vbi 0.2__tar.gz → 0.2.1__tar.gz

vbi-0.2.1/CHANGELOG.md

@@ -0,0 +1,112 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.2] - 2025-08-28
+
+### Added
+- **New Models:**
+  - Implemented Wong-Wang model with Numba JIT compilation and simulation functionality
+  - Added Numba-based Jansen-Rit model with initial state setup and integration functionality
+  - Implemented Bold model with parameter management and BOLD step functionality
+  - Added Wilson-Cowan CuPy implementation and example notebook
+  - Added Wong-Wang full (EI) model with CuPy implementation
+
+- **Feature Enhancements:**
+  - Added `__str__` method to JR_sde class for improved model parameter representation
+  - Added average parameter to `spectrum_moments` function for optional averaging of moments
+  - Enhanced `integrate` function to filter recorded data based on `t_cut`, with assertion for validity
+  - Added `dtype_convert` function and enhanced `prepare_vec_2d` for flexible input handling
+  - Added optional parameter 'k' to `fcd_stat` function for flexible window length calculation
+  - Added functions to check data location on CPU/GPU
+  - Enhanced parameter handling in KM_sde class
+  - Added SKIP_CPP environment variable to control C++ compilation during setup
+  - Added error handling for PCA transformation in `matrix_stat` function
+  - Allow customizable wavelet function in wavelet method (replaced ricker with morlet2)
+  - Added `allocate_memory` method in Bold class to accept dtype parameter
+
+- **Documentation:**
+  - Updated installation instructions to include SKIP_CPP environment variable
+  - Added Colab links and enhanced example notebooks with additional markdown headers
+  - Updated installation instructions in README to include pip install options
+  - Added docstring for train method in Inference class with parameter descriptions
+  - Added new example directories for mpr_sde_cpp and wilson_cowan_cupy
+  - Enhanced Jansen-Rit model documentation and improved CSS styles
+  - Added custom CSS styles and updated documentation structure
+  - Updated VBI toolkit description and improved presentation
+
+- **Infrastructure:**
+  - Added tvbk module integration with connectivity setup and MPR class implementation
+  - Added CONTRIBUTING.md for contribution guidelines
+  - Enhanced Docker support with NVIDIA CUDA base image and Python 3.10
+  - Added GitHub Actions workflow for publishing to PyPI
+  - Added Docker build badge and usage instructions
+
+### Changed
+- **Version Updates:**
+  - Updated project version from 0.1.3 to 0.2 in both `_version.py` and `pyproject.toml`
+  - Refactored DO_cpp class to DO
+
+- **Code Improvements:**
+  - Refactored Numba models and removed unused files
+  - Improved code formatting and style in Inference class methods
+  - Enhanced parameter handling in JR_sde and MPR_sde classes
+  - Updated buffer size calculation and streamlined data recording in WC_sde class
+  - Renamed `cupy/wilsoncowan.py` to `cupy/wilson_cowan.py` for naming compatibility
+
+- **Build System:**
+  - Updated MANIFEST.in and setup.py to include additional data files and C++ extensions
+  - Cleaned up pyproject.toml by removing commented sections
+  - Updated Docker workflow and improved build process
+
+### Fixed
+- Corrected weights array transposition in JR_sde class for proper data handling
+- Removed unnecessary transpose operation on weights in MPR_sde class
+- Updated noise_amp handling and added dependent parameter updates in MPR_sde class
+- Restored dtype definition in MPR class initialization
+- Updated import error messages to clarify C++ compilation or linking issues
+- Extended r_period calculation and improved RV recording condition in MPR_sde class
+- Fixed wavelet function imports and implementation
+
+### Removed
+- Removed tvbk_ext module and associated imports
+- Removed pre-commit configuration
+- Cleaned up deprecated test files and unnecessary dependencies
+- Removed outdated publish workflow steps from GitHub Actions
+
+## [0.1.3.3] - 2025-02-17
+
+### Changed
+- Updated package_data in setup.py to include Python files in vbi.models.cpp._src directory
+
+## [0.1.3.2] - 2025-02-17
+
+### Added
+- Updated wavelet functions to allow None as default for customizable wavelet function
+
+## [0.1.3.1] - 2025-02-17
+
+### Added
+- Imported models module in vbi package initialization
+- Implemented Bold class for balloon model and integrated with MPR_sde class
+
+### Changed
+- Updated Python version in publish workflow to 3.10 for improved compatibility
+
+## [0.1.3] - 2025-02-17
+
+### Added
+- Dynamic version retrieval implementation
+- Enhanced documentation structure and API references
+
+### Changed
+- Bumped version to 0.1.3
+
+---
+
+**Note:** This changelog covers changes from version 0.1.3 to the current version 0.2. Earlier versions may have additional changes not documented here.

{vbi-0.2 → vbi-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vbi
-Version: 0.2
+Version: 0.2.1
 Summary: Virtual brain inference.
 Author-email: Abolfazl Ziaeemehr <a.ziaeemehr@gmail.com>, Meysam Hashemi <meysam.hashemi@gmail.com>, Marmaduke Woodman <marmaduke.woodman@gmail.com>
 License-Expression: Apache-2.0

{vbi-0.2 → vbi-0.2.1}/docs/conf.py

@@ -7,7 +7,7 @@ from setuptools_scm import get_version
 # sys.path.insert(0, os.path.abspath("../vbi"))
 sys.path.insert(0, os.path.abspath(".."))
 
-needs_sphinx = "1.3"
+needs_sphinx = "0.2.1"
 
 extensions = [
     "sphinx.ext.autodoc",