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Merge branch 'master' of github.com:sandialabs/SpecUtils
2 parents 9e00e5a + e6773e6 commit f1e9570

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‎.github/workflows/pip.yml

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# From https://github.com/wjakob/nanobind_example/blob/5ce5ce57143a469e92d9ebaee9c47949ee77caa8/.github/workflows/pip.yml
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name: Pip
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on:
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workflow_dispatch:
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pull_request:
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push:
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branches:
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- master
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jobs:
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build:
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name: Build with Pip
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runs-on: ${{ matrix.platform }}
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strategy:
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fail-fast: false
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matrix:
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platform: [windows-latest, macos-latest, ubuntu-latest]
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#python-version: ["3.9", "3.12"]
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python-version: ["3.12"]
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Set min macOS version
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if: runner.os == 'macOS'
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run: |
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echo "MACOSX_DEPLOYMENT_TARGET=10.14" >> $GITHUB_ENV
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- name: Build and install
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run: |
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python -m pip install pytest
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pip install --verbose ./bindings/python
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- name: Test
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run: python -m unittest discover ./bindings/python/tests

‎.github/workflows/wheels.yml

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# From https://github.com/wjakob/nanobind_example/blob/5ce5ce57143a469e92d9ebaee9c47949ee77caa8/.github/workflows/wheels.yml
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name: Wheels
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on:
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workflow_dispatch:
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pull_request:
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push:
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branches:
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- master
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release:
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types:
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- published
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jobs:
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build_sdist:
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name: Build SDist
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- name: Build SDist
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run: pipx run build --sdist ./bindings/python
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- name: Check metadata
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run: pipx run twine check ./bindings/python/dist/*
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- uses: actions/upload-artifact@v4
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with:
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name: dist-sdist
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path: dist/*.tar.gz
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build_wheels:
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name: Wheels on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-13, macos-14, macos-latest, windows-latest]
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- uses: pypa/[email protected]
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env:
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CIBW_ARCHS_MACOS: "universal2"
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with:
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package-dir: ./bindings/python
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- name: Verify clean directory
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run: git diff --exit-code
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shell: bash
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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path: wheelhouse/*.whl
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name: dist-${{ matrix.os }}
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upload_all:
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name: Upload if release
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needs: [build_wheels, build_sdist]
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/SandiaSpecUtils
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permissions:
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id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
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if: github.event_name == 'release' && github.event.action == 'published'
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steps:
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- uses: actions/setup-python@v5
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- uses: actions/download-artifact@v4
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with:
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pattern: dist-*
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merge-multiple: true
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- shell: bash
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run: |
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pwd
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ls
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- uses: pypa/gh-action-pypi-publish@release/v1
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with:
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packages-dir: /home/runner/work/SpecUtils/SpecUtils
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user: __token__
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password: ${{ secrets.pypi_password }}

‎CMakeLists.txt

+7-41
Original file line numberDiff line numberDiff line change
@@ -19,22 +19,13 @@ option( SpecUtils_BUILD_UNIT_TESTS "Builds unit tests" OFF )
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option( SpecUtils_BUILD_FUZZING_TESTS "Builds fuzzing tests, requires clang" OFF )
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option( SpecUtils_BUILD_REGRESSION_TEST "Creates executable to perform interactive regression test" OFF )
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option( SpecUtils_BUILD_EXAMPLE "Builds example SpecUtil applications" OFF )
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option( SpecUtils_PYTHON_BINDINGS "Creates python bindings to the c++ code" OFF )
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option( SpecUtils_JAVA_SWIG "Creates swig/java bindings to the c++ code" OFF )
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option( SpecUtils_C_BINDINGS "Creates C bindings to the c++ code" OFF )
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option( SpecUtils_INJA_TEMPLATES "Creates inja template interface" OFF )
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option( SpecUtils_USE_SIMD "Use SIMD operations; i386/x64 only right now, and very alpha, and extremely minimally used" OFF )
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option( SpecUtils_ENABLE_EQUALITY_CHECKS "Enables the equal_enough(...) functions for comparing two spectrum files." OFF ) #code size is only reason to default to off, I think
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option( PERFORM_DEVELOPER_CHECKS "Performs additional computationally expensive tests during execution (requires linking to boost)" OFF )
29-
30-
31-
if( SpecUtils_PYTHON_BINDINGS )
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option( SpecUtils_SHARED_LIB "Whether to compile a shared, or static library" ON )
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list( APPEND sources bindings/python/SpecFile_py.cpp )
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else()
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#default to building a static lib
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option( SpecUtils_SHARED_LIB "Whether to compile a shared, or static library" OFF )
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endif()
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option( SpecUtils_SHARED_LIB "Whether to compile a shared, or static library" OFF )
3829

