diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 85309e718a752ec541f18893d7431bc8c455c280..bac8fe2a2f5f0ac7024296a86491d992159c2856 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,11 @@
+Changes in Release 4.4.0
+--------------------------------------------------------------------------------
+
+* Updates build system: Removed custom boost setup code and silenced cmake
+ warnings.
+* Several minor bug fixes, improvements
+
+
Changes in Release 4.3.1
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index e7d729192dec522e627cd4263c6d639ccecf7fd6..cd502e1bc634e5d54451cd46f1d88068b773e143 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,7 +1,7 @@
#-------------------------------------------------------------------------------
# Author: Marco Biasini
#-------------------------------------------------------------------------------
-cmake_minimum_required(VERSION 3.12.1 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.22 FATAL_ERROR)
# Set CMake policies
# Behaviour of target_link_libraries, always link by full path. CMP0060 can
@@ -10,9 +10,29 @@ cmake_minimum_required(VERSION 3.12.1 FATAL_ERROR)
# manually forced CMake to the new scheme.
cmake_policy(SET CMP0060 NEW)
+if(CMAKE_VERSION VERSION_GREATER_EQUAL "3.31.0")
+ # See CMP0177 for more information
+ # To summarize: all paths given to the install command are normalized starting
+ # from cmake version 3.31. Starting from 3.31 you'll start to see warnings if
+ # you use the OLD behaviour but some paths would need normalization.
+ # The problem with ost: some of the paths that we give install look like:
+ # xyz/./bla. So its actually a good thing to run them through normalization
+ # which would give xyz/bla
+ cmake_policy(SET CMP0177 NEW)
+endif()
+
+if(CMAKE_VERSION VERSION_GREATER_EQUAL "3.30.0")
+ # See CMP0167 for more information
+ # to summarize: Starting from boost 1.70, boost comes with a package
+ # configuration file BoostConfig.cmake. Starting from cmake 3.30,
+ # this is the way to go and users get warned if the old FindBoost module
+ # gets used.
+ cmake_policy(SET CMP0167 NEW)
+endif()
+
set (QMEAN_VERSION_MAJOR 4)
-set (QMEAN_VERSION_MINOR 3)
-set (QMEAN_VERSION_PATCH 1)
+set (QMEAN_VERSION_MINOR 4)
+set (QMEAN_VERSION_PATCH 0)
set (QMEAN_VERSION_STRING ${QMEAN_VERSION_MAJOR}.${QMEAN_VERSION_MINOR}.${QMEAN_VERSION_PATCH} )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
@@ -72,9 +92,13 @@ list(GET _python_version_list 1 Python_VERSION_MINOR)
# where Python modules live
set(PYTHON_MODULE_PATH "python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages/")
-setup_boost()
+find_package(Boost ${_BOOST_MIN_VERSION}
+ COMPONENTS filesystem
+ python
+ REQUIRED)
+
-find_package(OPENSTRUCTURE 2.4.0 REQUIRED
+find_package(OPENSTRUCTURE 2.10.0 REQUIRED
COMPONENTS mol seq seq_alg mol_alg conop db)
include_directories(${Boost_INCLUDE_DIRS}
diff --git a/cmake_support/QMEAN2.cmake b/cmake_support/QMEAN2.cmake
index afa2c52cdb15c51e18210f764b8402390aadfc64..68af4a3ed356adf77d91c0e5101b8997b6a35a03 100644
--- a/cmake_support/QMEAN2.cmake
+++ b/cmake_support/QMEAN2.cmake
@@ -82,10 +82,9 @@ macro(compile_py_files module out_dir compiled_files_name)
list(APPEND ${compiled_files_name} ${_out_file})
get_filename_component(_in_name ${input_file} NAME)
file(MAKE_DIRECTORY ${out_dir})
- add_custom_command(TARGET ${module}
+ add_custom_command(TARGET ${module} POST_BUILD
COMMAND ${Python_EXECUTABLE} -c "import py_compile;py_compile.compile(\"${_in_file}\",\"${_out_file}\",\"${_in_name}\",doraise=True)"
- VERBATIM DEPENDS ${input_file}
- )
+ VERBATIM)
endforeach()
endmacro()
@@ -147,9 +146,7 @@ macro(copy_if_different FROM_DIR TO_DIR FILES TARGETS TARGET)
set(TO ${TO_DIR}/${TOFILE})
endif()
file(MAKE_DIRECTORY ${TO_DIR})
- #message("copy following stuff: ${FROM} ${TO}")
add_custom_command(TARGET "${TARGET}" PRE_BUILD
- DEPENDS ${FROM}
COMMAND ${CMAKE_COMMAND} -E copy_if_different ${FROM} ${TO}
COMMENT ""
)
@@ -487,7 +484,7 @@ macro(pymod)
endif()
target_link_libraries("_${_LIB_NAME}" ${_PARENT_LIB_NAME}
- ${Python_LIBRARIES} ${BOOST_PYTHON_LIBRARIES})
+ ${Python_LIBRARIES} Boost::python)
set_target_properties("_${_LIB_NAME}"
PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${PYMOD_STAGE_DIR})
@@ -900,66 +897,13 @@ macro(find_path_recursive VARIABLE)
endwhile(_fst_subs)
endmacro(find_path_recursive)
+macro(setup_compiler_flags)
-function(get_compiler_version _OUTPUT_VERSION)
- exec_program(${CMAKE_CXX_COMPILER}
- ARGS ${CMAKE_CXX_COMPILER_ARG1} -dumpversion
- OUTPUT_VARIABLE _COMPILER_VERSION
- )
