scinumtools3 0.4.1__tar.gz

scinumtools3-0.4.1/.clang-format

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+BasedOnStyle: LLVM
+
+IndentWidth: 4
+TabWidth: 4
+UseTab: Never
+
+NamespaceIndentation: All
+
+BreakBeforeBraces: Attach
+
+# Important for preventing giant one-line pybind11 calls
+ColumnLimit: 120
+
+AllowShortFunctionsOnASingleLine: Inline
+AllowShortLambdasOnASingleLine: Inline
+
+# Better formatting for env.def(...) style calls
+BinPackArguments: false
+BinPackParameters: false
+AlignAfterOpenBracket: BlockIndent
+PenaltyBreakBeforeFirstCallParameter: 1
+
+# Prevent return type wrapping
+PenaltyReturnTypeOnItsOwnLine: 1000
+AlwaysBreakAfterReturnType: None
+
+DerivePointerAlignment: false
+PointerAlignment: Left
+
+SortIncludes: true
+IncludeBlocks: Regroup
+
+IncludeCategories:
+  - Regex: '^<(exs|val|puq|dip|mat)/.*>$'
+    Priority: 1
+
+  - Regex: '^"(exs|val|puq|dip|mat)/.*"$'
+    Priority: 1
+
+  - Regex: '^".*"$'
+    Priority: 2
+
+  - Regex: '^<.*>$'
+    Priority: 3

scinumtools3-0.4.1/.clang-format-ignore

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+src/snt/puq/systems/dmaps/**
+apps/snt-server/external/**

scinumtools3-0.4.1/.clang-tidy

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+Checks: >
+  clang-analyzer-*,
+  -clang-analyzer-cplusplus*,
+  performance-*,
+  llvm-include-cleaner,
+  modernize-use-nullptr,
+  modernize-use-override,
+  modernize-loop-convert,
+  modernize-use-equals-default,
+  modernize-use-equals-delete,
+  modernize-use-using,
+  cppcoreguidelines-pro-type-const-cast,
+  cppcoreguidelines-slicing,
+  cppcoreguidelines-pro-type-member-init,
+  cppcoreguidelines-narrowing-conversions,
+  cppcoreguidelines-virtual-class-destructor
+  modernize-use-forward-declaration
+  misc-forward-declarations
+  misc-include-cleaner
+  misc-unused-include
+  llvm-include-order
+  clang-analyzer-optin.cplusplus.IncludeWhatYouUse
+  readability-*
+  readability-identifier-naming
+   
+CheckOptions:
+  - key: readability-identifier-naming.ClassCase
+    value: CamelCase
+  - key: readability-identifier-naming.StructCase
+    value: CamelCase
+  - key: readability-identifier-naming.FunctionCase
+    value: camelBack         # e.g., `computeResult`
+  - key: readability-identifier-naming.VariableCase
+    value: lower_case        # e.g., `time_step`
+  - key: readability-identifier-naming.ParameterCase
+    value: lower_case
+  - key: readability-identifier-naming.PrivateMemberCase
+    value: m_lower_case      # if members are prefixed by `m_`
+  - key: readability-identifier-naming.ConstantCase
+    value: UPPER_CASE        # e.g., `MAX_ITER`
+  - key: readability-identifier-naming.GlobalConstantPrefix
+    value: k                 # if global constants are like `kMaxValue`
+  - key: readability-identifier-naming.EnumCase
+    value: CamelCase
+  - key: readability-identifier-naming.EnumConstantCase
+    value: UPPER_CASE
+
+WarningsAsErrors: '*'

