LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
docs/index.rst
docs/methods_comparison.md
docs/api/dataset.rst
docs/api/graph_analysis.rst
docs/api/models.rst
docs/api/utils.rst
docs/developer/contributing.rst
docs/examples/basic_usage.rst
docs/examples/fep_benchmark_tutorial.rst
docs/examples/parameter_sweeps.rst
docs/tutorials/index.rst
docs/user_guide/architecture.rst
docs/user_guide/installation.rst
docs/user_guide/parameter_optimization.rst
docs/user_guide/quickstart.rst
docs/user_guide/tutorials.rst
examples/benchmark_all_datasets.py
examples/parameter_optimization_example.py
examples/performance_tracking_example.py
examples/quick_performance_demo.py
src/maple_fep/__init__.py
src/maple_fep/py.typed
src/maple_fep.egg-info/PKG-INFO
src/maple_fep.egg-info/SOURCES.txt
src/maple_fep.egg-info/dependency_links.txt
src/maple_fep.egg-info/requires.txt
src/maple_fep.egg-info/top_level.txt
src/maple_fep/dataset/FEP_benchmark_dataset.py
src/maple_fep/dataset/__init__.py
src/maple_fep/dataset/base_dataset.py
src/maple_fep/dataset/dataset.py
src/maple_fep/dataset/synthetic_dataset.py
src/maple_fep/graph_analysis/__init__.py
src/maple_fep/graph_analysis/graph_cycle_analysis.py
src/maple_fep/graph_analysis/graph_setup.py
src/maple_fep/graph_analysis/performance_stats.py
src/maple_fep/graph_analysis/plotting_performance.py
src/maple_fep/models/__init__.py
src/maple_fep/models/base.py
src/maple_fep/models/config.py
src/maple_fep/models/graph_data.py
src/maple_fep/models/deterministic/__init__.py
src/maple_fep/models/deterministic/cycle_closure.py
src/maple_fep/models/deterministic/spectral_correction.py
src/maple_fep/models/probabilistic/__init__.py
src/maple_fep/models/probabilistic/gaussian_mixture_vi.py
src/maple_fep/models/probabilistic/variational_estimator.py
src/maple_fep/utils/__init__.py
src/maple_fep/utils/parameter_sweep.py
src/maple_fep/utils/performance_tracker.py