Bump version to 0.8.0

- Spinal network simulator improvements
- Strict mode for NEURON mechanism loading
- API documentation additions (HillModel, Network, SimulationRunner, etc.)
- Watanabe examples updated with 2015 citation
- NEO blocks documentation consolidated
- ReadTheDocs configuration with uv support
- Examples documentation paths fixed

Author: RaulSimpetru

.readthedocs.yaml

@@ -3,26 +3,21 @@
 
 version: 2
 
-# Set the OS, Python version, and other tools
 build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
-    uv: "latest"
   apt_packages:
-    # Required for NEURON and MPI support
+    - libegl1-mesa-dev
     - libopenmpi-dev
     - openmpi-bin
-  jobs:
-    # Install using uv sync (includes docs dependencies)
-    post_create_environment:
-      - uv sync --group docs
-    # First build pass (generates sphinx-gallery examples and autosummary stubs)
-    pre_build:
-      - uv run sphinx-build -b html docs/source $READTHEDOCS_OUTPUT/html
-
-# Build documentation in the "docs/" directory with Sphinx
-# This is the second pass - RTD runs this automatically after pre_build
-sphinx:
-  configuration: docs/source/conf.py
-  fail_on_warning: false
+    - openmpi-common
+    - libgtk2.0-dev
+  commands:
+    # Install uv and sync dependencies
+    - pip install uv
+    - uv sync --group dev --group docs
+    # Setup myogen (compile NEURON mechanisms)
+    - uv run poe setup_myogen
+    # Build docs (first pass generates stubs, second pass succeeds)
+    - uv run sphinx-build -b html docs/source $READTHEDOCS_OUTPUT/html || uv run sphinx-build -b html docs/source $READTHEDOCS_OUTPUT/html

CHANGELOG.md

@@ -7,6 +7,45 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.8.0] - 2025-12-28
+
+### Added
+- **Spinal Network Simulator**: Enhanced connectivity and afferent population support
+  - Improved interneuron and motor neuron connectivity patterns
+  - Added Group II (GII) afferent pathway support
+  - Enhanced afferent population configuration options
+- **Strict Mode for NEURON**: New error handling mode for mechanism loading
+  - Added `strict` parameter to `load_nmodl_files()` function
+  - Warnings by default, exceptions opt-in with `strict=True`
+  - Clearer error messages when NEURON mechanisms fail to load
+- **API Documentation**: Added missing classes to API docs and module exports
+  - `HillModel` - Hill-type muscle model
+  - `Network` - Spinal network container
+  - `SimulationRunner` - Simulation orchestration
+  - `JointDynamics` - Joint dynamics model
+  - `SpindleModel` - Muscle spindle proprioceptor
+  - `GolgiTendonOrganModel` - Golgi tendon organ proprioceptor
+  - `ContinuousSaver` and `convert_chunks_to_neo` utility functions
+- **ReadTheDocs Configuration**: New `.readthedocs.yaml` with uv package manager support
+  - Uses `uv sync --group docs` for dependency installation
+  - Double-build for sphinx-gallery (pre_build + sphinx section)
+  - MPI dependencies via apt packages
+
+### Changed
+- **NEO Blocks Documentation**: Consolidated 4 documentation files into single `docs/neo_blocks.md`
+  - Reduced from ~47KB across multiple files to ~4.5KB single digestible document
+  - Clearer structure with block types, access patterns, and troubleshooting
+- **API Documentation Order**: Reorganized `simulator_api.rst` to follow simulation workflow
+  - RecruitmentThresholds → Populations → Network → SimulationRunner → Muscle → Proprioception → JointDynamics → Force → Electrodes → EMG
+- **Watanabe Examples**: Updated paper citations from 2013 to 2015 (J. Neurosci.)
+  - Corrected DOI references across all example scripts
+  - Simplified README to essential information only
+- **README**: Rewritten for beginners with uv as primary installation method
+
+### Fixed
+- **Documentation Links**: Fixed examples toctree paths (`01_basic`, `02_finetune`)
+- **Literature Reproductions Link**: Added `watanabe-reproduction` ref label for cross-references
+
 ## [0.7.0] - 2025-12-24
 
 ### Added

README.md

@@ -8,7 +8,7 @@
 
   [![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://nsquaredlab.github.io/MyoGen/)
   [![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
-  [![Version](https://img.shields.io/badge/version-0.6.5-orange.svg)](https://github.com/NsquaredLab/MyoGen)
+  [![Version](https://img.shields.io/badge/version-0.8.0-orange.svg)](https://github.com/NsquaredLab/MyoGen)
 
   [Installation](https://nsquaredlab.github.io/MyoGen/#installation) •
   [Documentation](https://nsquaredlab.github.io/MyoGen/) •
@@ -39,6 +39,8 @@ MyoGen is designed for algorithm validation, hypothesis-driven research, and edu
 
 # Installation
 
+> **Requires Python 3.12+** — Check your version with `python --version`
+
 ## System Requirements
 
 | Platform | Before Installing MyoGen |
@@ -47,8 +49,6 @@ MyoGen is designed for algorithm validation, hypothesis-driven research, and edu
 | **Linux** | `sudo apt install libopenmpi-dev` (Ubuntu/Debian) or `sudo dnf install openmpi-devel` (Fedora) |
 | **macOS** | `brew install open-mpi` |
 
-**Python**: 3.12 or higher required
-
 > [!CAUTION]
 >
 > ## Windows Users: Install NEURON First

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "MyoGen"
-version = "0.7.0"
+version = "0.8.0"
 description = "Modular and extensible neuromuscular simulation framework for generating physiologically grounded motor-unit activity, muscle force, and EMG signals (surface and intramuscular)"
 readme = "README.md"
 requires-python = ">=3.12"