io', 'mol', 'seq', 'stutil' @ALL_ADDITIONAL_MODULES@]
 
+from _ost_base import *
+from stutil import *
 
 class StreamLogSink(LogSink):
   def __init__(self, stream):

modules/base/tests/test_log.py

@@ -30,6 +30,7 @@ class TestLog(unittest.TestCase):
         self.severity=severity
         ost.PushLogSink(ls)
     ls=CapturingLogSink()
+    ost.PushVerbosityLevel(1)
     ost.PushLogSink(ls)
     ost.LogError('error message')
     self.assertEqual(ls.message, 'error message\n')

modules/bindings/tests/test_blast.py

+import sys
 import unittest
 from ost import *
 from ost import settings

modules/bindings/tests/test_clustalw.py

+import sys
 import unittest
 from ost import *
 from ost import settings

modules/conop/tests/test_cleanup.py

+import sys
 import unittest
 from ost import geom, conop
 from ost.conop import cleanup

modules/gui/pymod/dng/init.py

@@ -12,6 +12,9 @@ try:
 except ImportError:
   _img_present=False
   pass
+ost.scene = gfx.Scene()
+ost.scene.Stereo=gfx.Stereo
+
 import httplib
 
 from PyQt4 import QtGui, QtCore

modules/io/tests/test_io_mmcif.py

 import unittest
+import ost
 from ost import *
 
 class TestMMCifInfo(unittest.TestCase):

modules/mol/alg/tests/test_convenient_superpose.py

+from ost import io,mol,geom
 import unittest
 import os
 import random

modules/seq/alg/tests/test_renumber.py

+import sys
 import unittest
 from ost import *
 from ost import settings

scripts/init_cl.py

@@ -34,6 +34,12 @@ else:
      
 from ost import *
 import ost
+try:
+  from ost import gfx
+  ost.scene = gfx.Scene()
+  ost.scene.Stereo=gfx.Stereo
+except ImportError:
+  pass
 
 ost.SetPrefixPath(os.getenv('DNG_ROOT'))
 def _InitRuleBasedBuilder():