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Build with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/settings, creating Pi skills/extensions/packages/themes/prompt templates, embedding Pi through the SDK, integrating over RPC or JSON event streams, parsing sessions, or developing custom Pi providers and TUI components.
Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.
Use when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.
| name | pi-agent |
| description | Build with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/settings, creating Pi skills/extensions/packages/themes/prompt templates, embedding Pi through the SDK, integrating over RPC or JSON event streams, parsing sessions, or developing custom Pi providers and TUI components. |
| license | MIT |
| compatibility | Requires Node.js/npm for Pi CLI and SDK usage. Pi package name is @earendil-works/pi-coding-agent. |
| metadata | {"version":"1.0","skill-author":"K-Dense Inc."} |
Use this skill when the user wants to operate Pi or build on top of Pi. Pi is a minimal terminal coding harness extended through TypeScript extensions, skills, prompt templates, themes, packages, custom models/providers, SDK integrations, RPC mode, JSON event streams, and TUI components.
Pick the reference before answering or coding:
| User intent | Read |
|---|---|
| Install, authenticate, first run | references/quickstart.md |
| Day-to-day CLI usage, commands, modes, flags | references/usage.md |
| Provider auth, API keys, cloud provider setup | references/providers.md |
| Custom model entries, local models, proxies | references/models.md |
| Extension development, custom tools, events, commands | references/extensions.md |
| Custom provider implementation, OAuth, custom streaming | references/custom-provider.md |
| Embed Pi in Node/TypeScript | references/sdk.md |
| Integrate from another process/language | references/rpc.md |
| Consume JSONL event output | references/json.md |
| Build terminal UI components | references/tui.md |
| Package extensions/skills/prompts/themes | references/packages.md |
| Author Pi skills | references/skills.md |
| Prompt templates or themes | references/prompt-templates.md, references/themes.md |
| Sessions, branching, compaction, parsing JSONL | references/sessions.md, references/compaction.md, references/session-format.md |
| Security, sandboxing, trust | references/security.md, references/containerization.md |
| Keyboard or terminal issues | references/keybindings.md, references/terminal-setup.md, references/tmux.md, references/windows.md, references/termux.md, references/shell-aliases.md |
| Working on Pi itself | references/development.md |
Prefer the SDK for Node/TypeScript apps that need type safety, direct state access, in-process custom tools/extensions, or custom resource loading. Use createAgentSession() for a single stable session; use createAgentSessionRuntime() when the app must replace sessions through new/resume/fork/clone/import flows.
Prefer RPC mode when the client is not Node.js, needs process isolation, or wants a language-agnostic JSONL protocol. Start with pi --mode rpc --no-session for stateless subprocess integration, then add session flags when persistence matters.
Prefer JSON mode for one-shot command-line pipelines that only need streamed events, not bidirectional control: pi --mode json "prompt".
Use extensions for Pi-native behavior: custom tools, command handlers, event hooks, provider registration, custom compaction, path protection, project trust policy, UI prompts, widgets, and TUI components.
Use packages when sharing or installing reusable extensions, skills, prompt templates, or themes across machines or projects.
Pi is local and not sandboxed by default. Treat extensions, packages, skills, shell commands, and project-local .pi resources as code with the permissions of the Pi process. For untrusted repos or unattended automation, isolate with Docker, OpenShell, Gondolin, a VM, or a remote sandbox.
Do not store secrets in project files. Prefer env vars, ~/.pi/agent/auth.json, OAuth via /login, or command-backed secret lookups in models.json/provider config.
npm install -g --ignore-scripts @earendil-works/pi-coding-agent
pi
pi -p "Summarize this codebase"
pi --mode json "List files"
pi --mode rpc --no-session
pi --provider anthropic --model claude-sonnet-4-5
pi --tools read,grep,find,ls -p "Review this repository"
These references summarize the Pi documentation at https://pi.dev/docs/latest and each docs page found under it as of this skill version. When exact API behavior matters, prefer the cited reference page and inspect installed TypeScript definitions under node_modules/@earendil-works/pi-coding-agent/dist/ and node_modules/@earendil-works/pi-ai/dist/.