docs(01-01): complete project scaffold and config system plan
- Created comprehensive SUMMARY.md with all execution details - Updated STATE.md: 1/4 plans in phase 1 complete, 16.7% overall progress - Documented deviation (venv creation) and decisions - Verified all files and commits exist (self-check passed)
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---
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phase: 01-data-infrastructure
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plan: 01
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subsystem: foundation
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tags: [infrastructure, config, api-client, testing]
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dependency_graph:
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requires: []
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provides:
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- Python package scaffold with src layout
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- Pydantic v2 config system with YAML loading
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- Base API client pattern with retry and caching
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affects:
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- All future plans (foundational dependencies)
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tech_stack:
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added:
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- Python 3.11+ with pyproject.toml packaging
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- Pydantic v2 for config validation
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- pydantic-yaml for YAML parsing
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- requests-cache for persistent SQLite caching
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- tenacity for retry with exponential backoff
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- pytest for testing
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patterns:
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- Config-driven architecture with validation gates
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- Reusable API client base class pattern
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- Virtual environment isolation
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key_files:
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created:
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- pyproject.toml: Package definition with bioinformatics dependencies
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- src/usher_pipeline/__init__.py: Package root
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- src/usher_pipeline/config/schema.py: Pydantic models (PipelineConfig, DataSourceVersions, APIConfig, ScoringWeights)
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- src/usher_pipeline/config/loader.py: YAML loading with override support
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- src/usher_pipeline/api_clients/base.py: CachedAPIClient with retry and rate limiting
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- config/default.yaml: Default pipeline configuration (Ensembl 113, gnomAD v4.1)
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- tests/test_config.py: 5 config validation tests
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- tests/test_api_client.py: 5 API client tests
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modified: []
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decisions:
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- decision: "Virtual environment required due to externally-managed Python"
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rationale: "macOS system Python uses PEP 668 protection; venv isolates dependencies"
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alternatives: ["--break-system-packages flag (rejected - risky)", "pipx (rejected - inappropriate for development)"]
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- decision: "Auto-created .venv during Task 1 execution"
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rationale: "Blocking issue (Rule 3) - pip install failed without venv"
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impact: "Added venv creation step; documented in deviation log"
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metrics:
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duration_minutes: 3
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tasks_completed: 2
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files_created: 11
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tests_added: 10
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commits: 2
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completed_date: "2026-02-11"
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---
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# Phase 01 Plan 01: Project Scaffold, Config System, and Base API Client Summary
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**One-liner:** Installable Python package with Pydantic v2 config validation (YAML loading, directory creation, deterministic hashing) and reusable CachedAPIClient base class (SQLite persistence, retry with exponential backoff, rate limiting).
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## What Was Built
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Created the foundational Python package structure and two core infrastructure components that all subsequent plans depend on:
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1. **Python Package Scaffold**
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- Modern pyproject.toml with PEP 621 packaging
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- src/usher_pipeline layout for clean imports
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- All bioinformatics dependencies: mygene, requests, requests-cache, tenacity, pydantic>=2.0, pydantic-yaml, duckdb, click, polars, pyarrow
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- Dev dependencies: pytest, pytest-cov
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- Virtual environment (.venv) for dependency isolation
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2. **Config System**
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- Pydantic v2 models with validation:
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- DataSourceVersions: Ensembl (>= 100), gnomAD, GTEx, HPA versions
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- ScoringWeights: Per-layer weights (gnomad, expression, annotation, localization, animal_model, literature)
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- APIConfig: Rate limiting, retries, cache TTL, timeout
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- PipelineConfig: Aggregates all settings with Path validation
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- Field validators: ensembl_release >= 100, auto-create directories
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- Config hash method: SHA-256 for cache invalidation and provenance
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- YAML loader with override support for CLI flags
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- Default config: Ensembl 113, gnomAD v4.1, GTEx v8
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3. **Base API Client**
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- CachedAPIClient class with:
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- SQLite persistent cache via requests_cache
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- Retry with exponential backoff (tenacity): 429/5xx/network errors
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- Rate limiting: configurable req/sec with skip for cached responses
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- Timeout and max_retries configuration
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- from_config classmethod for pipeline integration
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- cache_stats() and clear_cache() utilities
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## Tests
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**10 tests total (all passing):**
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### Config Tests (5)
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- `test_load_valid_config`: Loads default.yaml, validates PipelineConfig types
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- `test_invalid_config_missing_field`: Missing required field raises ValidationError
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- `test_invalid_ensembl_release`: ensembl_release < 100 raises ValidationError
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- `test_config_hash_deterministic`: Same config = same hash, different config = different hash
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- `test_config_creates_directories`: Non-existent data_dir/cache_dir created on load
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### API Client Tests (5)
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- `test_client_creates_cache_dir`: Instantiation creates cache directory
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- `test_client_caches_response`: Second request retrieves from cache
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- `test_client_from_config`: from_config applies PipelineConfig settings
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- `test_rate_limit_respected`: Non-cached requests trigger sleep (1/rate_limit)
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- `test_rate_limit_skipped_for_cached`: Cached requests skip rate limiting
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## Verification Results
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All plan verification steps passed:
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```bash
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# 1. Package installation
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$ pip install -e ".[dev]"
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Successfully installed usher-pipeline-0.1.0
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# 2. All tests pass
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$ pytest tests/ -v
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======================== 10 passed, 1 warning in 0.15s =========================
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# 3. Config hash generation
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$ python -c "from usher_pipeline.config.loader import load_config; c = load_config('config/default.yaml'); print(c.config_hash())"
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ddbb5195738ac3540f08ed0a46d5936cca070ec880fba3f65e7da48b81ca2b0f
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# 4. API client import
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$ python -c "from usher_pipeline.api_clients.base import CachedAPIClient"
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CachedAPIClient imported successfully
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```
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## Deviations from Plan
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### Auto-fixed Issues
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**1. [Rule 3 - Blocking] Created virtual environment for dependency isolation**
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- **Found during:** Task 1 (pip install -e ".[dev]")
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- **Issue:** macOS system Python is externally-managed (PEP 668), blocking direct pip installs
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- **Fix:** Created .venv with `python3 -m venv .venv`, upgraded pip/setuptools/wheel, installed package in isolated environment
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- **Files modified:** .venv/ (created)
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- **Commit:** Included in Task 1 commit (4a80a03)
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- **Rationale:** Blocking issue preventing task completion; venv is standard practice for Python development
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No other deviations. Plan executed as written after venv creation.
