flow-tdd
Enforces TDD Iron Law in flow-dev. NO PRODUCTION CODE WITHOUT A FAILING TEST FIRST.
flow-receiving-review
Handle code review feedback with technical rigor. Don't blindly agree - verify before implementing.
flow-finishing-branch
Decide how to complete a development branch: merge, PR, squash, or cleanup.
flow-debugging
4-phase systematic debugging for flow-fix. NO FIXES WITHOUT ROOT CAUSE INVESTIGATION FIRST.
flow-brainstorming
在 /flow-init 阶段强制触发，用于捕捉需求的原始意图、探索方案、记录决策。确保后续流程有明确的北极星可追溯。
devflow-tdd-enforcer
Enforces TDD order in TASKS.md - Tests MUST be marked complete before Implementation tasks. Blocks violations in real-time.
devflow-file-standards
File naming conventions, directory structure, and YAML frontmatter standards for CC-DevFlow. Consolidates shared conventions from all agents.
devflow-constitution-quick-ref
Quick reference guide to CC-DevFlow Constitution v2.0.0 with links to full text. Covers all 10 Articles and Phase -1 Gates.
constitution-guardian
Real-time Constitution compliance checker for devflow documents. Blocks partial implementations and hardcoded secrets during file editing.
cc-devflow-orchestrator
CC-DevFlow workflow router and agent recommender. Use when starting requirements, running flow commands, or asking about devflow processes.
swiftui-view-refactor
Refactor and review SwiftUI view files for consistent structure, dependency injection, and Observation usage. Use when asked to clean up a SwiftUI view’s layout/ordering, handle view models safely (non-optional when possible), or standardize how dependencies and @Observable state are initialized and passed.
swiftui-ui-patterns
Best practices and example-driven guidance for building SwiftUI views and components. Use when creating or refactoring SwiftUI UI, designing tab architecture with TabView, composing screens, or needing component-specific patterns and examples.
swiftui-performance-audit
Audit and improve SwiftUI runtime performance from code review and architecture. Use for requests to diagnose slow rendering, janky scrolling, high CPU/memory usage, excessive view updates, or layout thrash in SwiftUI apps, and to provide guidance for user-run Instruments profiling when code review alone is insufficient.
swiftui-liquid-glass
Implement, review, or improve SwiftUI features using the iOS 26+ Liquid Glass API. Use when asked to adopt Liquid Glass in new SwiftUI UI, refactor an existing feature to Liquid Glass, or review Liquid Glass usage for correctness, performance, and design alignment.
swift-concurrency-expert
Swift Concurrency review and remediation for Swift 6.2+. Use when asked to review Swift Concurrency usage, improve concurrency compliance, or fix Swift concurrency compiler errors in a feature or file.
macos-spm-app-packaging
Scaffold, build, and package SwiftPM-based macOS apps without an Xcode project. Use when you need a from-scratch macOS app layout, SwiftPM targets/resources, a custom .app bundle assembly script, or signing/notarization/appcast steps outside Xcode.
ios-debugger-agent
Use XcodeBuildMCP to build, run, launch, and debug the current iOS project on a booted simulator. Trigger when asked to run an iOS app, interact with the simulator UI, inspect on-screen state, capture logs/console output, or diagnose runtime behavior using XcodeBuildMCP tools.
gh-issue-fix-flow
End-to-end GitHub issue fix workflow using gh, local code changes, builds/tests, and git push. Use when asked to take an issue number, inspect the issue via gh, implement a fix, run XcodeBuildMCP builds/tests, commit with a closing message, and push.
app-store-changelog
Create user-facing App Store release notes by collecting and summarizing all user-impacting changes since the last git tag (or a specified ref). Use when asked to generate a comprehensive release changelog, App Store "What's New" text, or release notes based on git history or tags.
route-tester
Test authenticated routes in the your project using cookie-based authentication. Use this skill when testing API endpoints, validating route functionality, or debugging authentication issues. Includes patterns for using test-auth-route.js and mock authentication.
error-tracking
Add Sentry v8 error tracking and performance monitoring to your project services. Use this skill when adding error handling, creating new controllers, instrumenting cron jobs, or tracking database performance. ALL ERRORS MUST BE CAPTURED TO SENTRY - no exceptions.
file-header-guardian
文件头三行契约注释。触发：create file、新建文件、编写代码。
simpy
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.
shap
Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
security-compliance
Guides security professionals in implementing defense-in-depth security architectures, achieving compliance with industry frameworks (SOC2, ISO27001, GDPR, HIPAA), conducting threat modeling and risk assessments, managing security operations and incident response, and embedding security throughout the SDLC.
seaborn
Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.
scvi-tools
This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction, dimensionality reduction, differential expression, cell type annotation, multimodal integration, and spatial analysis tasks.
scikit-survival
Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions with concordance index or Brier score, handling competing risks, or implementing any survival analysis workflow with the scikit-survival library.
scikit-learn
Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
scientific-writing
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
scientific-visualization
Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.
scientific-slides
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
scientific-schematics
Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
scientific-critical-thinking
Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.
scientific-brainstorming
Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving.
when-training-neural-networks-use-flow-nexus-neural
This SOP provides a systematic workflow for training and deploying neural networks using Flow Nexus platform with distributed E2B sandboxes. It covers architecture selection, distributed training, ...
scholar-evaluation
Apply the ScholarEval framework to systematically evaluate scholarly and research work. This skill provides structured evaluation methodology based on peer-reviewed research assessment criteria, en...
scanpy
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
research-lookup
Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations.
research-grants
Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
browser-automation
Enterprise-grade browser automation using WebDriver protocol. Use when the user needs to automate web browsers, perform web scraping, test web applications, fill forms, take screenshots, monitor performance, or execute multi-step browser workflows. Supports Chrome, Firefox, and Edge with connection pooling and health management.
qutip
Quantum mechanics simulations and analysis using QuTiP (Quantum Toolbox in Python). Use when working with quantum systems including: (1) quantum states (kets, bras, density matrices), (2) quantum operators and gates, (3) time evolution and dynamics (Schrödinger, master equations, Monte Carlo), (4) open quantum systems with dissipation, (5) quantum measurements and entanglement, (6) visualization (Bloch sphere, Wigner functions), (7) steady states and correlation functions, or (8) advanced methods (Floquet theory, HEOM, stochastic solvers). Handles both closed and open quantum systems across various domains including quantum optics, quantum computing, and condensed matter physics.
qiskit
Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits. Use when working with quantum algorithms, simulations, or quantum hardware including (1) Building quantum circuits with gates and measurements, (2) Running quantum algorithms (VQE, QAOA, Grover), (3) Transpiling/optimizing circuits for hardware, (4) Executing on IBM Quantum or other providers, (5) Quantum chemistry and materials science, (6) Quantum machine learning, (7) Visualizing circuits and results, or (8) Any quantum computing development task.
pytorch-lightning
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.
pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
pyopenms
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.
pymoo
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
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