maintain-awepep-tooling

name	maintain-awepep-tooling
description	Maintain the awesome-peptide Python tooling and generated README workflow. Use when Codex needs to fix or update awepep package code, Liquid templates, validation checks, pyproject.toml metadata, console scripts, dependency issues, README generation behavior, CI, or documentation for running awe-pep and awe-check.

Maintain Awepep Tooling

Use this skill for code and workflow maintenance in the awesome-peptide repository. Keep tooling changes separate from paper curation unless the user asks for both.

Quick Start

1. Inspect the worktree and relevant code:

git status --short
rg "awe-pep|awe-check|awepep|awecheck|python-liquid|Template|README" .

2. Read the relevant references:

• references/tooling-maintenance.md for package, dependency, and validation behavior.
• references/generated-readme.md for generator/template rules.

3. Install dependencies if validation imports fail:

pip install -e .

4. Run focused checks after changes:

awe-check
python - <<'PY'
from awepep.paper import PaperList
md = PaperList("data/paper.csv").get_md(write=False)
print(len(md), md.splitlines()[0])
PY
awe-pep
git diff -- README.md

Maintenance Workflow

For package, generator, or validation changes:

1. Identify whether the task affects generation, validation, packaging, documentation, or all of them.
2. Read the current implementation before editing. Important files are awepep/paper.py, awepep/template.py, awepep/check.py, awepep/config.py, awepep/main.py, pyproject.toml, CONTRIBUTING.md, README.md, DATABASE.md, and .github/workflows/ci.yml.
3. Preserve the CSV schema and generated Markdown shape unless the user asks for a migration.
4. If changing templates or generation order, regenerate README.md and inspect the diff for unintended content loss.
5. If changing validation logic, test both passing data and at least one failing condition when practical.
6. Keep unrelated paper metadata changes out of tooling fixes.

Known Audit Points

• Runtime package metadata lives in pyproject.toml; keep console scripts, CI, and docs aligned when changing command names.
• README.md contains a top note about update frequency and MolAstra links; keep it in awepep/template.py so regeneration preserves it.
• License metadata should stay aligned with the GPLv3 LICENSE file.
• awepep.check.main should raise validation errors so CI fails on invalid data.

Guardrails

• Use apply_patch for manual source edits.
• Do not run formatters that rewrite unrelated files.
• Do not change taxonomy spelling or CSV content while fixing command/dependency issues unless that is required for the task.
• Treat README.md as generated output except for deliberate template or generator migrations.
• Mention any validation that could not run because dependencies are missing.

References

• Read references/tooling-maintenance.md before source changes.
• Read references/generated-readme.md before changing templates, generation flow, or README.md.