WIP: Scaffold Python/Docker CLI architecture for BioSimulators curation (#68)

[dyrpsf]

Problem

This PR addresses Issue #68, aiming to reach Level 5 curation on BioSimulators, which requires a containerized command-line interface.

Architectural Setup

This Draft PR scaffolds the recommended architecture:

1. Py4J Integration: Added py4j to pom.xml and created BioSimulatorsGateway.java to act as the Java-side server for the SBSCL engine.
2. Python CLI: Created biosimulators/main.py utilizing biosimulators-utils to handle SED-ML parsing and interface with the Java Gateway.
3. Containerization: Created a Dockerfile and entrypoint.sh to package the Fat JAR along with its dependencies, initialize the Java server in the background, and expose the Python CLI.
4. Tested: Verified the Docker build and the Python entrypoint locally.

Next Steps

• Submitting this as a WIP to get maintainer feedback on the Py4J/Docker architectural approach before fully mapping the SED-ML tasks.
• Once approved, the main.py script needs the specific SED-ML variables mapped to the sbscl_engine via the Py4J gateway.

[draeger]

I did not spot any obvious errors in the implementation, but I am unsure about the project structure. In particular, is biosimulators in the repository root the right location for the biosimulators.org compatibility code, or should this be placed under src instead? I would appreciate the other reviewer’s opinion before approving.

[dyrpsf]

I did not spot any obvious errors in the implementation, but I am unsure about the project structure. In particular, is biosimulators in the repository root the right location for the biosimulators.org compatibility code, or should this be placed under src instead? I would appreciate the other reviewer’s opinion before approving.

Thank you for the review, @draeger ! I'm really glad the core Py4J and Docker implementation looks solid.

I am completely flexible on the project structure. Since these are Python scripts, a Dockerfile, and shell scripts rather than Java source code, I initially placed them in a root biosimulators directory to keep them distinct from the Maven src tree. However, I can easily move the entire directory inside src/ (or any other preferred location) if that aligns better with the repository's conventions.

I will hold off on making any changes and wait for @matthiaskoenig and @tyzerrr to share their thoughts. Once there is a consensus, I'll update the folder structure immediately!