From 27b2b1aabb22af15c942a7ea7de4f836ee251fad Mon Sep 17 00:00:00 2001
From: Stefan <stefanbienert@me.com>
Date: Thu, 31 Oct 2013 22:14:18 +0100
Subject: [PATCH] Shorten module path, extended documentationsystem for autodoc
---
cmake_support/PROMOD3.cmake | 13 +++++++------
doc/CMakeLists.txt | 5 ++++-
doc/conf.py.in | 3 ++-
meld/CMakeLists.txt | 1 +
meld/tests/CMakeLists.txt | 8 ++++++++
meld/tests/test_raw_modeling.py | 12 ++++++------
scripts/pm.in | 8 ++++----
7 files changed, 32 insertions(+), 18 deletions(-)
create mode 100644 meld/tests/CMakeLists.txt
diff --git a/cmake_support/PROMOD3.cmake b/cmake_support/PROMOD3.cmake
index 4715b551..1f625e8b 100644
--- a/cmake_support/PROMOD3.cmake
+++ b/cmake_support/PROMOD3.cmake
@@ -163,7 +163,7 @@ endmacro()
# [HEADER_OUTPUT_DIR dir]
# [LINK link_cmds])
# Description:
-# Define an OpenStructure module.
+# Define a ProMod3 module.
#-------------------------------------------------------------------------------
macro(module)
#-----------------------------------------------------------------------------
@@ -513,9 +513,9 @@ macro(pymod)
return()
endif()
if (_ARG_OUTPUT_DIR)
- set(PYMOD_DIR "python${PYTHON_VERSION}/site-packages/promod3/${_ARG_OUTPUT_DIR}")
+ set(PYMOD_DIR "python${PYTHON_VERSION}/site-packages/${_ARG_OUTPUT_DIR}")
else()
- set(PYMOD_DIR "python${PYTHON_VERSION}/site-packages/promod3/${_ARG_PREFIX}/${_ARG_NAME}")
+ set(PYMOD_DIR "python${PYTHON_VERSION}/site-packages/${_ARG_PREFIX}/${_ARG_NAME}")
endif()
set(PYMOD_STAGE_DIR "${LIB_STAGE_PATH}/${PYMOD_DIR}")
file(MAKE_DIRECTORY ${PYMOD_STAGE_DIR})
@@ -691,7 +691,8 @@ macro(promod3_unittest)
if(python_path)
set(python_path "${python_path}:")
endif(python_path)
- set(python_path "${python_path}${LIB_STAGE_PATH}/python${PYTHON_VERSION}/site-packages")
+ # we just add OST manually here until we find a more flexible way
+ set(python_path "${python_path}${LIB_STAGE_PATH}/python${PYTHON_VERSION}/site-packages:${OST_ROOT}/lib/python${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"
@@ -701,8 +702,8 @@ macro(promod3_unittest)
sh -c "${PY_TESTS_CMD} ${CMAKE_CURRENT_SOURCE_DIR}/${py_test} xml || echo"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
COMMENT "running checks ${py_test}" VERBATIM)
- add_dependencies("${py_test}_run_xml" promod3_scripts "_${_ARG_PREFIX}_${_ARG_MODULE}")
- add_dependencies("${py_test}_run" promod3_scripts "_${_ARG_PREFIX}_${_ARG_MODULE}")
+ add_dependencies("${py_test}_run_xml" "_${_ARG_PREFIX}_${_ARG_MODULE}")
+ add_dependencies("${py_test}_run" "_${_ARG_PREFIX}_${_ARG_MODULE}")
add_dependencies(check "${py_test}_run")
add_dependencies(check_xml "${py_test}_run_xml")
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index e36c9cfe..1e924ad4 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -14,7 +14,10 @@ set(_SPHINX_CONF_PY "${_RST_SOURCE_DIR}/conf.py")
set(_SPHINX_CONF_SUBST_DICT PROMOD3_VERSION_MAJOR="${PROMOD3_VERSION_MAJOR}"
PROMOD3_VERSION_MINOR="${PROMOD3_VERSION_MINOR}"
PROMOD3_VERSION_PATCH="${PROMOD3_VERSION_PATCH}"
- PYTHON_DOC_URL="${PYTHON_DOC_URL}")