scinumtools3-0.4.1/.github/workflows/c-cpp-linux.yml

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+name: Linux Build
+
+on:
+  push:
+    branches: [ "main" ]
+    paths:
+      - 'src/**'
+      - 'include/**'
+      - 'bindings/**'
+      - 'benchmarks/**'
+      - 'examples/**'
+      - 'apps/**'
+      - 'tests/**'
+  pull_request:
+    branches: [ "main" ]
+    paths:
+      - 'src/**'
+      - 'include/**'
+      - 'bindings/**'
+      - 'benchmarks/**'
+      - 'examples/**'
+      - 'apps/**'
+      - 'tests/**'
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgtest-dev pybind11-dev
+          
+      - name: Build
+        run: ./setup.sh --github-workflows -b
+
+      - name: Test
+        run: ./setup.sh -t
+
+#jobs:
+#  build:
+#
+#    runs-on: ubuntu-latest
+#    
+#    steps:
+#    - uses: actions/checkout@v4
+#      with:
+#        submodules: recursive
+#    
+#    - name: Set up Python
+#      
+#      uses: actions/setup-python@v5
+#      with:
+#        python-version: '3.13'  
+#        
+#    - name: Install dependencies
+#      run: |
+#        python -m pip install --upgrade pip
+#        pip install -r requirements.txt
+#      
+#    - name: Install and build GTest
+#      run: |
+#        sudo apt-get update
+#        sudo apt-get install -y cmake
+#        sudo apt-get install -y libgtest-dev
+#        sudo apt-get install -y pybind11-dev
+#        cd /usr/src/gtest
+#        sudo cmake .
+#        sudo make
+#        sudo cp lib/*.a /usr/lib
+#        
+#    - name: build
+#      run: ./setup.sh --github-workflows -b
+#      
+#    - name: test
+#      run: ./setup.sh -t

scinumtools3-0.4.1/.github/workflows/c-cpp-macos.yml

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+name: macOS Build
+
+on:
+  push:
+    branches: [ "main" ]
+    paths:
+      - 'src/**'
+      - 'include/**'
+      - 'bindings/**'
+      - 'benchmarks/**'
+      - 'examples/**'
+      - 'apps/**'
+      - 'tests/**'
+  pull_request:
+    branches: [ "main" ]
+    paths:
+      - 'src/**'
+      - 'include/**'
+      - 'bindings/**'
+      - 'benchmarks/**'
+      - 'examples/**'
+      - 'apps/**'
+      - 'tests/**'
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [macos-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: macOS dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install googletest pybind11
+
+      - name: Build
+        run: ./setup.sh --github-workflows -b
+
+      - name: Test
+        run: ./setup.sh -t

scinumtools3-0.4.1/.github/workflows/pypi-wheels.yml

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+name: Build and Publish on PyPi
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build_wheels:
+    name: Build wheels (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          #- windows-latest
+          - macos-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.23
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    runs-on: ubuntu-latest
+
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build source distribution
+        run: |
+          python -m pip install build
+          python -m build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  publish:
+    needs:
+      - build_wheels
+      - build_sdist
+
+    runs-on: ubuntu-latest
+
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+
+    steps:
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: dist
+
+      - name: Flatten artifact directories
+        run: |
+          mkdir upload
+          find dist -type f \( -name "*.whl" -o -name "*.tar.gz" \) -exec cp {} upload/ \;
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: upload
+

scinumtools3-0.4.1/.github/workflows/static.yml

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+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+    paths:
+      - 'docs/**'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Build documentation
+        run:
+          sudo apt install -y doxygen graphviz;
+          pip3 install -r requirements.txt;
+          ./setup.sh -d
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: './docs/build/html/'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

scinumtools3-0.4.1/.gitignore

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+# Custom
+build/*
+CMakeFiles/*
+CMakeCache.txt
+helpers/*
+docs/build/*
+docs/doxy/*
+dist/*
+**/__pycache__/*
+.venv
+**/.DS_STORE
+
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app

scinumtools3-0.4.1/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "apps/snt-server/external/cpp-httplib"]
+	path = apps/snt-server/external/cpp-httplib
+	url = git@github.com:yhirose/cpp-httplib.git