3930

4031
set( SpecUtils_FLT_PARSE_METHOD "default_value" CACHE STRING [[How to parse lists of numbers.
@@ -82,7 +73,7 @@ endif()
8273

8374

8475
# If we are building this on Windows, not as a sub-project, lets enable selecting C++ runtime
85-
if( MSVC AND (SpecUtils_PYTHON_BINDINGS OR SpecUtils_BUILD_UNIT_TESTS) )
76+
if( MSVC AND SpecUtils_BUILD_UNIT_TESTS )
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get_directory_property(hasParent PARENT_DIRECTORY)
8778
if(NOT hasParent)
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option(${PROJECT_NAME}_USE_MSVC_MultiThreadDLL "Use dynamically-link runtime library." OFF)
@@ -96,7 +87,7 @@ if( MSVC AND (SpecUtils_PYTHON_BINDINGS OR SpecUtils_BUILD_UNIT_TESTS) )
9687
endif()
9788
message(STATUS "Using CMAKE_MSVC_RUNTIME_LIBRARY ${CMAKE_MSVC_RUNTIME_LIBRARY}")
9889
endif(NOT hasParent)
99-
endif( MSVC AND (SpecUtils_PYTHON_BINDINGS OR SpecUtils_BUILD_UNIT_TESTS) )
90+
endif( MSVC AND SpecUtils_BUILD_UNIT_TESTS )
10091

10192

10293
if( SpecUtils_BUILD_EXAMPLE )
@@ -121,14 +112,6 @@ endif( SpecUtils_JAVA_SWIG )
121112

122113
set( THIRD_PARTY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/3rdparty" )
123114

124-
if( SpecUtils_PYTHON_BINDINGS )
125-
FIND_PACKAGE(Python3 COMPONENTS Development )
126-
IF(NOT Python3_FOUND)
127-
MESSAGE(FATAL_ERROR "Unable to find PythonLibs.")
128-
ENDIF()
129-
message( "Python include dirs: ${Python3_INCLUDE_DIRS}")
130-
endif()
131-
132115
set( sources
133116
src/SpecFile.cpp
134117
src/SpecFile_pcf.cpp
@@ -255,10 +238,6 @@ if( SpecUtils_ENABLE_URI_SPECTRA )
255238
find_package( ZLIB REQUIRED )
256239
endif( SpecUtils_ENABLE_URI_SPECTRA )
257240

258-
if( SpecUtils_PYTHON_BINDINGS )
259-
list( APPEND sources bindings/python/SpecFile_py.cpp )
260-
endif( SpecUtils_PYTHON_BINDINGS )
261-
262241
if( SpecUtils_JAVA_SWIG )
263242
list( APPEND sources bindings/swig/SpecUtils.i )
264243
endif( SpecUtils_JAVA_SWIG )
@@ -277,7 +256,6 @@ endif( SpecUtils_SHARED_LIB )
277256
add_library( SpecUtils ${SpecUtils_LIB_TYPE} ${sources} ${headers} ${OTHER_SUPPORT_FILES} )
278257
set_target_properties( SpecUtils PROPERTIES PREFIX "lib" OUTPUT_NAME "SpecUtils" )
279258

