Release v0.4.0

What's Changed

Features

• feat(M5.1): Environment._state_version + versioned_cached_property (9f4d375)
• feat(M3.4): add public exception hierarchy in neurospatial._exceptions (86315f3)
• feat(M3.1): EnvironmentNotFittedError supports free-function form (749c7f5)
• feat(environment): mark polar envs and refuse Cartesian-assuming methods (M1 1.3) (7377271)
• feat(encoding): surface batch metric failures via BatchScoresResult + warning (M1 1.5) (dea5404)
• feat(encoding): warn before silent interneuron exclusion in detect_place_fields (M1 1.4) (14291b3)
• feat(decoding): default decode_position to validate=True; add non-negative spike_counts and rate checks (M1 1.8) (8143baa)
• feat(encoding/decoding): validate env.is_fitted at compute*_rate(s) and decode_position entry (M1 1.6) (83cc42b)
• feat(encoding): validate spike_times shape/sortedness at compute_*_rate(s) entry (M1 1.7) (ac30a17)
• feat(M8): expose gaze_offsets parameter in compute_view_rate(s) API (b3bc49b)
• feat(M8): implement backend-aware JAX metrics for result classes (5641618)
• feat(M7): add _field_metrics.py and extend _metrics.py (472cecb)
• feat(M6): add NumPy vs JAX performance benchmarks (Task 6.7) (4bbffaa)
• feat(M6): make metrics backend-aware and wire view/egocentric to JAX smoothing (b6de96c)
• feat(M6): implement real JAX compute path for spatial rate computation (991ae80)
• feat(M6): wire up JAX backend dispatch in compute functions (68f3e69)
• feat(M6): fix JAX array detection and add backend awareness tests (Task 6.5) (0d6d02e)
• feat(M6): add backend parameter to all compute functions (Task 6.4) (13f49d8)
• feat(M6): implement JAX metric computations in _core_jax.py (Task 6.2) (61c9f6d)
• feat(M6): implement JAX smoothing operations in _core_jax.py (Task 6.1) (4e3c024)
• feat(M5): verify comprehensive tests for egocentric encoding (Task 5.9) (4bdfef3)
• feat(M5): implement compute_egocentric_rates() function (Task 5.8) (9b721c4)
• feat(M5): implement compute_egocentric_rate() function (Task 5.7) (98a9250)
• feat(M5): implement egocentric binning layer (Task 5.6) (14128b8)
• feat(M5): implement EgocentricRatesResult.to_dataframe() (Task 5.5) (8073457)
• feat(M5): implement EgocentricRatesResult batch methods (Task 5.4) (2f591bd)
• feat(M5): implement EgocentricRateResult classification (Task 5.3) (fda734f)
• feat(M5): implement EgocentricRateResult convenience methods (Task 5.2) (837212d)
• feat(M5): implement EgocentricRateResult and EgocentricRatesResult classes (Task 5.1) (3c2e823)
• feat(M4): implement compute_view_rates() batch function (Task 4.8) (4e9f740)
• feat(M4): implement compute_view_rate() function (Task 4.7) (c4a25f8)
• feat(M4): implement view binning layer for spatial view encoding (Task 4.6) (6407637)
• feat(M4): implement ViewRatesResult.to_dataframe() (Task 4.5) (3a151ee)
• feat(M4): implement ViewRatesResult batch methods (Task 4.4) (cc22358)
• feat(M4): implement ViewRateResult.is_view_cell() classification (Task 4.3) (dfe8597)
• feat(M4): implement ViewRateResult convenience methods (Task 4.2) (ce2b7b5)
• feat(M4): add ViewRateResult and ViewRatesResult classes (Task 4.1) (08433dd)
• feat(M3): add comprehensive tests for directional encoding (Task 3.11) (87cadbf)
• feat(M3): implement compute_directional_rates() function (2af04fe)
• feat(M3): implement compute_directional_rate() function (212dc4a)
• feat(M3): implement directional binning layer (db988f9)
• feat(M3): implement DirectionalRatesResult.to_dataframe() (b21ba4f)
• feat(M3): implement DirectionalRatesResult batch methods (9617198)
• feat(M3): implement DirectionalRateResult classification methods (115e7e2)
• feat(M3): implement DirectionalRateResult tuning metrics (4dd95a2)
• feat(M3): implement DirectionalRateResult convenience methods (89489c0)
• feat(encoding): add DirectionalRateResult and DirectionalRatesResult classes (8fae7f0)
• feat(encoding): implement compute_spatial_rates() batch function (b89cc93)
• feat(encoding): implement compute_spatial_rate() function (b5c39af)
• feat(encoding): implement binning layer for spatial encoding (6a6f42d)
• feat(encoding): add SpatialRatesResult.to_dataframe() method (462116f)
• feat(encoding): add SpatialRatesResult batch metrics methods (e1a170d)
• feat(encoding): add SpatialRatesResult batch convenience methods (9df1e90)
• feat(encoding): add SpatialRateResult cell type metric methods (9db2b9e)
• feat(encoding): add SpatialRateResult convenience methods (72b1263)
• feat(encoding): add SpatialRateResult and SpatialRatesResult classes (3ec6ca8)
• feat(encoding): add batch_border_scores to _metrics.py (11e1ed8)
• feat(encoding): add batch_grid_scores to _metrics.py (b790877)
• feat(encoding): add _smoothing.py with shared smoothing implementations (9fcac0b)
• feat(encoding): add _metrics.py with spatial information and sparsity (b0872a5)
• feat(encoding): add _core_jax.py with stub functions (27ec643)
• feat(encoding): add _core_numpy.py with stub functions (99cf92b)
• feat(encoding): add _backend.py with backend selection (1c366af)
• feat(encoding): add _spikes.py with spike format normalization (b7356ef)
• feat(encoding): add _base.py with shared protocols and helpers (7424105)
• feat(M13): add comprehensive import test suite (009e91a)
• feat(M5): complete integration and documentation for behavioral metrics (57e3a52)
• feat(M4): implement VTE metrics module (a517953)
• feat(M3): implement spatial decision analysis module (be179d6)
• feat(M2): implement goal-directed navigation metrics module (bd56410)
• feat(M1): implement path efficiency metrics module (73b38e4)
• feat(M3.4): implement spatial view cell metrics module (0e077d5)
• feat(M3.3): implement spatial view field analysis (4bc2b53)
• feat(M3.2): implement spatial view cell simulation model (74fba03)
• feat(M3.1): implement visibility/gaze computation module (6dff4ec)
• feat(M2.6): complete object-vector cells integration and documentation (31a7cd0)
• feat(M2.4): implement ObjectVectorOverlay for animation (4be296e)
• feat(M2.3): implement ObjectVectorFieldResult and compute_object_vector_field (bd3e901)
• feat(M2.2): implement ObjectVectorMetrics and analysis functions (d7bd14f)
• feat(M2.1): implement ObjectVectorCellModel simulation (04c4623)
• feat(M1.3): implement egocentric polar environment factory (4d75906)
• feat(M1): implement egocentric reference frames module (26aa1d6)
• feat(M8): add top-level exports and documentation for events module (59955bc)
• feat(M7): implement NWB integration for events module (04c5d76)
• feat(M6): implement peri-event analysis functions (7f5ade7)
• feat(M4): implement interval utilities for events module (6da1016)
• feat(M3.4): implement add_positions() spatial event utility (af9eb4d)
• feat(M2.3): implement event_indicator() temporal GLM regressor (ebd5234)
• feat(M2.2): implement event_count_in_window() temporal GLM regressor (75f2d06)
• feat(M2.1): implement time_since_event() temporal GLM regressor (a5080cb)
• feat(M1): implement events module core infrastructure (02ff340)
• feat(basis): add maze-aware spatial basis functions for GLMs (e491364)
• feat(M6): add confidence bands to plot_circular_basis_tuning() (a209d4f)
• feat(M3): add plot_circular_basis_tuning() visualization for GLM tuning curves (faaba7a)
• feat(M2): add is_modulated() convenience function for GLM circular modulation (252a5dc)
• feat(M1): add circular basis functions for GLM design matrices (bb9ad19)
• feat(M4.7-M5): add property-based tests and complete integration (76b41a8)
• feat(M3.5): implement plot_head_direction_tuning for HD cell visualization (911b874)
• feat(M3.3-M3.4): implement HeadDirectionMetrics and HD cell classification (8480fb8)
