├── .gitattributes ├── .github ├── copilot-instructions.md └── workflows │ └── PR-test.yml ├── .gitignore ├── .readthedocs.yaml ├── CITATION.cff ├── CLAUDE.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── _static │ └── fra_11_04_0001.gif ├── _templates │ ├── custom-class-template.rst │ └── custom-module-template.rst ├── api.rst ├── conf.py ├── index.md ├── installation.md ├── make.bat ├── requirements-docs.txt └── tutorials.rst ├── environment.yml ├── notebooks ├── tutorial │ ├── 01-Introduction_and_Data_Format.ipynb │ ├── 02-Decoding_with_Sorted_Spikes.ipynb │ ├── 03-Decoding_with_Clusterless_Spikes.ipynb │ ├── 04-Classifying_with_Sorted_Spikes.ipynb │ └── 05-Classifying_with_Clusterless_Spikes.ipynb └── work_in_progress │ ├── 1D_respecting_connectivity.ipynb │ ├── AREADNE_Poster │ ├── diffusion_continuous_transition.pdf │ ├── env_with_cell_numbers.pdf │ ├── env_with_cell_numbers_alt.pdf │ ├── envs.pdf │ ├── movement_model_prev_posterior.pdf │ ├── replay_env1.pdf │ ├── replay_env1_alt.pdf │ ├── replay_env1_field_sequence.pdf │ ├── replay_env1_field_sequence_alt.pdf │ ├── replay_env1_one_env.pdf │ ├── replay_env1_one_env_alt.pdf │ ├── replay_env2.pdf │ ├── replay_env2_alt.pdf │ ├── replay_env2_field_sequence.pdf │ ├── replay_env2_field_sequence_alt.pdf │ ├── replay_env2_one_env.pdf │ ├── replay_env2_one_env_alt.pdf │ ├── replay_no_env.pdf │ ├── replay_no_env_alt.pdf │ ├── replay_no_env_field_sequence.pdf │ ├── replay_no_env_field_sequence_alt.pdf │ ├── replay_no_env_one_env.pdf │ └── replay_no_env_one_env_alt.pdf │ ├── Density_estimation.ipynb │ ├── EM.ipynb │ ├── Numba_GPU_KDE.ipynb │ ├── Numba_multiunit_likelihood.ipynb │ ├── Spatial_boundaries.ipynb │ ├── Test_1D.ipynb │ ├── Test_2D_Diffusion.ipynb │ ├── Test_EM.ipynb │ ├── Test_EM2.ipynb │ ├── Test_Inbound_Outbound.ipynb │ ├── Test_Inbound_Outbound_Directionality.ipynb │ ├── Test_Real_Data.ipynb │ ├── Test_no_spike.ipynb │ ├── Test_normalizing_flows.ipynb │ ├── Two_Environments.ipynb │ ├── Two_Environments2.ipynb │ ├── Two_Environments2b.ipynb │ ├── Two_Environments2c.ipynb │ ├── Two_Environments3.ipynb │ ├── Viterbi.ipynb │ ├── simulate_deconvolved_calcium.ipynb │ └── test_simulated_circular_track.ipynb ├── postBuild ├── pyproject.toml ├── pytest.ini ├── replay_trajectory_classification ├── __init__.py ├── classifier.py ├── clusterless_simulation.py ├── continuous_state_transitions.py ├── core.py ├── decoder.py ├── discrete_state_transitions.py ├── environments.py ├── initial_conditions.py ├── likelihoods │ ├── __init__.py │ ├── calcium_likelihood.py │ ├── diffusion.py │ ├── multiunit_likelihood.py │ ├── multiunit_likelihood_gpu.py │ ├── multiunit_likelihood_integer.py │ ├── multiunit_likelihood_integer_gpu.py │ ├── multiunit_likelihood_integer_gpu_log.py │ ├── multiunit_likelihood_track_graph.py │ ├── spiking_likelihood_glm.py │ ├── spiking_likelihood_kde.py │ └── spiking_likelihood_kde_gpu.py ├── observation_model.py ├── simulate.py ├── sorted_spikes_simulation.py ├── 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