Update virtual ecosystem to latest version + lots of renaming

[alexdewar]

This PR updates Virtual Ecosystem to the latest version. We were previously using a version that was sufficiently old that it was still called Virtual Rainforest, so I had to rename a few things to make it work. Besides that, there was one small tweak to the Snakefile that was needed to find the example data path correctly.

I figured I should rename all the documentation/code in this repo to use "Ecosystem" too while I was at it.

The newer version of VE supports Python 3.12 (but not Python 3.13), so I've added support for that to this repo too.

Closes #50. Closes #40.

[Copilot]

Pull Request Overview

This PR updates the repository to use Virtual Ecosystem instead of Virtual Rainforest. Key changes include:

• Renaming of resources, experiments, and associated variables from “VR” to “VE” across config files, tests, and helper modules.
• Updates to documentation, dependency names, and project metadata (pyproject.toml and README.md) to reflect the new naming.
• Adjustments in test cases and mock patches to ensure consistency with the new VE naming.

Reviewed Changes

Copilot reviewed 8 out of 12 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
workflow-profile/config.yaml	Renamed resource key from “vr” to “ve”.
tests/test_ve_experiment.py	Updated test fixture, class references, and log file names to “VE”.
snakemake_helper/ve_experiment.py	Changed imports, log file name, and experiment class from VR to VE.
snakemake_helper/init.py	Updated the default export to use VEExperiment.
pyproject.toml	Adjusted project name, description, and dependency names to “ecosystem”.
README.md	Updated title, badges, and repository links to reflect the new naming.

Files not reviewed (4)

• .gitmodules: Language not supported
• Snakefile: Language not supported
• virtual_ecosystem: Language not supported
• virtual_rainforest: Language not supported