Installation

Installation pathways for evaluation, internal testing, and reproducible command-line workflows.

Recommended approach. For most users, installation from PyPI is the fastest and most straightforward option. Wheel, source archive, and GitHub-based installation paths are also provided for environments that require manual package handling, source inspection, or local modification.

Good practice. In institutional or shared environments, install NeuroCGMD inside a dedicated Python virtual environment so the package version and dependencies used for a given evaluation remain easy to track.

Recommended environment setup

python3 -m venv .venv
source .venv/bin/activate      # macOS / Linux
# .venv\Scripts\activate       # Windows PowerShell
python -m pip install --upgrade pip

Option 1: pip install (recommended)

This is the most direct installation route and is appropriate for standard macOS, Linux, and Windows Python environments.

Open a terminal. On macOS, use Terminal. On Windows, use Command Prompt or PowerShell.
Install the package:

pip install neurocgmd

Allow the installation to complete. NeuroCGMD and its runtime dependencies, including NumPy and Matplotlib, will be installed automatically.
Proceed to the verification step below.

Troubleshooting. If the command fails, try pip3 install neurocgmd or python3 -m pip install neurocgmd. If the environment reports a permissions issue, use pip install --user neurocgmd when appropriate for your local setup.

Option 2: Install from the wheel file (.whl)

This method installs a pre-built package file manually and is useful when the distribution artifact is downloaded first for review or internal staging.

Open the package files page on PyPI: pypi.org/project/neurocgmd/1.0.0/#files
Download neurocgmd-1.0.0-py3-none-any.whl.
Open a terminal and move to the download location, typically the Downloads folder:

cd ~/Downloads

Install the wheel file:

pip install neurocgmd-1.0.0-py3-none-any.whl

Option 3: Install from the source archive (.tar.gz)

This method is appropriate when the source distribution should be unpacked and installed locally from the extracted project directory.

Open the package files page on PyPI: pypi.org/project/neurocgmd/1.0.0/#files
Download neurocgmd-1.0.0.tar.gz.
Open a terminal and move to the directory containing the downloaded archive:

cd ~/Downloads

# Extract the source archive
tar xzf neurocgmd-1.0.0.tar.gz

# Enter the extracted source directory
cd neurocgmd-1.0.0

# Install from the current directory
pip install .

Note. The final . in pip install . tells pip to install the package from the current directory.

Option 4: Install from GitHub source

This path is appropriate when the latest source code should be inspected, modified, or installed directly from the repository.

Using git

git clone https://github.com/sciencemaths-collab/neurocgmd.git
cd neurocgmd
pip install .

Without git

Download the repository ZIP archive: main.zip
Extract the ZIP archive.
Open a terminal and change into the extracted directory:

cd neurocgmd-main
pip install .

Verify the installation

After installation with any method above, confirm that the command-line interface is available.

neurocgmd --version

The command should report the installed version, for example:

neurocgmd 1.0.0

Then inspect the installed capability summary:

neurocgmd info

If the neurocgmd command is not found, try the module form instead:

python3 -m neurocgmd info

Next step: run with a parameter file

For a professional evaluation workflow, the recommended next step is to prepare a single TOML parameter file in the working directory and launch the run from that file rather than relying on ad hoc command changes.

project/
  structure.pdb
  run.toml

neurocgmd run run.toml

Page	Purpose
Quickstart	Reviewed starter layout, example `run.toml`, and first-pass command sequence.
Configuration	Parameter definitions and recommended TOML organization.
Running Simulations	Primary CLI commands for preparation, execution, and analysis.

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