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boettiger-labboettiger-lab/agent-skills/python-env/SKILL.md

python-env

Skill4 starsChanged 15 days agoBSD-3-ClauseView on GitHub

Never install into or run the system Python. Consult BEFORE `pip install`, before running a Python script or module, and before choosing an interpreter: prefer an existing project venv, then a container image, then a project-local venv you create. Triggers on: pip install, python3 script.py, python -m, venv, virtualenv, uv, conda, "which python", ModuleNotFoundError, externally-managed-environment.

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1 other project uses a version of this.

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We split this skill into the rules it gives an agent

2 rules. About 0 are common, 1 is distinctive, and 1 is very specific to this project.

  • ≈0

    Common · estimate

    Many files like this have a rule of this kind.

  • ≈1

    Distinctive · estimate

    This author's own choices. Worth a look.

  • 1

    Very specific

    Tied to their project's names, files or tools. Probably skip.

  • Common
  • Distinctive
  • Very specific
  1. Very specific:

    Never use system Python directly: Do not pip install into the system environment.

    line 17
  2. Distinctive:

    Always pull the latest image before running:

    line 30

≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.
Files
SKILL.md

Python Environment

Never use system Python directly. Do not pip install into the system environment.

Preferred approaches (in order)

  1. Local venv — Check for a .venv/ or venv/ in the current working directory. If one exists, activate it before running Python:
    source .venv/bin/activate  # or venv/bin/activate

  2. Docker — If no local venv exists, use a container:

    • ghcr.io/boettiger-lab/datasets:latest — DuckDB, GDAL, geopandas, h3, rasterio, pyarrow, and other geospatial/data tooling
    • ghcr.io/rocker-org/ml:latest — R + Python ML stack (torch, scikit-learn, etc.)

    Always pull the latest image before running:

    docker pull ghcr.io/boettiger-lab/datasets:latest

    Example:

    docker run --rm -v "$(pwd):/work" -w /work ghcr.io/boettiger-lab/datasets:latest python3 script.py
  3. Create a venv — If neither option above fits, create a project-local venv:
    python3 -m venv .venv && source .venv/bin/activate && pip install ...

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