diff --git a/CHANGELOG b/CHANGELOG
index bcfe0e157fa1a99532d33e26cf714e9951345177..2a1fc7b16a30e197ded81d00c08fd93af3e11b6b 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,6 +5,18 @@
Changelog
================================================================================
+Release 3.2.x
+--------------------------------------------------------------------------------
+
+* Remove outdated configuration scripts (Fedora 19 / ancient Mac)
+* Construct CB atoms if only N,CA and C atoms are present in
+ ReconstructSidechains input structure.
+* Detect Python using functionality provided by CMake instead of our own code.
+ You might have to adapt CMake flags when building ProMod3 to variables
+ specified here: https://cmake.org/cmake/help/latest/module/FindPython.html
+* Several minor bug fixes, improvements, and speed-ups.
+
+
Release 3.1.1
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1dd665c0179a07cbe951f8f2ef888dee4c59f5af..2ba70913c454ae129f7e9567d43137bdf129221b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -87,17 +87,19 @@ file(MAKE_DIRECTORY ${STAGE_DIR}
setup_compiler_flags()
# Python needed before Boost
-find_package(Python 3.6 REQUIRED)
+find_package(Python 3.6 REQUIRED COMPONENTS Interpreter Development)
# Split version string
-string(REPLACE "." ";" _python_version_list ${PYTHON_VERSION})
-list(GET _python_version_list 0 PYTHON_VERSION_MAJOR)
-list(GET _python_version_list 1 PYTHON_VERSION_MINOR)
+string(REPLACE "." ";" _python_version_list ${Python_VERSION})
+list(GET _python_version_list 0 Python_VERSION_MAJOR)
+list(GET _python_version_list 1 Python_VERSION_MINOR)
+# where Python modules live
+set(PYTHON_MODULE_PATH "python${Python_VERSION_MAJOR}${Python_VERSION_MINOR}/site-packages/")
setup_boost()
if(NOT DISABLE_DOCUMENTATION)
find_package(Sphinx REQUIRED)
- set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
+ set(PYTHON_DOC_URL "https://docs.python.org/${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}")
# this URL should always point to the latest version of OST
set(OST_DOC_URL "https://www.openstructure.org/docs")
endif()
@@ -125,7 +127,7 @@ endif()
# This is somewhat experimental: Checking if Boost is compiled with the same
# Python version used for Promod3. The very same macro is disabled in OST so
# it may fail at some point.
-#promod3_match_boost_python_version(${PYTHON_LIBRARIES})
+#promod3_match_boost_python_version(${Python_LIBRARIES})
# basic environment
include_directories(${Boost_INCLUDE_DIRS}
@@ -162,5 +164,5 @@ message(STATUS "${PROJECT_NAME} will be built with the following options:\n"
" OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"
" Compound library (-DCOMPOUND_LIB): ${occp}\n"
" Optimized (-DOPTIMIZE) : ${_OPT}\n"
- " Python : ${PYTHON_BINARY}\n"
+ " Python : ${Python_EXECUTABLE}\n"
" Eigen3 : ${EIGEN3_INCLUDE_DIR}\n")
diff --git a/cmake_support/FindOPENSTRUCTURE.cmake b/cmake_support/FindOPENSTRUCTURE.cmake
index 5e21d7262ca508e87cbe7c41d7ba31f95fd830e4..7677d6c0162bdbdebc150c554da49660fbad9663 100644
--- a/cmake_support/FindOPENSTRUCTURE.cmake
+++ b/cmake_support/FindOPENSTRUCTURE.cmake
@@ -27,7 +27,7 @@ macro(find_OPENSTRUCTURE OST_ROOT HEADER_NAMES PYMOD_NAME)
set(FOUND_LIB FOUND_LIB-NOTFOUND)
find_library(FOUND_LIB
NAMES ost_${LIB}
- HINTS "${PYTHON_ROOT}"
+ HINTS "${Python_ROOT}"
PATH ${OST_ROOT}
PATH_SUFFIXES lib lib64
NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
diff --git a/cmake_support/FindPython.cmake b/cmake_support/FindPython.cmake
deleted file mode 100644
index b0fb4cdf1b6308ec77d6257f29bd2f68b9cf769e..0000000000000000000000000000000000000000
--- a/cmake_support/FindPython.cmake
+++ /dev/null
@@ -1,188 +0,0 @@
-#-------------------------------------------------------------------------------
-# Check for Python Libraries
-#
-# PYTHON_IGNORE_FRAMEWORKS if set, do not check for python frameworks.
