Add tests, sequence viewer, loading skeletons, pagination, CI pipeline#1
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marcoloco23 merged 4 commits intomainfrom Mar 1, 2026
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- API tests: 42 pytest tests covering all endpoints (search, taxa, graph,
neighbors, sequences) plus MI distance unit tests
- Sequence viewer: new /taxa/{id}/sequences page with color-coded DNA bases,
composition bar chart, and expandable sequence cards
- Loading skeletons: shimmer animations for taxon detail and graph pages
replacing plain "Loading..." text
- Children pagination: /taxa/{id}/children endpoint with offset/limit,
inline limit of 100 with "load more" button on frontend
- Mobile responsive: additional breakpoints at 768px and 480px
- CI pipeline: GitHub Actions workflow for lint, typecheck, test, build
- Include sequence data in API response for viewer display
- Fix pyproject.toml build backend (hatchling.backends -> hatchling.build)
https://claude.ai/code/session_01NKQ34hreauk5SGYfSPEWFT
Documents architecture, conventions, pipeline order, testing strategy, type consistency rules, and remaining work for autonomous development. https://claude.ai/code/session_01NKQ34hreauk5SGYfSPEWFT
- Graph page: node search/filter with autocomplete dropdown and camera zoom - Pipeline tests: 11 tests for canonical selection scoring logic (53 total) - MI network endpoint: in-memory cache with 5-minute TTL - Dockerfile health checks: API, Web, PostgreSQL, Redis - docker-compose: service health checks with depends_on conditions - Fix all ruff lint warnings (unused imports, f-string, unused variable) - Fix Cytoscape type: Stylesheet → StylesheetStyle for newer @types - Update TODO.md and CLAUDE.md with current status https://claude.ai/code/session_01NKQ34hreauk5SGYfSPEWFT
Database: - Migration 002: pg_trgm GIN index for ILIKE search, composite indexes for neighbor queries (src_ott_id, distance), canonical checks (ott_id, is_canonical), pipeline selection (ott_id, marker), rank filtering - Connection pooling: 10 persistent + 20 overflow, pre-ping, 5min recycle Query optimization: - Lineage: recursive CTE replaces N+1 individual parent lookups - Subtree: recursive CTE replaces Python BFS with per-level queries - Canonical check: EXISTS subquery instead of fetching full row - Search: LIKE pattern escaping, prefix matches ranked first API: - GZip middleware compresses responses > 500 bytes - Updated MockDB to support execute() and exists() for CTE tests https://claude.ai/code/session_01NKQ34hreauk5SGYfSPEWFT
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neighbors, sequences) plus MI distance unit tests
composition bar chart, and expandable sequence cards
replacing plain "Loading..." text
inline limit of 100 with "load more" button on frontend
https://claude.ai/code/session_01NKQ34hreauk5SGYfSPEWFT