.gitattributes
.pre-commit-config.yaml
.radon.cfg
.readthedocs.yaml
.vulture_whitelist.py
CHANGELOG.md
Chi-squared Calculation.txt
DEVELOPMENT.md
LICENSE
MANIFEST.in
Makefile
README.md
pyproject.toml
requirements-dev.txt
requirements-optional.txt
requirements.txt
.github/fix-commit-errors/knowledge.json
.github/workflows/ci.yml
.github/workflows/docs.yml
.github/workflows/release.yml
docs/CHANGELOG.md
docs/Makefile
docs/conf.py
docs/deploy_docs.py
docs/index.rst
docs/performance.rst
docs/requirements.txt
docs/_static/.gitkeep
docs/api-reference/analysis-core.md
docs/api-reference/core.rst
docs/api-reference/index.rst
docs/api-reference/overview.md
docs/api-reference/robust.rst
docs/api-reference/utilities.rst
docs/api-reference/_autosummary/heterodyne.analysis.core.rst
docs/api-reference/_autosummary/heterodyne.core.config.rst
docs/api-reference/_autosummary/heterodyne.core.io_utils.rst
docs/api-reference/_autosummary/heterodyne.core.kernels.rst
docs/api-reference/_autosummary/heterodyne.core.rst
docs/api-reference/_autosummary/heterodyne.optimization.classical.rst
docs/developer-guide/architecture.rst
docs/developer-guide/completion-comparison.md
docs/developer-guide/completion-features.md
docs/developer-guide/contributing.rst
docs/developer-guide/index.rst
docs/developer-guide/optimization.md
docs/developer-guide/performance.rst
docs/developer-guide/security.rst
docs/developer-guide/testing-coverage.md
docs/developer-guide/testing.rst
docs/developer-guide/troubleshooting.rst
docs/developer-guide/version-updates.md
docs/developer-guide/optimization/cpu-performance.md
docs/developer-guide/optimization/distributed-optimization.md
docs/developer-guide/optimization/monitoring.md
docs/developer-guide/optimization/optimization-report.md
docs/research/computational_methods.rst
docs/research/index.rst
docs/research/methodology.md
docs/research/publications.rst
docs/research/theoretical_framework.rst
docs/user-guide/analysis-modes.rst
docs/user-guide/configuration.rst
docs/user-guide/examples.rst
docs/user-guide/getting-started.md
docs/user-guide/installation.rst
docs/user-guide/ml-acceleration.md
docs/user-guide/plotting.rst
docs/user-guide/quickstart.rst
docs/user-guide/troubleshooting.md
heterodyne/.coveragerc
heterodyne/__init__.py
heterodyne/_version.py
heterodyne/py.typed
heterodyne/analysis/__init__.py
heterodyne/analysis/core.py
heterodyne/analysis/helpers.py
heterodyne/cli/__init__.py
heterodyne/cli/core.py
heterodyne/cli/create_config.py
heterodyne/cli/enhanced_runner.py
heterodyne/cli/import_manager.py
heterodyne/cli/optimization.py
heterodyne/cli/parser.py
heterodyne/cli/run_heterodyne.py
heterodyne/cli/simulation.py
heterodyne/cli/utils.py
heterodyne/cli/visualization.py
heterodyne/config/__init__.py
heterodyne/config/heterodyne_template.json
heterodyne/config/template.json
heterodyne/core/__init__.py
heterodyne/core/analysis.py
heterodyne/core/blas_kernels.py
heterodyne/core/caching.py
heterodyne/core/composed_analysis.py
heterodyne/core/composition.py
heterodyne/core/config.py
heterodyne/core/cpu_optimization.py
heterodyne/core/initialization_optimizer.py
heterodyne/core/io_utils.py
heterodyne/core/kernels.py
heterodyne/core/lazy_imports.py
heterodyne/core/mathematical_optimization.py
heterodyne/core/migration.py
heterodyne/core/optimization_utils.py
heterodyne/core/performance_analytics.py
heterodyne/core/result_memoization.py
heterodyne/core/secure_io.py
heterodyne/core/security_metrics.py
heterodyne/core/security_performance.py
heterodyne/core/workflows.py
heterodyne/data/__init__.py
heterodyne/data/xpcs_loader.py
heterodyne/optimization/__init__.py
heterodyne/optimization/blas_optimization.py
heterodyne/optimization/classical.py
heterodyne/optimization/distributed.py
heterodyne/optimization/ml_acceleration.py
heterodyne/optimization/robust.py
heterodyne/optimization/utils.py
heterodyne/performance/__init__.py
heterodyne/performance/baseline.py
heterodyne/performance/cpu_profiling.py
heterodyne/performance/integrated_monitoring.py
heterodyne/performance/monitoring.py
heterodyne/performance/regression_prevention.py
heterodyne/performance/simple_monitoring.py
heterodyne/performance/startup_monitoring.py
heterodyne/statistics/__init__.py
heterodyne/statistics/chi_squared.py
heterodyne/typings/__init__.py
heterodyne/typings/mpl_toolkits/__init__.pyi
heterodyne/typings/mpl_toolkits/mplot3d.pyi
heterodyne/ui/__init__.py
heterodyne/ui/cli_enhancer.py
heterodyne/ui/error_reporter.py
heterodyne/ui/interactive.py
heterodyne/ui/progress.py
heterodyne/ui/visualization_optimizer.py
heterodyne/ui/completion/README.md
heterodyne/ui/completion/__init__.py
heterodyne/ui/completion/adapter.py
heterodyne/ui/completion/cache.py
heterodyne/ui/completion/core.py
heterodyne/ui/completion/fast_handler.py
heterodyne/ui/completion/install_completion.py
heterodyne/ui/completion/installer.py
heterodyne/ui/completion/monitor_performance.py
heterodyne/ui/completion/optimize_performance.py
heterodyne/ui/completion/plugins.py
heterodyne/ui/completion/uninstall_completion.py
heterodyne/validation/performance_validation.py
heterodyne/visualization/__init__.py
heterodyne/visualization/enhanced_plotting.py
heterodyne/visualization/plotting.py