pysjef 1.45.6__tar.gz

pysjef-1.45.6/.clang-format

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+---
+Language: Cpp
+BasedOnStyle: LLVM
+ColumnLimit: 120
+DerivePointerAlignment: true
+PointerAlignment: Left
+AlwaysBreakTemplateDeclarations: Yes
+...
+

pysjef-1.45.6/.gitattributes

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+CMakeLists.txt export-subst

pysjef-1.45.6/.github/workflows/build-and-test.yml

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+name: Build and test
+
+on:
+  push:
+    branches: [ "main" , "master" ]
+  pull_request:
+    branches: [ "main" , "master" ]
+  workflow_dispatch:
+
+env:
+  CMAKE_BUILD_TYPE: Release
+
+jobs:
+
+  cmake-build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm]
+    runs-on: ${{ matrix.os }}
+    container:
+      image: ghcr.io/${{ github.repository }}
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Check existence of build configuration file
+        id: check_configuration
+        uses: andstor/file-existence-action@v1
+        with:
+          files: "CMakeLists.txt"
+
+      - name: ccache
+        uses: hendrikmuhs/ccache-action@v1.2
+
+      - name: Configure CMake
+        if: steps.check_configuration.outputs.files_exists == 'true'
+        run: |
+          git config --global --add safe.directory /__w/sjef/sjef
+          cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.CMAKE_BUILD_TYPE}} -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache  --log-level=DEBUG
+
+      - name: Build
+        if: steps.check_configuration.outputs.files_exists == 'true'
+        run: cmake --build ${{github.workspace}}/build --config ${{env.CMAKE_BUILD_TYPE}}
+
+      - name: Test
+        if: steps.check_configuration.outputs.files_exists == 'true'
+        run: |
+          service ssh restart
+          service ssh status
+          ssh localhost hostname || ssh -v localhost hostname
+          cd ${{github.workspace}}/build && ctest -C ${{env.CMAKE_BUILD_TYPE}} || ctest -C ${{env.CMAKE_BUILD_TYPE}} -V --rerun-failed --output-on-failure
+
+      - name: Build doxygen
+        run: cmake --build ${{github.workspace}}/build --target sjef-doc
+
+  unix-python:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm]
+    runs-on: ${{ matrix.os }}
+    container:
+      image: ghcr.io/${{ github.repository }}
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    timeout-minutes: 5
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build
+        run: |
+          git config --global --add safe.directory /__w/sjef/sjef
+          . /opt/conda/etc/profile.d/conda.sh
+          python -m pip install .
+      - name: Test
+        run: |
+          mkdir -p /var/run/sshd
+          /usr/sbin/sshd
+          pytest
+  windows-python:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ windows-latest ] #, windows-11-arm ]
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+
+      - name: Environment
+        shell: pwsh
+        run: |
+          conda activate test
+          $CMAKE_INSTALL_PREFIX = $Env:CONDA_PREFIX -replace '\\','/'
+          echo ('CMAKE_INSTALL_PREFIX={0}' -f $CMAKE_INSTALL_PREFIX) | Out-File -FilePath $Env:GITHUB_ENV -Encoding utf8 -Append
+      - name: Build
+        shell: pwsh
+        run: |
+          conda activate test
+          python -m pip install .
+      - name: Minimal test
+        shell: pwsh
+        run: |
+          conda activate test
+          python -c "import pysjef; p=pysjef.Project('test'); print(p); print(pysjef.__version__);print(p.filename())"
+

pysjef-1.45.6/.github/workflows/docker-publish.yml

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+name: Docker build and publish
+
+on:
+  push:
+    paths:
+      - docker/Dockerfile
+      - .github/workflows/docker-publish.yml
+  workflow_dispatch:
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@v3.12.0
+
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3.7.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            latest
+
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v6.19.2
+        with:
+          context: docker
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          platforms: linux/amd64,linux/arm64

