Refactor code structure for improved readability and maintainability

Author: RaulSimpetru

CHANGELOG.md

@@ -31,12 +31,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - `neuron==8.2.7` now only installed automatically on Linux and macOS
   - Windows users must manually install NEURON before pip installing MyoGen
   - Combined dependency declaration for both Linux and macOS using `sys_platform` conditions
-- **Elephant Dependency**: Made elephant an optional dependency (PyPI compatibility)
-  - Removed elephant from core dependencies (PyPI doesn't allow git dependencies)
-  - Available as optional extra: `pip install myogen[elephant]`
-  - Provides spike train conversion (`BinnedSpikeTrain`) and statistics (`isi`) for simulations
-  - Used in EMG simulations, force modeling, and firing rate/CV analysis
-  - Automatically included in docs and dev environments
+- **Elephant Dependency**: Added elephant from PyPI as required dependency
+  - Elephant 1.1.1 included for spike train conversion and statistics
+  - Provides `BinnedSpikeTrain` conversion and `isi` for EMG/force simulations
+  - Graceful error handling if elephant import fails (development safety)
+- **NumPy Version**: Pinned to numpy <2.0 for elephant compatibility
+  - Elephant 1.1.1 requires numpy <2.0
+  - Ensures stable, tested dependency versions
 - **Sphinx Workflow**: Kept `setup_myogen` call in documentation build workflow
   - Required for editable installs used in CI/CD environments
   - Ensures NMODL mechanisms are compiled for documentation examples

README.md

@@ -47,14 +47,10 @@ MyoGen is designed for algorithm validation, hypothesis-driven research, and edu
 ## From PyPI (recommended)
 
 ```bash
-# Basic installation
 pip install myogen
-
-# With intramuscular EMG support (includes elephant)
-pip install myogen[elephant]
 ```
 
-NEURON mechanisms compile automatically during installation!
+NEURON mechanisms compile automatically during installation.
 
 ## From Source (for development)
 
@@ -83,17 +79,6 @@ uv run poe setup_myogen
 pip install cupy-cuda12x
 ```
 
-**Spike train analysis** (required for most simulations):
-
-```bash
-pip install myogen[elephant]
-# or
-pip install git+https://github.com/INM-6/elephant@389f53830d37290611af34e363d1d382a05e4d1e
-```
-
-Elephant provides:
-- `BinnedSpikeTrain` conversion for EMG and force simulations
-- `isi` (inter-spike interval) statistics for firing rate and CV analysis
 
 # Quick Start
 

pyproject.toml

@@ -7,6 +7,7 @@ requires-python = ">=3.12"
 dependencies = [
     "beartype>=0.21.0",
     "cython>=3.1.3",
+    "elephant>=1.1.1",
     "impi-rt>=2021.15.0 ; sys_platform == 'win32'",
     "matplotlib>=3.10.1",
     "mpi4py>=4.0.3",
@@ -15,7 +16,7 @@ dependencies = [
     #"neuron-nightly>=9.0a1.dev1492",
     "noise>=1.2.2",
     "numba>=0.61.2",
-    "numpy>=1.26",
+    "numpy>=1.26,<2.0",
     "optuna>=4.5.0",
     "pyqt6>=6.9.0",
     "quantities>=0.16.2",
@@ -34,19 +35,13 @@ dependencies = [
 invalid-syntax-in-forward-annotation = "ignore"
 possibly-unbound-import = "ignore"
 
-[project.optional-dependencies]
-elephant = [
-    "elephant @ git+https://github.com/INM-6/elephant@389f53830d37290611af34e363d1d382a05e4d1e",
-]
-
 [dependency-groups]
 dev = [
     "pandas-stubs>=2.3.0.250703",
     "poethepoet>=0.37.0",
     "scipy-stubs>=1.16.1.0",
 ]
 docs = [
-    "elephant @ git+https://github.com/INM-6/elephant@389f53830d37290611af34e363d1d382a05e4d1e",
     "enum-tools[sphinx]>=0.12.0",
     "linkify-it-py>=2.0.3",
     "memory-profiler>=0.61.0",