Add iEMG simulation + docs updates

.vscode/settings.json

@@ -15,7 +15,6 @@
         "C:/nrn/lib/python"
     ],
     "python.analysis.autoImportCompletions": true,
-    "editor.fontFamily": "Fira Code",
     "editor.fontSize": 16,
     "editor.fontLigatures": true,
     "svg.preview.background": "dark-transparent",

CHANGELOG.md

@@ -13,6 +13,32 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+## [0.3.0] - 2025-08-08
+
+### Added
+- **Intramuscular EMG Framework**: Enhanced intramuscular EMG simulation capabilities with improved framework
+- Optional CUDA/CuPy support for accelerated computations in intramuscular EMG
+- New type definitions for EMG simulation components:
+  - `CORTICAL_INPUT__MATRIX` type for cortical input data
+  - `INTRAMUSCULAR_MUAP_SHAPE__TENSOR` for intramuscular electrode arrays
+
+### Changed
+- **Major Refactor**: Improved intramuscular EMG simulation framework with better type annotations and imports
+- Enhanced `IntramuscularEMG` class with better parameter handling
+- Optimized bioelectric field calculations for needle electrodes
+- Updated surface EMG components for consistency with intramuscular framework
+- Enhanced muscle model integration with electrode positioning
+- Improved motor unit simulation with better parameter handling
+- Enhanced recruitment thresholds plotting utilities
+- Updated project dependencies and compatibility with latest package versions
+- Enhanced Sphinx documentation configuration with better type aliases and extensions
+- Renamed `MUAP_SHAPE__TENSOR` to `SURFACE_MUAP_SHAPE__TENSOR` for better clarity
+
+### Fixed
+- Ensured Mermaid diagrams have consistent white background in documentation
+- Improved readability and visual consistency in documentation
+- Enhanced development experience with updated VSCode settings
+
 ## [0.2.0] - 2025-07-26
 
 ### Added

docs/source/_static/custom.css

@@ -27,4 +27,8 @@ html[data-theme="dark"] .bd-content img:not(.only-dark):not(.dark-light) {
 
 .sphx-glr-footer.sphx-glr-footer-example.docutils.container {
     display: none;
-}
+}
+
+.mermaid {
+    background-color: #ffffff;
+}

docs/source/api/simulator_api.rst

@@ -33,6 +33,16 @@ Muscle Model
 
    Muscle
 
+Force Model
+^^^^^^^^^^^
+
+.. autosummary::
+   :toctree: ../generated/
+   :template: autosummary/class.rst
+   :recursive:
+
+   ForceModel
+
 EMG Generation
 ^^^^^^^^^^^^^^
 
@@ -41,4 +51,17 @@ EMG Generation
    :template: autosummary/class.rst
    :recursive:
 
-   SurfaceEMG 
+   SurfaceEMG 
+   IntramuscularEMG
+
+Electrodes
+^^^^^^^^^^^^^^
+
+
+.. autosummary::
+   :toctree: ../generated/
+   :template: autosummary/class.rst
+   :recursive:
+
+   SurfaceElectrodeArray 
+   IntramuscularElectrodeArray

docs/source/api/types_api.rst

@@ -11,6 +11,9 @@ This module contains type definitions for structured data and type safety.
    :recursive:
 
    INPUT_CURRENT__MATRIX
+   CORTICAL_INPUT__MATRIX
    SPIKE_TRAIN__MATRIX
-   MUAP_SHAPE__TENSOR
-   SURFACE_EMG__TENSOR 
+   SURFACE_MUAP_SHAPE__TENSOR
+   INTRAMUSCULAR_MUAP_SHAPE__TENSOR
+   SURFACE_EMG__TENSOR
+   INTRAMUSCULAR_EMG__TENSOR 

docs/source/conf.py

@@ -38,8 +38,11 @@
     "sphinx_gallery.gen_gallery",
     "sphinx.ext.doctest",
     "myst_parser",
+    "sphinxcontrib.mermaid",
 ]
 
+mermaid_version = "11.9.0"
+
 napoleon_use_admonition_for_examples = False
 napoleon_use_admonition_for_references = False
 napoleon_numpy_docstring = True
@@ -70,6 +73,7 @@
     "list[float] | None": ":class:`list`\\[:class:`float`] | :class:`None`",
     "list[str] | None": ":class:`list`\\[:class:`str`] | :class:`None`",
     "tuple[int, int]": ":class:`tuple`\\[:class:`int`, :class:`int`]",
+    "tuple[float, float]": ":class:`tuple`\\[:class:`float`, :class:`float`]",
     "list[int]": ":class:`list`\\[:class:`int`]",
     "list[float]": ":class:`list`\\[:class:`float`]",
     "list[str]": ":class:`list`\\[:class:`str`]",
@@ -78,6 +82,10 @@
     "SPIKE_TRAIN__MATRIX": ":data:`~myogen.utils.types.SPIKE_TRAIN__MATRIX`",
     "MUAP_SHAPE__TENSOR": ":data:`~myogen.utils.types.MUAP_SHAPE__TENSOR`",
     "SURFACE_EMG__TENSOR": ":data:`~myogen.utils.types.SURFACE_EMG__TENSOR`",
+    "INTRAMUSCULAR_EMG__TENSOR": ":data:`~myogen.utils.types.INTRAMUSCULAR_EMG__TENSOR`",
+    "CORTICAL_INPUT__MATRIX": ":data:`~myogen.utils.types.CORTICAL_INPUT__MATRIX`",
+    "SURFACE_MUAP_SHAPE__TENSOR": ":data:`~myogen.utils.types.SURFACE_MUAP_SHAPE__TENSOR`",
+    "INTRAMUSCULAR_MUAP_SHAPE__TENSOR": ":data:`~myogen.utils.types.INTRAMUSCULAR_MUAP_SHAPE__TENSOR`",
     "INPUT_CURRENT__MATRIX | None": ":class:`~myogen.utils.types.INPUT_CURRENT__MATRIX` | :class:`None`",
     # Beartype and Annotated type patterns - map to clean aliases
     "Annotated[ndarray[tuple[int, ...], dtype[bool]], beartype.vale.Is[lambda x: x.ndim == 3]]": ":data:`~myogen.utils.types.SPIKE_TRAIN__MATRIX`",