+ PYTHON_DOC_URL="${PYTHON_DOC_URL}"
+ LIB_STAGE_PATH="${LIB_STAGE_PATH}"
+ PYTHON_VERSION="${PYTHON_VERSION}"
+ OST_ROOT="${OST_ROOT}")
set(_CONF_SUBST_DICT -DINPUT_FILE=${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in -DOUT_FILE=${_SPHINX_CONF_PY})
foreach(_subst ${_SPHINX_CONF_SUBST_DICT})
list(APPEND _CONF_SUBST_DICT -D${_subst})
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 3d502970..77d7836d 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -19,7 +19,8 @@ import sys, os
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, '@LIB_STAGE_PATH@/python@PYTHON_VERSION@/site-packages')
+sys.path.insert(1, '@OST_ROOT@/lib/python@PYTHON_VERSION@/site-packages')
# -- General configuration -----------------------------------------------------
diff --git a/meld/CMakeLists.txt b/meld/CMakeLists.txt
index 842ebb33..3cc88cad 100644
--- a/meld/CMakeLists.txt
+++ b/meld/CMakeLists.txt
@@ -1,4 +1,5 @@
add_subdirectory(src)
add_subdirectory(pymod)
add_subdirectory(data)
+add_subdirectory(tests)
add_subdirectory(doc)
diff --git a/meld/tests/CMakeLists.txt b/meld/tests/CMakeLists.txt
new file mode 100644
index 00000000..d64ff2df
--- /dev/null
+++ b/meld/tests/CMakeLists.txt
@@ -0,0 +1,8 @@
+set(OST_BASE_UNIT_TESTS
+ test_raw_modeling.py
+)
+
+promod3_unittest(MODULE base
+ SOURCES "${OST_BASE_UNIT_TESTS}"
+ LINK ost_mol)
+
diff --git a/meld/tests/test_raw_modeling.py b/meld/tests/test_raw_modeling.py
index a24350ff..797f94a7 100644
--- a/meld/tests/test_raw_modeling.py
+++ b/meld/tests/test_raw_modeling.py
@@ -1,6 +1,7 @@
-from sm.core import *
-from sm.core.test import *
-from sm.meld import *
+import unittest
+from promod3 import *
+from promod3.meld import *
+from ost import seq
class RawModelingTests(unittest.TestCase):
def testRaiseNoAttachedView(self):
@@ -86,6 +87,5 @@ class RawModelingTests(unittest.TestCase):
if __name__ == "__main__":
- run()
-
-
+ from ost import testutils
+ testutils.RunTests()
diff --git a/scripts/pm.in b/scripts/pm.in
index de48aca8..24908896 100755
--- a/scripts/pm.in
+++ b/scripts/pm.in
@@ -8,7 +8,7 @@ SCRIPT_NAME=$0
BIN_DIR=$( cd `dirname "$SCRIPT_NAME"`; pwd)
export PROMOD3_ROOT="$BIN_DIR/.."
PROMOD3_EXEC_PATH="$PROMOD3_ROOT/libexec"
-export PYTHONPATH="${PROMOD3_ROOT}/@LIBDIR@/python@PYTHON_VERSION@/site-packages/promod3:${PYTHONPATH}"
+export PYTHONPATH="${PROMOD3_ROOT}/@LIBDIR@/python@PYTHON_VERSION@/site-packages:${PYTHONPATH}"
export PATH="$BIN_DIR:@OST_ROOT@/bin:$PATH"
export LD_LIBRARY_PATH="${PROMOD3_ROOT}/@LIBDIR@:$LD_LIBRARY_PATH"
if [ -n "@QMEAN_ROOT@" ] ; then
@@ -17,9 +17,9 @@ fi
if [ $# == 0 ] ; then
echo "usage:"
- echo " promod3 <action>"
+ echo " pm <action>"
echo ""
- echo "type promod3 help to get a list of commonly used actions"
+ echo "type pm help to get a list of commonly used actions"
exit
fi
@@ -36,5 +36,5 @@ fi
case "$ACTION_BASENAME" in
*.py ) ost "$ACTION" $@;;
* ) echo "unknown action '${ACTION}'"
- echo "type promod3 help to get started" ;;
+ echo "type pm help to get started" ;;
esac
--
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