-# has meaning on MacOS X only
-# PYTHON_ROOT Prefix for python libraries
-# PYTHON_MIN_VERSION minimal python version required
-#
-# When Python is found, the result is placed in the following variables:
-#
-# PYTHON_LIBRARIES is set to the library and linker flags used to
-# link against python
-# PYTHON_VERSION is set to the version of python
-# PYTHON_INCLUDE_PATH is set to the path that contains Python.h
-# PYTHON_BINARY is set to the path to the python executable
-# PYTHON_MODULE_PATH is set as path-component where modules should live
-#
-# Author: Marco Biasini/ Stefan Bienert
-#-------------------------------------------------------------------------------
-
-set(PYTHON_VERSIONS 3.8 3.7 3.6 )
-set(PYTHON_MIN_VERSION 3.6.0)
-
-#-------------------------------------------------------------------------------
-# check for python framework
-# this macro honours the values of PYTHON_ROOT
-#-------------------------------------------------------------------------------
-macro(check_for_python_framework)
- set(_FRAMEWORK_SEARCH_PATHS /Library/Frameworks/ /System/Library/Frameworks)
- if(PYTHON_ROOT)
- set(_FRAMEWORK_SEARCH_PATHS ${PYTHON_ROOT}/Library/Frameworks)
- endif()
- foreach(_PATH ${_FRAMEWORK_SEARCH_PATHS})
- set(_FULL_FRAMEWORK_NAME "${_PATH}/Python.framework")
- if(EXISTS ${_FULL_FRAMEWORK_NAME})
- set(PYTHON_FRAMEWORK ON)
- set(PYTHON_INCLUDE_PATH "${_FULL_FRAMEWORK_NAME}/Headers")
- set(PYTHON_FRAMEWORK_PATH "${_FULL_FRAMEWORK_NAME}/Python")
- endif()
- endforeach()
-endmacro()
-
-
-
-macro(_find_python PYTHON_ROOT VERSION)
- string(REPLACE "." "" _VERSION_NO_DOTS "${VERSION}")
- if(PYTHON_ROOT)
- find_library(PYTHON_LIBRARIES
- NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
- "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
- HINTS "${PYTHON_ROOT}"
- PATH_SUFFIXES lib libs
- NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
- )
- find_path(PYTHON_INCLUDE_PATH
- NAMES Python.h
- HINTS "${PYTHON_ROOT}/include"
- PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"
- "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
- NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
- )
- else()
- find_library(PYTHON_LIBRARIES
- NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
- "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
- PATH_SUFFIXES lib
- )
- find_path(PYTHON_INCLUDE_PATH
- NAMES Python.h
- PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"
- "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
- )
- endif()
-endmacro()
-
-macro(_find_python_bin PYTHON_ROOT VERSION)
- string(REPLACE "." "" _VERSION_NO_DOTS "${VERSION}")
- if(PYTHON_ROOT)
- find_program(PYTHON_BINARY
- NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}" python.exe
- HINTS "${PYTHON_ROOT}"
- PATH_SUFFIXES bin
- NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
- )
- else()
- find_program(PYTHON_BINARY
- NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
- HINTS "${CMAKE_PREFIX_PATH}"
- PATH_SUFFIXES bin
- )
- endif()
-endmacro()
-
-#-------------------------------------------------------------------------------
-# check for python lib
-#
-# this macro honours the values of PYTHON_ROOT and PYTHON_VERSION
-#-------------------------------------------------------------------------------
-macro(check_for_python_lib)
- if(PYTHON_VERSION)
- _find_python("${PYTHON_ROOT}" "${PYTHON_VERSION}")
- else()
- foreach(_VERSION ${PYTHON_VERSIONS})
- if((${PYTHON_MIN_VERSION} VERSION_LESS ${_VERSION}) OR
- (${PYTHON_MIN_VERSION} VERSION_EQUAL ${_VERSION}))
- _find_python("${PYTHON_ROOT}" "${_VERSION}")
- if(PYTHON_LIBRARIES)
- set(PYTHON_VERSION "${_VERSION}")
- break()
- endif()
- endif()
- endforeach()
- endif()
- # fallback to non-versioned naming scheme
- if (NOT $PYTHON_LIBRARIES)
- _find_python("${PYTHON_ROOT}" "")
- endif()
-endmacro()
-
-macro(check_for_python_binary)
- if(PYTHON_VERSION)
- _find_python_bin("${PYTHON_ROOT}" "${PYTHON_VERSION}")
- else()
- foreach(_VERSION ${PYTHON_VERSIONS})
- if((${PYTHON_MIN_VERSION} VERSION_LESS ${_VERSION}) OR
- (${PYTHON_MIN_VERSION} VERSION_EQUAL ${_VERSION}))
- _find_python_bin("${PYTHON_ROOT}" "${_VERSION}")
- if(PYTHON_BINARY)
- set(PYTHON_VERSION "${_VERSION}")
- # disallow all versions except for the one we just found. This makes
- # sure we don't mismatch the python binary and the libraries.