• feat(M3.2): implement head_direction_tuning_curve for HD cell analysis (118820d)
• feat(M3.1): create head_direction.py module with setup (dc5c3d8)
• feat(M2.3): implement plot_phase_precession for phase precession visualization (31344ff)
• feat(M2.2): implement phase_precession for place cell analysis (dc271be)
• feat(M1.4): implement circular_circular_correlation for phase coherence analysis (4d0e103)
• feat(M1.3): implement circular_linear_correlation for phase-position analysis (9a51ee1)
• feat(M1.2): implement rayleigh_test for circular uniformity testing (d605fa0)
• feat(M1.1): add circular statistics module with internal helpers (d5eb130)
• feat(phase6.1): add automated pytest-benchmark suite for napari playback (417d089)
• feat(phase5.2): audit layer.data assignments and add test documentation (da10c43)
• feat(phase5.1): complete callback audit and document findings (e078fdc)
• feat(phase4.2): add rapid scrubbing debounce to PlaybackController (1c246cf)
• feat(phase3.2): add throttle parameters and xlim caching for time series (39aa50b)
• feat(phase3.1): add update_mode parameter to TimeSeriesOverlay (ee8febc)
• feat(phase2.2): add configurable cache_size and async prefetching for video (1284873)
• feat(phase2.1): add time-indexed image layer for in-memory video (3709383)
• feat(phase1.2): integrate PlaybackController into render_napari() (7d0fa42)
• feat(phase1): add PlaybackController class for frame-skipping playback (82e75d4)
• feat(phase0): complete baseline measurements for napari playback (adb270e)
• feat(phase0): add video/timeseries tracing to perfmon config (5d0c78b)
• feat(phase0): add napari playback benchmark script (34fc1d1)
• feat(M7): update demo scripts to use speed-based API (9288fcc)
• feat(animation): make frame_times required and add speed parameter (Task 3.1) (d128325)
• feat(animation): add playback speed constants and helper function (d986f2e)
• feat(animation): add HTML backend warning for TimeSeriesOverlay (8cae4a2)
• feat(animation): add time series support to widget backend (82981f6)
• feat(animation): add napari dock widget for time series overlays (bdab281)
• feat(animation): add TimeSeriesArtistManager for matplotlib rendering (302246d)
• feat(animation): add TimeSeriesOverlay for continuous variable visualization (4b239bb)
• feat(F24): complete M6 testing milestone - all EventOverlay tests verified (07e6392)
• feat(F24): implement HTML backend event overlay rendering (M4) (20d4ef6)
• feat(F24): implement matplotlib event overlay rendering (M3) (d37eb2f)
• feat(F24): implement napari backend for EventOverlay (M2) (f1c3d07)
• feat(F24): implement EventOverlay core data structures (M1) (afa5a43)
• feat(M5.2): implement DecodingResult visualization methods (fe1a97e)
• feat(M5.1): finalize public API exports (6298bbf)
• feat(decoding): implement significance testing functions (Milestone 4.5) (a66ea07)
• feat(decoding): implement Poisson surrogate generation (Milestone 4.4) (1fa6c19)
• feat(decoding): implement posterior shuffles (Milestone 4.3) (799095b)
• feat(decoding): implement cell identity shuffles (Milestone 4.2) (8caeb61)
• feat(decoding): implement core temporal shuffles (Milestone 4.1) (8d870cb)
• feat(decoding): implement detect_trajectory_radon (Milestone 3.4) (465e749)
• feat(decoding): implement fit_linear_trajectory (Milestone 3.3) (aa3d105)
• feat(decoding): implement fit_isotonic_trajectory (Milestone 3.2) (732c4e3)
• feat(decoding): implement trajectory result dataclasses (Milestone 3.1) (2dc27d3)
• feat(decoding): implement decoding_correlation (Milestone 2.3) (0aa884f)
• feat(decoding): implement confusion_matrix (Milestone 2.2) (364fa8e)
• feat(decoding): implement error metrics (Milestone 2.1) (3a01e7b)
• feat(decoding): implement estimate functions (Milestone 1.5) (7375e6d)
• feat(decoding): implement posterior normalization (Milestone 1.4) (4c9e27d)
• feat(decoding): implement likelihood functions (Milestone 1.3) (e645fbe)
• feat(decoding): implement DecodingResult container (Milestone 1.2) (3fa9ac3)
• feat(decoding): add decoding subpackage structure (Milestone 1.1) (9eacfe3)
• feat(M4): export helper functions from animation module (Task 4.3) (985f750)
• feat(M4): add large_session_napari_config helper (Task 4.2) (f2b2f17)
• feat(M4): add estimate_colormap_range_from_subset helper (Task 4.1) (6e97d70)
• feat(M3): disable multiscale pyramids in napari viewer (Task 3.3) (48d0d04)
• feat(M3): add large dataset warning and subsampling for colormap range (Task 3.2) (332ab7f)
• feat(M3): add streaming path to compute_global_colormap_range (Task 3.1) (e204029)
• feat(M2): add benchmark comparing LazyFieldRenderer vs Dask (Task 2.6) (3f86107)
• feat(M2): add array input support to lazy field renderers (Tasks 2.2-2.4) (a8b844b)
• feat(M2): add array input support to render_napari (Task 2.1) (1d5352c)
• feat(animation): preserve array format for napari backend (Milestone 1) (ea81920)
• feat(exports): add ScaleBarConfig to public API (M4) (91b075a)
• feat(animation): add scale_bar parameter to all backends (M3) (7a42cd7)
• feat(visualization): add scale bar support for static plots (M1-M2) (c226be5)
• feat(exports): add directional place fields to public API (Tasks 4.1-4.3) (44dec0e)
• feat(metrics): add directional_field_index function (Task 3.1) (653cdf7)
• feat(behavioral): add heading_direction_labels function (Task 2.2) (b1b9b97)
• feat(behavioral): add goal_pair_direction_labels function (Task 2.1) (42b4a69)
• feat(spike_field): add compute_directional_place_fields function (Task 1.3) (f7b0a6f)
• feat(spike_field): add _subset_spikes_by_time_mask helper (Task 1.2) (672e2f2)
• feat(spike_field): add DirectionalPlaceFields dataclass (Task 1.1) (a33f4af)
• feat(annotation): implement 1D preview for track graph (Task 4.2) (331a2bf)
• feat(annotation): implement edge order editing UI (Task 4.1) (e237764)
• feat(annotation): add Task 3.3 - module exports for track graph (7fada5b)
• feat(annotation): implement Task 3.2 - annotate_track_graph entry point (ab7bfb0)
• feat(annotation): implement Task 3.1 - TrackGraphResult in track_graph.py (a2a4815)
• feat(annotation): implement Task 2.3 - create control widget for track graph (04f3a34)
• feat(annotation): implement Task 2.2 - event handlers for track widget (465d105)
• feat(annotation): implement Task 2.1 - create layer setup for track graph (c61f0ea)
• feat(annotation): complete Task 1.4 - unit tests for state management (dd8810c)
• feat(annotation): implement graph building helpers for track annotation (8031b54)
• feat(annotation): implement TrackBuilderState for track graph annotation (55af604)
• feat(annotation): add TrackGraphMode type definition (2820f6b)
• feat(mazes): implement T-Maze (Milestone 2.2) (89e9259)
• feat(mazes): implement Linear Track maze (Milestone 2.1) (691d7e5)
• feat(mazes): implement Milestone 1 - foundation for simulation mazes (e55b701)
• feat(M4-M7): complete boundary seeding feature (3df9890)
• feat(M3): wire boundary seeding into annotate_video() (f307b65)
• feat(M2): add napari integration for boundary seeding (3f7c6f0)
• feat(annotation): add boundary inference from position data (M1) (09ad454)
• feat(behavioral): implement graph_turn_sequence for turn classification (b3cb24c)
• feat(behavioral): implement cost_to_goal with cost maps and terrain difficulty (8a27bc2)
• feat(behavioral): implement compute_trajectory_curvature with smoothing (1624063)
• feat(behavioral): implement time_to_goal with temporal countdown (d6a27b7)
• feat(behavioral): implement distance_to_region for scalar and dynamic targets (69a0289)
• feat(behavioral): implement path_progress with geodesic/euclidean metrics (e3ab9ea)
