Changelog#

This document records notable changes to the CaliBrain package.

Note

This page summarizes notable package, workflow, and documentation changes.

Version 1.0.2 (2026-06-16)#

  • [DOCS] Reworked the installation documentation into separate beginner-oriented PyPI, pip, and conda guides with clearer step-by-step instructions.

  • [DOCS] Refined the tutorial and documentation structure around the current workflow, conceptual overview, glossary, datasets, and runnable gallery pages.

  • [DOCS] Added manual Examples using calibrain.XXX sections to API reference pages so core classes and workflow entry points link directly to relevant tutorials.

Version 1.0.1 (2026-06-16)#

  • [BREAKING] Raised the supported Python version floor to >=3.10 and aligned package metadata, documentation builds, and contributor setup instructions accordingly.

  • [DOCS] Reworked documentation CI so GitHub Actions validates documentation builds while Read the Docs remains the canonical published documentation host.

  • [DOCS] Fixed the documentation version switcher to use explicit Read the Docs latest, stable, and tagged release targets.

  • [BUGFIX] Completed package dependency declarations for wheel-based installation and clean-environment imports.

  • [FEATURE] Added Publishing GitHub Actions workflow for PyPI releases triggered from published GitHub releases, with manual dispatch retained as a fallback.

  • [FEATURE] Added Zenodo DOI citation metadata and surfaced the software DOI throughout the package documentation.

  • [FEATURE] Added a root CITATION.cff file with author metadata, ORCID identifiers, release metadata, and Zenodo DOI information.

  • [DOCS] Added Read the Docs, PyPI, downloads, license, release, workflow, and DOI badges to the README and documentation landing page.

  • [DOCS] Consolidated the root project README around README.rst and removed the duplicate Markdown copy.

  • [DOCS] Standardized software citation text across the README, documentation landing page, and citation page using full author names and Zenodo DOI-based software references.

  • [ENHANCEMENT] Refined the package description and synchronized the README and docs landing page around the current package scope and workflow summary.

Version 1.0.0 (2026-06-11)#

  • Version 1.0.0 marks a major consolidation of the CaliBrain package around a stable, production-ready workflow. The package is now centered on simulation-based uncertainty estimation and calibration in EEG/MEG inverse source imaging, with robust support for fixed and free-orientation source models.

  • [BREAKING] Consolidated the supported inverse workflow around gamma_map_sflex, gamma_lambda_map_sflex, BMN, and BMN_joint. Older methods such as gamma_map, eLORETA, and related cross-validation branches have been removed from the supported pipeline.

  • [BREAKING] Reworked calibration from within-subject, across-source fitting to pooled source datasets across subjects, with isotonic regression now fit on subject-level splits rather than a single subject at a time.

  • [FEATURE] Introduce five calibration modes (precal, post_oracle, post_pooled, post_pooled_mismatch, and post_fixed) for evaluating calibration performance under different fitting conditions.

  • [FEATURE] Expanded the core simulation stack with stronger support for source simulation, sensor simulation, and leadfield handling across fixed and free-orientation settings.

  • [FEATURE] Added and extended uncertainty estimation and calibration capabilities, including pointwise and aggregated uncertainty modes, full_cov and marginal free-orientation interval types, componentwise uncertainty handling, and the multiple calibration modes.

  • [FEATURE] Added manifest workflow modules for data generation, aggregation, calibration, and calibration-figure generation, and documented their main entry points and helper methods.

  • [ENHANCEMENT] Refined MetricEvaluator and related evaluation logic for mse, mae, rmse, rmae, mean_posterior_std, emd, mean_signed_deviation, mean_absolute_deviation, max_underconfidence_deviation, and max_overconfidence_deviation.

  • [BREAKING] Removed the legacy benchmarking class and replaced it with DataGenerator, which wraps solver grids, SourceSimulator, SensorSimulator, LeadfieldBuilder, and posterior-summary generation in a single workflow abstraction.

  • [BUGFIX] Fixed unit handling and source/sensor projection consistency across the simulation pipeline.

Version 0.1.2 (2025-08-19)#

  • [FEATURE] Refactored entire codebase into a modular, class-based architecture: SourceSimulator, SensorSimulator, MetricEvaluator, Visualizer.

  • [FEATURE] Added empirical evaluation metrics: - Uncertainty: mean_posterior_std - Calibration: mean_calibration_error, max_underconfidence_deviation, max_overconfidence_deviation, mean_absolute_deviation, mean_signed_deviation - Spatial Accuracy: emd, jaccard_error, mse - Detection Performance: euclidean_distance, f1, accuracy

  • [FEATURE] Integrated eLORETA as a new inverse estimator for distributed source reconstruction.

  • [FEATURE] Introduced unit-aware visualization utilities with automatic label scaling for EEG/MEG/source signals.

  • [FEATURE] Added comprehensive examples and tutorials covering simulation, evaluation, and visualization.

  • [FEATURE] Overhauled and expanded documentation with updated installation and usage instructions.

  • [ENHANCEMENT] Streamlined simulation engine with clearer logic, improved configuration handling, and consistent SI unit usage.

  • [ENHANCEMENT] Improved leadfield projection with support for orientation handling and channel filtering.

  • [BUGFIX] Fixed inconsistent unit handling across simulation pipeline ([Issue #18](braindatalab/calibrain#18)): - Converted source dipole moments from nAm to Am - Standardized EEG/MEG projections to SI units (V, T) - Added logic to format plot labels according to unit scaling

Version 0.1.1 (2025-05-24)#

  • [FEATURE] Include ERP signal generation. Add Multi trial simulation and refactor DataSimulator (Issue #6, implemented in PR #7).

  • [ENHANCEMENT] Refactored ERP signal generation for smoother waveforms and support for random Hanning window length/duration (Commit 035d65c <https://github.com/braindatalab/CaliBrain/commit/035d65c0f434ae614d675eb3e03e0585a2bc6254>_).

  • [BUGFIX] Enhance noise handling in data simulation

Version 0.1.0 (2025-04-28)#

  • Initial release.

  • Added LeadfieldSimulator for simulating leadfields.

  • Added DataSimulator for generating synthetic data.

  • Added SourceEstimator for estimating source activity using gamma MAP and eLORETA.

  • Added UncertaintyEstimator for estimating uncertainty in source activity.

  • Added DataGenerator class for orchestrating source-estimation data generation.

  • Added utils module for utility functions.