Agentic Ecology Project Initialization Skill

Use this skill when you need to initialize a fresh, local project directory for ecological modeling workflows (such as bioacoustics or camera trap analysis) without cloning the entire agentic_ecology repository into the user's project workspace.

Workflow Overview

Follow these sequential steps to set up the local workspace:

1. Identify Target Working Directory:
   • Confirm the root directory of the user's project workspace.
2. Initialize Project & Scaffolding:
   • Ensure the target project directory exists.
   • Run uv init --python 3.12 --no-readme && rm main.py in the project directory if it has not already been initialized. This pins .python-version to 3.12, generates .gitignore, initializes version control tracking, and removes the placeholder entrypoint.
   • Install the google-deepmind/agentic_ecology and googlecolab/google-colab-cli (colab-operator) skills locally with npx skills add.
   • Create standard working subdirectories:
     • agent_workspace/: Sandboxed folder for agent scripts, server
     • databases/: Destination folder for Hoplite vector databases.
     • data/: Destination folder for raw datasets (e.g., audio, images).
3. Copy Reference Dependency Configurations:
   • Overwrite the generated pyproject.toml and copy uv.lock from this skill's references/ directory into the target project root.
   • Adjust the package name in pyproject.toml to match the user's project name if desired, keeping all core dependencies (perch-hoplite, speciesnet), constraints, and build configurations intact.
4. Install Workspace Rules (AGENTS.md):
   • Copy the reference AGENTS.md from this skill's references/ directory into the appropriate location in the project workspace to establish standard Agentic Ecology guidelines (compute assessment and offloading protocols, macOS dynamic library deadlock rules, Linux PyTorch/TensorFlow import order rules, and SQL log suppression filters).
5. Synchronize Environment with uv:
   • Execute uv sync from the target project root to create the local virtual environment (.venv) and install all pinned dependencies.
6. Verify Environment Setup:
   • Run a verification command via uv run python to confirm that key libraries (perch_hoplite, speciesnet, soundfile, tensorflow) import cleanly.

Technical Reference

For detailed command options, directory layout specifications, and verification code snippets, see:

• Initialization Technical Reference