Local runtime setup

Wisp starts and runs native biological tools without Python, R, uv, or Node. First-run model setup and Settings → Models show a background path check. Cmd/Ctrl+P → Quick setup (快速配置) reopens setup and refreshes the check. It never runs installers or creates a virtualenv. Detected executable paths are saved in the Local execution context without replacing existing choices. A found path does not establish version compatibility or installed packages.

Task	Optional tools
Python analysis / persistent python tool	Existing Python environment; uv can help create one
R analysis / persistent r tool	Rscript with jsonlite
User-configured Python MCP	That server's own interpreter and dependencies
bear-* literature skills	Node >= 20, npm, sci (scimaster-cli)
Bioinformatics workflows	pixi for isolated conda/pip environments

Start with the user's task and existing environment. Install only what it needs. Do not treat every missing optional tool as a broken installation. After changing PATH, use Check paths again in model settings; restart Wisp only if the GUI process needs to inherit a changed PATH. Interpreter settings can be saved directly without restarting the app.

Step 0 — Detect platform, region, and current state

Read the Environment section in the system prompt (Operating system, Working directory).

0a — Region / network (mirror or not)

Before any install or pip/npm/pixi add, decide whether the user is on mainland China and needs mirrors.

Signals (use several; do not rely on one):

Signal	Mainland likely
User writes in Chinese and mentions 国内 / 镜像 / 翻墙 / 清华 / 阿里	yes
TZ / system timezone Asia/Shanghai, Asia/Chongqing, Asia/Urumqi	hint
Locale zh_CN, zh-Hans-CN	hint
curl -s --connect-timeout 3 https://pypi.org/simple/ fails or >5s; tuna mirror responds in <2s	yes
User explicitly says they are not in China / have full international access	no

If ambiguous, ask once: "Are you on mainland China? I'll use domestic mirrors for pip/npm/conda if yes."

When mainland mirrors apply, set these before installs (user shell profile or session env):

# PyPI / uv (Python environments + pixi pip deps)
export UV_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple
export PIP_INDEX_URL=https://pypi.tuna.tsinghua.edu.cn/simple

# npm (scimaster-cli)
npm config set registry https://registry.npmmirror.com

Windows (PowerShell, persist for user):

[Environment]::SetEnvironmentVariable("UV_INDEX_URL", "https://pypi.tuna.tsinghua.edu.cn/simple", "User")
[Environment]::SetEnvironmentVariable("PIP_INDEX_URL", "https://pypi.tuna.tsinghua.edu.cn/simple", "User")
npm config set registry https://registry.npmmirror.com

Pixi conda channels (global or per-project pixi.toml):

[project]
channels = ["https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/"]

[pypi-config]
index-url = "https://pypi.tuna.tsinghua.edu.cn/simple"

Or global:

pixi config set --global pypi-config.index-url https://pypi.tuna.tsinghua.edu.cn/simple

Alternatives if tuna is slow: Aliyun PyPI https://mirrors.aliyun.com/pypi/simple/, USTC conda mirrors.

If international access works, do not set mirrors — use defaults.

0b — Tool presence

Run with shell (PowerShell on Windows, sh -c elsewhere):

Windows:

Get-Command python,python3,Rscript,uv,node,npm,sci,pixi -ErrorAction SilentlyContinue | Select-Object Name,Source
uv --version 2>$null; node --version 2>$null; npm --version 2>$null; sci --version 2>$null; pixi --version 2>$null

macOS / Linux:

for c in python3 python Rscript uv node npm sci pixi; do command -v $c && $c --version 2>/dev/null; done

The optional environment panel in onboarding, model settings, and Capabilities shows detected paths. Inspect the saved Local interpreter settings before choosing another environment.

Python and R, when requested

Reuse an existing project environment when suitable. In the desktop app, set_runtime_interpreter saves a path on the execution context:

{"context_id":"local","language":"python","executable":"/absolute/path/to/python"}

For R, use "language":"r" and an absolute Rscript path. Users can also open Runtime interpreters and browse for either executable. Running REPLs keep their previous interpreter until restarted; the agent tool restarts the current conversation's matching REPL and clears its variables.

For Python, invoke the chosen executable to verify its version and install only needed packages. python/requirements-kernel.txt lists common analysis packages shipped as a requirements file; native biological tools require none of them. The kernel worker itself uses the Python standard library. For R, verify Rscript -e 'library(jsonlite)' using the chosen absolute path; install jsonlite in that environment if needed, then test the Wisp r tool.

The CLI uses an existing environment at <workspace>/.wisp/python/.venv if present, otherwise Python on PATH. The desktop retains these legacy fallback locations for users who already prepared them; it never creates them on launch:

OS	Desktop venv path
Windows	%APPDATA%\science.wisp-science\wisp-science\python\.venv
macOS	~/Library/Application Support/science.wisp-science/wisp-science/python/.venv
Linux	~/.local/share/science.wisp-science/wisp-science/python/.venv

Install uv

International:

# Windows
powershell -ExecutionPolicy Bypass -c "irm https://astral.sh/uv/install.ps1 | iex"

# macOS / Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

Mainland China: prefer winget / Homebrew / distro package if the astral installer is slow or blocked; set UV_INDEX_URL (above) before uv pip install.

winget install --id astral-sh.uv -e          # Windows

brew install uv                               # macOS

Default binary: ~/.local/bin/uv (Unix) or %USERPROFILE%\.local\bin\uv.exe (Windows). Ensure that dir is on PATH.

Python via uv

uv python install 3.11
uv python list

Target: Python 3.11+. With mainland mirrors, export UV_INDEX_URL first.