• feat(behavioral): implement trials_to_region_arrays helper (0de2c87)
• feat(api): export segmentation functions to public API (a738b5e)
• feat(M3): extend write_laps() with region columns (1a91141)
• feat(M2): add write_trials() and read_trials() NWB functions (91f54e5)
• feat(M1): add start_region field to Trial, rename outcome to end_region (3bf40e2)
• feat(nwb): add 1D GraphLayout round-trip support and preserve is_1d property (66c8c14)
• feat(nwb): implement read_environment() for NWB round-trip (M3.2.1) (81cc8f2)
• feat(nwb): implement write_environment() for saving Environment to NWB scratch (M3.1.1) (8b9420b)
• feat(nwb): implement write_region_crossings() for saving region crossing events (M2.2.2) (7f3d585)
• feat(nwb): implement write_laps() for saving lap events (M2.2.1) (99d6d61)
• feat(nwb): implement write_occupancy() for saving occupancy maps (M2.1.2) (77dc16c)
• feat(nwb): implement write_place_field() for saving spatial fields (M2.1.1) (73cab07)
• feat(nwb): implement environment_from_position() factory function (M1.4.4) (68a2d99)
• feat(nwb): implement head_direction_overlay_from_nwb() factory function (M1.4.3) (f0af9f0)
• feat(nwb): implement bodypart_overlay_from_nwb() factory function (M1.4.2) (78c80e3)
• feat(nwb): implement position_overlay_from_nwb() factory function (M1.4.1) (05a0e57)
• feat(nwb): implement read_intervals() function (M1.3.2) (73cf6e6)
• feat(nwb): implement read_events() function (M1.3.1) (152bf51)
• feat(nwb): implement read_pose() function (M1.2.1) (c3caab5)
• feat(nwb): implement read_head_direction() function (M1.1.3) (9ada46d)
• feat(nwb): implement read_position() function (M1.1.2) (10e3d8e)
• feat(nwb): add NWB integration module structure (M0.1) (5ac9f92)
• feat(annotation): improve widget UX and add validation (649994a)
• feat(annotation): export annotation API from main package (dd565eb)
• feat(annotation): add napari widget and core annotation entry point (43e7688)
• feat(annotation): add IO module for LabelMe/CVAT import (ff749d3)
• feat(annotation): implement converters module with TDD (6b7ac0f)
• feat(8.5): add VideoReaderProtocol for type safety (dd54f96)
• feat(6.3): add video overlay backend integration tests (9727d7f)
• feat(6.2): add video fixture utilities for testing (a0e87d8)
• feat(6.1): add calibration edge case tests and ill-conditioned landmark check (b304a75)
• feat(5.1): add calibrate_video() convenience function (1b4a38e)
• feat(4.3): add widget and HTML backend video overlay support (5a68b7d)
• feat(4.2): add video export backend support for video overlays (37773af)
• feat(4.1): add napari video layer rendering support (ba65888)
• feat(3.2): add pipeline integration for VideoOverlay (8f40fbf)
• feat(3.1): add VideoReader class with LRU caching (b79c257)
• feat(2.2): add VideoData internal container (59c7dca)
• feat(2.1): add VideoOverlay dataclass (6d1cfa5)
• feat(1.2): add VideoCalibration dataclass (a9edcfb)
• feat(1.1): add video calibration helpers (f189618)
• feat(I.2-I.6): complete M0 integration pre-requisites for VideoOverlay (34a1c93)
• feat(P6.2): add adjacency property to Skeleton for graph traversal (6908667)
• feat(P6.1): add skeleton edge canonicalization and deduplication (f4ea368)
• feat(P5.3): add DPI warning for video export (b1bb9d1)
• feat(P4.3): add optional JPEG image format support to widget backend (5a6834a)
• feat(P4.1): fix widget set_array optimization and add fallback diagnostics (d5aa081)
• feat(P3): complete Phase 3 - Overlay Conversion & Core Orchestration (f48a075)
• docs(P2.3): verify tracks color_by workaround is correct for napari 0.5.6 (ad6ca4b)
• feat(P2.2): add per-viewer transform fallback warning tracking (6ec55a9)
• feat(P1.2): add layout_type and is_grid_compatible properties to layouts (376708a)
• feat(P1.1): centralize coordinate transforms in shared module (dec6581)
• feat(P0.3): add benchmark scripts and record baseline metrics (70c0994)
• feat(P0.2): add benchmark dataset generators for animation performance testing (dd82407)
• feat(P0.1): add timing instrumentation for animation backends (d21a2b0)
• feat(M2): replace Shapes-based skeleton with precomputed Vectors layer (4fc1773)
• feat(napari): add _build_skeleton_vectors for precomputed skeleton rendering (7482c05)
• feat(M7.4): complete CLAUDE.md updates and address code review feedback (5ba933c)
• feat(M7.3): create comprehensive overlay example notebook (2675b56)
• feat(M7.2): add overlay examples to animate_fields() docstring (3f04a99)
• feat(M7.1): add comprehensive overlay API documentation (bb231c8)
• feat(M6.3): add backend capability matrix tests (b88e2ec)
• feat(animation): add visual regression tests for overlay rendering (M6.2) (4deec69)
• feat(animation): add comprehensive integration tests for overlay system (M6.1) (ae8d0fb)
• feat(animation): implement widget backend overlay rendering (M5.3) (b57db14)
• feat(animation): implement HTML overlay size guardrails (M5.2) (0b94364)
• feat(animation): implement HTML backend overlay rendering (M5.1) (17f2d89)
• feat(animation): implement video overlay optimization and performance tests (M4.3, M4.5) (fdeaf40)
• feat(animation): add pickle-ability validation for parallel video rendering (M4.2) (0693e5c)
• feat(animation): implement video backend overlay rendering (M4.1) (5775939)
• feat(animation): add napari performance benchmarks (M3.6) (f50ea35)
• feat(animation): implement napari overlay rendering (M3.1) (349f886)
• feat(animation): integrate overlay system into core dispatcher (M2.2) (99a7616)
• feat(animation): update animate_fields() signature for overlay support (dede6d4)
• feat(animation): implement conversion funnel for overlay data alignment (f1633a3)
• feat(animation): implement validation functions with WHAT/WHY/HOW error messages (6b9b37c)
• feat(animation): add multi-field viewer support for Napari (2fafc13)
• feat(napari): improve UX with larger slider and spacebar playback (3b07b7f)
• feat(napari): add interactive playback speed slider widget (95fb53f)
• feat(napari): add playback controls - start at frame 0 and configure FPS (b74ef30)
• feat(M6): integrate animate_fields() method into Environment class (58692db)
• feat(M5): implement Jupyter widget backend with interactive controls (6c0c2d8)
• feat(M4): implement napari GPU-accelerated backend with LRU caching (b9740cf)
• feat(M3): add -r and -threads ffmpeg flags from original gist (7f361cc)
• feat(M3): implement parallel video backend with ffmpeg (7b8af5d)
• feat(animation): implement core dispatcher and backend stubs (626679c)
• feat(animation): add optional dependencies for animation backends (111f052)
• feat(animation): implement HTML backend with embedded player (M2) (9c3fa5a)
• feat(animation): implement rendering utilities for multi-backend animation (d801f41)
• feat(M3.2): rename map_probabilities_to_nearest_target_bin() to map_probabilities() (a555454)
• feat(M2.1): rename shortest_path() to path_between() (83ad2d9)
• feat(M1.3): add env.apply_transform() method (5a92d4b)
• feat(M1.2): add env.region_mask() method (3aafe6e)
• feat(M1.1): add selective clearing to env.clear_cache() (5f0f931)
• feat(M4): implement EnvironmentNotFittedError custom exception (Tasks 4.6-4.8) (22cdf15)
• feat(M4): add PathLike type alias and comprehensive pathlib tests (Task 4.1) (c4647b9)
• feat(M2): implement scipy connected components (Task 2.8-2.12) - 6.16x speedup (3b7abfa)
• feat(M2): add comprehensive cache management system (Task 2.11) (90940b7)
• feat(M2): standardize scale parameter naming across transforms and alignment (Task 2.10) (d969611)
• feat(api): fix import inconsistencies and add comprehensive tests (56286f9)
