Python Conventions

Single source of truth for Python code standards. Other skills reference this.

Copyright Boilerplate

All new source files must start with:

# Copyright (c) 2026 Genome Research Ltd.
#
# Author: Sendu Bala <sb10@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to
# the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Project Layout

pyproject.toml          # single config file (no setup.py, setup.cfg, requirements.txt)
src/<pkg>/              # all source code under src/
  __init__.py
  py.typed              # PEP 561 marker
tests/                  # mirrors src/ structure

• uv for dependency management and virtualenvs. Never pip install directly.
• All tool config (ruff, pyright, pytest) lives in pyproject.toml.

Python 3.14 Specifics

LLMs trained on older code will get these wrong. Pay attention.

• PEP 649 deferred annotations are the default. Do NOT add from __future__ import annotations. It is unnecessary and discouraged. All annotations are evaluated lazily at runtime automatically.
• PEP 728 TypedDict with extra_items. Use closed=True on TypedDicts that should reject extra keys; use extra_items=<type> for known-extra patterns. These replace @final workarounds.
• PEP 742 TypeIs narrowing: use TypeIs[T] (not TypeGuard[T]) for type-narrowing functions that narrow in both branches. TypeGuard only narrows the truthy branch. TypeIs is the default choice now.
• type statement (3.12+): Prefer type Alias = ... over TypeAlias: TypeAlias = .... The type statement supports forward references natively.
• Generic syntax (3.12+): Use class Foo[T]: and def bar[T](x: T) -> T: instead of TypeVar + Generic[T]. Only use TypeVar if you need bound= or constraints= that can't be expressed inline.
• match statements (3.10+): Prefer match/case over long if/elif chains for structural pattern matching where appropriate.
• Exception groups and except* (3.11+): Use for concurrent error handling where multiple exceptions may be raised simultaneously.
• f-string improvements (3.12+): Nested quotes and backslashes are allowed inside f-string expressions. No need for workarounds.

Code Quality

Typing

• Strict mode. No Any. Every function has full parameter and return type annotations. pyright strict must pass clean.
• Use collections.abc for abstract types (Sequence, Mapping, Callable, Iterator, AsyncIterator), not typing equivalents.
• X | None (not Optional[X]). X | Y (not Union[X, Y]).
• Annotated[T, ...] for metadata (Pydantic Field, Typer Option/ Argument).
• Pydantic models for structured data, dataclasses for plain value objects. No raw dicts for structured data.
• Self return type for fluent/builder methods.
• @overload for functions with distinct return types based on input.
• Never for functions that always raise.

Style

• Functions ~30 lines max, excluding type annotations and docstrings.
• Early returns/guard clauses over nested if/else.
• Docstrings on all public modules, classes, functions (imperative mood, one line if sufficient).
• One responsibility per module; filenames describe the responsibility.
• Import grouping: stdlib | third-party | local (enforced by ruff isort).
• __all__ in every public module.
• Context managers (with) for all resource handling.
• Prefer comprehensions over map/filter with lambdas.
• pathlib.Path over os.path.

Pydantic v2

• model_validator, field_validator (not v1 @validator, @root_validator).
• model_dump() / model_validate() (not .dict() / .parse_obj()).
• ConfigDict class attribute (not inner class Config).
• Annotated[T, Field(...)] for field metadata.
• model_json_schema() for JSON Schema export.
• Strict mode where appropriate: model_config = ConfigDict(strict=True).

CLI (Typer)

• Typer app per CLI module. Commands as decorated functions.
• Annotated[T, typer.Option(...)] / Annotated[T, typer.Argument(...)] for all params (not default-value style).
• Rich help panels for grouped options.
• raise typer.Exit(code=1) for errors (not sys.exit).

Error Handling

• Custom exception hierarchy rooted in a project base exception.
• Never bare except: or except Exception: without re-raise or logging.
• logging module with structured fields, not print statements.

Testing (pytest)

• pytest with pytest-asyncio (auto mode) for async tests.
• Fixtures over setup/teardown. tmp_path for filesystem ops.
• pytest.raises for expected exceptions with match= pattern.
• pytest.mark.parametrize for data-driven tests.
• No mutable global state between tests.
• Test files mirror src/ structure: tests/test_<module>.py.
• Assertions use plain assert (pytest introspection rewrites them).
• Follow testing-principles for test intent; this section covers pytest mechanics.
• Every spec.md acceptance test MUST have a corresponding pytest test. No stubs, no hardcoded results, no swallowed failures.

Commands

# Deps
uv sync                                    # install/sync all deps
uv add <pkg>                               # add dependency
uv add --group dev <pkg>                   # add dev dependency

# Tests
uv run pytest tests/ -v                    # all tests
uv run pytest tests/ -v -k <name>          # specific test

# Lint + format
uv run ruff check --fix src/ tests/        # lint + autofix
uv run ruff format src/ tests/             # format
uv run ruff check src/ tests/              # lint check only
uv run ruff format --check src/ tests/     # format check only

# Type checking
uv run pyright                             # strict type check