From 75c977b5da010f34998b3218b86f978912a781b2 Mon Sep 17 00:00:00 2001
From: Andreas Schenk <andreas_schenk@hms.harvard.edu>
Date: Sun, 11 Nov 2012 23:57:50 -0500
Subject: [PATCH] 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 | 11 ++++++--
modules/base/pymod/CMakeLists.txt | 25 ++++++++++++++++++-
.../pymod/{__init__.py => __init__.py.in} | 21 +++-------------
modules/base/tests/test_log.py | 1 +
modules/bindings/tests/test_blast.py | 1 +
modules/bindings/tests/test_clustalw.py | 1 +
modules/conop/tests/test_cleanup.py | 1 +
modules/gui/pymod/dng/init.py | 3 +++
modules/io/tests/test_io_mmcif.py | 1 +
.../alg/tests/test_convenient_superpose.py | 1 +
modules/seq/alg/tests/test_renumber.py | 1 +
scripts/init_cl.py | 6 +++++
12 files changed, 52 insertions(+), 21 deletions(-)
rename modules/base/pymod/{__init__.py => __init__.py.in} (67%)
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index fb478ec08..1145f5cdb 100644
--- a/cmake_support/OST.cmake
+++ b/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}
diff --git a/modules/base/pymod/CMakeLists.txt b/modules/base/pymod/CMakeLists.txt
index 6a011018f..433dfeb9f 100644
--- a/modules/base/pymod/CMakeLists.txt
+++ b/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")
+
diff --git a/modules/base/pymod/__init__.py b/modules/base/pymod/__init__.py.in
similarity index 67%
rename from modules/base/pymod/__init__.py
rename to modules/base/pymod/__init__.py.in
index 8ecfacd79..4b1be9f6c 100644
--- a/modules/base/pymod/__init__.py
+++ b/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):
diff --git a/modules/base/tests/test_log.py b/modules/base/tests/test_log.py
index cec9378ed..2527159d4 100644
--- a/modules/base/tests/test_log.py
+++ b/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')
diff --git a/modules/bindings/tests/test_blast.py b/modules/bindings/tests/test_blast.py
index 54a5c4ef8..85a65ea24 100644
--- a/modules/bindings/tests/test_blast.py
+++ b/modules/bindings/tests/test_blast.py
@@ -1,3 +1,4 @@
+import sys
import unittest
from ost import *
from ost import settings
diff --git a/modules/bindings/tests/test_clustalw.py b/modules/bindings/tests/test_clustalw.py
index fa5a5e6b5..9aaf210f8 100644
--- a/modules/bindings/tests/test_clustalw.py
+++ b/modules/bindings/tests/test_clustalw.py
@@ -1,3 +1,4 @@
+import sys
import unittest
from ost import *
from ost import settings
diff --git a/modules/conop/tests/test_cleanup.py b/modules/conop/tests/test_cleanup.py
index 1dc280f4f..11df64187 100644
--- a/modules/conop/tests/test_cleanup.py
+++ b/modules/conop/tests/test_cleanup.py
@@ -1,3 +1,4 @@
+import sys
import unittest
from ost import geom, conop
from ost.conop import cleanup
diff --git a/modules/gui/pymod/dng/init.py b/modules/gui/pymod/dng/init.py
index d46af73d8..ef122cd97 100644
--- a/modules/gui/pymod/dng/init.py
+++ b/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
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index 94eb06330..46eda067e 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -1,4 +1,5 @@
import unittest
+import ost
from ost import *
class TestMMCifInfo(unittest.TestCase):
diff --git a/modules/mol/alg/tests/test_convenient_superpose.py b/modules/mol/alg/tests/test_convenient_superpose.py
index eb4331ca3..728f315de 100644
--- a/modules/mol/alg/tests/test_convenient_superpose.py
+++ b/modules/mol/alg/tests/test_convenient_superpose.py
@@ -1,3 +1,4 @@
+from ost import io,mol,geom
import unittest
import os
import random
diff --git a/modules/seq/alg/tests/test_renumber.py b/modules/seq/alg/tests/test_renumber.py
index 51e4727d3..8f234f859 100644
--- a/modules/seq/alg/tests/test_renumber.py
+++ b/modules/seq/alg/tests/test_renumber.py
@@ -1,3 +1,4 @@
+import sys
import unittest
from ost import *
from ost import settings
diff --git a/scripts/init_cl.py b/scripts/init_cl.py
index bb8090b5e..2c7a04810 100644
--- a/scripts/init_cl.py
+++ b/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():
--
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