AGENTS.md

Agent Instructions for sdrf-pipelines

Package Manager

Use uv (not pip):

uv sync --group dev
uv run pytest
uv run pre-commit run --all-files

Related Repositories

• sdrf-templates: YAML schema definitions (submodule at src/sdrf_pipelines/sdrf/sdrf-templates). Template changes go there, not here.
• proteomics-metadata-standard: SDRF-Proteomics specification and guidelines.

Style

• Type hints required, checked by mypy
• Format with ruff format, lint with ruff check
• Run pre-commit run --all-files before committing

Testing

• Use ErrorCode enums and ValidationManifest in tests, not string matching on error messages
• Skip slow ontology tests by default; use --run-ontology to include them

Auto-generated Files

• COMMANDS.md: Auto-generated from CLI help. Don't edit manually.

CLI

parse_sdrf --help
parse_sdrf validate-sdrf -s file.sdrf.tsv