- set(PYTHON_VERSIONS "${_VERSION}")
- break()
- endif()
- endif()
- endforeach()
- endif()
- if (NOT PYTHON_BINARY)
- _find_python("${PYTHON_ROOT}" "")
- endif()
-endmacro()
-
-if(NOT PYTHON_ROOT)
- if(WIN32)
- set(PYTHON_ROOT "${CMAKE_PREFIX_PATH}")
- else()
- set(PYTHON_ROOT "/usr")
- endif()
-endif()
-if(APPLE AND NOT PYTHON_IGNORE_FRAMEWORKS)
- check_for_python_framework()
-endif()
-
-# first check for python binary.
-check_for_python_binary()
-
-if(NOT PYTHON_FRAMEWORK_FOUND)
- check_for_python_lib()
-endif()
-
-set(PYTHON_MODULE_PATH "python${PYTHON_VERSION}/site-packages/")
-
-mark_as_advanced(
- PYTHON_LIBRARIES
- PYTHON_INCLUDE_PATH
- PYTHON_VERSION
- PYTHON_BINARY
- PYTHON_MODULE_PATH
-)
-
-if(PYTHON_LIBRARIES)
- if(PYTHON_FRAMEWORK)
- set(PYTHON_LIBRARIES "${PYTHON_FRAMEWORK_PATH}"
- CACHE FILEPATH "Python Libraries" FORCE)
- else()
- set(PYTHON_LIBRARIES "${PYTHON_LIBRARIES}"
- CACHE FILEPATH "Python Libraries" FORCE)
- endif()
- set(PYTHON_INCLUDE_PATH "${PYTHON_INCLUDE_PATH}"
- CACHE FILEPATH "Python Include Path" FORCE)
-endif()
-
-if (PYTHON_BINARY)
- set(PYTHON_VERSION "${PYTHON_VERSION}"
- CACHE STRING "Python Version" FORCE)
- set(PYTHON_BINARY "${PYTHON_BINARY}"
- CACHE FILEPATH "Python Binary" FORCE)
-endif()
diff --git a/cmake_support/FindSphinx.cmake b/cmake_support/FindSphinx.cmake
index 956b18248d4ca013ba1f3e9727855e28413da540..28bce054877838c4db5ddc12f52edc709e0da29d 100644
--- a/cmake_support/FindSphinx.cmake
+++ b/cmake_support/FindSphinx.cmake
@@ -1,5 +1,5 @@
-IF(PYTHON_BINARY)
- EXEC_PROGRAM ("${PYTHON_BINARY}"
+IF(Python_EXECUTABLE)
+ EXEC_PROGRAM ("${Python_EXECUTABLE}"
ARGS "-c 'import sphinx; print(sphinx.__version__)'"
OUTPUT_VARIABLE VERSION_STRING
RETURN_VALUE SPHINX_NOT_FOUND)
@@ -9,13 +9,13 @@ IF(PYTHON_BINARY)
set(SPHINX_FOUND TRUE)
set(SPHINX_VERSION ${VERSION_STRING})
endif (SPHINX_NOT_FOUND)
-ENDIF(PYTHON_BINARY)
+ENDIF(Python_EXECUTABLE)
if (SPHINX_FOUND)
message(STATUS "Sphinx version: " ${SPHINX_VERSION})
else (SPHINX_FOUND)
if (Sphinx_FIND_REQUIRED)
- message (FATAL_ERROR "Could not import sphinx in " ${PYTHON_BINARY}
+ message (FATAL_ERROR "Could not import sphinx in " ${Python_EXECUTABLE}
" make it available or disable documentation with -DDISABLE_DOCUMENTATION")
endif (Sphinx_FIND_REQUIRED)
endif (SPHINX_FOUND)
diff --git a/cmake_support/PROMOD3.cmake b/cmake_support/PROMOD3.cmake
index f42ac97d137dc170880b4add0e1dc3879c638b1a..01f5f74ccc169f108467bf5cf2483c3f063f6de8 100644
--- a/cmake_support/PROMOD3.cmake
+++ b/cmake_support/PROMOD3.cmake
@@ -70,7 +70,7 @@ endmacro(check_architecture)
#
# Set variable VAR (in parent scope) to an updated PYTHONPATH env. variable
# which includes OST and PM3 paths. This can then be used to call python scripts
-# with commands such as: sh -c "PYTHONPATH=${VAR} ${PYTHON_BINARY} ..."
