agentic-flow 1.9.0 → 1.9.1

package/agentic-flow/examples/crispr-cas13-pipeline/.github/workflows/ci.yml

@@ -1,341 +0,0 @@
-name: CI/CD Pipeline
-
-on:
-  push:
-    branches: [ main, develop ]
-  pull_request:
-    branches: [ main, develop ]
-
-env:
-  CARGO_TERM_COLOR: always
-  RUST_BACKTRACE: 1
-
-jobs:
-  # Job 1: Code quality checks
-  lint:
-    name: Lint and Format
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Install Rust toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          components: rustfmt, clippy
-          override: true
-
-      - name: Cache cargo registry
-        uses: actions/cache@v3
-        with:
-          path: ~/.cargo/registry
-          key: ${{ runner.os }}-cargo-registry-${{ hashFiles('**/Cargo.lock') }}
-
-      - name: Cache cargo index
-        uses: actions/cache@v3
-        with:
-          path: ~/.cargo/git
-          key: ${{ runner.os }}-cargo-index-${{ hashFiles('**/Cargo.lock') }}
-
-      - name: Cache cargo build
-        uses: actions/cache@v3
-        with:
-          path: target
-          key: ${{ runner.os }}-cargo-build-target-${{ hashFiles('**/Cargo.lock') }}
-
-      - name: Check code formatting
-        run: cargo fmt --all -- --check
-
-      - name: Run clippy
-        run: cargo clippy --all-targets --all-features -- -D warnings
-
-  # Job 2: Build project
-  build:
-    name: Build
-    runs-on: ubuntu-latest
-    needs: lint
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Install Rust toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          override: true
-
-      - name: Cache cargo dependencies
-        uses: actions/cache@v3
-        with:
-          path: |
-            ~/.cargo/registry
-            ~/.cargo/git
-            target
-          key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}
-
-      - name: Build workspace
-        run: cargo build --release --all-features
-
-      - name: Archive build artifacts
-        uses: actions/upload-artifact@v3
-        with:
-          name: build-artifacts
-          path: target/release/
-          retention-days: 7
-
-  # Job 3: Unit and integration tests
-  test:
-    name: Test
-    runs-on: ubuntu-latest
-    needs: build
-
-    services:
-      postgres:
-        image: postgres:16
-        env:
-          POSTGRES_USER: test_user
-          POSTGRES_PASSWORD: test_password
-          POSTGRES_DB: crispr_test
-        ports:
-          - 5432:5432
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-
-      mongodb:
-        image: mongo:7
-        env:
-          MONGO_INITDB_ROOT_USERNAME: test_user
-          MONGO_INITDB_ROOT_PASSWORD: test_password
-        ports:
-          - 27017:27017
-        options: >-
-          --health-cmd "mongosh --eval 'db.runCommand({ping: 1})'"
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-
-      redis:
-        image: redis:7-alpine
-        ports:
-          - 6379:6379
-        options: >-
-          --health-cmd "redis-cli ping"
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Install Rust toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          override: true
-
-      - name: Cache cargo dependencies
-        uses: actions/cache@v3
-        with:
-          path: |
-            ~/.cargo/registry
-            ~/.cargo/git
-            target
-          key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}
-
-      - name: Run unit tests
-        env:
-          DATABASE_URL: postgres://test_user:test_password@localhost:5432/crispr_test
-          MONGODB_URL: mongodb://test_user:test_password@localhost:27017/crispr_test
-          REDIS_URL: redis://localhost:6379
-        run: cargo test --lib --all-features -- --nocapture
-
-      - name: Run integration tests
-        env:
-          DATABASE_URL: postgres://test_user:test_password@localhost:5432/crispr_test
-          MONGODB_URL: mongodb://test_user:test_password@localhost:27017/crispr_test
-          REDIS_URL: redis://localhost:6379
-        run: cargo test --test '*' --all-features -- --nocapture
-
-      - name: Run doc tests
-        run: cargo test --doc --all-features
-
-  # Job 4: Code coverage
-  coverage:
-    name: Code Coverage
-    runs-on: ubuntu-latest
-    needs: test
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Install Rust toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          override: true
-
-      - name: Install tarpaulin
-        run: cargo install cargo-tarpaulin
-
-      - name: Generate coverage report
-        run: cargo tarpaulin --all-features --workspace --timeout 300 --out Xml
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
-        with:
-          files: ./cobertura.xml
-          fail_ci_if_error: false
-
-      - name: Check coverage threshold
-        run: |
-          COVERAGE=$(cargo tarpaulin --all-features --workspace --timeout 300 --out Stdout | grep -oP '\d+\.\d+(?=%)' | head -1)
-          echo "Coverage: $COVERAGE%"
-          if (( $(echo "$COVERAGE < 85" | bc -l) )); then
-            echo "Coverage $COVERAGE% is below 85% threshold"
-            exit 1
-          fi
-
-  # Job 5: Performance benchmarks
-  benchmark:
-    name: Performance Benchmarks
-    runs-on: ubuntu-latest
-    needs: test
-    if: github.event_name == 'pull_request'
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Install Rust toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          override: true
-
-      - name: Cache cargo dependencies
-        uses: actions/cache@v3
-        with:
-          path: |
-            ~/.cargo/registry
-            ~/.cargo/git
-            target
-          key: ${{ runner.os }}-cargo-${{ hashFiles('**/Cargo.lock') }}
-
-      - name: Run benchmarks
-        run: cargo bench --all-features -- --output-format bencher | tee benchmark_results.txt
-
-      - name: Download baseline benchmarks
-        uses: actions/cache@v3
-        with:
-          path: ./target/criterion
-          key: ${{ runner.os }}-benchmark-${{ github.base_ref }}
-
-      - name: Compare with baseline
-        run: |
-          if [ -f ./target/criterion/baseline.txt ]; then
-            echo "Comparing with baseline..."
