styxsingularity 0.2.0

Singularity/Apptainer integration for Styx compiled wrappers

Singularity/Apptainer Runner for Styx compiled wrappers

styxsingularity is a Python package that provides Singularity/Apptainer integration for Styx compiled wrappers. It allows you to run Styx functions within Singularity containers, offering improved isolation and reproducibility for your workflows.

Installation

You can install styxsingularity using pip:

pip install styxsingularity

Usage

from styxdefs import set_global_runner
from styxsingularity import SingularityRunner

# Initialize the SingularityRunner with your container images
runner = SingularityRunner(
    images={
        "ubuntu:20.04": "/path/to/ubuntu_20.04.sif",
        "python:3.9": "/path/to/python_3.9.sif"
    }
)

# Set the global runner for Styx
set_global_runner(runner)

# Now you can use any Styx functions as usual, and they will run in Singularity containers

Advanced Configuration

The SingularityRunner class accepts several parameters for advanced configuration:

• images: A dictionary mapping container image tags to their local paths
• singularity_executable: Path to the Singularity executable (default: "singularity")
• data_dir: Directory for temporary data storage
• environ: Environment variables to set in the container

Example:

runner = SingularityRunner(
    images={"ubuntu:20.04": "/path/to/ubuntu_20.04.sif"},
    singularity_executable="/usr/local/bin/singularity",
    data_dir="/tmp/styx_data",
    environ={"PYTHONPATH": "/app/lib"}
)

Error Handling

styxsingularity provides a custom error class, StyxSingularityError, which is raised when a Singularity execution fails. This error includes details about the return code, command arguments, and Singularity arguments for easier debugging.

Contributing

Contributions to styxsingularity are welcome! Please refer to the GitHub repository for information on how to contribute, report issues, or submit pull requests.

License

styxsingularity is released under the MIT License. See the LICENSE file for details.

Documentation

For detailed API documentation, please visit our API Docs.

Support

If you encounter any issues or have questions, please open an issue on the GitHub repository.

Requirements

• Python 3.10+
• Singularity or Apptainer installed and running on your system

Comparison with styxdocker

While styxdocker and styxsingularity serve similar purposes, they have some key differences:

• Container Technology: styxdocker uses Docker, while styxsingularity uses Singularity/Apptainer.
• Platform Support: styxdocker works on Windows, Linux, and macOS, whereas styxsingularity is not supported on Windows.
• User Permissions: styxdocker can run containers as the current user on POSIX systems, which can help with file permission issues.

Choose the package that best fits your infrastructure and requirements.