feat: add Python bindings

[aaravm]

Adding python bindings for creating structs: Configuration, Transport, ServiceInfo, TES, and adding tests for testing the python bindings. This is done using maturin and pytest, inspired from https://github.com/vemonet/nanopub-rs

Summary by Sourcery

Add Python bindings for the GA4GH SDK using PyO3, enabling interaction with GA4GH services from Python. Implement a Rust module for the TES API, providing task management functionalities. Include comprehensive tests for both the Python bindings and the Rust TES client.

New Features:

• Introduce Python bindings for the GA4GH SDK, allowing interaction with GA4GH services through Python using PyO3.
• Add support for creating and managing tasks in the GA4GH Task Execution Service (TES) via Python bindings.

Enhancements:

• Implement a new module in Rust for interacting with the TES API, including functionalities for creating, retrieving, canceling, and listing tasks.

Documentation:

• Add a README file for the Python bindings, providing instructions for installation, development, and building the Python package.

Tests:

• Add unit tests for the Python bindings using pytest to ensure the functionality of the Configuration, Transport, ServiceInfo, and TES classes.
• Include tests for the Rust TES client to verify task creation, status retrieval, cancellation, and task listing.

[sourcery-ai[bot]]

Reviewer's Guide by Sourcery

This pull request adds Python bindings for the GA4GH SDK, focusing on creating structs like Configuration, Transport, ServiceInfo, TES, and adding tests for these bindings. The implementation uses maturin for building Python extensions and pytest for testing. The changes include modifications to the Rust TES client, addition of Python bindings, and creation of Python tests and documentation.

Class diagram for TES and Task structs with Python bindings

classDiagram
    class TES {
        +Configuration config
        +Result<Service, Box<dyn std::error::Error>> service
        +Transport transport
        +new(config: &Configuration) Result<Self, Box<dyn std::error::Error>>
        +create(task: TesTask) Result<Task, Box<dyn std::error::Error>>
        +get(view: &str, id: &str) Result<TesTask, Box<dyn std::error::Error>>
        +list_tasks(params: Option<ListTasksParams>) Result<TesListTasksResponse, Box<dyn std::error::Error>>
    }
    class Task {
        +String id
        +Transport transport
        +new(id: String, transport: Transport) Self
        +status() Result<TesState, Box<dyn std::error::Error>>
        +cancel() Result<serde_json::Value, Box<dyn std::error::Error>>
    }
    TES --> Task
    TES --> Transport
    TES --> Configuration
    TES --> Service
    Task --> Transport
    class PyTES {
        +TES inner
        +new(config: &PyConfiguration) PyResult<Self>
        +create(task: &PyTesTask) PyResult<PyTask>
        +get(view: &str, id: &str) PyResult<PyTesTask>
    }
    class PyTask {
        +Task inner
        +new(id: String, transport: &PyTransport) PyResult<Self>
        +status() PyResult<String>
        +cancel() PyResult<String>
    }
    PyTES --> TES
    PyTask --> Task
    class PyConfiguration {
        +Configuration inner
        +new(base_path: String) PyResult<Self>
        +set_base_path(base_path: String) PyResult<()>
        +get_base_path() String
    }
    class PyTransport {
        +Transport inner
        +new(py_config: &PyConfiguration) PyResult<Self>
        +get(endpoint: String, params: Option<String>) PyResult<String>
        +post(endpoint: String, data: Option<String>) PyResult<String>
        +put(endpoint: String, data: String) PyResult<String>
        +delete(endpoint: String) PyResult<String>
    }
    PyConfiguration --> Configuration
    PyTransport --> Transport

File-Level Changes

Change	Details	Files
Implemented Python bindings for GA4GH SDK structs	Created PyO3 bindings for Configuration, Transport, ServiceInfo, TES, and Task structs Implemented methods for each struct to expose functionality to Python Added error handling and conversion between Rust and Python types Created a Python module initialization function	python/src/lib.rs
Modified TES client implementation in Rust	Added documentation for TES client methods Implemented new methods for TES client (create, get, list_tasks) Added structs for ListTasksParams and TesListTasksResponse Improved error handling and added more comprehensive tests	lib/src/clients/tes/mod.rs lib/src/clients/tes/model.rs
Added Python tests for the new bindings	Created test cases for Configuration, Transport, ServiceInfo, and TES classes Implemented mock objects and patching for testing HTTP requests Added tests for various HTTP methods (GET, POST, PUT, DELETE)	python/tests/test_all.py python/tests/__init__.py
Added documentation and build instructions for Python bindings	Created a README with installation and usage instructions Added information about development and testing processes Included instructions for building the wheel using maturin	python/README.md

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[pavelnikonorov]

@Xforsa thanks for reviewing!