AUTOCOPASI: Installation & Setup
===============================

AUTOCOPASI is a Python script designed to automate the setup and analysis of kinetic models for chemical reaction networks, particularly those generated by SPECI. This guide covers how to obtain, install, and configure AUTOCOPASI for integration with your workflows.

Obtaining AUTOCOPASI
--------------------

1. **Download the Code**

   AUTOCOPASI is distributed as a Python script and can be obtained from:
   - The [main SPECI repository](https://github.com/Manting-Mu/OLIGO) (if included)
   - Or, directly from the `AUTOCOPASI.zip` archive provided.

2. **Extract the Files**

   If you have a ZIP archive (e.g., `AUTOCOPASI.zip`), extract it to your desired location using your system's file explorer or the terminal:

   .. code-block:: bash

      unzip AUTOCOPASI.zip

   This will create a folder containing the AUTOCOPASI Python scripts and associated files.

Python Environment Setup
------------------------

AUTOCOPASI is compatible with Python 3 and requires a small set of dependencies. It is recommended to use the same Conda environment as SPECI for seamless workflow integration.

1. **Ensure Python is Installed**

   SPECI’s recommended environment (`speci-env`) includes all typical dependencies.

2. **Install Required Packages (if needed)**

   If using a separate environment, ensure the following packages are available:

   - `pandas`
   - `numpy`
   - `lxml`
   - `xml.etree.ElementTree` (standard in Python 3)
   - Any other libraries specified in the AUTOCOPASI README or requirements.txt

   Install them with pip if needed:

   .. code-block:: bash

      pip install pandas numpy lxml

Usage & Integration
-------------------

1. **Running AUTOCOPASI**

   Navigate to the AUTOCOPASI directory and run the main script, e.g.:

   .. code-block:: bash

      python AUTOCOPASI.py

   (Replace `AUTOCOPASI.py` with the actual script name if different.)

2. **Input Files**

   - AUTOCOPASI expects input files (reaction network, species list, kinetic parameters) generated by SPECI or prepared manually.
   - Make sure all paths and filenames are correct and adjust any configuration variables as needed.

3. **Output**

   - Results (COPASI models, kinetic analysis, simulation outputs) will be saved in the output directory specified in the script.
   - Review the output files for COPASI-compatible formats (`.cps`, `.xml`) for further simulation and visualization.

Best Practices
--------------

- Keep AUTOCOPASI scripts together with your project files for reproducibility.
- Always check the script header or README for specific requirements, updates, or usage notes.
- For detailed kinetic analysis, consider visualizing results directly in [COPASI](https://copasi.org/).

Troubleshooting & Support
-------------------------

- For issues running AUTOCOPASI, consult error messages for missing dependencies or file path errors.
- If additional help is needed, open an issue on the main repository or contact the script author.

References & Related Links
--------------------------

- [COPASI Project](https://copasi.org/)
- [SPECI Documentation](index.html)