Skip to content

CHANGELOG.md

Latest commit

 

History

History
103 lines (78 loc) · 4.3 KB

CHANGELOG.md

File metadata and controls

103 lines (78 loc) · 4.3 KB
Raw

Changelog

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning. While the major version is 0.x, breaking API changes may land in any release; treat the package as alpha-stage until 1.0.

[0.1.4] — 2026-06-08

Changed

  • Maze 1D occupancy now bins each arm independently into an integer number of ~bin_width_mm bins, so every arm boundary falls exactly on a bin edge. Previously a single global grid spanned the whole linearized axis, letting a bin straddle an arm/direction junction and pool frames from two segments. Maze rate maps, spatial information, and place-cell classification can change slightly (mostly near junctions); re-run the maze pipeline to regenerate existing bundles. Arena pipelines are unaffected.

Added

  • compute_occupancy_map_1d accepts an optional edges argument for explicit (possibly non-uniform) bin edges; the uniform n_bins/ pos_range path is unchanged.

[0.1.3] — 2026-05-06

Fixed

  • clip_to_arena now logs the number of clamped frames and the maximum out-of-bounds deviation at INFO. Previously silent — closes the "no silent data repair" policy gap.

[0.1.2] — 2026-05-06

Fixed

  • Stability shuffle no longer injects 0.0 for degenerate iterations; the p-value denominator now uses the count of valid shuffles (Phipson & Smyth 2010). Previously anti-conservative for stable units on sparse or short sessions.

Changed

  • Arena preprocess_behavior step order: perspective → Hampel → clip → mm (was Hampel first). Bundle outputs unchanged for existing data.
  • oasis-deconv ImportError reformatted with install commands on separate lines.

[0.1.1] — 2026-05-06

Fixed

  • Project URLs in pyproject.toml, README.md, and docs now use the canonical PascalCase GitHub repository name miniscope/CaMAP. The previously-listed lowercase paths returned 404 on GitHub Pages (which is case-sensitive on case-sensitive filesystems).

Added

  • Python 3.13 support (requires-python = ">=3.11,<3.14"). PyPI classifier and black target-version updated; the matrix in test.yml already exercised 3.13.

[0.1.0] — 2026-05-05

Initial public release. CaMAP was previously developed internally as placecell; this is the first version published to PyPI under the new name.

Added

  • CLI (camap): analysis runs the full pipeline (load → preprocess → deconvolve → match → analyze → save bundle); define-zones and detect-zones build and apply maze zone graphs.
  • Datasets: ArenaDataset for 2D open-field analysis, MazeDataset for 1D arm/maze analysis, sharing a common abstract base (BaseCaMAPDataset).
  • Analysis primitives (camap.analysis): rate maps, spatial information (Skaggs 1993), split-half stability with multi-scale block configurations, shuffle-based significance, place-field detection (Guo et al. 2023), coverage maps and curves, arm-by-arm population vector overlap (compute_dataset_arm_pvo).
  • Bundle format (.camap): self-contained directory with config, per-neural-frame canonical table, occupancy/footprint arrays, per-unit results, summary figures, and a versioned metadata.json. Round-trips via BaseCaMAPDataset.save_bundle() / load_bundle().
  • Notebook viewers for arena and maze bundles (notebook/view_results_*.ipynb).
  • Docs: installation, quickstart, pipeline reference, CLI reference, workflows, notebooks (built with Sphinx + sphinx-book-theme).

Notes

  • Alpha-stage. APIs may change without notice in 0.x; the Development Status :: 3 - Alpha classifier is set on PyPI and the alpha signal is carried by the leading 0.x per common scientific-Python practice (rather than a strict PEP 440 aN suffix that would force pip install --pre).
  • Companion paper. A CITATION.cff will be added when the associated publication is finalized.
  • Internal history. placecell git tags v0.1.0–v0.7.0 (private dev before the rename) were deleted from origin; this 0.1.0 is the first publicly-tagged release.
  • No backward compatibility for legacy .pcellbundle directories — loading raises with explicit rename instructions. Re-run the pipeline to produce a .camap directory.