agentic-flow 1.9.0 → 1.9.2

package/agentic-flow/examples/crispr-cas13-pipeline/Cargo.toml

@@ -1,105 +0,0 @@
-[package]
-name = "crispr-cas13-pipeline"
-version = "0.1.0"
-edition = "2021"
-rust-version = "1.75"
-authors = ["rUv <contact@ruv.io>", "Agentic Flow Contributors"]
-description = "High-performance Rust pipeline for CRISPR-Cas13 off-target analysis & immune response profiling in primate models"
-documentation = "https://docs.rs/crispr-cas13-pipeline"
-homepage = "https://ruv.io"
-repository = "https://github.com/ruvnet/agentic-flow"
-license = "MIT"
-keywords = ["crispr", "cas13", "bioinformatics", "genomics", "rna-editing"]
-categories = ["science", "command-line-utilities", "web-programming"]
-readme = "README.md"
-exclude = [
-    ".github/",
-    ".swarm/",
-    ".claude-flow/",
-    "target/",
-    "benchmarks/",
-]
-
-[workspace]
-members = [
-    "crates/data-models",
-    "crates/alignment-engine",
-    "crates/offtarget-predictor",
-    "crates/immune-analyzer",
-    "crates/api-service",
-    "crates/processing-orchestrator",
-]
-
-[dependencies]
-tokio = { version = "1.40", features = ["full"] }
-serde = { version = "1.0", features = ["derive"] }
-serde_json = "1.0"
-anyhow = "1.0"
-thiserror = "1.0"
-tracing = "0.1"
-tracing-subscriber = { version = "0.3", features = ["env-filter"] }
-uuid = { version = "1.10", features = ["v4", "serde"] }
-chrono = { version = "0.4", features = ["serde"] }
-
-# Database
-sqlx = { version = "0.8", features = ["runtime-tokio-native-tls", "postgres", "uuid", "chrono"] }
-mongodb = "3.1"
-
-# API
-axum = "0.7"
-tower = "0.5"
-tower-http = { version = "0.6", features = ["cors", "trace"] }
-
-# Distributed computing
-rdkafka = "0.36"
-redis = { version = "0.27", features = ["tokio-comp", "cluster"] }
-
-# Scientific computing
-ndarray = "0.16"
-bio = "2.0"
-rust-htslib = "0.47"
-
-# Configuration
-config = "0.14"
-dotenv = "0.15"
-
-# Privacy and Cryptography
-rand = "0.8"
-rand_distr = "0.4"
-sha2 = "0.10"
-hex = "0.4"
-
-# Workspace dependencies (will be published separately)
-data-models = { version = "0.1.0", path = "crates/data-models" }
-offtarget-predictor = { version = "0.1.0", path = "crates/offtarget-predictor" }
-immune-analyzer = { version = "0.1.0", path = "crates/immune-analyzer" }
-
-[dev-dependencies]
-criterion = { version = "0.5", features = ["html_reports"] }
-proptest = "1.5"
-mockall = "0.13"
-wiremock = "0.6"
-
-[profile.release]
-opt-level = 3
-lto = "fat"
-codegen-units = 1
-
-[profile.bench]
-inherits = "release"
-
-[[bench]]
-name = "alignment_benchmark"
-harness = false
-
-[[bench]]
-name = "offtarget_prediction_benchmark"
-harness = false
-
-[[bench]]
-name = "immune_analysis_benchmark"
-harness = false
-
-[[bench]]
-name = "comprehensive_benchmarks"
-harness = false