280-
281259
set( SpecUtils_USE_FAST_FLOAT OFF ) # Uses https://github.com/fastfloat/fast_float . If fast_float.h isnt found, will be fetched
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set( SpecUtils_USE_FROM_CHARS OFF ) # Supported by MSVC >= 2019, and gcc >= 12. Not supported by Apple clang. In MSVC, about 50% slower than boost::spirit
283261
set( SpecUtils_USE_BOOST_SPIRIT OFF ) # Uses boost::spirit, and fasted method (maybe a hair faster than fastfloat)
@@ -335,28 +313,22 @@ if( SpecUtils_USE_FAST_FLOAT )
335313
endif( NOT FAST_FLOAT_FILE_PATH )
336314
endif( SpecUtils_USE_FAST_FLOAT )
337315

338-
# We only need boost libraries if we are using boost to parse floats, if we are performing developer
339-
# checks, or we are creating Python bindings
340-
if( SpecUtils_USE_BOOST_SPIRIT OR PERFORM_DEVELOPER_CHECKS OR SpecUtils_PYTHON_BINDINGS )
316+
# We only need boost libraries if we are using boost to parse floats, if we are performing developer checks
317+
if( SpecUtils_USE_BOOST_SPIRIT OR PERFORM_DEVELOPER_CHECKS )
341318

342319
if( DEFINED boost_SOURCE_DIR )
343320
# We used CMake Fetch to get boost (e.g., in InterSpec)
344321
target_link_libraries( SpecUtils PUBLIC Boost::system Boost::spirit Boost::fusion Boost::algorithm Boost::functional Boost::crc )
345322

346323
else( DEFINED boost_SOURCE_DIR )
347-
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if( SpecUtils_PYTHON_BINDINGS )
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list( APPEND boost_libs_required python )
350-
endif( SpecUtils_PYTHON_BINDINGS )
351-
352324
find_package( Boost REQUIRED COMPONENTS system ${boost_libs_required} )
353325
if( NOT Boost_FOUND )
354326
message(FATAL_ERROR "Couldnt Find Boost")
355327
endif( NOT Boost_FOUND )
356328

357329
target_link_libraries( SpecUtils PUBLIC Boost::system )
358330
endif( DEFINED boost_SOURCE_DIR )
359-
endif( SpecUtils_USE_BOOST_SPIRIT OR PERFORM_DEVELOPER_CHECKS OR SpecUtils_PYTHON_BINDINGS )
331+
endif( SpecUtils_USE_BOOST_SPIRIT OR PERFORM_DEVELOPER_CHECKS )
360332

361333
if( SpecUtils_USE_FROM_CHARS )
362334
if( NOT (MSVC AND (MSVC_VERSION GREATER_EQUAL 1920)) )
@@ -402,17 +374,11 @@ elseif( NOT SpecUtils_USING_NO_THREADING )
402374
endif( SpecUtils_USE_WT_THREADPOOL )
403375

404376

405-
406377
if( SpecUtils_ENABLE_URI_SPECTRA )
407378
target_link_libraries( SpecUtils PUBLIC ZLIB::ZLIB )
408379
endif( SpecUtils_ENABLE_URI_SPECTRA )
409380

410381

411-
if( SpecUtils_PYTHON_BINDINGS )
412-
target_link_libraries( SpecUtils PUBLIC Boost::python ${Boost_PYTHON_LIBRARY} ${Python3_LIBRARIES} )
413-
endif( SpecUtils_PYTHON_BINDINGS )
414-
415-
416382
if( SpecUtils_JAVA_SWIG )
417383
target_link_libraries( SpecUtils PUBLIC ${JAVA_LIBRARIES} )
418384
endif( SpecUtils_JAVA_SWIG )
@@ -428,7 +394,7 @@ elseif( WIN32 )
428394
endif( MINGW )
429395

430396
target_include_directories( SpecUtils PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR}
431-
PRIVATE ${THIRD_PARTY_DIR} ${Python3_INCLUDE_DIRS} )
397+
PRIVATE ${THIRD_PARTY_DIR} )
432398

433399
if( SpecUtils_BUILD_REGRESSION_TEST )
434400
if( NOT SpecUtils_ENABLE_EQUALITY_CHECKS )

