[rosspeili]

Description

Fixes #427

Introduces the new bio life-sciences category and the foundational bio/sequence_ops (v0.1.0) skill bundle adhering to Manifest v2 Universal Taxonomy standards.

Acceptance Criteria Mapping

• Sequence operations engine: skills/bio/sequence_ops/ops.py (typing, validation, revcom, transcription, multi-table translation, Needleman-Wunsch/Smith-Waterman alignment, variant calling, 6-frame ORF discovery, k-mer entropy, and FASTA export).
• Skill execution & envelopes: skills/bio/sequence_ops/skill.py (subclasses BaseSkill, resolves parameter aliases, returns structured envelopes).
• Manifest v2 contract: skills/bio/sequence_ops/manifest.yaml (shape: atomic, tier: core, 10 governed tags, full schema).
• Directive & Presentation: skills/bio/sequence_ops/instructions.md (persona-free directive) and skills/bio/sequence_ops/card.json + tests/fixtures/card_ui_schema/bio__sequence_ops.json.
• Knowledge Base: skills/bio/sequence_ops/kb/ (codon_table.json, genetic_codes.json, iupac_codes.json, amino_acids.json).
• Tests & Assurance: skills/bio/sequence_ops/test_skill.py (24 unit tests) and tests/skills/bio/test_sequence_ops_simulations.py (8 multi-step biology simulations and stress tests).
• Category docs & catalog: docs/skills/bio/README.md (category hub) and docs/skills/bio/sequence_ops.md (5 provider loops: Gemini, Claude, OpenAI, DeepSeek, Ollama).
• Repo governance & index: README.md, docs/skills/README.md, docs/sitemap.md, docs/usage/agent_loops.md, .github/labels.json, .github/ISSUE_TEMPLATE/01_skill_proposal.yml, and CHANGELOG.md.
• Packaging & Extras: skillware/core/extras.py ("biopython": "Bio" alias) and synced pyproject.toml extras.
• Runnable demo: examples/bio_sequence_ops_demo.py and examples/README.md.

Type of Change

• New Skill — new registry bundle under skills/
• Skill Upgrade — changes to an existing skill under skills/
• Bug Fix — incorrect runtime or framework behavior
• Documentation — docs, README, CONTRIBUTING only
• Framework Feature — skillware/core/ loader, env, adapters
• CLI — skillware/cli.py, docs/usage/cli.md
• Examples — examples/*.py, agent loops, examples/README.md
• Packaging — PyPI wheel, pyproject.toml, MANIFEST.in
• RFC / meta — templates, labels, CI, or large design doc

Checklist (all PRs)

• Linked GitHub issue (Fixes #427)
• Scope matches the issue — no unrelated refactors
• Contribution complies with Legal notice and code ownership (original work, MIT license grant, no malicious logic)
• python -m black --check ., flake8, and ruff check . pass locally (or CI-equivalent subset)
• pytest skills/ and pytest tests/ pass locally when relevant
• CHANGELOG.md updated under [Unreleased] when user-visible behavior changes
• examples/README.md updated if this PR adds, renames, or removes a runnable script
• Ran pytest tests/test_registry_docs.py when skills, examples index, or agent-loops matrix changed
• Ran pytest tests/test_skill_docs.py when catalog Usage Examples or provider snippets changed

New or updated skill

Bundle and metadata

• Skill at skills/bio/sequence_ops/
• manifest.yaml: name (bio/sequence_ops), version (0.1.0), description, parameters, constitution, real issuer
• Optional: short_description, issuer.github, issuer.org, requirements, env_vars

Effect, Directive, Assurance

• Deterministic skill.py (Effect; purely offline in-silico Biopython operations)
• instructions.md (Directive) explains when and how to use the skill without persona framing
• card.json (Presentation) issuer matches manifest (rosspeili / ARPAHLS)
• test_skill.py (Assurance) covers execution, all 11 actions, and schema expectations (24 tests pass)
• SkillLoader.load_skill("bio/sequence_ops") succeeds

Documentation and catalog

• docs/skills/bio/sequence_ops.md, category hub row in docs/skills/bio/README.md, row in docs/skills/README.md, and docs/sitemap.md
• Usage Examples for Gemini, Claude, OpenAI, DeepSeek, Ollama per skill usage template

Constitution and safety (skills only)

1. In-Silico Modeling Only: Purely computational evaluations; no medical diagnostic or clinical claims.
2. Strict Determinism: Zero stochastic drift; bitwise-identical results across platforms.
3. Air-gapped Confidentiality: Zero outbound network requests; proprietary sequence strings remain local.
4. No Hallucinated Bases: Rejects unknown alphabets; reports exact IUPAC positions without fabrication.

Related Issues

Fixes #427