• feat(docs): replace T-maze with 2D Shapely polygon in notebook 11 (a6ba6f3)
• feat(docs): add place field shift measurement examples to notebook 11 (28e2a57)
• feat(M3): implement grid_cell_session() with 18 tests (feecbfa)
• feat(M3): implement boundary_cell_session() with mixed cell types (03033b9)
• feat(M3): implement tmaze_alternation_session() with trial metadata (5e1d9d1)
• feat(M3): implement linear_track_session() convenience function (5f07f92)
• feat(M3): implement open_field_session() convenience function (9edc3c4)
• feat(M3): implement plot_session_summary() visualization (b947396)
• feat(M3): implement validate_simulation() validation helper (1908357)
• feat(M3): implement simulate_session() convenience function (e28045e)
• feat(M3): implement SimulationSession dataclass (017cd79)
• feat(M3): implement GridCellModel with hexagonal firing pattern (5504ff2)
• feat(M2): implement add_modulation() with parameter validation (5b90bc5)
• feat(M2): implement BoundaryCellModel with TDD (8558b68)
• feat(simulation): implement simulate_trajectory_laps (6024dcc)
• feat(simulation): complete Milestone 1 - core simulation framework (ad96365)
• feat(visualization): add plot_field() method for spatial field visualization (3fa792b)
• feat(spike_field): implement unified place field API with diffusion KDE default (82ad0ba)
• feat(M4.6): add behavioral segmentation example notebook (7547f9a)
• feat(M4.6): add trajectory analysis example notebook (2049764)
• feat(M4.4): implement trial segmentation for behavioral tasks (cb9740b)
• feat(M4.2): implement region-based segmentation (b4e482f)
• feat(M4.1): implement trajectory characterization metrics (4fcd3fa)
• feat(M3.3): implement border_score for boundary cell analysis (9f17b69)
• feat(M3.2): implement population-level place field metrics (3bed01b)
• feat(M3.1): implement place field detection and spatial metrics (9f1083e)
• feat(M2.2): implement convolve() spatial convolution primitive (7364cf7)
• feat(M2.1): implement neighbor_reduce() spatial signal processing primitive (136c004)
• feat(M1.3): implement divergence operator and rename KL divergence (a255207)
• feat(M1.2): implement gradient operator (1051dc7)
• feat(M1.1): implement differential operator infrastructure (4e2be9f)
• feat(M0.3): add comprehensive example notebook for Phase 0 primitives (d515e89)
• feat(M0.2): add reward field primitives for RL applications (ad87427)
• feat: add spike-to-field conversion and occupancy options (69e9106)
• feat(M11): complete comprehensive testing and verification (94c1a89)
• feat(M10): create package init and extract remaining methods (7b18695)
• feat(M9): create core module with mixin inheritance (519b40e)
• feat(M8): extract factory methods to mixin (237aa54)
• feat(M4): extract analysis methods to mixin (bf8baf7)
• feat(M6): extract serialization methods to mixin (bd3a18b)
• feat(M5): extract region methods to mixin (3938948)
• feat(M3): extract visualization methods to mixin (5581cfd)
• feat(M2): extract check_fitted decorator (ff34c31)
• feat(M1): complete Milestone 1 - Preparation (5a4c187)

Bug Fixes

• test(encoding): act on four-agent PR review of d864b6d (cb25580)
• fix(M5.8): preserve None vs '' distinction in Environment.repr; add str (9a1709c)
• fix(M4.5): set env.units in HeadDirectionCellModel doctest + numpy bool wrap (63ed531)
• fix(M4.5): add speed_units to remaining source-file doctests (1d7dc22)
• fix(M4): repair user-facing docs/examples broken by M4.5 + finish M4.1, M4.3 (ad1ef4d)
• fix(M3): finish four reviewer-flagged gaps (616c186)
• fix(M2.D): align remaining distance_to_reward call sites with current signature (14f6256)
• fix(M2.D): repoint Bayesian decoding examples + docs to canonical stats imports (1f01755)
• fix(M2): README CI snippet + batch wrappers reject bad API params (22736ac)
• fix(M2): drop dedup= from bin_sequence_with_runs; bins shape is per-run (0795927)
• fix(M2): bin_sequence dedup is gap-blind; tighten test naming + stale docs (408b8f8)
• fix(M2): tighten bin_sequence_with_runs gap semantics + batch_grid_scores irregular-env contract (7b5f54b)
• docs(M2): close M2.A/M2.B review-response findings (9 items) (f5ad3bf)
• fix(M1): match plain-ndarray copy=False semantics in BatchScoresResult (cd02b24)
• fix(M1): close remaining review-response findings (4 items) (6ead6a5)
• fix(M1): bundle review-response findings (10 items) (312b7a5)
• fix(environment): rewrite Environment.subset() to return a MaskedGrid for grid envs (M1 1.1) (3f93811)
• fix(environment): align Environment.occupancy with bin_sequence on out-of-env samples (M1 1.2) (2e3dfed)
• fix(decoding): reject zero-mass and array-like priors at validate=True boundary (M1 1.8 second follow-up) (c6745f2)
• fix(decoding): tighten decode_position validation per review (M1 1.8 follow-up) (85bf631)
• docs(examples): rewrite examples/README and place notebook 21 in canonical home (M0 0.6, 0.7) (76a236d)
• fix(encoding): enable JAX x64 in production; gate JAX tests on the optional extra (055ba08)
• fix(encoding): three more review findings (precision, validation, test unpack) (23614c0)
• fix(encoding): address review findings on M3, M4 and M2.5 (cf7ce0a)
• fix(encoding): make _backend.py doctests platform-independent (63cef8a)
• fix(M8): enforce monotonic time validation in single-neuron binning (91bf041)
• fix(M8): handle NaN in egocentric nearest-object selection (c50c947)
• fix(test): update segment_trials parameter validation test (8b71f9f)
• fix(M6): skip JAX dispatch for binned smoothing method (ea92811)
• fix(M6): add backend validation to compute_spatial_rate(s) (Task 6.4 follow-up) (5a1c547)
• fix(M6): add backend validation to compute_spatial_rate(s) (Task 6.4 follow-up) (322ad00)
• fix(encoding): add time validation parity and fix docs (95f1946)
• fix(encoding): complete remaining code review fixes (0cd005d)
• fix(encoding): correct view occupancy calculation and add validation (b0ce142)
• fix(M3): address code review findings for directional encoding (cbf1001)
• fix(M0): change head_direction.py angle_unit default from deg to rad (dcdeb91)
• fix(phase6.2): add QTimer for automatic debounce trailing-edge flush (89b85ac)
• fix(tests): add missing random seeds to prevent flaky tests (dec0588)
• fix(behavioral): fix test fixture and test assertion (a7259cd)
• fix(nwb): address code review feedback and add timestamps parameter (1762302)
• fix(annotation): deselect shape after naming using processEvents (631ecd4)
• fix(annotation): deselect shape after Enter with QTimer delay (79dbe56)
• fix(annotation): clear selection after applying name with Enter (76ec8fb)
• fix(annotation): address code and UX review feedback (c0d32a6)
• fix(8.1): add warning for VideoOverlay interp='linear' not implemented (d930e81)
• fix(4.1): add video frame update callback for scrubbing (bd1798c)
• fix(4.1): get VideoReader dimensions for affine transform (2048ff3)
• fix(4.1): use VideoReader subscript access in VideoData.get_frame() (7a4f287)
• fix(P5.2): control ffmpeg I/O to avoid buffer issues (33dc134)
• fix(P4.2): fix skeleton initialization IndexError and add overlay artist tests (349a12a)
• fix(P2.4): only throttle frame info updates during playback (0f19282)
• fix(napari): use line style for skeleton vectors (hide arrow heads) (3e3ec4e)
• fix(napari): use [position, direction] format for skeleton vectors (e6e87ca)
• fix(animation): map overlay coordinates to pixel indices for napari (d02406f)
• fix(animation): invert Y-axis for napari image coordinate system (439347c)
• fix(animation): transpose RGB image for napari (y, x) convention (6bf6dc6)
