Merge branch 'develop' into hmm_score

f7b6d6e7 · Studer Gabriel · 1ccd8359 · 5012fa87 · f7b6d6e7 · f7b6d6e7
Commit f7b6d6e7 authored 5 years ago by Studer Gabriel
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -71,8 +71,8 @@ test:centos7.3:
             -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include
             -DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so
             -DOPTIMIZE=1
-             -DCMAKE_C_FLAGS='-L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
-             -DCMAKE_CXX_FLAGS='-L/scicore/soft/apps/libpng/1.6.34-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/LibTIFF/4.0.9-GCCcore-7.3.0/lib/ -L/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include' 
+             -DCMAKE_C_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
+             -DCMAKE_CXX_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
             -DCMAKE_EXE_LINKER_FLAGS=" -pthread"
  - make -j 2
  - echo "    ... done building OST."

--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
+Changes in Release 2.0.0
+--------------------------------------------------------------------------------
+
+ * Port OpenStructure to Python 3 (3.6).
+ * Updated versions of dependencies
+ * Reduced amount of warnings during compilation.
+ * Removed OpenMM density plugin and out-dated bindings (3dcomb, MMalign).
+ * Several minor bug fixes and improvements.
+
+Changes in Release 1.11.0
+--------------------------------------------------------------------------------
+
+ * This is expected to be the last release supporting Python 2.
+ * Read revision version numbers from mmCIF files.
+ * Several minor bug fixes and improvements.
+
 Changes in Release 1.10.0
 --------------------------------------------------------------------------------


--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,11 +2,19 @@
 # Author: Marco Biasini
 #-------------------------------------------------------------------------------

-cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.10.2 FATAL_ERROR)
+
+# Set CMake policies
+# Behaviour of target_link_libraries, always link by full path. CMP0060 can
+# disable this to stay compatible with old projects. We want the new behaviour
+# since before we needed to provide the full path ourselves, that is: we
+# manually forced CMake to the new scheme.
+cmake_policy(SET CMP0060 NEW)
+
 project(OpenStructure CXX C)
 set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
-set (OST_VERSION_MAJOR 1)
-set (OST_VERSION_MINOR 10)
+set (OST_VERSION_MAJOR 2)
+set (OST_VERSION_MINOR 0)
 set (OST_VERSION_PATCH 0)
 set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
@@ -23,7 +31,9 @@ option(PROFILE "whether to compile with profiling support"
 option(ENABLE_GUI "whether the graphical user interface should be enabled"
       ON)
 option(ENABLE_GFX "whether graphics support should be enabled"
-      ON)
+       ON)
+option(OPENGLPREFERENCE_LEGACY "whether to use the OpenGL Legacy GL implementation"
+       OFF)
 option(ENABLE_IMG "whether the image processing module should be compiled"
       ON)
 option(ENABLE_INFO "whether openstructure should be compiled with support for the info library"
@@ -213,6 +223,11 @@ else()
  endif()
 endif()
 if (ENABLE_GFX)
+  if (OPENGLPREFERENCE_LEGACY)
+    set(OpenGL_GL_PREFERENCE LEGACY)
+  else()
+    set(OpenGL_GL_PREFERENCE GLVND)
+  endif(OPENGLPREFERENCE_LEGACY)
  find_package(OpenGL REQUIRED)
 endif()

@@ -262,8 +277,8 @@ if (ENABLE_GUI)
  find_package(Qt5Widgets REQUIRED)
  find_package(Qt5OpenGL REQUIRED)
  set(QT_LIBRARIES ${QT_LIBRARIES} Qt5::Gui Qt5::Widgets Qt5::Core)
-  ost_find_python_module(sip)
  ost_find_python_module(PyQt5)
+  ost_find_python_module_alt("PyQt5.sip;sip")
 endif()

 if (ENABLE_SPNAV)
@@ -289,6 +304,13 @@ if (CMAKE_COMPILER_IS_GNUCXX)
  endif(HIDDEN_VISIBILITY)
 endif()

+if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unknown-warning-option")
+endif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+if(CMAKE_C_COMPILER_ID MATCHES "Clang")
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unknown-warning-option")
+endif(CMAKE_C_COMPILER_ID MATCHES "Clang")
+
 # basic environment
 include_directories(${Boost_INCLUDE_DIRS} 
                    ${FFTW_INCLUDE_DIRS} 
@@ -362,3 +384,5 @@ message(STATUS
        "   Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ${_UBUNTU_LAYOUT}"
        ${HIDDEN_VIS_MSG})