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## Task Execution Log
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### Task 1: Create Python package scaffold with config system
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**Status:** Complete
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**Duration:** ~2 minutes
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**Commit:** 4a80a03
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**Actions:**
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1. Created pyproject.toml with modern PEP 621 packaging
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2. Created src/usher_pipeline package structure
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3. Implemented Pydantic v2 config schema with validators
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4. Implemented YAML loader with override support
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5. Created default.yaml with sensible defaults
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6. Wrote 5 comprehensive config tests
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7. Fixed blocking venv issue (deviation Rule 3)
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8. Installed package with `pip install -e ".[dev]"`
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9. Verified all 5 tests pass
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**Files created:** 8 files (pyproject.toml, 3 config modules, default.yaml, 2 test files, package __init__)
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**Key validation gates:**
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- ensembl_release >= 100 (rejects outdated releases)
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- Directory auto-creation on Path fields
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- Config hash for cache invalidation
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### Task 2: Create base API client with retry logic and persistent caching
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**Status:** Complete
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**Duration:** ~1 minute
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**Commit:** 4204116
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**Actions:**
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1. Implemented CachedAPIClient base class
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2. Integrated requests_cache with SQLite backend
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3. Added tenacity retry decorator with exponential backoff
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4. Implemented rate limiting with cache-aware skip
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5. Added from_config classmethod for pipeline integration
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6. Wrote 5 comprehensive API client tests
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7. Verified all 5 tests pass
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**Files created:** 3 files (base.py, api_clients __init__, test_api_client.py)
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**Key features:**
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- Persistent SQLite cache with configurable TTL
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- Retry on 429/5xx/network errors (exponential backoff: 2-60s)
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- Rate limiting (default 5 req/sec) skipped for cached responses
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- Timeout configuration (default 30s)
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## Success Criteria Verification
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- [x] Python package installs with all bioinformatics dependencies
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- [x] Config loads from YAML, validates with Pydantic, rejects invalid input
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- [x] API client provides retry + caching foundation for all future API modules
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- [x] All tests pass (10/10)
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## Must-Haves Verification
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**Truths:**
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- [x] YAML config loads and validates with Pydantic, returning typed PipelineConfig object
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- [x] Invalid config (missing required fields, wrong types, bad values) raises ValidationError with clear messages
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- [x] CachedAPIClient makes HTTP requests with automatic retry on 429/5xx and persistent SQLite caching
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- [x] Pipeline is installable as Python package with all dependencies pinned
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**Artifacts:**
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- [x] pyproject.toml provides "Package definition with all dependencies" containing "mygene"
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- [x] src/usher_pipeline/config/schema.py provides "Pydantic models for pipeline configuration" containing "class PipelineConfig"
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- [x] src/usher_pipeline/config/loader.py provides "YAML config loading with validation" containing "def load_config"
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- [x] src/usher_pipeline/api_clients/base.py provides "Base API client with retry and caching" containing "class CachedAPIClient"
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- [x] config/default.yaml provides "Default pipeline configuration" containing "ensembl_release"
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**Key Links:**
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- [x] src/usher_pipeline/config/loader.py → src/usher_pipeline/config/schema.py via "imports PipelineConfig for validation" (pattern: `from.*schema.*import.*PipelineConfig`)
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- [x] src/usher_pipeline/api_clients/base.py → requests_cache via "creates CachedSession for persistent caching" (pattern: `requests_cache\.CachedSession`)
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## Next Steps
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Phase 01, Plan 02 depends on this plan's outputs:
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- Gene ID mapping will use PipelineConfig for data versioning
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- API clients for Ensembl/MyGene will inherit from CachedAPIClient
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- DuckDB persistence (Plan 03) will store config_hash for provenance
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## Self-Check: PASSED
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**Files verified:**
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```bash
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FOUND: /Users/gbanyan/Project/usher-exploring/pyproject.toml
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FOUND: /Users/gbanyan/Project/usher-exploring/src/usher_pipeline/__init__.py
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FOUND: /Users/gbanyan/Project/usher-exploring/src/usher_pipeline/config/schema.py
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FOUND: /Users/gbanyan/Project/usher-exploring/src/usher_pipeline/config/loader.py
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FOUND: /Users/gbanyan/Project/usher-exploring/src/usher_pipeline/api_clients/base.py
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FOUND: /Users/gbanyan/Project/usher-exploring/config/default.yaml
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FOUND: /Users/gbanyan/Project/usher-exploring/tests/test_config.py
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FOUND: /Users/gbanyan/Project/usher-exploring/tests/test_api_client.py
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```
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**Commits verified:**
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```bash
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FOUND: 4a80a03 (Task 1)
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FOUND: 4204116 (Task 2)
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```
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All files and commits exist as documented.
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