+# with commands such as: sh -c "PYTHONPATH=${VAR} ${Python_EXECUTABLE} ..."
#-------------------------------------------------------------------------------
macro(get_python_path VAR)
set(${VAR} $ENV{PYTHONPATH})
@@ -521,7 +521,7 @@ macro(pymod)
set(_PARENT_LIB_NAME "${_PARENT_NAME}")
endif()
target_link_libraries("_${_ARG_NAME}" ${_PARENT_LIB_NAME}
- ${PYTHON_LIBRARIES} ${BOOST_PYTHON_LIBRARIES})
+ ${Python_LIBRARIES} ${BOOST_PYTHON_LIBRARIES})
set_target_properties("_${_ARG_NAME}"
PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${PYMOD_STAGE_DIR})
if(NOT ENABLE_STATIC)
@@ -589,7 +589,7 @@ macro(pymod)
add_custom_target("${_ARG_NAME}_${_trans_py_source}_pymod" ALL DEPENDS ${_trans_py_file_to})
add_dependencies("${_ARG_NAME}_pymod" "${_ARG_NAME}_${_trans_py_source}_pymod")
add_dependencies("_${_ARG_NAME}" "${_ARG_NAME}_pymod")
- include_directories(${PYTHON_INCLUDE_PATH})
+ include_directories(${Python_INCLUDE_DIRS})
install(FILES ${_trans_py_file_to} DESTINATION "${LIB_DIR}/${PYMOD_DIR}")
if(NOT DISABLE_DOCUMENTATION)
add_doc_dependency(NAME ${_ARG_NAME} DEP "${_ARG_NAME}_${_trans_py_source}_pymod")
@@ -641,7 +641,7 @@ macro(pymod)
copy_if_different("./" "${PYMOD_STAGE_DIR}" "${_ABS_PY_FILES}" "TARGETS"
"${_ARG_NAME}_pymod")
add_dependencies("_${_ARG_NAME}" "${_ARG_NAME}_pymod")
- include_directories(${PYTHON_INCLUDE_PATH})
+ include_directories(${Python_INCLUDE_DIRS})
install(FILES ${_PY_FILES} DESTINATION "${LIB_DIR}/${PYMOD_DIR}")
endif()
endif()
@@ -798,7 +798,7 @@ macro(promod3_unittest)
message(FATAL_ERROR "Python test script does not exist: ${py_twp}")
endif()
get_python_path(python_path)
- set (PY_TESTS_CMD "PYTHONPATH=${python_path} ${PYTHON_BINARY}")
+ set (PY_TESTS_CMD "PYTHONPATH=${python_path} ${Python_EXECUTABLE}")
add_custom_target("${py_test}_run"
sh -c "${PY_TESTS_CMD} ${py_twp}"
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -863,8 +863,8 @@ endmacro(add_unit_test_data_target)
#-------------------------------------------------------------------------------
macro(promod3_find_python_module MODULE)
if(NOT PYTHON_MODULE_${MODULE})
- message(STATUS "Searching for python module ${MODULE} for ${PYTHON_BINARY}")
- execute_process(COMMAND ${PYTHON_BINARY} -c "import ${MODULE}"
+ message(STATUS "Searching for python module ${MODULE} for ${Python_EXECUTABLE}")
+ execute_process(COMMAND ${Python_EXECUTABLE} -c "import ${MODULE}"
OUTPUT_QUIET ERROR_QUIET
RESULT_VARIABLE _IMPORT_ERROR)
if(_IMPORT_ERROR)
@@ -900,9 +900,9 @@ macro(promod3_match_boost_python_version)
list(GET _BOOST_PYTHON_LIBRARY ${_LIB_INDEX} _BP_LIB_PATH)
set(_BOOST_PYTHON_LIBRARY ${_BP_LIB_PATH})
endif()
- set(CMAKE_REQUIRED_FLAGS "-I${PYTHON_INCLUDE_PATH}")