-            # TODO: Add benchmark comparison logic
-          else
-            echo "No baseline found, saving current as baseline"
-            cp benchmark_results.txt ./target/criterion/baseline.txt
-          fi
-
-      - name: Upload benchmark results
-        uses: actions/upload-artifact@v3
-        with:
-          name: benchmark-results
-          path: |
-            benchmark_results.txt
-            target/criterion/**/*.html
-          retention-days: 30
-
-      - name: Post benchmark comment
-        if: github.event_name == 'pull_request'
-        uses: actions/github-script@v6
-        with:
-          script: |
-            const fs = require('fs');
-            const results = fs.readFileSync('benchmark_results.txt', 'utf8');
-            github.rest.issues.createComment({
-              issue_number: context.issue.number,
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              body: `## 📊 Benchmark Results\n\n\`\`\`\n${results}\n\`\`\``
-            });
-
-  # Job 6: Security audit
-  security:
-    name: Security Audit
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Install cargo-audit
-        run: cargo install cargo-audit
-
-      - name: Run security audit
-        run: cargo audit
-
-  # Job 7: Deploy documentation (on main branch only)
-  docs:
-    name: Build and Deploy Docs
-    runs-on: ubuntu-latest
-    needs: [test, coverage]
-    if: github.ref == 'refs/heads/main'
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Install Rust toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          override: true
-
-      - name: Generate documentation
-        run: cargo doc --no-deps --all-features
-
-      - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./target/doc
-          cname: docs.crispr-pipeline.dev
-
-  # Job 8: Performance regression detection
-  performance-check:
-    name: Performance Regression Check
-    runs-on: ubuntu-latest
-    needs: benchmark
-    if: github.event_name == 'pull_request'
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Download benchmark artifacts
-        uses: actions/download-artifact@v3
-        with:
-          name: benchmark-results
-
-      - name: Check for performance regressions
-        run: |
-          echo "Checking for performance regressions..."
-          # TODO: Implement regression detection logic
-          # Fail CI if performance degrades by >10%
-
-  # Job 9: Notification
-  notify:
-    name: Notify on Completion
-    runs-on: ubuntu-latest
-    needs: [lint, build, test, coverage, security]
-    if: always()
-    steps:
-      - name: Send notification
-        run: |
-          echo "CI/CD pipeline completed"
-          echo "Status: ${{ job.status }}"

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

@@ -1,388 +0,0 @@
-# Contributing to CRISPR-Cas13 Pipeline
-
-Thank you for your interest in contributing! This project was built using [SPARC methodology](https://github.com/ruvnet/agentic-flow) and [rUv.io](https://ruv.io) AI coordination.