pysjef-1.45.6/.github/workflows/doxygen-gh-pages.yml

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+name: Build doxygen pages and publish to github pages
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - master
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    container:
+      # relies on repository name being all lower case
+      image: ghcr.io/${{ github.repository }}
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Configure CMake
+        run: |
+          git config --global --add safe.directory ${{github.workspace}}
+          cmake -B ${{github.workspace}}/build
+
+      - name: Build
+        run: |
+          git config --global --add safe.directory ${{github.workspace}}
+          cmake --build ${{github.workspace}}/build --target sjef-doc
+          rsync -av ${{github.workspace}}/build/html .
+          mkdir -p html/DoxygenTagFiles
+          find ${{github.workspace}}/build -name '*.tag' -exec cp {} html/DoxygenTagFiles \;
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3.8.0
+        if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' }}
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./html

pysjef-1.45.6/.github/workflows/wheels.yml

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+name: wheels
+
+on:
+  push:
+    tags: [ "[0-9]+.[0-9]+.[0-9]+" ]   # matches existing tag style, e.g. 1.45.4
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+          - os: ubuntu-24.04-arm
+          - os: macos-15-intel      # Intel
+          - os: macos-latest      # Apple Silicon
+          - os: windows-latest
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0   # setuptools_scm and LibraryManager both need tag history
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.22
+        env:
+          CIBW_MACOS_DEPLOYMENT_TARGET: 11.0
+          CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=11.0"
+          CIBW_BEFORE_ALL_LINUX: >
+            set -eux &&
+            if command -v yum >/dev/null 2>&1; then
+              yum -y install libxml2-devel libxslt-devel;
+            elif command -v apt-get >/dev/null 2>&1; then
+                        apt-get update && apt-get install -y libxml2-dev libxslt1-dev;
+            elif command -v apk >/dev/null 2>&1; then
+              apk add --no-cache libxml2-dev libxslt-dev;
+            fi
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl
+
+  build_sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - run: pipx run build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  publish:
+    needs: [ build_wheels, build_sdist ]
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pysjef/
+    permissions:
+      id-token: write   # trusted publishing to PyPI, no API token needed
+      contents: read
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+      - uses: pypa/gh-action-pypi-publish@release/v1

pysjef-1.45.6/.gitignore

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+build/
+.idea
+record.txt
+cmake-build*/
+dependencies/*/
+*_lockfile
+env/
+__pycache__/
+*.pyc
+*.so
+*.vim
+*.sw*
+ycm_extra_conf.py
+_build/
+cy.sh
+scrap/
+.ipynb_checkpoints
+.vs
+CMakeSettings.json
+Doxyfile.in.bak
+.DS_Store

