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Merge pull request #12 from ilias-karimalis/main
Scikit-Learn compatible rewrite
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‎.github/workflows/main.yml

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‎.gitignore

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# Python Ignores
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notebooks/.ipynb_checkpoints/*
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*.pyc
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*.pyo
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# Build Objects
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*.o
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*.tmp
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# C extensions
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*.so
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gosdt_test
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# Autobuild Ignores
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# Distribution / packaging
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wheelhouse/
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.Python
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pyproject-build/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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Makefile
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config.log
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config.status
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autom4te.cache/*
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aclocal.m4
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m4
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libtool
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.deps
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gosdt_test
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bin
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.scon*
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.DS_Store
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## Xcode User settings
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xcuserdata/
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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.idea/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# setuptools_scm
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src/*/_version.py
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# ruff
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.ruff_cache/
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# OS specific stuff
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.DS_Store
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._DS_Store
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__private/
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cmake*/
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_skbuild/
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dist/
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wheelhouse/
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*.egg-info/
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/gosdt.xcodeproj/xcuserdata/
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.DS_Store?
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._*
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.Spotlight-V100
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.Trashes
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ehthumbs.db
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Thumbs.db
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# Common editor files
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*~
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*.swp
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# Cmake files
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compile_commands.json

‎CMakeLists.txt

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cmake_minimum_required(VERSION 3.10)
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cmake_minimum_required(VERSION 3.15...3.27)
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project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
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# Project `Name` and `Language`
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project(GOSDT)
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set(CMAKE_CXX_STANDARD 20)
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# Set the language standard to `c++11`
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set(CMAKE_CXX_STANDARD 11)
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set(TARGET "_libgosdt")
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set(CLI_TARGET "gosdt_cli")
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# Set the compiler flags
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if (MSVC)
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set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
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set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} /DDEBUG")
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set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE}")
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message(STATUS "PATH environment variable: $ENV{PATH}")
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message(STATUS "LD_LIBRARY_PATH environment variable: $ENV{LD_LIBRARY_PATH}")
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# `#define NOMINMAX` prevents expansion of min and max macros on Windows,
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# otherwise `std::numeric_limits<T>::max()/min()` leads to MSVC compiler errors.
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# Reference: https://stackoverflow.com/questions/27442885/syntax-error-with-stdnumeric-limitsmax
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj /w /DNOMINMAX")
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set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /DDEBUG")
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set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}")
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else()
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set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -Wextra")
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set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -DDEBUG")
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set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE}")
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# Python Target
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if (SKBUILD)
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# Find the module development requirements (requires FindPython from 3.17 or
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# scikit-build-core's built-in backport)
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find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
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find_package(pybind11 CONFIG REQUIRED)
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra")
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set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -DDEBUG")
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set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}")
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endif()
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# Python Target
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file(GLOB_RECURSE SOURCE_FILES src/libgosdt/src/*.cpp src/libgosdt.cpp)
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python_add_library(${TARGET} MODULE ${SOURCE_FILES} WITH_SOABI)
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target_link_libraries(${TARGET} PRIVATE pybind11::module)
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target_include_directories(${TARGET} PUBLIC src/libgosdt/include/)
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install(TARGETS ${TARGET} DESTINATION ${SKBUILD_PROJECT_NAME})
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#
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# MARK: - Targets
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#
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# In the case where wer're running on Windows with packages installed via vcpkg, we include
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# the vcpkg.cmake file to find the packages.
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if (WIN32)
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include($ENV{VCPKG_INSTALLATION_ROOT}/scripts/buildsystems/vcpkg.cmake)
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endif()
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# Target Definition
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set(TARGET_CLI "gosdt")
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set(TARGET_TESTS "gosdt_tests")
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set(TARGET_PYTHON "libgosdt")
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# Target: GOSDT CLI
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file(GLOB_RECURSE SOURCE_FILES_CLI src/*.cpp)
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list(REMOVE_ITEM SOURCE_FILES_CLI "${CMAKE_SOURCE_DIR}/src/python_extension.cpp")
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add_executable(${TARGET_CLI} ${SOURCE_FILES_CLI})
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target_include_directories(${TARGET_CLI} PUBLIC ${CMAKE_SOURCE_DIR}/include)
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endif()
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# Target: GOSDT Tests
