Merge remote-tracking branch 'origin/master' into issue/31-spectra-io-out-of-fortran

Author: hbivens

.github/workflows/pip.yml

@@ -0,0 +1,40 @@
+# From https://github.com/wjakob/nanobind_example/blob/5ce5ce57143a469e92d9ebaee9c47949ee77caa8/.github/workflows/pip.yml
+name: Pip
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+
+jobs:
+  build:
+    name: Build with Pip
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [windows-latest, macos-latest, ubuntu-latest]
+        #python-version: ["3.9", "3.12"]
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Set min macOS version
+      if: runner.os == 'macOS'
+      run: |
+        echo "MACOSX_DEPLOYMENT_TARGET=10.14" >> $GITHUB_ENV
+
+    - name: Build and install
+      run: |
+        python -m pip install pytest
+        pip install --verbose ./bindings/python
+
+    - name: Test
+      run: python -m unittest discover ./bindings/python/tests

.github/workflows/wheels.yml

@@ -0,0 +1,91 @@
+# From https://github.com/wjakob/nanobind_example/blob/5ce5ce57143a469e92d9ebaee9c47949ee77caa8/.github/workflows/wheels.yml
+
+name: Wheels
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+     - master
+  release:
+    types:
+      - published
+
+jobs:
+  build_sdist:
+    name: Build SDist
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - name: Build SDist
+      run: pipx run build --sdist ./bindings/python
+
+    - name: Check metadata
+      run: pipx run twine check ./bindings/python/dist/*
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: dist-sdist
+        path: dist/*.tar.gz
+
+
+  build_wheels:
+    name: Wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-13, macos-14, macos-latest, windows-latest]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - uses: pypa/[email protected]
+      env:
+        CIBW_ARCHS_MACOS: "universal2"
+      with:
+        package-dir: ./bindings/python
+
+    - name: Verify clean directory
+      run: git diff --exit-code
+      shell: bash
+
+    - name: Upload wheels
+      uses: actions/upload-artifact@v4
+      with:
+        path: wheelhouse/*.whl
+        name: dist-${{ matrix.os }}
+
+  upload_all:
+    name: Upload if release
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/SandiaSpecUtils
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+    - uses: actions/setup-python@v5
+    - uses: actions/download-artifact@v4
+      with:
+        pattern: dist-*
+        merge-multiple: true
+    - shell: bash
+      run: |
+        pwd
+        ls
+
+    - uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages-dir: /home/runner/work/SpecUtils/SpecUtils
+        user: __token__
+        password: ${{ secrets.pypi_password }}

CMakeLists.txt

@@ -20,7 +20,6 @@ option( SpecUtils_BUILD_UNIT_TESTS "Builds unit tests" OFF )
 option( SpecUtils_BUILD_FUZZING_TESTS "Builds fuzzing tests, requires clang" OFF )
 option( SpecUtils_BUILD_REGRESSION_TEST "Creates executable to perform interactive regression test" OFF )
 option( SpecUtils_BUILD_EXAMPLE "Builds example SpecUtil applications" OFF )
-option( SpecUtils_PYTHON_BINDINGS "Creates python bindings to the c++ code" OFF )
 option( SpecUtils_JAVA_SWIG "Creates swig/java bindings to the c++ code" OFF )
 option( SpecUtils_FORTRAN_SWIG "Enables build/test of swig/FORTRAN bindings" OFF )
 option( SpecUtils_FORTRAN_SWIG_GEN "When this is on, cmake will attemp to generate swig fortran bindings. 
@@ -30,15 +29,7 @@ option( SpecUtils_INJA_TEMPLATES "Creates inja template interface" OFF )
 option( SpecUtils_USE_SIMD "Use SIMD operations; i386/x64 only right now, and very alpha, and extremely minimally used" OFF )
 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
 option( PERFORM_DEVELOPER_CHECKS "Performs additional computationally expensive tests during execution (requires linking to boost)" OFF )
-
-
-if( SpecUtils_PYTHON_BINDINGS )
-  option( SpecUtils_SHARED_LIB "Whether to compile a shared, or static library" ON )
-  list( APPEND sources bindings/python/SpecFile_py.cpp )
-else()
-  #default to building a static lib
-  option( SpecUtils_SHARED_LIB "Whether to compile a shared, or static library" OFF )
-endif()
+option( SpecUtils_SHARED_LIB "Whether to compile a shared, or static library" OFF )
 
 
 set( SpecUtils_FLT_PARSE_METHOD "default_value" CACHE STRING [[How to parse lists of numbers.
@@ -86,7 +77,7 @@ endif()
 
