| name | coding-in-python |
| description | 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. |
| related | ["programming-and-coding","running-python","parallel-python","accelerating-python","code-review"] |
| updated | 2026-05-22T00:00:00.000Z |
Coding in Python
Rule: locked env, portable paths, thin notebooks, runnable scripts.
For cluster execution, also load running Python.
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.
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.
Layout
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/....
from pathlib import Path
REPO = Path(__file__).resolve().parents[1]
DATA = REPO / "data" / "raw" / "panel.parquet"
For scripts, accept paths as args:
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
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
uv run ruff format .
uv run ruff check .
Checklist
Further reading