- string(REGEX REPLACE "([0-9])\\.([0-9])(\\.[0-9])?" "\\1\\2"
- _COMPILER_VERSION ${_COMPILER_VERSION})
-
- set(${_OUTPUT_VERSION} ${_COMPILER_VERSION} PARENT_SCOPE)
-endfunction(get_compiler_version)
-
+ set(CMAKE_CXX_STANDARD 17)
-macro(setup_compiler_flags)
- if(CMAKE_COMPILER_IS_GNUCXX)
- get_compiler_version(_GCC_VERSION)
+ if (CMAKE_COMPILER_IS_GNUCXX)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall" )
- if(_GCC_VERSION MATCHES "44")
- # gcc 4.4. is very strict about aliasing rules. the shared_count
- # implementation that is used boost's shared_ptr violates these rules. To
- # silence the warnings and prevent miscompiles, enable
- # -fno-strict-aliasing
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-strict-aliasing" )
- endif()
- #message(STATUS "GCC VERSION " ${_GCC_VERSION})
- if (_GCC_VERSION LESS "60")
- # for older compilers we need to enable C++11
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
- endif()
endif()
-endmacro(setup_compiler_flags)
+endmacro(setup_compiler_flags)
-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)
- # 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}
- python)
- find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS ${_python_lib_name} QUIET)
- if(Boost_FOUND)
- message(STATUS "Found Boost package: " ${_python_lib_name})
- set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
- break()
- else()
- message(STATUS "Boost package not found: " ${_python_lib_name}
- ". Trying alternative names!")
- endif()
- endforeach(_python_lib_name)
- if(NOT BOOST_PYTHON_LIBRARIES)
- message(FATAL_ERROR "Failed to find any Boost Python library!")
- endif()
- set(Boost_LIBRARIES)
- find_package(Boost ${_BOOST_MIN_VERSION}
- COMPONENTS filesystem system REQUIRED)
- set(BOOST_LIBRARIES ${Boost_LIBRARIES})
-endmacro(setup_boost)
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 7bc511e81aaf7d9dca61c4091a3fb6832d86d9c9..5ebe19be0a95646acbe6ca2bafdad4757c7452ef 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -70,9 +70,9 @@ copyright = u'2016-2020, Gabriel Studer'
# built documents.
#
# The short X.Y version.
-release = '4.3.1'
+release = '4.4.0'
# The full version, including alpha/beta/rc tags.
-release = '4.3.1'
+release = '4.4.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/doc/source/example_scripts/test_doctests.py b/doc/source/example_scripts/test_doctests.py
index 036bf0c32fe488359d2d3f702fd8ee69ec7d1cd4..7d80cb335bd70f5398fbc3dded4b9f02702a1920 100644
--- a/doc/source/example_scripts/test_doctests.py
+++ b/doc/source/example_scripts/test_doctests.py
@@ -29,6 +29,7 @@ import subprocess
import shutil
from ost import io, settings, table
import qmean
+import numpy as np
class DocTests(unittest.TestCase):
@@ -409,7 +410,8 @@ class DocTests(unittest.TestCase):
self.assertAlmostEqual(a,b,4)
def testAssessModelQualityExample(self):
- return_code, sout, serr = self.runScript('assess_model_quality_example.py')
+ return_code, sout, serr = self.runScript('assess_model_quality_example.py')
+
self.assertEqual(return_code, 0)
self.assertTrue(os.path.exists("local_profile.png"))
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 32e36f3ae8b7288b0b1436994f05837e6ac7afe0..811aa6b43b85d6d8d29b212bfa7b5690bd93c622 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -79,5 +79,5 @@ configure_file(version.hh.in ${VERSION_HH_FILE})
module(NAME qmean SOURCES ${QMEAN_SOURCES} HEADERS ${QMEAN_HEADERS}
PREFIX "" HEADER_OUTPUT_DIR qmean
- LINK ${OST_LIBRARIES} ${BOOST_LIBRARIES})
+ LINK ${OST_LIBRARIES} Boost::filesystem)
diff --git a/src/disco.cc b/src/disco.cc
index 019421d8e86865f067ade610fdc795b2b885c177..169d267e3e6b7fc308fb93fed5efeb837801f370 100644
--- a/src/disco.cc
+++ b/src/disco.cc
@@ -55,7 +55,7 @@ void PairwiseSequenceSimilarities(const ost::seq::AlignmentHandle& aln,
typedef std::vector<std::vector<char> > idx_mat_type;
idx_mat_type idx_mat(aln_length, std::vector<char>(num_sequences));
for(int i = 0; i < num_sequences; ++i) {
- const String& s = aln.GetSequence(i + 1).GetString();
+ String s = aln.GetSequence(i + 1).GetString();
for(int j = 0; j < aln_length; ++j) {
idx_mat[j][i] = static_cast<char>(ToIdx(s[j]));
}
@@ -116,7 +116,7 @@ void PairwiseSequenceSimilarities(const ost::seq::AlignmentHandle& aln,
// lets fill in the sequence similarities to the SEQRES in a separate step
// (code duplication I know)
- const String& seqres = aln.GetSequence(0).GetString();
+ String seqres = aln.GetSequence(0).GetString();
summed_weights.assign(num_sequences, 0);
counts.assign(num_sequences, 0);
seqsim_to_seqres.resize(num_sequences);