pysjef-1.45.6/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.15)
+project(sjef LANGUAGES CXX C)
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+include(FetchContent)
+FetchContent_Declare(
+        LibraryManager
+        GIT_REPOSITORY https://github.com/molpro/library-manager.git
+        GIT_TAG 71c0165d48924610b65edbfbd99e336bfc7909df
+)
+FetchContent_MakeAvailable(LibraryManager)
+
+LibraryManager_Project(DEFAULT_VERSION "$Format:%(describe:tags)$")
+message(VERBOSE "PROJECT_VERSION=${PROJECT_VERSION}")
+message(VERBOSE "PROJECT_VERSION_FULL=${PROJECT_VERSION_FULL}")
+
+option(BUILD_TESTS "Whether to build tests or not" OFF)
+option(BUILD_PROGRAM "Whether to build sjef command-line program or not" ON)
+
+project(sjef LANGUAGES CXX C VERSION ${PROJECT_VERSION})
+set(SJEF_VERSION ${PROJECT_VERSION_FULL})
+set(CMAKE_OSX_DEPLOYMENT_TARGET "10.15" CACHE STRING "Minimum macOS deployment target")
+
+set(PROGRAM_FILENAME "sjef")
+set(PROGRAM_NAME "sjef-program")
+
+if (MSVC)
+    add_compile_options(/EHsc /permissive-)
+
+    # Define Windows target architecture
+    if(CMAKE_SIZEOF_VOID_P EQUAL 8)
+        add_compile_options(/D_WIN64)
+    else()
+        add_compile_options(/D_WIN32)
+    endif()
+
+    # Define minimum Windows version
+    add_compile_definitions(_WIN32_WINNT=0x0601)
+endif ()
+
+option(BUILD_PYTHON "Whether to build the Python bindings or not" ON)
+set(CMAKE_POLICY_DEFAULT_CMP0048 NEW)
+if (BUILD_PYTHON)
+    set (BUILD_SHARED_LIBS OFF)
+endif()
+
+
+set(BOOST_BUILD_HINTS "")
+foreach(prefix IN LISTS CMAKE_PREFIX_PATH)
+    if(IS_DIRECTORY "${prefix}/libboost_headers/include/boost")
+        set(BOOST_BUILD_HINTS "${prefix}/libboost_headers/include")
+        break()
+    endif()
+endforeach()
+
+if(BOOST_BUILD_HINTS)
+    message(STATUS "Using libboost-headers from: ${BOOST_BUILD_HINTS}")
+    add_library(Boost::boost INTERFACE IMPORTED)
+    target_include_directories(Boost::boost INTERFACE "${BOOST_BUILD_HINTS}")
+else()
+    if(POLICY CMP0167)
+        cmake_policy(SET CMP0167 NEW)
+    endif()
+    find_package(Boost REQUIRED)
+endif()
+
+
+add_subdirectory(src)
+
+if (BUILD_PYTHON)
+    set (BUILD_SHARED_LIBS OFF)
+    find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
+    find_program(CYTHON_EXECUTABLE cython REQUIRED)
+
+    set(CYTHON_SRC ${CMAKE_CURRENT_SOURCE_DIR}/src/pysjef/project_wrapper.pyx)
+    set(CYTHON_CPP ${CMAKE_CURRENT_SOURCE_DIR}/src/pysjef/project_wrapper.cpp)
+
+    add_custom_command(OUTPUT ${CYTHON_CPP}
+            COMMAND ${CYTHON_EXECUTABLE} --cplus -3 -I ${CMAKE_CURRENT_SOURCE_DIR}/src ${CYTHON_SRC} -o ${CYTHON_CPP}
+            DEPENDS ${CYTHON_SRC}
+            COMMENT "Generating C++ code from Cython"
+    )
+    python_add_library(project_wrapper MODULE ${CYTHON_CPP} WITH_SOABI)
+    target_link_libraries(project_wrapper PRIVATE sjef)
+    target_include_directories(project_wrapper PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/src)
+    install(TARGETS project_wrapper DESTINATION pysjef)
+
+endif()
+
+if (BUILD_TESTS)
+    enable_testing()
+    add_subdirectory(test)
+endif ()
+
+if (BUILD_PROGRAM)
+    add_subdirectory(program)
+endif ()
+
+option(BUILD_DOCUMENTATION "Generate documentation" ON)
+if (BUILD_DOCUMENTATION)
+    find_package(Doxygen)
+    if (DOXYGEN_FOUND)
+        configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+        add_custom_target(${PROJECT_NAME}-doc ALL
+                DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
+        )
+        file(GLOB_RECURSE headers src/*.h */*.md *.md src/*.cpp)
+        add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
+                COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+                DEPENDS ${headers} ${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                COMMENT "Generating API documentation with Doxygen" VERBATIM
+        )
+    endif (DOXYGEN_FOUND)
+endif ()
+
+add_custom_target(_version.py
+        COMMAND echo "__version__ = \"${CMAKE_PROJECT_VERSION}\"" > _version.py
+)
+
+
+if (WIN32)
+    FetchContent_Declare(rsync
+            GIT_REPOSITORY https://github.com/molpro/cwrsync
+            GIT_TAG main
+    )
+    FetchContent_MakeAvailable(rsync)
+    install(DIRECTORY ${rsync_SOURCE_DIR}/ DESTINATION ./rsync PATTERN .git EXCLUDE)
+endif ()