LICENSE
MANIFEST.in
README.md
pyproject.toml
docs/cookbook/README.md
docs/cookbook/analysis-quick-reference.md
docs/cookbook/tutorial-constructing-and-analysing-an-ssn.md
docs/cookbook/tutorial-ml-training-and-inference-on-an-ssn.md
docs/cookbook/tutorial-quantitative-analysis-of-an-ssn.md
docs/cookbook/accessibility/README.md
docs/cookbook/accessibility/basins-of-attraction.md
docs/cookbook/accessibility/greedy-accessible-paths.md
docs/cookbook/accessibility/high-fitness-reachability-audit.md
docs/cookbook/accessibility/local-optima.md
docs/cookbook/accessibility/neutral-networks.md
docs/cookbook/accessibility/stochastic-adaptive-walks.md
docs/cookbook/data/README.md
docs/cookbook/epistasis/README.md
docs/cookbook/epistasis/categorical-and-multiallelic.md
docs/cookbook/epistasis/choose-an-estimand.md
docs/cookbook/epistasis/estimand-contracts.md
docs/cookbook/epistasis/known-answer-and-sensitivity-checks.md
docs/cookbook/epistasis/regression-sampled-binary.md
docs/cookbook/epistasis/walsh-complete-binary.md
docs/cookbook/foundations/README.md
docs/cookbook/foundations/annotations-and-queries.md
docs/cookbook/foundations/external-networkx-graphs.md
docs/cookbook/foundations/first-empirical-landscape.md
docs/cookbook/foundations/fitness-layers.md
docs/cookbook/foundations/preparing-sequences.md
docs/cookbook/foundations/public-api.md
docs/cookbook/graph-construction/README.md
docs/cookbook/graph-construction/compare-representations.md
docs/cookbook/graph-construction/diffusion-semantics.md
docs/cookbook/graph-construction/edge-semantics.md
docs/cookbook/graph-construction/embedding-diffusion.md
docs/cookbook/graph-construction/evolutionary-diffusion.md
docs/cookbook/graph-construction/external-adjacency.md
docs/cookbook/graph-construction/hamming.md
docs/cookbook/graph-construction/input-contracts.md
docs/cookbook/graph-construction/knn-embedding-domains.md
docs/cookbook/graph-construction/knn-sequence-space.md
docs/cookbook/graph-construction/plm-knn.md
docs/cookbook/graph-construction/tda.md
docs/cookbook/installation/README.md
docs/cookbook/installation/feature-availability.md
docs/cookbook/io/README.md
docs/cookbook/io/command-line-workflows.md
docs/cookbook/io/csv-import-and-export.md
docs/cookbook/io/cytoscape-and-python-visualization.md
docs/cookbook/io/lsbundle-archives.md
docs/cookbook/io/portable-directory-bundles.md
docs/cookbook/io/provenance-and-integrity.md
docs/cookbook/ml/README.md
docs/cookbook/ml/adding-predictions-back-to-a-landscape.md
docs/cookbook/ml/evaluation-without-leakage.md
docs/cookbook/ml/feature-and-target-preparation.md
docs/cookbook/ml/pytorch-geometric-export.md
docs/cookbook/ml/sequence-tensor-export.md
docs/cookbook/ruggedness/README.md
docs/cookbook/ruggedness/autocorrelation-contract.md
docs/cookbook/ruggedness/comparing-graph-views.md
docs/cookbook/ruggedness/dirichlet-energy.md
docs/cookbook/ruggedness/graph-fourier-analysis.md
docs/cookbook/ruggedness/local-dirichlet-contributions.md
docs/cookbook/ruggedness/random-walk-autocorrelation.md
docs/cookbook/ruggedness/spectral-operators.md
docs/cookbook/scaling/README.md
docs/cookbook/scaling/component-wise-pipelines.md
docs/cookbook/scaling/diffusion-resource-guards.md
docs/cookbook/scaling/esm-embeddings.md
docs/cookbook/scaling/knn-backends.md
docs/cookbook/scaling/plm-embeddings.md
docs/cookbook/scaling/ray-and-parallel-construction.md
docs/cookbook/scaling/reproducibility-checklist.md
docs/cookbook/scaling/sparse-spectral-analysis.md
docs/cookbook/simulation/README.md
docs/cookbook/simulation/binary-nk.md
docs/cookbook/simulation/elementary-landscapes.md
docs/cookbook/simulation/generalized-nk.md
docs/cookbook/simulation/method-validation.md
docs/cookbook/simulation/rough-mount-fuji.md