+
+# LocalWords:  CMake CMP
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -522,7 +522,7 @@ def _CheckConsistency(alignments, log_error):
    for alignment in alignments:
        ref_chain = Renumber(alignment.GetSequence(0)).CreateFullView()
        mdl_chain = Renumber(alignment.GetSequence(1)).CreateFullView()
-        new_is_cons = ResidueNamesMatch(ref_chain, mdl_chain, log_error)
+        new_is_cons = ResidueNamesMatch(mdl_chain, ref_chain, log_error)
        is_cons = is_cons and new_is_cons
    return is_cons


--- a/build_configs/buildconfig_bc2
+++ b/build_configs/buildconfig_bc2
-set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/include/" CACHE PATH "")
-set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3f.a"  CACHE PATH "")
-set(PYTHON_ROOT "/scicore/soft/apps/Python/2.7.5-goolf-1.4.10"  CACHE PATH "")
-set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.2.1-goolf-1.4.10/include/Eigen" CACHE PATH "")
-set(BOOST_ROOT "/import/bc2/apps/Boost/1.53.0-goolf-1.4.10-Python-2.7.5"  CACHE PATH "")
-set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt4" CACHE PATH "")
-set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
+set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.8-gompi-2018b/include/" CACHE PATH "")
+set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.8-gompi-2018b/lib/libfftw3f.a"  CACHE PATH "")
+set(PYTHON_ROOT "/scicore/soft/apps/Python/3.6.6-foss-2018"  CACHE PATH "")
+set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.3.1/include/Eigen" CACHE PATH "")
+set(BOOST_ROOT "/scicore/soft/apps/Boost/1.68.0-foss-2018b-Python-3.6.6"  CACHE PATH "")
+set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt5" CACHE PATH "")
+set(COMPOUND_LIB "/scicore/home/schwede/GROUP/OpenStructure/ChemLib/1.8/compounds.chemlib" CACHE PATH "")
 set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
--- a/build_configs/buildconfig_bc2_static
+++ b/build_configs/buildconfig_bc2_static
-set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/include/" CACHE PATH "")
-set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3f.a"  CACHE PATH "")
+set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.8-gompi-2018b/include/" CACHE PATH "")
+set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.8-gompi-2018b/lib/libfftw3f.a"  CACHE PATH "")
 set(DL_LIBRARIES "/usr/lib64/libdl.a"  CACHE PATH "")
 set(PTHREAD_LIBRARIES "/usr/lib64/libpthread.a"  CACHE PATH "")
-set(ZLIB_LIBRARY "/scicore/soft/apps/zlib/1.2.8-goolf-1.4.10/lib/libz.a"  CACHE PATH "")
-set(PYTHON_ROOT "/scicore/soft/apps/Python/2.7.5-goolf-1.4.10"  CACHE PATH "")
-set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.2.1-goolf-1.4.10/include/Eigen" CACHE PATH "")
-set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt4" CACHE PATH "")
-set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
+set(ZLIB_LIBRARY "/scicore/soft/apps/zlib/1.2.11-GCCcore-7.3.0/lib/libz.a"  CACHE PATH "")
+set(PYTHON_ROOT "/scicore/soft/apps/Python/3.6.6-foss-2018"  CACHE PATH "")
+set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.3.1/include/Eigen" CACHE PATH "")
+set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt5" CACHE PATH "")
+set(COMPOUND_LIB "/scicore/home/schwede/GROUP/OpenStructure/ChemLib/1.8/compounds.chemlib" CACHE PATH "")
 set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
--- a/cmake_support/CheckLSBTypes.cmake
+++ b/cmake_support/CheckLSBTypes.cmake
@@ -23,11 +23,11 @@
 #   CoR-Lab, Research Institute for Cognition and Robotics
 #     Bielefeld University

-SET(LSB_DISTRIBUTOR_ID "unkown")
-SET(LSB_RELEASE "unkown")
-SET(LSB_CODENAME "unkown")
-SET(LSB_BIT_TYPE "unkown")
-SET(LSB_ARCH_TYPE "unkown")
+SET(LSB_DISTRIBUTOR_ID "unknown")
+SET(LSB_RELEASE "unknown")
+SET(LSB_CODENAME "unknown")
+SET(LSB_BIT_TYPE "unknown")
+SET(LSB_ARCH_TYPE "unknown")