• fix(animation): correct napari add_tracks API usage for position overlays (37f697e)
• fix(tests): reduce memory safety test grid size to prevent CI timeout (dd6df73)
• fix(ci): sync mypy configuration between pre-commit and CI (970a358)
• fix(tests): prevent Qt crashes in napari tests with xdist_group (b6cd89a)
• fix(napari): use correct API for spacebar playback toggle (9a82171)
• fix(napari): fix deprecation warnings and notebook blocking issues (5fe723e)
• fix(napari): ensure only time slider visible, improve control docs (f57e9c6)
• fix(napari): remove contrast_limits for RGB images (c7fae05)
• fix(examples): add napari.run() to block and keep windows open (fc296f1)
• fix(napari): add ndim property and tuple indexing support to LazyFieldRenderer (9fe2606)
• fix(M2): remove incorrect type annotations from SubsetLayout (Task 2.8) (b4f9918)
• fix(regions): prevent metadata mutation with deep copy (f74e6e7)
• fix(hexagonal): improve numerical stability with MIN_HEX_RADIUS validation (d0ccbf4)
• fix(trajectory): improve numerical stability with named EPSILON constant (d320438)
• fix(security): prevent path traversal attacks in io.py (5a8cd24)
• fix(docs): simplify T-maze to clean T shape with uniform corridors (3a1588b)
• fix(docs): connect T-maze arms to form continuous horizontal bar (50c84ca)
• fix(docs): sync examples/11_place_field_analysis with Part 9 additions (00c1588)
• fix(viz): fix grey checkerboard artifacts in grid field visualizations (555beb7)
• fix(docs): fix f-string-missing-placeholders in 08_spike_field_basics.ipynb (12afc63)
• fix(docs): fix CI failures - formatting and broken links (3038cf0)
• fix: remove unused variables instead of prefixing with underscore (a178917)
• fix(M3.5): increase duration to 100s in notebook 08 for better coverage (bb1f93d)
• fix(M3.5): improve 2D exploration in 08_spike_field_basics.ipynb (a25d090)
• fix(examples): update notebooks 11 and 12 with corrected OU parameters (49fd1e0)
• fix(simulation): correct OU process sigma formula to match RatInABox (6edfda1)
• fix(M3.5): correct ground_truth access in 11_place_field_analysis.ipynb (2d2e75d)
• fix(visualization): address code review improvements for plot_field() (013a9db)
• fix: resolve linting errors in example scripts (8b3e5a0)
• fix(M4.6): correct trajectory/times length mismatch in behavioral segmentation notebook (edde6fc)
• fix(M3.1): remove internal min peak rate filter (ceea9aa)
• fix(M1.4): correct Laplacian verification to use weighted NetworkX comparison (4b7a312)

Documentation

• docs(examples): finish M7.4 — wire _style.py into notebooks 01-23 (52e2044)
• docs: act on ux-reviewer findings on PR #2 (1c800eb)
• docs(encoding): fix dangling See-Also in object_vector_score (25285ec)
• docs(M6,M7): act on suggestion-tier PR review findings (abe6de9)
• docs(M6,M7): act on three-agent PR review of b30e9e1 (b430e2b)
• docs(M6): add notebooks 24-27 (OVC, HD, PSTH, NWB) (6757eff)
• docs(M6.11): add Prerequisites lines + convert bold notebook refs to MD links (1f5d7fc)
• docs(M6): land M6.5–M6.10 and M6.12 — docs infrastructure + bandit skip (9f99d94)
• docs(M5): correct differential-operator docstrings + composite parity claim (1609cc2)
• docs(M5): close reviewer-flagged gaps (0b848e3)
• docs(M5.4): add T-maze, plus-maze, and linear-track examples to from_graph (3258d56)
• docs(M4.3): document heading-convention on every public heading consumer (7a211da)
• docs(M2.C): add directional-exception note to compute_directional_rates (9d467af)
• docs(M2): fix border_score arg order in stale public docs (81b2a2d)
• docs(M2): close M2.A/M2.B review-response findings (9 items) (f5ad3bf)
• docs(M1): close out doc drift left by review-response bundle (62b837d)
• docs(plan): mark M1 1.1, 1.2, 1.3 complete in TASKS.md (1e58b0b)
• docs(plan): mark M1 1.4 and 1.5 complete in TASKS.md (1d21413)
• docs(plan): mark M1 1.6/1.7/1.8 complete in TASKS.md (6423a8b)
• docs/ci: address second-pass review (multi-line +SKIP, README placeholder snippet) (bf44732)
• docs/ci: address M0 code-review findings (H1-H3, I1, I3, I4, M2, M4) (5bedcab)
• docs(plan): mark M0 tasks complete in TASKS.md (0c523ee)
• ci: add curated doc-snippet smoke test (M0 0.10) (b9a4df8)
• docs/examples: regenerate notebook 15/20 outputs, fix QUICKSTART bin_at example (M0 0.3 follow-up, 0.8) (842e8c6)
• docs(examples): rewrite examples/README and place notebook 21 in canonical home (M0 0.6, 0.7) (76a236d)
• docs: fix broken first-run snippets in README, QUICKSTART, package docstring (M0 0.1-0.5) (a30dc4e)
• docs(plan): add v0.4 UX cleanup plan, tasks, and source review (98831fc)
• test: fix Python-3.10/11/12 docstring tests and Windows test failures (84e64a4)
• docs: align README, CLAUDE.md, and QUICKSTART with current encoding API (e0b5e9e)
• docs/tests: clean up post-deletion legacy references (2055987)
• docs(M6): add legacy parity tests as xfail; record M6 hold in plan (e452f45)
• docs: update SCRATCHPAD.md with Milestone 7 completion notes (19296b1)
• docs(M7): mark Task 7.6 complete (full test suite passes) (9446be9)
• docs(M7): update QUICKSTART.md with new encoding API (8ac2bc1)
• docs(M7): update documentation with new encoding API (730d9e7)
• docs(M7): update example notebooks to new encoding API (99e1f73)
• docs(M7): mark Task 7.2 migration subtasks as complete (ac4a22e)
• docs(M6): mark Task 6.6 complete - JAX-specific tests verified (5d058e7)
• docs(M6): skip Task 6.3 - JAX grid/border score not feasible (a57d103)
• docs(M4): verify comprehensive test coverage for view encoding (Task 4.9) (63e449f)
• docs: update TASKS.md and SCRATCHPAD.md for Task 4.2 completion (56592c7)
• docs(encoding): mark Task 2.10 and Milestone 2 as complete (8213a97)
• docs(M14): complete final verification for package reorganization (dae73e2)
• docs: add doctest skip annotations and fix docstring examples (59dfe73)
• docs(M12): mark milestone 12 complete (b617308)
• docs(M12): update remaining notebooks with new import paths (e008efc)
• docs(M12): update example notebooks with new import paths (9db19a7)
• docs(M11): mark milestone 11 complete (cddaa17)
• docs(M11): update import paths in documentation and docstrings (f07d097)
• docs: update TASKS.md and SCRATCHPAD.md for Milestone 10 (db0e194)
• docs(M2): mark all Milestone 2 tasks as complete (45e5f6e)
• docs(M2): update progress for transforms.py migration (7c791a3)
• docs(M3.6): complete spatial view cells integration and documentation (65c2001)
• docs(M3.5): verify all spatial view cell tests passing (f1f0d0b)
• docs(M1.5): add egocentric reference frames documentation (784ec6c)
• docs: add circular basis functions to QUICKSTART and API_REFERENCE (41878df)
• docs(M7): add basis functions to QUICKSTART and API_REFERENCE (24b76eb)
• docs(M5.6): enhance circular basis docs with multi-domain examples (72dcf0a)
• docs(profiling): add napari performance profiling guide (a99437a)
• docs(M8): update CLAUDE.md with speed-based animation API (bbb1adb)
• docs: update TASKS.md to reflect actual completion status from code inspection (224f369)
• docs(M4): update Environment.animate_fields() signature and docstring (e026aa0)
• docs: mark Milestone 3 tasks complete in TASKS.md (40a1fac)
• docs: update SCRATCHPAD with Milestone 1 & 2 completion status (2a9d9f6)
• docs(animation): add TimeSeriesOverlay documentation to CLAUDE.md (30e7c89)
• docs(decoding): add animate_fields guidance to plot() docstring (3abad65)
• docs(M6/M7): complete example scripts & documentation updates (72144d0)
• docs: mark Milestone 4 as complete in TASKS.md (f6906ba)
• docs(scale_bar): add scale bar examples to CLAUDE.md (M6) (1a4eec7)
• docs: add directional place fields example and CLAUDE.md reference (Tasks 6.1-6.2) (77239db)