docs/cookbook/statistics/README.md
docs/cookbook/statistics/fitness-distributions.md
docs/cookbook/statistics/graph-aware-reporting.md
docs/cookbook/statistics/inference-contract.md
docs/cookbook/statistics/pairwise-hypothesis-tests.md
docs/cookbook/statistics/permutation-tests.md
docs/cookbook/statistics/subsampling-sensitivity.md
docs/cookbook/topology/README.md
docs/cookbook/topology/category-diffusion-and-crossing.md
docs/cookbook/topology/community-annotations.md
docs/cookbook/topology/connected-components.md
docs/cookbook/topology/effective-resistance-contract.md
docs/cookbook/topology/effective-resistance.md
docs/cookbook/topology/graph-properties-and-support.md
docs/cookbook/topology/quotient-landscapes.md
docs/cookbook/tutorial_ml_ssn_figures/held_out_predictions_on_ssn.png
docs/cookbook/tutorial_ml_ssn_figures/ml_split.png
docs/cookbook/tutorial_ml_ssn_figures/mlp_performance.png
docs/cookbook/tutorial_ml_ssn_figures/mlp_training.png
docs/cookbook/tutorial_quantitative_ssn_figures/fitness_views.png
docs/cookbook/tutorial_quantitative_ssn_figures/graphical_analysis.png
docs/cookbook/tutorial_quantitative_ssn_figures/robustness.png
docs/cookbook/tutorial_quantitative_ssn_figures/spectral_analysis.png
docs/cookbook/tutorial_quantitative_ssn_figures/synthetic_fitness.png
docs/cookbook/tutorial_ssn_figures/annotations.png
docs/cookbook/tutorial_ssn_figures/category_diffusion.png
docs/cookbook/tutorial_ssn_figures/louvain_communities.png
docs/cookbook/tutorial_ssn_figures/phylum_quotient.png
src/fitness_landscape/__init__.py
src/fitness_landscape/__main__.py
src/fitness_landscape/_const.py
src/fitness_landscape/_optional.py
src/fitness_landscape/utils.py
src/fitness_landscape/analysis/__init__.py
src/fitness_landscape/analysis/adaptive_walk.py
src/fitness_landscape/analysis/diffusion_scale.py
src/fitness_landscape/analysis/dirichlet_energy.py
src/fitness_landscape/analysis/epistasis.py
src/fitness_landscape/analysis/graph.py
src/fitness_landscape/analysis/graph_induction_alignment.py
src/fitness_landscape/analysis/random_walk.py
src/fitness_landscape/analysis/statistics.py
src/fitness_landscape/core/__init__.py
src/fitness_landscape/core/annotation.py
src/fitness_landscape/core/edge_schema.py
src/fitness_landscape/core/fitness.py
src/fitness_landscape/core/graph.py
src/fitness_landscape/core/landscape.py
src/fitness_landscape/core/sequence.py
src/fitness_landscape/core/superscape.py
src/fitness_landscape/embedding/__init__.py
src/fitness_landscape/embedding/esm.py
src/fitness_landscape/embedding/soft_embedding.py
src/fitness_landscape/graph_matching/__init__.py
src/fitness_landscape/graph_matching/hierarchical_alignment.py
src/fitness_landscape/graph_matching/isorank.py
src/fitness_landscape/graph_matching/latent_alignment.py
src/fitness_landscape/graph_matching/minimum_spanning_graph.py
src/fitness_landscape/io/__init__.py
src/fitness_landscape/io/bundle.py
src/fitness_landscape/io/exceptions.py
src/fitness_landscape/models/__init__.py
src/fitness_landscape/models/elementary_landscape.py
src/fitness_landscape/models/nk.py
src/fitness_landscape/models/rmf.py
src/fitness_landscape/phylo/__init__.py
src/fitness_landscape/phylo/_sub_matrices.py
src/fitness_landscape/phylo/model.py
src/fitness_landscape/phylo/phylogenetic_asr.py
src/fitness_landscape/transforms/__init__.py
src/fitness_landscape/transforms/eigenmode.py
src/fitness_landscape/transforms/graph_fourier.py
src/fitness_landscape/transforms/walsh_hadamard.py
src/landscapy.egg-info/PKG-INFO
src/landscapy.egg-info/SOURCES.txt
src/landscapy.egg-info/dependency_links.txt
src/landscapy.egg-info/entry_points.txt
src/landscapy.egg-info/requires.txt
src/landscapy.egg-info/top_level.txt