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Resolved conflict in conf/modules.config by combining: - Published container image from add-ci-cd (ghcr.io/bostongene/pyigmap-fastp:1.0.0) - FastpSingle process support from main (#135) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…eline Implement a comprehensive CI/CD architecture with three separate workflows: - ci.yml: Fast quality checks (lint, type, unit-tests) on every PR/push - Runs in ~5 minutes for immediate feedback - No Docker builds required - Removed component and integration tests - cd.yml: Build and push Docker images on version changes - Added path filter to trigger only on bin/*/pyproject.toml changes - Removed pull_request trigger - Removed add-ci-cd branch from triggers - Only builds when cutting releases (version bumps) - e2e.yml: End-to-end testing after image deployment (new) - Triggers automatically after cd.yml completes successfully - Pulls production images from GHCR - Correctly maps GHCR image names to local tags - Runs component and integration tests against production images Benefits: - Fast feedback loop: quality checks in ~5 min on every PR - Resource efficiency: only build images on version bumps - Production validation: E2E tests use actual GHCR images - Clear separation: CI = quality, CD = build, E2E = validate Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…nd unit tests
Fix CI type checking and unit testing by ensuring all component packages
and their dependencies are available in the root venv:
- pyproject.toml: Add reporter visualization dependencies (panel, plotly,
bokeh, matplotlib, seaborn, logomaker) to dev dependency group
- Required for pyrefly type checker to resolve imports in reporter/viz.py
- justfile: Modify update-dev to install all component packages in editable mode
- Installs pyumi, calib_dedup, reporter, fastp, vidjil, igblast,
cdr3nt-error-corrector, fq-downloader in editable mode
- Allows unit tests to import from component packages using absolute imports
- uv.lock: Update with new dev dependencies
Fixes:
- Type checking: reporter now passes (was failing on missing panel/plotly/bokeh)
- Unit tests: pyumi and cdr3nt-error-corrector tests now pass (were failing on
ModuleNotFoundError for component packages)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Add ffq==0.3.1 to dev dependencies to fix type checking for fq-downloader. The type checker was failing because it couldn't find the ffq.ffq module imported in bin/fq-downloader/src/fq_downloader/run.py. All components now pass type checking with 0 errors. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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