Command Line Tools

cython [options] sourcefile.pyx

Options:
  -o FILE, --output-file FILE   Output file name
  -D, --output-dir DIR         Output directory  
  -3                           Compile for Python 3
  -2                           Compile for Python 2
  --cplus                      Generate C++ code
  -X DIRECTIVE                 Set compiler directive
  -E, --directive DIRECTIVE    Set compiler directive (alternative form)
  -s, --option OPTION          Set compiler option
  -p, --embed-pos-in-filename  Embed source position in filename
  -z, --pre-import MODULE      Pre-import module
  --cleanup LEVEL              Cleanup intermediate files (0-3)
  -w, --working DIR            Working directory
  -v, --verbose                Verbose output
  -l, --include-dir DIR        Add include directory
  -I DIR                       Add include directory (alternative)
  --gdb                        Generate debugging information
  --gdb-outdir DIR             GDB debugging output directory
  -a, --annotate               Generate annotated HTML output
  --annotate-coverage COVERAGE Use coverage data for annotation
  -f, --force                  Force recompilation
  --timestamps                 Only compile newer sources
  -q, --quiet                  Quiet operation
  --fast-fail                  Stop on first error
  --warning-errors             Treat warnings as errors
  --Werror                     Treat warnings as errors (alternative)
  -M                           Generate dependency file
  --depfile FILE               Dependency output file

cythonize [options] sources...

Positional arguments:
  sources                      Source files (.pyx, .py) or glob patterns

Options:
  -b, --build                  Build extension modules
  -i, --inplace                Build extensions in-place
  -j N, --parallel N           Parallel compilation (N processes)
  -f, --force                  Force recompilation
  -q, --quiet                  Quiet operation  
  -k, --keep-going             Continue despite errors
  -X DIRECTIVE                 Set compiler directive
  --lenient                    Lenient error handling
  --no-docstrings              Remove docstrings
  -M                           Generate dependency files
  --depfile                    Dependency file template
  -s OPTION                    Set compiler option
  --annotate                   Generate annotated HTML
  -3                           Compile for Python 3
  -2                           Compile for Python 2
  --cplus                      Generate C++ code
  --fast-fail                  Stop on first error
  --verbose                    Verbose output
  -h, --help                   Show help

cygdb [options] [path-to-project-directory] [gdb-args...]

Positional arguments:
  path-to-project-directory    Path to project with cython_debug/ directory
  gdb-args                     Additional arguments passed to GDB

Options:
  --gdb-executable GDB         GDB executable to use (default: gdb)
  --verbose                    Verbose output
  -h, --help                   Show help

# Compile a single .pyx file to C
cython my_module.pyx

# Compile for Python 3 with C++ output
cython -3 --cplus my_module.pyx -o my_module.cpp

# Generate annotated HTML for performance analysis
cython -a my_module.pyx

# Compile with specific directives
cython -X boundscheck=False -X wraparound=False my_module.pyx

# Include debugging information
cython --gdb my_module.pyx

# Compile with custom include directories
cython -I /usr/local/include -I ./headers my_module.pyx

# Generate dependency files
cython -M --depfile my_module.dep my_module.pyx

# Build extension module in-place
cythonize -i my_module.pyx

# Build with parallel compilation
cythonize -j 4 -b src/*.pyx

# Build with specific Python version
cythonize -3 -b my_module.pyx

# Build C++ extensions
cythonize --cplus -b *.pyx

# Force rebuild with annotations
cythonize -f --annotate -b my_module.pyx

# Build with compiler directives
cythonize -X language_level=3 -X boundscheck=False -b *.pyx

# Build with custom options and keep going on errors
cythonize -k -s -j 8 -b src/**/*.pyx

# Quiet build with dependency tracking
cythonize -q -M -b my_package/*.pyx

# Debug in current directory (requires cython_debug/ folder)
cygdb

# Debug specific project
cygdb /path/to/my/project

# Debug with custom GDB executable
cygdb --gdb-executable gdb-multiarch

# Debug with additional GDB arguments
cygdb . --args python my_script.py arg1 arg2

# 1. Write Cython code in my_module.pyx
# 2. Build with debugging and annotations
cythonize -i --gdb --annotate my_module.pyx

# 3. Test the module
python -c "import my_module; print(my_module.test_function())"

# 4. Debug if needed
cygdb

# 5. Optimize based on annotations
# Open my_module.html in browser to see performance bottlenecks

# Compile with optimizations for production
cythonize -X boundscheck=False \
          -X wraparound=False \
          -X cdivision=True \
          -X language_level=3 \
          -j 8 -b src/*.pyx

# Set environment variables for cross-compilation
export CC=arm-linux-gnueabihf-gcc
export CXX=arm-linux-gnueabihf-g++

# Compile with custom include paths
cythonize -I /usr/arm-linux-gnueabihf/include \
          -b my_module.pyx

# Makefile example
CYTHON = cython
CYTHONIZE = cythonize

%.c: %.pyx
	$(CYTHON) -3 $< -o $@

build: src/*.pyx
	$(CYTHONIZE) -3 -b $^

debug: src/*.pyx
	$(CYTHONIZE) -3 --gdb --annotate -i $^

clean:
	rm -f src/*.c src/*.cpp src/*.html src/*.so

# CMakeLists.txt example
find_program(CYTHON_EXECUTABLE cython)

function(add_cython_module module_name pyx_file)
    get_filename_component(pyx_file_we ${pyx_file} NAME_WE)
    set(c_file "${CMAKE_CURRENT_BINARY_DIR}/${pyx_file_we}.c")
    
    add_custom_command(
        OUTPUT ${c_file}
        COMMAND ${CYTHON_EXECUTABLE} -3 ${pyx_file} -o ${c_file}
        DEPENDS ${pyx_file}
    )
    
    add_library(${module_name} MODULE ${c_file})
endfunction()

# Compiler selection
export CC=clang
export CXX=clang++

# Python configuration
export PYTHON_CONFIG=python3-config

# Build flags
export CFLAGS="-O3 -march=native"
export CXXFLAGS="-O3 -march=native"

# Include paths
export CPATH="/usr/local/include:/opt/include"

# Library paths  
export LIBRARY_PATH="/usr/local/lib:/opt/lib"