Style: PEP 8; 4‑space indents; add type hints where practical.
Naming: functions/variables
```
snake_case
```
, classes
```
CapWords
```
, modules
```
lower_snake_case
```
.
Imports: stdlib → third‑party → local, grouped and alphabetized.
Docstrings: concise, imperative summaries; include Args/Returns when helpful.

Testing Guidelines

Framework:
```
pytest
```
.
Layout: tests live in
```
tests/
```
; files named
```
test_*.py
```
; functions
```
test_*
```
.

Example: validate

getSnake

with

tests/make_files/workflow_common.smk

targets.

Coverage focus: core package
```
snakehelper
```
; prefer unit tests over heavyweight integration.

Commit & Pull Request Guidelines

Commits: short, imperative summaries (e.g., "add option to skip working dir change"); optional tags like
```
[feature]
```
,
```
[doc]
```
as seen in history.
PRs: describe change, rationale, and scope; link issues; include updated tests and relevant logs/screens.
Expectations: PRs pass
```
pytest
```
locally; keep diffs minimal and focused.

Security & Configuration Tips

Windows builds: Snakemake may require Microsoft C++ Build Tools (see README screenshots).
Interactive dev: set
```
SNAKEMAKE_DEBUG_ROOT
```
(or add to
```
.env
```
) to auto‑switch working dir when exploring in notebooks/VS Code.
Secrets: never commit credentials;
```
.env
```
is for local use only and should not contain production secrets.

Repository Guidelines

Project Structure & Module Organization

Source:
```
src/snakehelper/
```
(core logic in
```
SnakeIOHelper.py
```
).

Tests:

tests/

(e.g.,

tests/test_snakehelper.py

; sample Snakefile in

tests/make_files/

Docs & examples:
```
docs/
```
,
```
examples/
```
.
Build/config:
```
pyproject.toml
```
,
```
.coveragerc
```
,
```
uv.lock
```
.

Build, Test, and Development Commands

*- Environment: Python 3.11+.

Install (editable):
```
pip install -e .
```
(or
```
uv pip install -e .
```
).
Run tests:
```
uv run pytest -q
```
from repo root.

Coverage:

uv run pytest -q --cov=snakehelper

(honors

.coveragerc

; requires

pytest-cov

Clean caches: remove
```
__pycache__/
```
,
```
.pytest_cache/
```
, and
```
.snakemake/
```
if needed.

Coding Style & Naming Conventions

Style: PEP 8; 4‑space indents; add type hints where practical.
Naming: functions/variables
```
snake_case
```
, classes
```
CapWords
```
, modules
```
lower_snake_case
```
.
Imports: stdlib → third‑party → local, grouped and alphabetized.
Docstrings: concise, imperative summaries; include Args/Returns when helpful.

Testing Guidelines

Framework:
```
pytest
```
.
Layout: tests live in
```
tests/
```
; files named
```
test_*.py
```
; functions
```
test_*
```
.

Example: validate

getSnake

with

tests/make_files/workflow_common.smk

targets.

Coverage focus: core package
```
snakehelper
```
; prefer unit tests over heavyweight integration.

Commit & Pull Request Guidelines

Commits: short, imperative summaries (e.g., "add option to skip working dir change"); optional tags like
```
[feature]
```
,
```
[doc]
```
as seen in history.
PRs: describe change, rationale, and scope; link issues; include updated tests and relevant logs/screens.
Expectations: PRs pass
```
pytest
```
locally; keep diffs minimal and focused.

Security & Configuration Tips

Windows builds: Snakemake may require Microsoft C++ Build Tools (see README screenshots).
Interactive dev: set
```
SNAKEMAKE_DEBUG_ROOT
```
(or add to
```
.env
```
) to auto‑switch working dir when exploring in notebooks/VS Code.
Secrets: never commit credentials;
```
.env
```
is for local use only and should not contain production secrets.

Repository Guidelines

Repository Guidelines

Project Structure & Module Organization

Build, Test, and Development Commands

Coding Style & Naming Conventions

Testing Guidelines

Commit & Pull Request Guidelines

Security & Configuration Tips

Related Skills

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Repository Guidelines

Project Structure & Module Organization

Build, Test, and Development Commands

Coding Style & Naming Conventions

Testing Guidelines

Commit & Pull Request Guidelines

Security & Configuration Tips