-
-## 🚀 Quick Start
-
-1. **Fork the repository**
-   ```bash
-   git clone https://github.com/YOUR_USERNAME/agentic-flow.git
-   cd agentic-flow/agentic-flow/examples/crispr-cas13-pipeline
-   ```
-
-2. **Set up development environment**
-   ```bash
-   # Install Rust (if not already installed)
-   curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
-
-   # Install development tools
-   cargo install cargo-tarpaulin  # Code coverage
-   cargo install cargo-audit      # Security auditing
-   cargo install cargo-machete    # Unused dependency detection
-
-   # Build and test
-   cargo build
-   cargo test --all
-   ```
-
-## 📋 Development Workflow
-
-### 1. Create a Feature Branch
-
-```bash
-git checkout -b feature/your-feature-name
-# or
-git checkout -b fix/your-bug-fix
-```
-
-### 2. Write Tests First (TDD)
-
-We follow Test-Driven Development:
-
-```rust
-// tests/my_feature_test.rs
-#[test]
-fn test_my_new_feature() {
-    let result = my_new_feature();
-    assert_eq!(result.status, "success");
-}
-```
-
-### 3. Implement Your Feature
-
-```rust
-// crates/my-crate/src/lib.rs
-pub fn my_new_feature() -> Result<Output> {
-    // Implementation here
-    Ok(Output { status: "success" })
-}
-```
-
-### 4. Run Quality Checks
-
-```bash
-# Run all tests
-cargo test --all
-
-# Check formatting
-cargo fmt --all -- --check
-
-# Run linter
-cargo clippy -- -D warnings
-
-# Security audit
-cargo audit
-
-# Check for unused dependencies
-cargo machete
-
-# Test coverage (minimum 80%)
-cargo tarpaulin --out Html
-```
-
-### 5. Update Documentation
-
-```bash
-# Generate and check documentation
-cargo doc --no-deps --open
-
-# Update relevant markdown files
-# - README.md (if public API changed)
-# - CHANGELOG.md (add your changes)
-# - docs/ (if architecture/algorithms changed)
-```
-
-### 6. Commit Your Changes
-
-We use [Conventional Commits](https://www.conventionalcommits.org/):
-
-```bash
-git add .
-git commit -m "feat: add new off-target scoring algorithm"
-# or
-git commit -m "fix: correct DESeq2 normalization edge case"
-# or
-git commit -m "docs: update API documentation for immune analyzer"
-```
-
-Commit types:
-- `feat`: New feature
-- `fix`: Bug fix
-- `docs`: Documentation only
-- `style`: Code style changes (formatting)
-- `refactor`: Code refactoring
-- `perf`: Performance improvements
-- `test`: Adding tests
-- `chore`: Maintenance tasks
-
-### 7. Push and Create Pull Request
-
-```bash
-git push origin feature/your-feature-name
-```
-
-Then open a Pull Request on GitHub.
-
-## 🧪 Testing Guidelines
-
-### Unit Tests
-
-```rust
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn test_function_name() {
-        // Arrange
-        let input = setup_test_data();
-
-        // Act
-        let result = function_under_test(input);
-
-        // Assert
-        assert_eq!(result.expected_field, expected_value);
-    }
-}
-```
-
-### Integration Tests
-
-```rust
-// tests/integration_test.rs
-use crispr_cas13_pipeline::prelude::*;
-
-#[tokio::test]
-async fn test_complete_workflow() {
-    let target = create_test_target();
-    let predictor = DefaultPredictor::new(Default::default()).unwrap();
-    let prediction = predictor.predict(&target).await.unwrap();
-    assert!(!prediction.off_targets.is_empty());
-}
-```
-
-### Property-Based Tests
-
-```rust
-use proptest::prelude::*;
-
-proptest! {
-    #[test]
-    fn test_score_normalization(score in 0.0f64..1.0f64) {
-        let normalized = normalize_score(score);
-        assert!(normalized >= 0.0 && normalized <= 1.0);
-    }
-}
-```
-
-### Benchmark Tests
-
-```rust
-use criterion::{black_box, criterion_group, criterion_main, Criterion};
-
-fn alignment_benchmark(c: &mut Criterion) {
-    c.bench_function("align 1000 reads", |b| {
-        let reads = generate_test_reads(1000);
-        b.iter(|| align_reads(black_box(&reads)))
-    });
-}
-
-criterion_group!(benches, alignment_benchmark);
-criterion_main!(benches);
-```
-
-## 📝 Code Standards
-
-### Style Guide
-
-- Use `rustfmt` for formatting (enforced by CI)
-- Follow [Rust API Guidelines](https://rust-lang.github.io/api-guidelines/)
-- Maximum line length: 100 characters
-- Use meaningful variable names (no single-letter variables except in math formulas)
-
-### Documentation
-
-```rust
-/// Calculate CFD (Cutting Frequency Determination) score for off-target sites.
-///
-/// # Arguments
-///
-/// * `guide` - Guide RNA sequence (22-30nt)
-/// * `target` - Target RNA sequence to score
-///
-/// # Returns
-///
-/// Returns a score between 0.0 (no match) and 1.0 (perfect match).