 # ---- (mgoettin 10/17/2011) TODO: Update this to match all OS ----
 SET(LSB_PROCESSOR_ARCH ${CMAKE_SYSTEM_PROCESSOR})

--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -759,6 +759,34 @@ macro(ost_find_python_module MODULE)
  endif()
 endmacro()

+#-------------------------------------------------------------------------------
+# make sure the previously detected Python interpreter has the given module
+# while allowing alternative module names
+#-------------------------------------------------------------------------------
+macro(ost_find_python_module_alt MODULES)
+  set(_PY_MODS "")
+  foreach(py_mod ${MODULES})
+    if (NOT PYTHON_MODULE_${py_mod})
+      set(_PY_MODS "${_PY_MODS} ${py_mod}")
+      message(STATUS "Searching for python module ${py_mod} for ${PYTHON_BINARY}")
+      execute_process(COMMAND ${PYTHON_BINARY} -c "import ${py_mod}"
+                      OUTPUT_QUIET ERROR_QUIET
+                      RESULT_VARIABLE _IMPORT_ERROR)
+      if (NOT _IMPORT_ERROR)
+        message(STATUS "Found python module ${py_mod}")
+        set("PYTHON_MODULE_${py_mod}" FOUND CACHE STRING "" FORCE)
+        break()
+      endif (NOT _IMPORT_ERROR)
+    else ()
+      message(STATUS "Already found python module ${py_mod}")
+      unset(_IMPORT_ERROR)
+      break()
+    endif (NOT PYTHON_MODULE_${py_mod})
+  endforeach(py_mod ${MODULES})
+  if (_IMPORT_ERROR)
+    message(FATAL_ERROR "Could not find one of python modules ${_PY_MODS}. Please install one of them.")
+  endif ()    
+endmacro()

 #-------------------------------------------------------------------------------
 # this macro tries to detect a very common problem during configuration stage:

--- a/deployment/CMakeLists.txt
+++ b/deployment/CMakeLists.txt
@@ -11,7 +11,7 @@ if(${PROJECT_SOURCE_DIR} STREQUAL ${CMAKE_SOURCE_DIR})
  INCLUDE(InstallRequiredSystemLibraries)
  
  set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "OpenStructure Framework")
-  set(CPACK_PACKAGE_VENDOR "2008-2010 -- The OpenStructure Team")
+  set(CPACK_PACKAGE_VENDOR "2008-2020 -- The OpenStructure Team")
  set(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/ReadMe.txt")
  set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/LICENSE.txt")
  set(CPACK_PACKAGE_VERSION_MAJOR ${OST_VERSION_MAJOR})

--- a/deployment/README.html.in
+++ b/deployment/README.html.in
@@ -18,7 +18,7 @@
 -----------------------------README----------------------------------------<br/>
 This file is part of the OpenStructure project <www.openstructure.org><br/>
 <br/>
- Copyright (C) 2008-2011 by the OpenStructure authors<br/>
+ Copyright (C) 2008-2020 by the OpenStructure authors<br/>
 <br/>
 This library is free software; you can redistribute it and/or modify it under<br/>
 the terms of the GNU Lesser General Public License as published by the Free<br/>

--- a/deployment/win/dng.bat
+++ b/deployment/win/dng.bat
@@ -2,7 +2,7 @@
 REM ------------------------------------------------------------------------------
 REM This file is part of the OpenStructure project <www.openstructure.org>
 REM
-REM Copyright (C) 2008-2011 by the OpenStructure authors
+REM Copyright (C) 2008-2020 by the OpenStructure authors
 REM
 REM This library is free software; you can redistribute it and/or modify it under
 REM the terms of the GNU Lesser General Public License as published by the Free

--- a/doc/conf/conf.py
+++ b/doc/conf/conf.py
@@ -48,8 +48,8 @@ source_suffix = '.rst'
 master_doc = 'index'

 # General information about the project.
-project = 'OpenStructure'
-copyright = '2019, OpenStructure authors'
+project = u'OpenStructure'
+copyright = u'2020, OpenStructure authors'

 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

--- a/doc/make.py
+++ b/doc/make.py
@@ -113,7 +113,7 @@ for builder in builders:
  Sphinx(
    srcdir='doc/source',
    confdir='doc/conf',
-    outdir='doc/build/html',
+    outdir='doc/build/%s' % builder,
    doctreedir='doc/build/html/.doctrees',
    buildername=builder,
    **extra_args).build(True)
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -2,7 +2,7 @@ FROM ubuntu:18.04