scinumtools3-0.4.1/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.22)
+cmake_policy(SET CMP0074 NEW)
+set(CMAKE_TRY_ENABLE_TARGET_TYPE STATIC_LIBRARY)
+
+project(scinumtools VERSION 1.0 LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+if(NOT MSVC)
+    add_compile_options(-Wno-deprecated)
+endif()
+
+set(MODULE_NAME snt)
+#set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}/install")
+set(CMAKE_INSTALL_BINDIR bin)
+set(CMAKE_INSTALL_LIBDIR lib)
+set(CMAKE_INSTALL_INCLUDEDIR include)
+
+# limit error number
+if (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+    add_compile_options(-ferror-limit=3)
+elseif (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+    add_compile_options(-fmax-errors=3)
+endif()
+
+# ensure all targets (executables, static libs, shared libs) are built with -fPIC if required
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+# set environmental variables
+file(READ "settings.env" ENV_CONTENTS)
+string(REGEX MATCH "CODE_VERSION=([^\n\r]*)" _ ${ENV_CONTENTS})
+string(REGEX REPLACE ".*CODE_VERSION=([^\n\r]*).*" "\\1" CODE_VERSION "${_}")
+
+# set preprocessor flags
+add_compile_definitions(CODE_VERSION="${CODE_VERSION}")
+configure_file(
+    ${CMAKE_SOURCE_DIR}/cmake/settings.h.in
+    ${CMAKE_BINARY_DIR}/settings.h
+)
+
+# analyze code compilation
+option(ENABLE_TIME_TRACE "Enable Clang time tracing" OFF)
+if(ENABLE_TIME_TRACE)
+    add_compile_options(-ftime-trace)
+endif()
+
+# enable apps
+option(ENABLE_APP_SNT_SERVER "Enable SNT REST-API server app" OFF)
+option(ENABLE_APP_SNT_GUI "Enable SNT graphical user interface" OFF)
+
+# set generic options
+function(set_module_options NAME DEFAULT)
+    # set default values
+    option(ENABLE_${NAME} "Enable ${NAME}" ${DEFAULT})
+    option(ENABLE_${NAME}_GTEST "Enable ${NAME} gtests" ${DEFAULT})
+    option(ENABLE_${NAME}_PYBIND "Enable ${NAME} pytests" ${DEFAULT})
+    option(ENABLE_${NAME}_PYTEST "Enable ${NAME} pytests" ${DEFAULT})
+    # set parts off if main switch is off
+    if(NOT ENABLE_${NAME})
+        set(ENABLE_${NAME}_GTEST OFF CACHE BOOL "" FORCE)
+        set(ENABLE_${NAME}_PYBIND OFF CACHE BOOL "" FORCE)
+    endif()
+    if(NOT ENABLE_${NAME}_PYBIND)
+        set(ENABLE_${NAME}_PYTEST OFF CACHE BOOL "" FORCE)
+    endif()
+    message(STATUS "ENABLE_${NAME}=${ENABLE_${NAME}}")
+    message(STATUS "ENABLE_${NAME}_GTEST=${ENABLE_${NAME}_GTEST}")
+    message(STATUS "ENABLE_${NAME}_PYBIND=${ENABLE_${NAME}_PYBIND}")
+    message(STATUS "ENABLE_${NAME}_PYTEST=${ENABLE_${NAME}_PYTEST}")
+endfunction()
+# set options for all modules
+set_module_options(SNT ON)
+set_module_options(EXS ON)
+set_module_options(VAL ON)
+set_module_options(PUQ ON)
+set_module_options(DIP ON)
+set_module_options(MAT ON)
+
+# import GTest
+###############
+
+# this needs to be here, so that ctest notice it!
+if(
+    ENABLE_SNT_GTEST OR
+    ENABLE_EXS_GTEST OR
+    ENABLE_VAL_GTEST OR
+    ENABLE_PUQ_GTEST OR
+    ENABLE_DIP_GTEST OR
+    ENABLE_MAT_GTEST
+)
+  find_package(GTest REQUIRED)
+  include_directories(${GTEST_INCLUDE_DIRS})
+  include(GoogleTest)
+  enable_testing()
+endif()
+
+message("Scientific Numerical Tools (SNT)")
+message("Code version: ${CODE_VERSION}")
+
+# enable clang-tidy during the compilation
+##########################################
+
+option(ENABLE_CLANG_TIDY "Run clang-tidy during build" OFF)
+if(ENABLE_CLANG_TIDY)
+    find_program(CLANG_TIDY_COMMAND NAMES clang-tidy)
+    if(NOT CLANG_TIDY_COMMAND)
+        message(FATAL_ERROR "clang-tidy not found!")
+    else()
+        message(STATUS "Running with clang-tidy ${ENABLE_CLANG_TIDY}")
+    endif()
+
+    # This makes all targets run clang-tidy automatically during compilation
+    set(CMAKE_CXX_CLANG_TIDY ${CLANG_TIDY_COMMAND}
+    			     -p=${CMAKE_BINARY_DIR})
+endif()
+
+# compile libraries and executables
+###################################
+
+add_subdirectory(src)                  # build dip-cpp library
+add_subdirectory(apps)                 # build executable applications
+add_subdirectory(examples)             # build example applications
+add_subdirectory(tests)                # build gtest executable
+if (ENABLE_PUQ AND ENABLE_DIP)         
+   add_subdirectory(bindings/python/cpp)  # build Python bindings
+endif()
+
+# setup Google Benchmark
+########################
+
+option(ENABLE_BENCHMARKS "Build benchmarks" OFF)
+
+if(ENABLE_BENCHMARKS)
+
+  include(FetchContent)
+  
+  FetchContent_Declare(
+      benchmark
+      GIT_REPOSITORY https://github.com/google/benchmark.git
+      GIT_TAG v1.8.3
+  )
+  
+  set(BENCHMARK_ENABLE_TESTING OFF)
+
+  FetchContent_MakeAvailable(benchmark)
+
+  set_target_properties(
+      benchmark
+      benchmark_main
+      PROPERTIES
+      CXX_CLANG_TIDY ""
+  )
+
+  add_subdirectory(benchmarks)
+endif()
+
+# create cmake export files
+###########################
+
+include(CMakePackageConfigHelpers)
+
+configure_package_config_file(
+	${CMAKE_CURRENT_SOURCE_DIR}/cmake/${MODULE_NAME}-config.cmake.in
+  	"${CMAKE_CURRENT_BINARY_DIR}/${MODULE_NAME}-config.cmake"
+  	INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${MODULE_NAME}
+	PATH_VARS CMAKE_INSTALL_INCLUDEDIR
+)
+
+write_basic_package_version_file(
+	"${CMAKE_CURRENT_BINARY_DIR}/${MODULE_NAME}-config-version.cmake"
+    	VERSION ${CODE_VERSION}
+    	COMPATIBILITY AnyNewerVersion
+)
+
+# install files
+###############
+	
+install(DIRECTORY src/
+	INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+	FILES_MATCHING PATTERN "*.h")
+	
+install(FILES
+	"${CMAKE_CURRENT_BINARY_DIR}/${MODULE_NAME}-config.cmake"
+	"${CMAKE_CURRENT_BINARY_DIR}/${MODULE_NAME}-config-version.cmake"
+        DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${MODULE_NAME}
+)
+
+install(EXPORT TargetsSNT
+        FILE ${MODULE_NAME}-targets.cmake
+        DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/${MODULE_NAME}"
+)
+