-///
-/// # Examples
-///
-/// ```
-/// use crispr_cas13_pipeline::scoring::CfdScorer;
-///
-/// let score = CfdScorer::score("ACGUACGU", "ACGUACGU");
-/// assert_eq!(score, 1.0);
-/// ```
-///
-/// # References
-///
-/// Doench et al. (2016) Nature Biotechnology 34(2)
-pub fn score(guide: &str, target: &str) -> f64 {
-    // Implementation
-}
-```
-
-### Error Handling
-
-Use `thiserror` for custom errors:
-
-```rust
-use thiserror::Error;
-
-#[derive(Error, Debug)]
-pub enum PredictionError {
-    #[error("Invalid guide RNA length: {0} (expected 22-30nt)")]
-    InvalidGuideLength(usize),
-
-    #[error("ML model not found at path: {0}")]
-    ModelNotFound(String),
-
-    #[error("Prediction failed: {0}")]
-    PredictionFailed(#[from] anyhow::Error),
-}
-```
-
-### Performance
-
-- Use `rayon` for CPU-bound parallel work
-- Use `tokio` for I/O-bound async work
-- Minimize allocations (use `&str` over `String` when possible)
-- Benchmark critical paths with `criterion`
-
-## 🏗️ Architecture Guidelines
-
-### Crate Organization
-
-Each crate should have:
-- Clear single responsibility
-- Well-defined public API
-- Comprehensive tests (>80% coverage)
-- Examples in `examples/` directory
-
-### Adding a New Crate
-
-```bash
-# Create new crate
-cargo new --lib crates/my-new-crate
-
-# Add to workspace in root Cargo.toml
-[workspace]
-members = [
-    "crates/data-models",
-    # ... existing crates
-    "crates/my-new-crate",  # Add here
-]
-```
-
-### Dependencies
-
-- Minimize external dependencies
-- Use well-maintained crates only
-- Lock versions for stability
-- Document why each dependency is needed
-
-## 🤝 Code Review Process
-
-### As a Contributor
-
-- Respond to review comments promptly
-- Make requested changes in new commits (don't force push)
-- Mark conversations as resolved when addressed
-- Be open to feedback and suggestions
-
-### As a Reviewer
-
-- Be respectful and constructive
-- Focus on code quality, not personal preferences
-- Provide specific suggestions for improvement
-- Approve when all concerns are addressed
-
-## 🐛 Bug Reports
-
-Use the [bug report template](.github/ISSUE_TEMPLATE/bug_report.md):
-
-```markdown
-**Describe the bug**
-A clear and concise description of what the bug is.
-
-**To Reproduce**
-Steps to reproduce the behavior:
-1. Run command '...'
-2. With input '...'
-3. See error
-
-**Expected behavior**
-What you expected to happen.
-
-**Actual behavior**
-What actually happened.
-
-**Environment**
-- OS: [e.g. Ubuntu 22.04]
-- Rust version: [e.g. 1.75.0]
-- Package version: [e.g. 0.1.0]
-```
-
-## ✨ Feature Requests
-
-Use the [feature request template](.github/ISSUE_TEMPLATE/feature_request.md):
-
-```markdown
-**Is your feature request related to a problem?**
-A clear description of the problem.
-
-**Describe the solution you'd like**
-A clear description of what you want to happen.
-
-**Describe alternatives you've considered**
-Any alternative solutions or features you've considered.
-
-**Additional context**
-Any other context or screenshots about the feature request.
-```
-
-## 📚 Resources
-
-### Documentation
-- [Rust Book](https://doc.rust-lang.org/book/)
-- [Rust API Guidelines](https://rust-lang.github.io/api-guidelines/)
-- [SPARC Methodology](https://github.com/ruvnet/agentic-flow)
-- [rUv.io Platform](https://ruv.io)
-
-### Scientific References
-- [CRISPR-Cas13 Overview](https://www.nature.com/articles/s41576-018-0059-1)
-- [Off-Target Analysis](https://www.nature.com/articles/nbt.3437)
-- [DESeq2 Algorithm](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8)
-
-## 🎯 Current Priorities
-
-See [GitHub Projects](https://github.com/ruvnet/agentic-flow/projects) for current roadmap.
-
-High-priority areas:
-- [ ] GPU acceleration for ML models
-- [ ] Additional Cas13 variant support
-- [ ] Frontend UI development
-- [ ] Real-world validation studies
-
-## 💬 Communication
-
-- **GitHub Discussions**: For questions and general discussion
-- **Discord**: [Join our community](https://discord.gg/ruv)
-- **Email**: contribute@ruv.io
-
-## 📜 License
-
-By contributing, you agree that your contributions will be licensed under the MIT License.
-
----
-
-Thank you for contributing to CRISPR-Cas13 Pipeline! 🧬✨