 # ARGUMENTS
 ###########
-ARG OPENSTRUCTURE_VERSION="python3_port"
+ARG OPENSTRUCTURE_VERSION="2.0.0"
 ARG SRC_FOLDER="/usr/local/src"
 ARG CPUS_FOR_MAKE=2
 ARG MSMS_VERSION="2.6.1"
@@ -84,7 +84,9 @@ RUN cd ${SRC_FOLDER} && \
             -DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
             -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
             -DENABLE_GFX=ON \
-             -DENABLE_GUI=ON && \
+             -DENABLE_GUI=ON \
+             -DCMAKE_C_FLAGS="-isystem /usr/include/boost/ -isystem ${OPENMM_INCLUDE_PATH}/include" \
+             -DCMAKE_CXX_FLAGS="-isystem /usr/include/boost/ -isystem ${OPENMM_INCLUDE_PATH}/include" && \
    make -j ${CPUS_FOR_MAKE} && \
    wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz && \
    stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm && \

--- a/docker/README.rst
+++ b/docker/README.rst
@@ -6,10 +6,22 @@ OST Docker
  For many docker installations it is required to run docker commands as root. As
  this depends on set up, we skip the ``sudo`` in all commands.

+Obtain Docker image from the OST registry
+-----------------------------------------
+
+OST has its own container registry inside GitLab. There we try to keep one
+image for the latest stable version of OST. You can import it by
+
+.. code-block:: bash
+
+  docker pull registry.scicore.unibas.ch/schwede/openstructure:<TAG>
+
+and just start using it without the overhead to build it yourself.
+
+
 Build Docker image
 ------------------

-
 In order to build OST image:

 .. code-block:: bash
@@ -155,7 +167,9 @@ To see the help for compare-structures action run:
 Run GUI
 -------

-In order to run GUI do (tested on linux machine):
+The container is built with GUI support, but this is still to be considered an
+experimental feature as it is known to depend on some properties of the host
+where Docker is run. What works on some Linux machines is the following:

 .. code-block:: bash


--- a/doxygen/Doxyfile
+++ b/doxygen/Doxyfile
 # Doxyfile 1.5.7

+# RUN in OST_ROOT with "doxygen doxygen/Doxyfile" (assumes compiled in build)
+# -> outout in doc/html
+
 #---------------------------------------------------------------------------
 # Project related configuration options
 #---------------------------------------------------------------------------
@@ -91,7 +94,7 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT                  = ./modules ./stage
+INPUT                  = ./modules ./build/stage
 INPUT_ENCODING         = UTF-8
 FILE_PATTERNS          = *.hh \
                         *.dox \

--- a/examples/code_fragments/ui/mdi_example.py
+++ b/examples/code_fragments/ui/mdi_example.py
 #------------------------------------------------------------------------------
 # This file is part of the OpenStructure project <www.openstructure.org>
 #
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
 #
 # This library is free software; you can redistribute it and/or modify it under
 # the terms of the GNU Lesser General Public License as published by the Free

--- a/examples/code_fragments/ui/menubar_example.py
+++ b/examples/code_fragments/ui/menubar_example.py
 #------------------------------------------------------------------------------
 # This file is part of the OpenStructure project <www.openstructure.org>
 #
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
 #
 # This library is free software; you can redistribute it and/or modify it under
 # the terms of the GNU Lesser General Public License as published by the Free

--- a/examples/code_fragments/ui/widget_example.py
+++ b/examples/code_fragments/ui/widget_example.py
 #------------------------------------------------------------------------------
 # This file is part of the OpenStructure project <www.openstructure.org>
 #
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
 #
 # This library is free software; you can redistribute it and/or modify it under
 # the terms of the GNU Lesser General Public License as published by the Free

--- a/modules/base/pymod/__init__.py.in
+++ b/modules/base/pymod/__init__.py.in
 #------------------------------------------------------------------------------
 # This file is part of the OpenStructure project <www.openstructure.org>
 #
-# Copyright (C) 2008-2011 by the OpenStructure authors
+# Copyright (C) 2008-2020 by the OpenStructure authors
 #
 # This library is free software; you can redistribute it and/or modify it under
 # the terms of the GNU Lesser General Public License as published by the Free