package/agentic-flow/examples/crispr-cas13-pipeline/DELIVERABLES.md

@@ -1,140 +0,0 @@
-# Test Suite Deliverables - CRISPR-Cas13 Pipeline
-
-## 📦 Complete File Inventory
-
-### Unit Tests (5 files, ~2,500 lines)
-1. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/crates/data-models/tests/models_test.rs`
-2. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/crates/alignment-engine/tests/alignment_test.rs`
-3. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/crates/offtarget-predictor/tests/prediction_test.rs`
-4. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/crates/immune-analyzer/tests/analysis_test.rs`
-5. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/crates/api-service/tests/api_test.rs`
-
-### Integration & Property Tests (2 files, ~1,200 lines)
-6. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/tests/integration_test.rs`
-7. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/tests/property_tests.rs`
-
-### Performance Benchmarks (4 files, ~2,400 lines)
-8. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/benches/alignment_benchmark.rs`
-9. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/benches/offtarget_prediction_benchmark.rs`
-10. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/benches/immune_analysis_benchmark.rs`
-11. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/benches/api_benchmark.rs`
-
-### Load Testing Scripts (2 files, ~900 lines)
-12. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/tests/load_testing_k6.js`
-13. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/tests/load_testing_locust.py`
-
-### CI/CD Configuration (1 file, ~250 lines)
-14. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/.github/workflows/ci.yml`
-
-### Documentation (4 files, ~1,900 lines)
-15. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/docs/BENCHMARKS.md`
-16. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/docs/TESTING_GUIDE.md`
-17. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/tests/README.md`
-18. `/workspaces/agentic-flow/agentic-flow/examples/crispr-cas13-pipeline/TEST_SUITE_SUMMARY.md`
-
----
-
-## 📊 Statistics
-
-- **Total Files Created:** 18
-- **Total Lines of Code/Documentation:** ~8,261 lines
-- **Test Cases Defined:** 245+
-- **Benchmark Scenarios:** 50+
-- **Documentation Pages:** 4 comprehensive guides
-
----
-
-## ✅ Completion Checklist
-
-- [x] Unit tests for all 5 crates (data-models, alignment-engine, offtarget-predictor, immune-analyzer, api-service)
-- [x] Integration tests for end-to-end workflows
-- [x] Property-based tests for algorithm correctness
-- [x] Criterion benchmarks for all performance-critical components
-- [x] k6 load testing script with multiple scenarios
-- [x] Locust load testing script with user simulation
-- [x] GitHub Actions CI/CD workflow with multi-service orchestration
-- [x] Comprehensive benchmark report with performance targets
-- [x] Testing guide for contributors
-- [x] Test suite README with quick start
-- [x] Delivery summary with next steps
-
----
-
-## 🎯 Quality Metrics
-
-### Test Coverage
-- Target: >85% for all components
-- Includes: statements, branches, functions, lines
-
-### Performance Targets
-| Component | Metric | Target | Status |
-|-----------|--------|--------|--------|
-| Alignment Engine | Throughput | >10K reads/sec | ✅ Defined |
-| Off-target Predictor | Throughput | >100K sites/sec | ✅ Defined |
-| Immune Analyzer | Analysis Time | <30 sec (20K genes) | ✅ Defined |
-| API Service | Latency (p95) | <200 ms | ✅ Defined |
-| End-to-End Pipeline | Processing Time | <30 min (1M reads) | ✅ Defined |
-
-### CI/CD Pipeline
-- [x] Automated testing on push/PR
-- [x] Code coverage reporting (Codecov integration)
-- [x] Performance regression detection
-- [x] Security audit (cargo-audit)
-- [x] Documentation deployment
-- [x] Multi-service orchestration (PostgreSQL, MongoDB, Redis)
-
----
-
-## 🚀 Usage Instructions
-
-### Run All Tests
-```bash
-cargo test --all-features
-```
-
-### Run Benchmarks
-```bash
-cargo bench --all-features
-```
-
-### Run Load Tests
-```bash
-# k6
-k6 run --vus 100 --duration 5m tests/load_testing_k6.js
-
-# Locust
-locust -f tests/load_testing_locust.py --host=http://localhost:8080
-```
-
-### Generate Coverage
-```bash
-cargo install cargo-tarpaulin
-cargo tarpaulin --all-features --workspace --out Html
-open tarpaulin-report.html
-```
-
----
-
-## 📝 Next Steps
-
-1. **Implementation Phase:** Develop core functionality for each crate
-2. **Test Execution:** Run test suite and iterate on failures
-3. **Performance Tuning:** Run benchmarks and optimize bottlenecks
-4. **Load Testing:** Stress test API and identify scalability limits
-5. **Production Deployment:** Complete CI/CD setup and monitoring
-
----
-
-## 📚 Documentation References
-
-- **Testing Guide:** `docs/TESTING_GUIDE.md` - How to run and write tests
-- **Benchmark Report:** `docs/BENCHMARKS.md` - Performance analysis and targets
-- **Test Suite README:** `tests/README.md` - Quick start and overview
-- **Delivery Summary:** `TEST_SUITE_SUMMARY.md` - Complete deliverable list
-
----
-
-**Agent:** Testing & Benchmarking Agent (SPARC Phase 5)
-**Date:** 2024-10-12
-**Status:** ✅ COMPLETE
-**Version:** 1.0.0

package/agentic-flow/examples/crispr-cas13-pipeline/LICENSE

@@ -1,32 +0,0 @@
-MIT License
-
-Copyright (c) 2025 rUv.io and Agentic Flow Contributors
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
----
-
-## Additional Acknowledgments
-
-This project was built using:
-- SPARC Methodology: https://github.com/ruvnet/agentic-flow
-- rUv.io Platform: https://ruv.io
-
-Scientific algorithms and references are credited in the documentation.
-See docs/SPECIFICATION.md for complete citations.