• docs(Task 4.4): add docstrings and See Also sections (e33e5a5)
• docs(Task 4.3): add track graph annotation to CLAUDE.md (f8754cc)
• docs: mark M5.4 complete - all code quality checks pass (1807d2f)
• docs: update progress tracking for M5.3.1 completion (60b82df)
• docs(behavioral): update CLAUDE.md with v0.8.0 features (c109df1)
• docs: update SCRATCHPAD with review completion status (4232228)
• docs(behavioral): address code and UX review feedback (6b2dfc4)
• docs(behavioral): update TASKS.md - M4.2 complete (e4eda24)
• docs(behavioral): update TASKS.md - M4.1 complete (acd9ab1)
• docs: update TASKS.md - M3.2 complete (2ded57e)
• docs: update TASKS.md - M1.1 complete (e805291)
• docs(animation): fix griffe warning in OverlayProtocol docstring (9e6ebfe)
• docs(M5): update documentation for Trial.end_region field (fdb4e06)
• docs(nwb): complete M4.4 final verification - all milestones done (a9d76f8)
• docs(annotation): mark verification checklist complete and update scratchpad (b510d7b)
• docs(annotation): add annotation feature to CLAUDE.md (8b40c20)
• docs: update tracking files with final verification status (c18d666)
• docs: fix calibrate_from_landmarks parameter names in CLAUDE.md (a4622a0)
• docs(8.8): improve animate_fields docstring with multi-field mode (d9d726c)
• docs(8.6): document overlay JSON schema for HTML backend (6d2f7fc)
• docs(8.4): document coordinate conventions for video overlay (c7b70ea)
• docs(7.3): update animation guide with VideoOverlay documentation (aa3e71b)
• docs(7.2): create video overlay example notebook (4ce0981)
• docs(7.1): update CLAUDE.md with VideoOverlay documentation (f9388f3)
• docs(4.1): mark napari backend task complete (6392d7f)
• docs(UX): improve error messages and documentation consistency (37a9a8b)
• docs(P7.3): add backend selection guide and Skeleton class documentation (87ec8c6)
• docs(P7.1): verify unit tests already exist and pass (a103be1)
• docs(P5.4): complete video re-profiling - no performance regression (d880416)
• docs(P4.4): complete widget re-profiling - 1.8-2.2x speedup verified (27c5dad)
• docs(P2.5): re-profile napari - document 42-50x skeleton speedup (fc9681c)
• docs(P2.3): verify tracks color_by workaround is correct for napari 0.5.6 (ad6ca4b)
• docs(P1.3): verify no regressions after Phase 1 changes (340f486)
• docs: exclude research directory from build to fix CI (23120dd)
• docs(animation): fix broken links and add to navigation (86f3944)
• docs: mark code review complete in TASKS.md (f5d9269)
• docs: mark docstring review complete in TASKS.md (89cb31a)
• docs(animation): convert backend docstring examples to code-block format (c9c2da1)
• docs: add Session 25b docstring review progress (da0b3de)
• docs(animation): fix docstring examples to follow NumPy format (ee81505)
• docs: mark Error Message Review tasks complete in TASKS.md (623d663)
• docs(animation): add Session 25 error message review summary (d09cf0d)
• docs(animation): document subsample memory behavior investigation (dd2e611)
• docs(animation): update benchmark results with larger sample sizes (cd1ba2f)
• docs(animation): verify error message tests complete (824aa66)
• docs: add Session 19 notes for documentation enhancements (a5d901e)
• docs(napari): update render_napari docstring with multi-field features (02c6cfd)
• docs(animation): add multi-field viewer example and enhance documentation (d82b60a)
• docs(animation): update README with animation feature (6b4dc96)
• docs(animation): create comprehensive user guide (aa6e40e)
• docs(animation): update CLAUDE.md with animation documentation (57fe991)
• docs: add Milestone 7.5 (Enhanced Napari UX) to planning documents (dafdefc)
• docs(napari): correct playback control documentation (8a44a99)
• docs: mark milestones 1 and 2 complete and add HTML demo (fb93742)
• docs: update scratchpad with milestone 1 completion status (a68b975)
• docs: add notebook update steps to Milestone 3 tasks (5bb614d)
• docs: mark Milestone 2.2 as skipped (344d050)
• docs(M4): mark pathlib tasks 4.2-4.5 complete - already implemented (4dfa1b5)
• docs(M3): update task tracking - keep dual API decision (6e077db)
• docs(M3): clarify bin_at() vs map_points_to_bins() semantics (1aec606)
• docs(M2): update SCRATCHPAD with Tasks 2.8-2.12 completion (65d75bd)
• docs(M2): Task 2.7 complete - Connected Components investigation (09d574c)
• docs(M2): Document NetworkX incidence_matrix investigation (a6acf08)
• docs(M2): Task 2.4 complete - Laplacian investigation (KEEP CURRENT) (576c3ec)
• docs(M2): add scipy investigation report for Task 2.1 (b0dcfab)
• docs(M1): complete coverage audit for distance.py (Task 1.1) (aaf2d91)
• docs(M2): add comprehensive module-level docstring to init.py (Task 2.9) (92900c5)
• docs: mark Task 2.2 as completed in TASKS.md (22850fd)
• docs: mark Task 1.8 as completed in TASKS.md (500d2d9)
• docs: update task tracking for completed task 1.5 (93d1f71)
• docs: mark Task 1.4 as completed in TASKS.md (76c061b)
• docs: update task tracking for completed task 1.1 (3bbb7c5)
• fix(docs): sync examples/11_place_field_analysis with Part 9 additions (00c1588)
• docs: add learning objectives to notebooks 9-15 for pedagogical consistency (c27c53f)
• docs(M3.5): complete comprehensive pedagogical validation of notebook suite (99df3e0)
• docs(M3.5): complete validation of simulation notebooks and code quality (6879644)
• docs(M3.5): add simulation subpackage section to API reference (fec0bb0)
• docs(M3.5): add comprehensive Simulation section to README.md (fe81421)
• docs(M3.5): verify all documentation links work correctly (5c19ceb)
• docs(M3.5): update mkdocs config and examples index for all 15 notebooks (9cdf9db)
• docs(M3.5): sync all notebooks from examples/ to docs/examples/ (b5ca267)
• docs: document notebook 08 coverage investigation and 100s duration fix (007049b)
• docs: document OU process critical bug fix in SCRATCHPAD (455fc91)
• docs(M3.5): create comprehensive simulation workflows tutorial notebook (7565e7f)
• docs(M3.5): update 12_boundary_cell_analysis.ipynb to use simulation subpackage (fdcdee4)
• docs(M3.5): update 08_spike_field_basics.ipynb to use simulation subpackage (43eed0e)
• docs: update SCRATCHPAD.md with notebook execution verification (12e83d0)
• docs(M3.5): update 11_place_field_analysis.ipynb to use simulation subpackage (624304b)
• docs(M3): update SCRATCHPAD and TASKS for SimulationSession completion (b193f45)
• docs(M2): complete Milestone 2 documentation and validation (f19132b)
• docs: update SCRATCHPAD.md to reflect Milestone 1 completion (bac5f1d)
• docs: fix broken API reference links (faedcb6)
• docs(M4.6): add comprehensive trajectory and behavioral analysis user guide (c9b20e5)
• docs(M3.4): add boundary cell analysis notebook (c0a8858)
• docs(M3.4): add place field analysis notebook (9fb4040)
• docs(M3.4): add comprehensive neuroscience metrics documentation (ddec7bb)
• docs(M2.3): add comprehensive signal processing primitives documentation (0c21a1d)
• docs: document Laplacian verification bug fix in SCRATCHPAD (6ad54d0)
• docs(M1.4): add comprehensive differential operators documentation and examples (40e99df)
• docs(M0): mark all Milestone 0 success criteria complete (e5425b1)
• docs(M0.3): fix plotting errors and enable notebook execution (1fd85d6)
• docs(M0.3): add comprehensive user guides for Phase 0 primitives (2e609f2)
• docs: update README for v0.2.0 release (826d5ad)
• docs: update CHANGELOG.md for v0.2.0 (580b8eb)

Other Changes

• test(animation): skip PlaybackController tests when no Qt binding present (c7c2808)
• chore(release): prep v0.4.0 (CHANGELOG, version bump, _style, smoke) (b30e9e1)