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file(GLOB_RECURSE SOURCE_FILES_TESTS src/*.cpp)
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list(REMOVE_ITEM SOURCE_FILES_TESTS "${CMAKE_SOURCE_DIR}/src/python_extension.cpp")
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list(REMOVE_ITEM SOURCE_FILES_TESTS "${CMAKE_SOURCE_DIR}/src/main.cpp")
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list(INSERT SOURCE_FILES_TESTS 0 "${CMAKE_SOURCE_DIR}/test/test.cpp")
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add_executable(${TARGET_TESTS} ${SOURCE_FILES_TESTS})
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target_include_directories(${TARGET_TESTS} PUBLIC ${CMAKE_SOURCE_DIR}/include)
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# CLI Target
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file(GLOB_RECURSE SOURCE_FILES src/libgosdt/src/*.cpp src/cli.cpp)
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add_executable(${CLI_TARGET} ${SOURCE_FILES})
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target_include_directories(${CLI_TARGET} PUBLIC src/libgosdt/include/)
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#
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# MARK: - Dependencies
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# Link all needed dependencies to this project:
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#
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find_package(PkgConfig REQUIRED)
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include(FetchContent)
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# Dependencies: Intel TBB
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# TBB:
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find_package(TBB REQUIRED)
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target_link_libraries(${TARGET_CLI} PRIVATE TBB::tbb)
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target_link_libraries(${TARGET_CLI} PRIVATE TBB::tbbmalloc)
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target_link_libraries(${TARGET_TESTS} PRIVATE TBB::tbb)
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target_link_libraries(${TARGET_TESTS} PRIVATE TBB::tbbmalloc)
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if (SKBUILD)
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target_link_libraries(${TARGET} PRIVATE TBB::tbb)
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target_link_libraries(${TARGET} PRIVATE TBB::tbbmalloc)
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endif()
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target_link_libraries(${CLI_TARGET} PRIVATE TBB::tbb TBB::tbbmalloc)
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# Dependencies: GMP
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find_package(PkgConfig REQUIRED)
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# GMP:
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pkg_check_modules(GMP REQUIRED IMPORTED_TARGET gmp)
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target_link_libraries(${TARGET_CLI} PRIVATE PkgConfig::GMP)
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target_include_directories(${TARGET_CLI} PRIVATE ${GMP_INCLUDE_DIRS})
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target_link_libraries(${TARGET_TESTS} PRIVATE PkgConfig::GMP)
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target_include_directories(${TARGET_TESTS} PRIVATE ${GMP_INCLUDE_DIRS})
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# Dependencies: Threads (pthread on macOS and Ubuntu, win32 thread on Windows)
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# This is needed because the CentOS docker provided by manylinux reports linker errors
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set(THREADS_PREFER_PTHREAD_FLAG ON)
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find_package(Threads REQUIRED)
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target_link_libraries(${TARGET_CLI} PRIVATE Threads::Threads)
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target_link_libraries(${TARGET_TESTS} PRIVATE Threads::Threads)
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if (SKBUILD)
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target_link_libraries(${TARGET} PRIVATE PkgConfig::GMP)
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target_include_directories(${TARGET} PRIVATE ${GMP_INCLUDE_DIRS})
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endif()
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target_link_libraries(${CLI_TARGET} PRIVATE PkgConfig::GMP)
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target_include_directories(${CLI_TARGET} PRIVATE ${GMP_INCLUDE_DIRS})
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# Target: GOSDT Python Module
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# nlohmann::json:
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FetchContent_Declare(json URL https://github.com/nlohmann/json/releases/download/v3.11.3/json.tar.xz)
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FetchContent_MakeAvailable(json)
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if (SKBUILD)
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message(STATUS "GOSDT is built using scikit-build. Will build the Python module.")
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# Find the Python 3 development environment
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if (NOT DEFINED Python3_INCLUDE_DIR)
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message(FATAL_ERROR "The CMake variable Python3_INCLUDE_DIR should have been defined by scikit-build.")
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endif()
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# Create the list of source files needed to build the Python extension
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file(GLOB_RECURSE SOURCE_FILES_PY src/*.cpp)
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list(REMOVE_ITEM SOURCE_FILES_PY "${CMAKE_SOURCE_DIR}/src/main.cpp")
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# Define the CMake target for the Python extension
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add_library(${TARGET_PYTHON} MODULE ${SOURCE_FILES_PY})
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target_include_directories(${TARGET_PYTHON} PRIVATE ${CMAKE_SOURCE_DIR}/include ${Python3_INCLUDE_DIR} ${GMP_INCLUDE_DIRS})
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target_link_libraries(${TARGET_PYTHON} TBB::tbb TBB::tbbmalloc PkgConfig::GMP Threads::Threads)
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# Set up the Python extension
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find_package(PythonExtensions REQUIRED)
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## Use the suffix `.abi3.so` or `.pyd` so that Python 3 on other platforms can find the dylib and import it properly
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message(STATUS "The current Python extension suffix is \"${PYTHON_EXTENSION_MODULE_SUFFIX}\".")
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if (WIN32)
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set(PYTHON_EXTENSION_MODULE_SUFFIX ".pyd")
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else()
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set(PYTHON_EXTENSION_MODULE_SUFFIX ".abi3.so")
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endif()
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message(STATUS "The new Python extension suffix is \"${PYTHON_EXTENSION_MODULE_SUFFIX}\".")
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## Define the Python extension module target
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python_extension_module(${TARGET_PYTHON})
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# Install `libgosdt` to the root directory of the Python extension package
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install(TARGETS ${TARGET_PYTHON} LIBRARY DESTINATION .)
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target_link_libraries(${TARGET} PRIVATE nlohmann_json::nlohmann_json)
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endif()
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target_link_libraries(${CLI_TARGET} PRIVATE nlohmann_json::nlohmann_json)
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# Generate compile_commands.json for vscode
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set(CMAKE_EXPORT_COMPILE_COMMANDS
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ON
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CACHE INTERNAL "")

‎LICENSE

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BSD 3-Clause License
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Copyright (c) 2021, 2022 Chudi Zhong, Hayden McTavish, Jimmy Lin, Margo Seltzer,
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Cynthia Rudin, The University of British Columbia, Duke University
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Copyright (c) 2021, 2022, 2024, Chudi Zhong, Hayden McTavish, Jimmy Lin, Ilias Karimalis,
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Margo Seltzer, Cynthia Rudin, The University of British Columbia, Duke University
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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* Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
18-
contributors may be used to endorse or promote products derived from
19-
this software without specific prior written permission.
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* Neither the name of the copyright holder nor the names of its
18+
contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
2020

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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

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