Prerequisite Guide: Setting Up Virtual Environments for MuscleX Installation

Before installing MuscleX via Conda, pip, or directly from GitHub, it’s crucial to establish a virtual environment. This step ensures your project dependencies are managed in an isolated space, preventing conflicts. This guide emphasizes Conda as the recommended tool for environment management, with venv presented as an alternative option.

⚠️ Important Consideration

Conda is highly recommended for creating virtual environments, especially since it allows for the specification of Python versions within each environment, independent of the system’s Python interpreter. This flexibility is particularly beneficial for projects requiring a specific Python version or those aiming to avoid interference with system-wide Python settings.

Why Use a Virtual Environment?

A virtual environment is necessary for installations involving:

Conda: When installing MuscleX from a Conda channel.
Pip: For installations via the Python Package Index (PyPI) or from GitHub.
GitHub: When installing the latest development version from the GitHub repository.

Using a virtual environment ensures a clean, controlled setup, isolating MuscleX’s dependencies from other Python projects on your system.

Recommended: Conda Environment Management

Conda is an all-encompassing package and environment management system, ideal for handling complex dependencies across multiple platforms.

Advantages of Conda:

Cross-Platform Compatibility: Functions on Windows, macOS, and Linux.
Advanced Dependency Management: Excellently resolves complex dependencies to avert compatibility issues.
Environment Isolation: Safeguards your project by preventing cross-environment interference.

Setting Up Conda:

Install Miniconda: Refer to the Miniconda installation guide for your operating system.

Important note: On linux and macOS, you may need to run source ~/.bashrc or source ~/.bash_profile after installing Miniconda to activate the conda command, then close and reopen your terminal. On Windows, you will need to search for ‘Anaconda Prompt’ in the Start Menu and open it. It will open a terminal with the conda command available.

Create a New Environment: For an environment named myenv with Python 3.10, use:
```
conda create -n myenv python=3.10
```
Activate the Environment:
```
conda activate myenv
```

Given its extensive features and user-friendly nature, Conda is the preferred choice for most users.

Alternative: venv for Python Projects

venv is a viable alternative, provided with Python 3.3 and later.

⚠️ Important Consideration

Only use venv if you are installing MuscleX via pip or GitHub, because installing MuscleX via Conda requires a Conda environment. If you are using Conda, please refer to the Conda environment setup instructions above.

Advantages of venv:

Built-In with Python: No need for additional installations.

Setting Up venv:

Verify Python Version: Ensure you have Python 3.3 or newer by running python --version.
Create a New Environment: Within your project directory:
```
python -m venv myenv
```

Activate the Environment:

Windows:
```
myenv\Scripts\activate
```
macOS and Linux:
```
source myenv/bin/activate
```