• test(encoding): act on four-agent PR review of d864b6d (cb25580)
• test(encoding): simplify backend dispatch tests (review fixes) (d864b6d)
• test(encoding): close three reviewer findings on JAX guards and plot ax assertions (cont.) (15cd7bd)
• test(encoding): JAX-skip the remaining unguarded test + assert array type + cover backend="auto" (019fab0)
• test(encoding): close three reviewer findings on JAX guards and plot ax assertions (5700c26)
• test: address remaining best-practice gaps (test-order, weak tests, properties) (80e95cf)
• test(environment,nwb,simulation): strip env-attr / setup-recheck / docstring-only tests (batch 21) (27729a6)
• test(animation,visualization,regions): trim weak/mocked/setup-recheck tests (batch 20) (8ead868)
• test(encoding): strip import/dataclass/dtype tautologies across 7 files (batch 19) (f77bf87)
• test(ops): strip meta-tests on module exports and dataclass field echoes (batch 18) (d543926)
• test(segmentation): strip parameter-order tautologies (batch 17) (600c4ec)
• test(behavior): strip dataclass / summary-string / one-line-method tests (batch 16) (99f19f3)
• test(events): strip setup re-checks and return-type tautologies (batch 15) (910382a)
• test(decoding): strip return-type tautologies and success-criteria scaffolding (batch 14) (084d062)
• test(decoding): strip 34 copy-paste shuffle boilerplate methods (batch 13) (479df6a)
• test(decoding,encoding): drop @cached_property tautologies and plot-axes-not-None duplicates (batch 12) (d2d9076)
• test(mazes): strip per-maze dataclass-trivia classes (batch 11) (88e7697)
• test(encoding): trim tautological imports and duplicate _to_numpy variants (batch 10) (04e3094)
• test(ops): trim import-shim and all-pinning tests (batch 9) (caebf93)
• test(stats): remove import tautologies and consolidate circular tests (batch 8) (0a0155d)
• test(animation): remove self-referential constant/formula tests (batch 7) (f1f40ab)
• test(encoding): collapse 24 backend-dispatch passthrough tests to one parametrized validator (batch 6) (4636244)
• test: collapse top-level import-test files (batch 5) (1efd3fd)
• test: delete five more duplicate TDD-scaffolding test files (batch 4) (9483217)
• test: delete duplicate, import-only, and print-only test files (batch 3) (6c8d9ad)
• test: collapse parameter/path/layout-kind permutations (batch 2) (da10542)
• test: remove tautological and cosmetic-formatting tests (batch 1) (e9360cc)
• docs(M5): correct differential-operator docstrings + composite parity claim (1609cc2)
• docs(M5): close reviewer-flagged gaps (0b848e3)
• chore(M5): tick M5 checkboxes in TASKS.md (dee6b3e)
• refactor(M5.9): remove Environment.save / Environment.load (d0cf6e3)
• refactor(M5.7): remove Environment.mask_for_region in favor of region_mask (dce5cfb)
• refactor(M5.6): convert bin_attributes / edge_attributes / differential_operator to methods (c48d0ee)
• refactor(M5.5): finish Regions API consolidation by raising in remove() (9074804)
• refactor(M5.3): rename from_image/from_mask -> from_pixel_mask/from_grid_mask (6ae8ee1)
• chore(M4): tick M4 checkboxes in TASKS.md (7d90e66)
• refactor(M4.4, M4.5): coordinate-convention safety part 2 (2d5ec4c)
• refactor(M4.1, M4.2): coordinate-convention safety part 1 (134c57d)
• chore(M3): tick M3 checkboxes in TASKS.md (c11d4fc)
• refactor(M3.5-M3.9): error/warning hygiene sweep (c1eea2d)
• refactor(M3.3): expand @check_fitted coverage on Environment methods (3d64e21)
• refactor(M3.2): migrate manual not-fitted checks to EnvironmentNotFittedError (65221a0)
• refactor(M2.C): finish 2.19 + 2.15; tick M2.C/M2.D in TASKS.md (88a6f7d)
• refactor(M2.D): convert events.init lazy getattr to eager imports (7fbbe94)
• refactor(M2.D): remove cross-domain re-exports for one canonical import path (c6360d3)
• refactor(M2.D): remove path_efficiency, keep compute_path_efficiency (8ad0d24)
• refactor(M2.C): force kwarg-only on settings parameters across the API (751a591)
• refactor(M2.C): is_object_vector_cell takes raw data like sister classifiers (f956804)
• refactor(M2.C): align argument order with canonical conventions (5fe5886)
• test(properties): loosen rate_map_coherence smooth-field bound (08e37df)
• fix(M2): README CI snippet + batch wrappers reject bad API params (22736ac)
• refactor(M2.B 2.13): misc result-type cleanup (7ceaecc)
• refactor(M2.B): result-class consolidation (renames + structured returns) (53a4c66)
• refactor(M2.A): unify M2 parameter names across the public API (0e7aea8)
• feat(environment): mark polar envs and refuse Cartesian-assuming methods (M1 1.3) (7377271)
• feat(decoding): default decode_position to validate=True; add non-negative spike_counts and rate checks (M1 1.8) (8143baa)
• docs/ci: address second-pass review (multi-line +SKIP, README placeholder snippet) (bf44732)
• docs/ci: address M0 code-review findings (H1-H3, I1, I3, I4, M2, M4) (5bedcab)
• test: fix Python-3.10/11/12 docstring tests and Windows test failures (84e64a4)
• test: gate optional-extra tests on their actual dependencies (26efb25)
• docs/tests: clean up post-deletion legacy references (2055987)
• test(encoding): make x64-import regression actually fail without the fix (927d819)
• refactor(M4): symmetric NumPy/JAX backends; _metrics.py is dispatch only (561cc8b)
• refactor(M2): inherit SpatialResultMixin and vectorize directional batch ops (0a028d6)
• refactor(M1): unify input validation and fix egocentric arg order (14be540)
• refactor(M7): update remaining test imports to new module locations (3ea4b43)
• refactor(M7): clean up place.py and update test imports (3a10db3)
• refactor(M7): update encoding/init.py exports for new locations (e1e9a64)
• refactor(M7): migrate object_vector.py utilities to egocentric.py (32cf53e)
• refactor(M7): migrate spatial_view.py utilities to view.py (2f64b0d)
• refactor(M7): migrate head_direction.py utilities to directional.py (1462788)
• refactor(M7): migrate DirectionalPlaceFields and detect_place_fields to spatial.py (16b2a1b)
• refactor(M6): consolidate JAX helpers and add backend validation (00c83f6)
• refactor(M10): consolidate metrics modules into encoding (4303194)
• refactor(M10): delete old files and consolidate encoding modules (21d7222)
• refactor(M9): reduce top-level exports to 5 core classes (4c87ccf)
• refactor(M8): consolidate animation/ module - move scale bar config (807dbe1)
• refactor(M7): add re-exports from stats to decoding module (cd90a47)
• refactor(M6): update internal imports for encoding modules (cf02f62)
• refactor(M6): create encoding/population.py with population metrics re-exports (f40493b)
• refactor(M6): create encoding/phase_precession.py with phase precession re-exports (ebf9fc2)
• refactor(M6): create encoding/spatial_view.py with spatial view cell re-exports (1fc8145)
• refactor(M6): create encoding/object_vector.py with object-vector cell re-exports (4b9d129)
• refactor(M6): create encoding/border.py with border cell re-exports (494b28b)
• refactor(M6): create encoding/head_direction.py with head direction re-exports (7b9a8f2)
• refactor(M6): create encoding/grid.py with grid cell re-exports (3b123c4)
• refactor(M6): create encoding/place.py with place cell re-exports (5dfcdcc)
• refactor(M5): move reward.py to behavior/reward.py (f887c20)
• refactor(M5): create behavior/decisions.py with decision_analysis and VTE (1bfb0c4)
• refactor(M5): create behavior/navigation.py with path and goal metrics (e2ea4e7)
• refactor(M5): move segmentation/ to behavior/segmentation.py (e4d94cc)
• refactor(M5): move trajectory functions to behavior/trajectory.py (355a337)
• refactor(M2): remove backward compatibility shims (246fb63)
