mater 0.7.0

Metabolic Analysis for Transdisciplinary Ecological Research

MATER

Metabolic Analysis for Transdisciplinary Ecological Research

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📋 Requirements

• Python 3.12 or higher

We recommend using one virtual environment per Python project to manage dependencies and maintain isolation. You can use a package manager like uv to help you with library dependencies and virtual environments.

📦 Install the Mater Package

Install the mater package via pip:

pip install mater

⚙️ Run a Simulation

The mater command line interface (CLI) makes it easy to run simulations. Ensure the required Excel input file (chose a compatible version) is located in the root of your working directory.

Run the following command to start a simulation from your excel file:

mater run -i <YOUR_INPUT_FILE_NAME>

📊 Visualize Variables

Simulation results are stored locally in Parquet (.mater) files.

User Interface

Results can be visualize in a built-in user interface. Go to the directory containing the result folder and use the following command :

mater plot -o <YOUR_RESULT_FOLDER_NAME>

Accessing the Results from a Python Script

Below is an example Python script using pandas and matplotlib to plot specific simulation results. Each folder in the output directory corresponds to a variable that can be loaded with pandas.

# Import the MATER package and matplotlib.pyplot
import matplotlib.pyplot as plt
from mater import Mater

# Create a Mater instance
model = Mater()

# Select the output directory where the run results are stored
model.set_output_dir()  # Defaults to the working directory

# Set the run directory name
model.set_run_name("run0")

# Get a variable
in_use_stock = model.get("in_use_stock")

# Transform the dataframe and plot the results
in_use_stock.groupby(level=["location", "object"]).sum().T.plot()
plt.show()

This example demonstrates how to access and plot variables from simulation outputs. Adjust the code to fit your analysis needs.

🤝 Contributing

We welcome contributions to the MATER project! To get started, please refer to the CONTRIBUTING file for detailed guidelines.

📚 Online Documentation

For more information, refer to the official MATER documentation.