+ set(CMAKE_REQUIRED_FLAGS "-I${Python_INCLUDE_DIRS}")
set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} -I${Boost_INCLUDE_DIR}")
- set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} ${PYTHON_LIBRARIES}")
+ set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} ${Python_LIBRARIES}")
set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} ${_BOOST_PYTHON_LIBRARY}")
check_cxx_source_runs(
"#include <boost/python.hpp>
@@ -1016,12 +1016,12 @@ set(_BOOST_MIN_VERSION 1.53)
macro(setup_boost)
# starting with CMake 3.11 we could use the following instead of the foreach
# find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS
- # python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR} REQUIRED)
+ # python${Python_VERSION_MAJOR}${Python_VERSION_MINOR} REQUIRED)
# set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
# see https://cmake.org/cmake/help/v3.11/module/FindBoost.html
- foreach(_python_lib_name python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}
- python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
- python${PYTHON_VERSION_MAJOR}
+ foreach(_python_lib_name python${Python_VERSION_MAJOR}${Python_VERSION_MINOR}
+ python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}
+ python${Python_VERSION_MAJOR}
python)
find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS ${_python_lib_name} QUIET)
if(Boost_FOUND)
@@ -1331,7 +1331,7 @@ macro(convert_module_data)
# setup python call
set(_PY_PATH "${CMAKE_CURRENT_SOURCE_DIR}/${_ARG_SCRIPT}")
- set(_PY_CMD "${PYTHON_BINARY} '${_PY_PATH}' '${_SRC_PATH}' '${_TRG_PATH}' ${_ARG_ARGS}")
+ set(_PY_CMD "${Python_EXECUTABLE} '${_PY_PATH}' '${_SRC_PATH}' '${_TRG_PATH}' ${_ARG_ARGS}")
# set command to run (depends on _MODULE (pymod-target), FILE and SCRIPT)
# -> here we also make sure "import promod3" is ready
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index acaf8d0f77ff49b0e4b296003b70eae9022cd292..343dd02451528c4c198026f0064cd2b4a776f6f5 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -144,7 +144,7 @@ set(_SPHINX_INDEX_HTML "${_SPHINX_HTML_DIR}/index.html")
add_custom_command(OUTPUT ${_SPHINX_INDEX_HTML}
DEPENDS doc_wait_for_rst "${_SPHINX_CONF_PY}" ${_RST_DEPS}
${_DOC_MODULE_DEPS} doc_wait_for_modules
- COMMAND "${PYTHON_BINARY}" -m sphinx -b html -c "${_RST_SOURCE_DIR}"
+ COMMAND "${Python_EXECUTABLE}" -m sphinx -b html -c "${_RST_SOURCE_DIR}"
"${_RST_SOURCE_DIR}" "${_SPHINX_HTML_DIR}")
add_custom_target(html DEPENDS ${_SPHINX_INDEX_HTML})
@@ -156,7 +156,7 @@ set(_SPHINX_INDEX_JSON "${_SPHINX_JSON_DIR}/index.fjson")
add_custom_command(OUTPUT ${_SPHINX_INDEX_JSON}
DEPENDS doc_wait_for_rst "${_SPHINX_CONF_PY}" ${_RST_DEPS}
${_DOC_MODULE_DEPS} doc_wait_for_modules
