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initial Python 3 commit
- Edited CMakeLists.txt to search for Python with 3.6 as min version 3.6 is the Python version shipped by default with Ubuntu 18.04 LTS - Add version 3.6 to cmake_support/FindPython.cmake - Adapt setup_boost macro in cmake_support/OST.cmake to prefer versioned libraries and not first check for boost_python.so. In the example of Ubuntu 18.04, libboost_python.so is specific for Python 2 but libboost_python3.so is the one we want. - apply the following command: 2to3-2.7 -n -w <PROMOD3_DIR> - replace commands added in cmake to build documentation from sphinx-build <args> to python_executable -m sphinx <args> The reason is that sphinx-build is a short shell script starting with a shebang #!python. In Debian based systems this means by default Python 2 if you're not running a virtual env or manually changed that behaviour. PROBLEM: cmake is NOT looking for the presence of Sphinx anymore and you'll get errors at build time if its missing. A cmake macro that checks whether a certain module can be imported would be nice. - replace r.__next__ with r.next to get the next ResidueHandle - edit unit tests that expected strict string output (pm3_argparse) that might change depending on how json generates strings of dictionaries
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- CMakeLists.txt 5 additions, 2 deletionsCMakeLists.txt
- cmake_support/FindPython.cmake 2 additions, 2 deletionscmake_support/FindPython.cmake
- cmake_support/FindSphinx.cmake 0 additions, 35 deletionscmake_support/FindSphinx.cmake
- cmake_support/PROMOD3.cmake 3 additions, 3 deletionscmake_support/PROMOD3.cmake
- core/init/__init__.py.in 1 addition, 1 deletioncore/init/__init__.py.in
- core/pymod/CMakeLists.txt 0 additions, 1 deletioncore/pymod/CMakeLists.txt
- core/pymod/__init__.py 2 additions, 2 deletionscore/pymod/__init__.py
- core/pymod/_filecache.py 0 additions, 85 deletionscore/pymod/_filecache.py
- core/pymod/pm3argparse.py 26 additions, 29 deletionscore/pymod/pm3argparse.py
- core/tests/test_helper.py 1 addition, 1 deletioncore/tests/test_helper.py
- core/tests/test_pm3argparse.py 31 additions, 88 deletionscore/tests/test_pm3argparse.py
- doc/CMakeLists.txt 4 additions, 4 deletionsdoc/CMakeLists.txt
- doc/cmake.py 3 additions, 3 deletionsdoc/cmake.py
- doc/tests/scripts/loop_backbone.py 3 additions, 3 deletionsdoc/tests/scripts/loop_backbone.py
- doc/tests/scripts/loop_fragger.py 2 additions, 2 deletionsdoc/tests/scripts/loop_fragger.py
- doc/tests/scripts/loop_main.py 4 additions, 4 deletionsdoc/tests/scripts/loop_main.py
- doc/tests/scripts/loop_mm_sys_creation.py 3 additions, 3 deletionsdoc/tests/scripts/loop_mm_sys_creation.py
- doc/tests/scripts/modelling_allatomrelaxer.py 1 addition, 1 deletiondoc/tests/scripts/modelling_allatomrelaxer.py
- doc/tests/scripts/modelling_close_small_deletions.py 2 additions, 2 deletionsdoc/tests/scripts/modelling_close_small_deletions.py
- doc/tests/scripts/modelling_fill_loops_by_database.py 2 additions, 2 deletionsdoc/tests/scripts/modelling_fill_loops_by_database.py
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