Create a project environment when needed

Set ENV_DIR to a task-specific environment location and REQ to the bundled or repository python/requirements-kernel.txt when those analysis packages are wanted. Reuse an existing suitable environment instead of recreating it.

uv venv "$ENV_DIR"
uv pip install -r "$REQ" --python "$ENV_DIR/bin/python"
"$ENV_DIR/bin/python" -c "import sys; print(sys.executable)"

Windows PowerShell: use $envDir, $req, and Scripts\python.exe:

uv venv $envDir
uv pip install -r $req --python "$envDir\Scripts\python.exe"
& "$envDir\Scripts\python.exe" -c "import sys; print(sys.executable)"

Save that absolute interpreter through set_runtime_interpreter when available, then verify a small python tool call. If the tool is unavailable in the CLI, use the CLI fallback location above or launch with the prepared environment on PATH.

User-configured Python MCP servers

Read that server's installation requirements. Prepare its own environment and configure its MCP command with the absolute executable and appropriate arguments. Do not reinstall the removed mcp-servers/bio-tools tree or add Python MCP packages merely to use Wisp's native biological tools. Test the configured connection after setup.

Layer 2 — Literature: Node + scimaster-cli

Required for bundled bear-support, bear-counter, bear-map, bear-scoop, bear-trace, bear-review, bear-onboard, bear-propose.

Install Node >= 20

International: https://nodejs.org/ LTS, or winget install OpenJS.NodeJS.LTS, or brew install node.

Mainland China:

# Windows — winget often works; or npmmirror-hosted installer
winget install OpenJS.NodeJS.LTS

# macOS — brew or fnm with npmmirror
brew install node
# fnm alternative:
# export FNM_NODE_DIST_MIRROR=https://npmmirror.com/mirrors/node
# fnm install 20 && fnm use 20

After install, open a new terminal; verify node --version (v20+).

scimaster-cli

Set npm registry first if mainland (see 0a), then:

npm install -g scimaster-cli
sci init        # paste SciMaster API Key
sci --version
sci usage

API Key: SciMaster settings → API Key. Do not proceed with bear-* skills if sci --version fails.

In the wisp-science desktop app, you can also save the SciMaster key in Settings -> Credentials -> SCIMaster. Wisp will sync that key into ~/.scimaster/config.json for scimaster-cli.

Layer 3 — Bioinformatics: pixi

pixi manages isolated per-project environments (conda + pip) — use for scanpy/single-cell, variant calling stacks, etc. The Wisp python tool uses the selected context interpreter. The same environment can run standalone commands through pixi run python … or pixi run …, or supply the interpreter for persistent python/r analysis. Choose process lifetime according to state reuse, script requirements, and task lifecycle; installing an environment does not select an execution method. Scripts consuming existing runtime objects can use script_path and required_objects.

Workflow engines

For multi-step analysis pipelines (many rules, parallel execution, resume after failure), pair pixi with a dedicated workflow engine — pixi manages the environments, the engine schedules the steps. Run engines from shell in the project directory.

Engine	What it is	When to choose
snakemake	Python-defined rules, mature conda/mamba integration	Established rules; Python-centric teams
nextflow	Groovy DSL, container-first	nf-core ecosystem; HPC/cloud portability
oxo-flow	Rust-native, TOML-defined DAG engine; CLI + web UI	Lightweight single-binary install; rule-level conda/mamba/pixi/docker/singularity backends; checkpoint/resume

Install pixi

International:

curl -fsSL https://pixi.sh/install.sh | bash

powershell -ExecutionPolicy ByPass -c "irm -useb https://pixi.sh/install.ps1 | iex"

Mainland China: if install script is slow, try brew install pixi (macOS) or download release from GitHub mirror; then configure mirrors (0a).

Typical project workflow

In the user's analysis directory:

pixi init
pixi add scanpy anndata          # example; adjust to task
pixi run python analysis.py

Multiple envs: use [environments] / features in pixi.toml, or separate project dirs — see pixi docs.

With mainland mirrors, set [pypi-config] and channels in pixi.toml (0a) before large pixi add.

Verify pixi

pixi --version
pixi info    # shows config paths and channels

Workarounds

Issue	Fix
uv/node installed but app still says missing	Restart wisp-science; confirm tools on PATH for the GUI user (macOS: relaunch from Dock after shell profile update).
Cannot modify PATH	Set UV_PATH / PIXI_PATH to full binary paths before launching wisp-science.
Mainland: timeouts on pypi.org / registry.npmjs.org	Apply Step 0a mirrors; retry.
Corporate proxy / TLS	HTTPS_PROXY, trust store; still use mirrors if direct egress to US is blocked.
Broken Python environment	Diagnose or create a replacement environment, install needed packages, then save its interpreter. Restarting Wisp does not repair or recreate environments.
bear-* skill stops at CLI check	Install Node + scimaster-cli + sci init; do not fake citations.

Agent workflow

1. Load this skill for requested setup or a task blocked by a missing dependency.
2. Detect OS and existing paths; reuse the user's selected environment.
3. Before downloading, choose appropriate network mirrors (Step 0a).
4. Install only the Python/R, custom MCP, literature, or bioinformatics components needed.
5. Save interpreter paths to the chosen execution context and verify actual task/tool execution.
6. Report installed components, selected paths, and any task-specific dependencies still missing.

Not in scope

• Remote GPU or direct SSH → compute-env-setup; managed cloud backends are unavailable until Wisp implements a matching execution-context backend
• Replacing pixi with conda/micromamba when pixi suffices locally
• SciMaster API billing / key provisioning beyond pointing to sci init