scinumtools3-0.4.1/CONTRIBUTING.md

@@ -0,0 +1,95 @@
+# Contributing to scinumtools3
+
+Thank you for considering contributing to **scinumtools3**! We welcome all contributions, including bug reports, feature requests, documentation improvements, and code changes.
+
+---
+
+## How to Contribute
+
+1. **Fork the repository** from GitHub:  
+   [https://github.com/vrtulka23/scinumtools3](https://github.com/vrtulka23/scinumtools3)
+
+2. **Clone your fork locally**:
+   ```bash
+   git clone https://github.com/vrtulka23/scinumtools3.git
+   cd scinumtools3
+   ```
+
+3. **Create a new branch** for your work:
+
+   ```bash
+   git checkout -b feature/my-new-feature
+   ```
+
+4. **Make your changes**:
+
+   * Follow the coding style defined in `.clang-format`.
+   * Use modern C++ (C++17 or newer).
+   * Write Doxygen-style comments for public APIs.
+   * Add unit tests for new features or bug fixes (see `gtest/`).
+
+5. **Build and run tests**:
+
+   ```bash
+   cmake -B build
+   cd build
+   make
+   ctest
+   ```
+
+6. **Commit and push your changes**:
+
+   ```bash
+   git add .
+   git commit -m "Describe your change"
+   git push origin feature/my-new-feature
+   ```
+
+7. **Open a Pull Request**:
+
+   * Go to the original repository on GitHub.
+   * Submit a PR with a clear description of your changes.
+   * Link related issues if any.
+
+---
+
+## Coding Guidelines
+
+* Use descriptive variable and function names.
+* Keep functions small and focused.
+* Apply `.clang-format` for consistent style.
+* Document all public interfaces with Doxygen comments, for example:
+
+  ```cpp
+  /// \brief Short description
+  /// \param name Description of the parameter
+  /// \return Description of the return value
+  ```
+
+---
+
+## Reporting Issues
+
+If you find a bug or have a feature request:
+
+1. Check the issue tracker to see if it is already reported:
+   [https://github.com/vrtulka23/scinumtools3/issues](https://github.com/vrtulka23/scinumtools3/issues)
+
+2. If not, open a new issue and include:
+
+   * Steps to reproduce the problem
+   * Expected behavior
+   * Actual behavior
+   * System details (OS, compiler, version)
+
+---
+
+## Communication
+
+For questions or discussions:
+
+* Use GitHub Discussions (if enabled) or open an Issue.
+
+---
+
+Thank you for contributing to **scinumtools3**!