‎bindings/python/CMakeLists.txt

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1+
cmake_minimum_required(VERSION 3.15...3.26)
2+
3+
project(SpecUtils_py LANGUAGES CXX)
4+
5+
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
6+
7+
set( SpecUtils_ENABLE_D3_CHART ON CACHE BOOL "" )
8+
set( SpecUtils_D3_SUPPORT_FILE_STATIC ON CACHE BOOL "" )
9+
set( SpecUtils_ENABLE_URI_SPECTRA OFF CACHE BOOL "" ) #Lets not worry about linking to zlib right now
10+
set( SpecUtils_PYTHON_BINDINGS ON CACHE BOOL "Build the python bindings" )
11+
set( SpecUtils_ENABLE_EQUALITY_CHECKS OFF CACHE BOOL "" )
12+
set( PERFORM_DEVELOPER_CHECKS OFF CACHE BOOL "" )
13+
set( SpecUtils_SHARED_LIB OFF CACHE BOOL "" ) #we'll statically link SpecUtils into the lib we create here
14+
set( SpecUtils_FLT_PARSE_METHOD "strtod" CACHE STRING "Float parsing method" )
15+
16+
add_subdirectory( ${CMAKE_CURRENT_SOURCE_DIR}/../.. ${CMAKE_CURRENT_BINARY_DIR}/LibSpecUtils )
17+
18+
if (NOT SKBUILD)
19+
message(FATAL_ERROR "\
20+
This CMake file is must be executed using 'scikit-build'.
21+
If you are a user trying to install this package, please use the command
22+
below, which will install all necessary build dependencies, compile
23+
the package in an isolated environment, and then install it.
24+
=====================================================================
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$ pip install .
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=====================================================================
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If you are a software developer, and this is your own package, then
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it is usually much more efficient to install the build dependencies
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in your environment once and use the following command that avoids
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a costly creation of a new virtual environment at every compilation:
31+
=====================================================================
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$ pip install nanobind scikit-build-core
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$ pip install --no-build-isolation -ve .
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=====================================================================
35+
You may optionally add -Ceditable.rebuild=true to auto-rebuild when
36+
the package is imported. Otherwise, you need to re-run the above
37+
after editing C++ files.")
38+
endif()
39+
40+
# Try to import all Python components potentially needed by nanobind
41+
find_package(Python 3.8
42+
REQUIRED COMPONENTS Interpreter Development.Module
43+
OPTIONAL_COMPONENTS Development.SABIModule)
44+
45+
# Import nanobind through CMake's find_package mechanism
46+
find_package(nanobind CONFIG REQUIRED)
47+
48+
# We are now ready to compile the actual extension module
49+
nanobind_add_module(
50+
# Name of the extension
51+
PySpecUtils
52+
53+
# Target the stable ABI for Python 3.12+, which reduces
54+
# the number of binary wheels that must be built. This
55+
# does nothing on older Python versions
56+
STABLE_ABI
57+
58+
# Build libnanobind statically and merge it into the
59+
# extension (which itself remains a shared library)
60+
#
61+
# If your project builds multiple extensions, you can
62+
# replace this flag by NB_SHARED to conserve space by
63+
# reusing a shared libnanobind across libraries
64+
NB_STATIC
65+
66+
#Perform link time optimization.
67+
#LTO
68+
69+
70+
# Source code goes here
71+
SpecFile_py.cpp
72+
)
73+
74+
set_target_properties( PySpecUtils PROPERTIES OUTPUT_NAME "SpecUtils" )
75+
target_link_libraries( PySpecUtils PUBLIC SpecUtils )
76+
77+
# Install directive for scikit-build-core
78+
install(TARGETS PySpecUtils LIBRARY DESTINATION SpecUtils)
79+
install(FILES __init__.py DESTINATION SpecUtils)
80+
81+
nanobind_add_stub(
82+
SpecUtils_stub
83+
MODULE SpecUtils
84+
OUTPUT SpecUtils.pyi
85+
PYTHON_PATH $<TARGET_FILE_DIR:PySpecUtils>
86+
DEPENDS PySpecUtils
87+
)

‎bindings/python/Ex_pyconverted.chn

-64.5 KB
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