- COMMAND "${PYTHON_BINARY}" -m sphinx -b json -c "${_RST_SOURCE_DIR}"
+ COMMAND "${Python_EXECUTABLE}" -m sphinx -b json -c "${_RST_SOURCE_DIR}"
"${_RST_SOURCE_DIR}" "${_SPHINX_JSON_DIR}")
add_custom_target(json DEPENDS ${_SPHINX_INDEX_JSON})
@@ -167,7 +167,7 @@ set(_SPHINX_MAN "${_SPHINX_MAN_DIR}/promod3.1")
add_custom_command(OUTPUT ${_SPHINX_MAN}
DEPENDS doc_wait_for_rst "${_SPHINX_CONF_PY}" ${_RST_DEPS}
${_DOC_MODULE_DEPS} doc_wait_for_modules
- COMMAND "${PYTHON_BINARY}" -m sphinx -b man -c "${_RST_SOURCE_DIR}"
+ COMMAND "${Python_EXECUTABLE}" -m sphinx -b man -c "${_RST_SOURCE_DIR}"
"${_RST_SOURCE_DIR}" "${_SPHINX_MAN_DIR}")
add_custom_target(man DEPENDS ${_SPHINX_MAN})
@@ -180,7 +180,7 @@ add_dependencies(doc man)
set(_SPHINX_LINKCHECK_DIR "${CMAKE_CURRENT_BINARY_DIR}/linkcheck")
file(MAKE_DIRECTORY ${_SPHINX_LINKCHECK_DIR})
add_custom_target(linkcheck
- COMMAND "${PYTHON_BINARY}" -m sphinx -b linkcheck -c "${_RST_SOURCE_DIR}"
+ COMMAND "${Python_EXECUTABLE}" -m sphinx -b linkcheck -c "${_RST_SOURCE_DIR}"
"${_RST_SOURCE_DIR}" "${_SPHINX_LINKCHECK_DIR}"
DEPENDS "${_SPHINX_CONF_PY}" ${_RST_DEPS} ${_DOC_MODULE_DEPS})
diff --git a/doc/buildsystem.rst b/doc/buildsystem.rst
index 5960348cf6d2e6cb2598440d7ffa10784a63ef2e..df28ce02585ae1557e4af1d57b2d942fb396ea51 100644
--- a/doc/buildsystem.rst
+++ b/doc/buildsystem.rst
@@ -65,7 +65,7 @@ headers would be located in ``OST_ROOT/include/ost``).
Similarly, one can specify folders for |boost|, |python| and |eigen3|
if multiple versions exist and/or they are not installed in a default location.
These are set with the ``BOOST_ROOT`` (make sure that's the same as for |ost_s|),
-``PYTHON_ROOT`` and ``EIGEN3_INCLUDE_DIR``.
+``Python_ROOT`` and ``EIGEN3_INCLUDE_DIR``.
Here is a list of more options used within |project|:
diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index fd4ae8e6ec0d55b1c0f073f07cd132146b17e931..35af3b9a4a41b6dac2f51c5e4a3438615bd01f01 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -3,7 +3,7 @@ set(SUBST_DICT OST_ROOT="${OST_ROOT}"
LIBEXECPATH=${LIBEXEC_PATH}
PYTHON_MODULE_PATH=${PYTHON_MODULE_PATH}
OST_PYMOD_PATH=${OST_PYMOD_PATH}
- PYTHON_BINARY=${PYTHON_BINARY})
+ Python_EXECUTABLE=${Python_EXECUTABLE})
add_custom_target(promod3_scripts ALL)
diff --git a/scripts/pm.in b/scripts/pm.in
index d7c7e190828772497476b2e64222940ae95fe7ea..339c715b8ac4c7edc9bc323551ca11eaf3c67e0b 100755
--- a/scripts/pm.in
+++ b/scripts/pm.in
@@ -43,7 +43,7 @@ export PATH="$BIN_DIR:${OST_ROOT}/bin:$PATH"
export LD_LIBRARY_PATH="${PROMOD3_ROOT}/@LIBDIR@:${OST_ROOT}/lib64:$LD_LIBRARY_PATH"
# retrieve absolute path to python executable
-pyexec="@PYTHON_BINARY@"
+pyexec="@Python_EXECUTABLE@"
ACTION="$1"
PROMOD3_SCRIPT="${PROMOD3_EXEC_PATH}/pm-${ACTION}"