• refactor(M4): create stats/surrogates.py with surrogate generation functions (e808d0f)
• refactor(M4): move shuffle functions to stats/shuffle.py (89a588a)
• refactor(M4): move circular statistics to stats/circular.py (ff00e6e)
• refactor(M3): move nwb/ → io/nwb/ (20a2ecc)
• refactor(M2): move basis.py → ops/basis.py (63616af)
• refactor(M2): move visibility.py → ops/visibility.py (285a6c2)
• refactor(M2): move reference_frames.py → ops/egocentric.py (75243fb)
• refactor(M2): move alignment.py → ops/alignment.py (95cd446)
• refactor(M2): move transforms.py → ops/transforms.py (d2514de)
• refactor(M2): move differential.py → ops/calculus.py (f5bd05b)
• refactor(M2): move primitives.py → ops/graph.py (f92ed86)
• refactor(M2): move kernels.py → ops/smoothing.py (9248e66)
• refactor(M2): move field_ops.py → ops/normalize.py (7776cda)
• refactor(M2): move distance.py → ops/distance.py (4ae7995)
• refactor(M2): move spatial.py → ops/binning.py (770fa0a)
• refactor(M1): create new package directory structure (d0a9415)
• chore: defer M3.5-M3.8 spatial event utilities (dcdd2a6)
• chore: defer M2.4 exponential_kernel and M3.1-M3.3 detection functions (bb01fde)
• refactor(M2.1): replace time_since_event with time_to_nearest_event (67ecc2d)
• chore: update TASKS.md with completed milestone checkboxes (1727d72)
• chore: update SCRATCHPAD with completion status (f42fba2)
• test: add behavioral tests verifying plot_circular_basis_tuning math (671b26e)
• refactor: extract phase_precession module from circular.py (2b892f6)
• test(animation): remove skip markers for Task 3.2 (now implemented) (24ca1e9)
• refactor(animation): add _validate_frame_times function (8af7335)
• test(animation): add final integration tests for TimeSeriesOverlay (d8ae692)
• test(animation): add performance and edge case tests for TimeSeriesOverlay (8bf771c)
• refactor(M2): remove dask renderer after benchmark showed poor performance (38e952a)
• refactor(scale_bar): DRY helper, validation, and edge case tests (5cdc999)
• chore(Task 4.5): complete final review and testing (3fac478)
• test(annotation): complete Task 3.4 - end-to-end tests for track graph (37b8b74)
• test(annotation): complete Task 2.4 - widget integration tests (4563fde)
• chore(tests): complete Milestones 6 and 8 (fb91de4)
• refactor(tests): remove duplicate fixtures from test files (c2e0a8c)
• refactor(tests): move animation fixtures to local conftest (c03dcbd)
• refactor(tests): make simple_3d_env fixture deterministic (888ae95)
• refactor(tests): migrate animation tests to local RNG (b2ed549)
• refactor(tests): migrate segmentation tests to local RNG (73af5ef)
• refactor(tests): migrate test_population.py to local RNG (9194837)
• refactor(tests): migrate test_trajectory.py to local RNG (d3e6365)
• refactor(tests): migrate test_grid_cells.py to local RNG (1a44f86)
• chore: update TASKS.md with test_behavioral.py migration status (0b2b7ac)
• refactor(tests): migrate test_behavioral.py to deterministic fixtures (e9a1948)
• refactor(tests): migrate test_transforms_new.py to local RNG (7587fb3)
• refactor(tests): migrate test_differential.py to local RNG (7d07063)
• refactor(tests): migrate test_io.py to local RNG (fc39766)
• refactor(tests): migrate test_trajectory_metrics.py to local RNG (b62681b)
• refactor(tests): migrate test_interpolate.py to local RNG (363a697)
• refactor(tests): migrate test_validation_new.py to local RNG (fd9029f)
• refactor(tests): migrate test_transforms_3d.py to local RNG (1402b57)
• refactor(tests): migrate test_spike_field.py to local RNG (ef0b160)
• refactor(tests): migrate test_place_fields.py to local RNG (96a16fd)
• refactor(tests): reduce from_samples calls in test_transitions.py (3f6aba6)
• refactor(tests): reduce from_samples calls in test_occupancy.py (3071612)
• refactor(tests): reduce from_samples calls in test_boundary_cells.py (96052b7)
• test(behavioral): add coverage improvement tests (2161653)
• test(behavioral): add comprehensive curvature tests for multiple turns (c426c5c)
• test(nwb): add comprehensive parametrized tests for all layout types (2a995aa)
• test(nwb): add round-trip tests for all remaining layout types (806a78a)
• test(nwb): add file-based round-trip tests for Environment (246181d)
• test(nwb): add linked timestamps test for pose reading (a182672)
• test(nwb): add skeleton round-trip tests (M1.2.2) (67e45d2)
• test(nwb): add core discovery utilities tests (M1.1.1) (abd6e5c)
• test(nwb): add test infrastructure with NWB fixtures (M0.3) (0cd49cc)
• chore(nwb): add optional NWB dependencies (M0.2) (8710f75)
• chore(annotation): remove non-working features from help text (ae93477)
• chore(annotation): remove non-working UX features and update shortcuts (0c0525e)
• test(8.6): add TypedDict JSON schema conformance tests (f0eac94)
• chore: update verification status and code review results (44d9d60)
• refactor(8.3): centralize pickle validation messages (2cfdc62)
• refactor(8.2): normalize OverlayData.regions to dict format (96f1bf4)
• test(6.5): add shared environment fixtures for video overlay testing (20cc64b)
• test(6.4): add video validation and napari-free operation tests (a922ef4)
• test(P5.1): add frame naming pattern tests (5ac437f)
• refactor: move benchmark_datasets to scripts/ directory (5b23c41)
• chore(M4): remove dead skeleton callback code (5c0af5d)
• chore(animation): remove legacy overlay_trajectory tests (542c154)
• test: remove backup file and mark slow tests to prevent CI timeouts (1cbcbeb)
• test(memory): remove redundant test_very_large_environment_only_warns (bfbadad)
• chore(animation): remove unnecessary type ignore comments (19cf867)
• test(animation): add comprehensive error message tests (99a44ac)
• test(animation): add memory profiling tests (c5bb173)
• test(animation): increase benchmark sample sizes for robust baselines (ded4c69)
• test(animation): add comprehensive performance benchmarks (939270c)
• test(animation): add Session 20 integration tests and Pillow dependency (c4652eb)
• test(animation): add end-to-end layout integration tests (fbfdd0e)
• refactor(animation): apply code review recommendations (4bfe66f)
• chore(M2): cleanup investigation files and update task tracking (d343ec3)
• test(M1): achieve 95% coverage for place_fields.py (Task 1.4 complete) (bb52c0e)
• test(M1): achieve 100% coverage for kernels.py (Task 1.3 complete) (1355731)
• chore(M1): achieve 100% coverage for differential.py via dead code removal (Task 1.2 complete) (d3fac33)
• test(M1): achieve 100% coverage for distance.py (Task 1.1 complete) (735697a)
• chore(M2): remove dead code from utils.py (Task 2.12) (1520a91)
• refactor(M2): extract helper functions from _create_regular_grid() (Task 2.7) (c22f8c3)
• test(M2): add property-based tests with Hypothesis (Task 2.4) (3ca45bd)
• test(perf): complete performance regression test suite (Task 2.3) (f7e555d)
• refactor(M2): extract generic graph connectivity helper (Task 2.1) (7edf6e0)
• test: add comprehensive 3D environment test coverage (8d338cd)
• fix(trajectory): improve numerical stability with named EPSILON constant (d320438)
• chore: re-execute notebook 08 with seed=137 to update embedded outputs (a32da4e)
• docs(M2): complete Milestone 2 documentation and validation (f19132b)
• refactor: replace fragile type name checks with _layout_type_tag (6153ebb)
• refactor: reduce nesting with guard clauses in spike_field (7805e1b)
• refactor: standardize parameter order - env first in all functions (576cc14)
• chore(M4.6): update progress tracking for completed documentation (0a80dd0)
• test(M4.6): add comprehensive integration tests for trajectory analysis workflows (85bafd5)

Full Changelog: v0.2.0...v0.4.0