 
 # If we are building this on Windows, not as a sub-project, lets enable selecting C++ runtime
-if( MSVC )
+if( MSVC AND SpecUtils_BUILD_UNIT_TESTS )
   get_directory_property(hasParent PARENT_DIRECTORY)
   if(NOT hasParent)
     option(${PROJECT_NAME}_USE_MSVC_MultiThreadDLL "Use dynamically-link runtime library." OFF)
@@ -100,7 +91,7 @@ if( MSVC )
     endif()
     message(STATUS "Using CMAKE_MSVC_RUNTIME_LIBRARY ${CMAKE_MSVC_RUNTIME_LIBRARY}")
   endif(NOT hasParent)
-endif( MSVC )
+endif( MSVC AND SpecUtils_BUILD_UNIT_TESTS )
 
 
 if( SpecUtils_BUILD_EXAMPLE )
@@ -125,14 +116,6 @@ endif( SpecUtils_JAVA_SWIG )
 
 set( THIRD_PARTY_DIR "${CMAKE_CURRENT_SOURCE_DIR}/3rdparty" )
 
-if( SpecUtils_PYTHON_BINDINGS )
-  FIND_PACKAGE(Python3 COMPONENTS Development )
-  IF(NOT Python3_FOUND)
-    MESSAGE(FATAL_ERROR "Unable to find PythonLibs.")
-  ENDIF()
-  message( "Python include dirs: ${Python3_INCLUDE_DIRS}")
-endif()
-
 set( sources
      src/SpecFile.cpp
      src/SpecFile_pcf.cpp
@@ -259,10 +242,6 @@ if( SpecUtils_ENABLE_URI_SPECTRA )
   find_package( ZLIB REQUIRED )
 endif( SpecUtils_ENABLE_URI_SPECTRA )
 
-if( SpecUtils_PYTHON_BINDINGS )
-  list( APPEND sources bindings/python/SpecFile_py.cpp )
-endif( SpecUtils_PYTHON_BINDINGS )
-
 if( SpecUtils_JAVA_SWIG )
   list( APPEND sources bindings/swig/SpecUtils.i )
 endif( SpecUtils_JAVA_SWIG )
@@ -351,28 +330,22 @@ if( SpecUtils_USE_FAST_FLOAT )
   endif( NOT FAST_FLOAT_FILE_PATH )
 endif( SpecUtils_USE_FAST_FLOAT )
 
-# We only need boost libraries if we are using boost to parse floats, if we are performing developer
-#  checks, or we are creating Python bindings
-if( SpecUtils_USE_BOOST_SPIRIT OR PERFORM_DEVELOPER_CHECKS OR SpecUtils_PYTHON_BINDINGS )
+# We only need boost libraries if we are using boost to parse floats, if we are performing developer checks
+if( SpecUtils_USE_BOOST_SPIRIT OR PERFORM_DEVELOPER_CHECKS )
 
   if( DEFINED boost_SOURCE_DIR )
     # We used CMake Fetch to get boost (e.g., in InterSpec)
     target_link_libraries( SpecUtils PUBLIC Boost::system Boost::spirit Boost::fusion Boost::algorithm Boost::functional Boost::crc )
 
   else( DEFINED boost_SOURCE_DIR )
-  
-    if( SpecUtils_PYTHON_BINDINGS )
-      list( APPEND boost_libs_required python )
-    endif( SpecUtils_PYTHON_BINDINGS )
-  
     find_package( Boost REQUIRED COMPONENTS system ${boost_libs_required} )
     if( NOT Boost_FOUND )
       message(FATAL_ERROR "Couldnt Find Boost")
     endif( NOT Boost_FOUND )
 
     target_link_libraries( SpecUtils PUBLIC Boost::system )
   endif( DEFINED boost_SOURCE_DIR )
-endif( SpecUtils_USE_BOOST_SPIRIT OR PERFORM_DEVELOPER_CHECKS OR SpecUtils_PYTHON_BINDINGS )
+endif( SpecUtils_USE_BOOST_SPIRIT OR PERFORM_DEVELOPER_CHECKS )
 
 if( SpecUtils_USE_FROM_CHARS )
   if( NOT (MSVC AND (MSVC_VERSION GREATER_EQUAL 1920)) )
@@ -418,17 +391,11 @@ elseif( NOT SpecUtils_USING_NO_THREADING )
 endif( SpecUtils_USE_WT_THREADPOOL )
 
 
-
 if( SpecUtils_ENABLE_URI_SPECTRA )
   target_link_libraries( SpecUtils PUBLIC ZLIB::ZLIB )
 endif( SpecUtils_ENABLE_URI_SPECTRA )
 
 
-if( SpecUtils_PYTHON_BINDINGS )
-  target_link_libraries( SpecUtils PUBLIC Boost::python ${Boost_PYTHON_LIBRARY} ${Python3_LIBRARIES} )
-endif( SpecUtils_PYTHON_BINDINGS )
-
-
 if( SpecUtils_JAVA_SWIG )
   target_link_libraries( SpecUtils PUBLIC ${JAVA_LIBRARIES} )
 endif( SpecUtils_JAVA_SWIG )

SpecUtils/EnergyCalibration.h

@@ -279,7 +279,7 @@ namespace SpecUtils
      
      Values larger than this will cause an exception to be thrown when setting the calibration.
      */
-    static const size_t sm_max_channels; // = 65536 + 8
+    static const size_t sm_max_channels; // 131072 (previous to 20241112, used 65536 + 8)
 
     /** The largest positive value of the offset (zeroth energy cal term) allowed for normal polynomial energy calibration.
      i.e., if a gamma spectrum has a larger value than this, then the calibration coefficients will be considered garbage and not used.

