# Coding In Python

> How to write Python well — uv environments, formatting, CLI scripts, logging, seeds. TRIGGER when authoring or editing .py files. For running Python on the Yale SOM HPC cluster (sbatch, Slurm, uv on /gpfs), use running-python instead.

- **Type:** Skill
- **Install:** `agentstack add skill-yale-som-hpc-claude-code-marketplace-coding-in-python`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [yale-som-hpc](https://agentstack.voostack.com/s/yale-som-hpc)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** Unlicense
- **Upstream author:** [yale-som-hpc](https://github.com/yale-som-hpc)
- **Source:** https://github.com/yale-som-hpc/claude-code-marketplace/tree/main/plugins/hpc/skills/coding-in-python

## Install

```sh
agentstack add skill-yale-som-hpc-claude-code-marketplace-coding-in-python
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Coding in Python

Rule: locked env, portable paths, thin notebooks, runnable scripts.

For cluster execution, also load [running Python](../running-python/SKILL.md).

## Defaults

- `uv` for envs and lockfiles. Commit `pyproject.toml` and `uv.lock`; ignore `.venv/`.
- `ruff` for format + lint.
- `pathlib` for paths.
- `argparse` for scripts. Use `click` only for real subcommands.
- `logging`, not scattered `print()`, for long runs.
- `pytest` for reusable logic; smoke tests for analysis scripts.

```bash
uv init --app
uv add polars pyarrow duckdb pandas statsmodels
uv add --dev ruff pytest
uv sync --frozen
```

On HPC: sync/setup before large jobs. For long Slurm jobs call `.venv/bin/python` directly; see [running Python](../running-python/SKILL.md).

## Layout

```text
project/
├── pyproject.toml
├── uv.lock
├── README.md
├── scripts/       # entry points
├── src/           # shared helpers, or lib.py for tiny projects
├── notebooks/     # exploration
├── data/raw/      # immutable; usually ignored
├── data/derived/  # rebuildable
└── results/       # figures/tables/logs
```

## Paths

Never commit laptop/user paths: `/Users/...`, `C:\Users\...`, `/home/netid/...`, `/gpfs/scratch60/netid/...`.

```python
from pathlib import Path

REPO = Path(__file__).resolve().parents[1]
DATA = REPO / "data" / "raw" / "panel.parquet"
```

For scripts, accept paths as args:

```python
import argparse
from pathlib import Path

parser = argparse.ArgumentParser()
parser.add_argument("--input", type=Path, required=True)
parser.add_argument("--output", type=Path, required=True)
args = parser.parse_args()
```

## Style

- f-strings.
- Imports at top.
- Type hints on public/helper function signatures.
- `@dataclass(frozen=True)` for small immutable records.
- `pydantic` only for external/untrusted input.
- Context managers for every file/network/DB handle.
- Early returns to reduce nesting.
- Fixed seeds: `rng = np.random.default_rng(42)`; pass `rng` through.

## Logging

```python
import logging

log = logging.getLogger(__name__)

def main() -> None:
    logging.basicConfig(
        level=logging.INFO,
        format="%(asctime)s %(levelname)s %(name)s: %(message)s",
    )
    log.info("starting")
```

Log rows loaded, files written, model dimensions, task IDs.

## Notebooks

- Notebook for exploration/figures.
- Script for batch/rebuild/Slurm.
- Cell >30 lines: move to `src/` or `lib.py`.
- Do not import from notebooks.

## Checks

```bash
uv run ruff format .
uv run ruff check .
```

## Checklist

- [ ] Ruff clean
- [ ] No hardcoded personal paths
- [ ] Seeds set
- [ ] `uv.lock` updated if deps changed
- [ ] Small smoke test run
- [ ] HPC long jobs use `.venv/bin/python`

## Further reading

- [uv](https://docs.astral.sh/uv/)
- [ruff](https://docs.astral.sh/ruff/)
- [pathlib](https://docs.python.org/3/library/pathlib.html)
- [argparse](https://docs.python.org/3/howto/argparse.html)

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [yale-som-hpc](https://github.com/yale-som-hpc)
- **Source:** [yale-som-hpc/claude-code-marketplace](https://github.com/yale-som-hpc/claude-code-marketplace)
- **License:** Unlicense

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** yes
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-yale-som-hpc-claude-code-marketplace-coding-in-python
- Seller: https://agentstack.voostack.com/s/yale-som-hpc
- Browse the marketplace: https://agentstack.voostack.com/browse

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Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.