Using the SPARCED Command Line Interface (CLI)¶

The SPARCED package provides a convenient CLI tool to manage common tasks like compiling models, running simulations, benchmarking, and visualizing results.

This guide explains how to use the sparced CLI tool to streamline your workflows.

Getting Started¶

Before using the CLI, ensure the following:

SPARCED Installed as a CLI Tool: The sparced CLI tool is installed and available in your environment. If not, install it using the requirements file in the project directory:
```
chmod +x requirements.txt
./requirements.txt
```
Verify Installation: Run the following command to verify:
```
sparced --help
```
If installed correctly, this will display the help menu for the CLI.

Common Commands¶

The sparced CLI supports several commands for different operations:

General Usage¶

Use the following syntax:

sparced <command> [options]

Example:

sparced simulate --name SPARCED_standard

Available Commands¶

Compile Models: Compile an Antimony or SBML model:
```
sparced compile --name <model_name> --output <output_directory>
```
- –input: Path to the Antimony or SBML model file.
- –output: Directory to save the compiled model.
Example:
```
sparced compile --name SPARCED_standard --output compiled_models/
```
Run Simulations: Execute simulations using a specified model and condition file:
```
sparced simulate --name <model_name> --condition <condition_file>
```
- –model: Name of the model (e.g., SPARCED_standard).
- –condition: Path to the condition file.
Example:
```
sparced simulate --name SPARCED_standard --condition data/simulation/standard_GeneReg.txt
```
- –benchmark: Name of the benchmark.
- –Observable: Boolean flag for whether the validation pipeline returns all results (False)
or only the observable results (True).

Validate Benchmarks: Compare a model’s output to a benchmark:
```
sparced validate --benchmark <benchmark_file>
```
- –benchmark: Path to the benchmark YAML file.
Example:
```
sparced validate --benchmark benchmarks/TRAIL-response.yml
```

Advanced Options¶

To view all options for a specific command, use the –help flag:

sparced <command> --help

For example:

sparced simulate --help

This will display detailed information about the simulate command and its options.

Examples¶

Here are a few example workflows:

Compile and Run a Model:

sparced compile --name SPARCED_standard
sparced simulate --name SPARCED_standard

Validate a Benchmark:

sparced validate --benchmark benchmarks/TRAIL-response/TRAIL-response.yml

MPI Support¶

The SPARCED CLI supports MPI for parallel processing for (only) the validate function.

To enable MPI, call the mpiexec command before the sparced command:

::: mpiexec -n <num_processes> sparced validate [options]

For example:

::: mpiexec -n 4 sparced simulate –benchmark benchmarks/TRAIL-response/TRAIL-response.yml

Troubleshooting¶

If you encounter issues while using the CLI tool, check the following:

Environment: Ensure the CLI tool is installed in your environment and accessible via the sparced command.
Dependencies: Verify the command line Interface was installed properly:
```
pipx list
```
The output should include sparced.
Log Files: Some commands may produce log files for debugging. Check the output directory for logs.

For additional help, use:

sparced --help