SpecUtils/StringAlgo.h

@@ -224,7 +224,11 @@ namespace  SpecUtils
   size_t utf8_str_size_limit( const char * const str,
                              size_t num_in_bytes, const size_t max_bytes );
 
-  
+  /** Returns if the passed-in string is valid UTF-8.
+   @param str The string to evaluate.
+   @param num_in_bytes The length of the string - must not include (optional) null-terminator.
+   */
+  bool valid_utf8( const char * const str, const size_t num_in_bytes );
 
 
   /** \brief parses a string of ascii characters to their floating point value.

bindings/python/CMakeLists.txt

@@ -0,0 +1,87 @@
+cmake_minimum_required(VERSION 3.15...3.26)
+
+project(SpecUtils_py LANGUAGES CXX)
+
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+set( SpecUtils_ENABLE_D3_CHART ON CACHE BOOL "" )
+set( SpecUtils_D3_SUPPORT_FILE_STATIC ON CACHE BOOL "" )
+set( SpecUtils_ENABLE_URI_SPECTRA OFF CACHE BOOL "" )  #Lets not worry about linking to zlib right now
+set( SpecUtils_PYTHON_BINDINGS ON CACHE BOOL "Build the python bindings" )
+set( SpecUtils_ENABLE_EQUALITY_CHECKS OFF CACHE BOOL "" )
+set( PERFORM_DEVELOPER_CHECKS OFF CACHE BOOL "" )
+set( SpecUtils_SHARED_LIB OFF CACHE BOOL "" )  #we'll statically link SpecUtils into the lib we create here
+set( SpecUtils_FLT_PARSE_METHOD "strtod" CACHE STRING "Float parsing method" )
+
+add_subdirectory( ${CMAKE_CURRENT_SOURCE_DIR}/../.. ${CMAKE_CURRENT_BINARY_DIR}/LibSpecUtils )
+
+if (NOT SKBUILD)
+  message(FATAL_ERROR "\
+  This CMake file is must be executed using 'scikit-build'. 
+  If you are a user trying to install this package, please use the command
+  below, which will install all necessary build dependencies, compile
+  the package in an isolated environment, and then install it.
+  =====================================================================
+   $ pip install .
+  =====================================================================
+  If you are a software developer, and this is your own package, then
+  it is usually much more efficient to install the build dependencies
+  in your environment once and use the following command that avoids
+  a costly creation of a new virtual environment at every compilation:
+  =====================================================================
+   $ pip install nanobind scikit-build-core
+   $ pip install --no-build-isolation -ve .
+  =====================================================================
+  You may optionally add -Ceditable.rebuild=true to auto-rebuild when
+  the package is imported. Otherwise, you need to re-run the above
+  after editing C++ files.")
+endif()
+
+# Try to import all Python components potentially needed by nanobind
+find_package(Python 3.8
+  REQUIRED COMPONENTS Interpreter Development.Module
+  OPTIONAL_COMPONENTS Development.SABIModule)
+
+# Import nanobind through CMake's find_package mechanism
+find_package(nanobind CONFIG REQUIRED)
+
+# We are now ready to compile the actual extension module
+nanobind_add_module(
+  # Name of the extension
+  PySpecUtils
+
+  # Target the stable ABI for Python 3.12+, which reduces
+  # the number of binary wheels that must be built. This
+  # does nothing on older Python versions
+  STABLE_ABI
+
+  # Build libnanobind statically and merge it into the
+  # extension (which itself remains a shared library)
+  #
+  # If your project builds multiple extensions, you can
+  # replace this flag by NB_SHARED to conserve space by
+  # reusing a shared libnanobind across libraries
+  NB_STATIC
+
+  #Perform link time optimization.
+  #LTO
+
+
+  # Source code goes here
+  SpecFile_py.cpp
+)
+
+set_target_properties( PySpecUtils PROPERTIES OUTPUT_NAME "SpecUtils" )
+target_link_libraries( PySpecUtils PUBLIC SpecUtils )
+
+# Install directive for scikit-build-core
+install(TARGETS PySpecUtils LIBRARY DESTINATION SpecUtils)
+install(FILES __init__.py DESTINATION SpecUtils) 
+
+nanobind_add_stub(
+  SpecUtils_stub
+    MODULE SpecUtils
+    OUTPUT SpecUtils.pyi
+    PYTHON_PATH $<TARGET_FILE_DIR:PySpecUtils>
+    DEPENDS PySpecUtils
+)