Inside the sandbox
What is installed
Section titled “What is installed”The sandbox image is Debian with:
- Python with conda and mamba (conda-forge, from Miniforge), and uv
- Node.js, git, curl, ripgrep, and build tools (a C/C++ compiler and make)
- the agents: Claude Code (downloaded by the app, see Container engines), Codex, DeepSeek Harness and OpenCode
- storyteller, for reports
R, GPU tooling and other native libraries are not in the image: the agent installs what an analysis needs.
The project’s environment
Section titled “The project’s environment”The agent installs software into the project, not the image, so it is there next time:
- a Python virtual environment (
pip/uv pip install), which also sees the image’s own Python packages - conda environments (
mamba create), R libraries, npm and cargo packages - their download caches
codeflower-env-export writes a readable recipe of everything installed (requirements files and conda
.ymls), to recreate it elsewhere. Behind a network allowlist, installing needs
@pypi, @conda, @cran or similar.
Where the agent works
Section titled “Where the agent works”| Path | What |
|---|---|
/data/input/*, /data/output/*, /data/code/*, /data/skills/* |
your folders |
/codeflower-state/workspace |
its working directory: scripts, figures, results, draft reports, logs |
/codeflower-state/env |
the project’s software environment |
Its instructions (AGENTS.md, and CLAUDE.md for Claude Code) are in the workspace. They tell it how to work:
numbered, rerunnable scripts; checking its own results; showing figures; writing reports; delivering to
/data/output. You can edit them for a project; a newer image keeps your edits.
code flower’s tools
Section titled “code flower’s tools”The agent uses these by itself; you can also run them with a ! command in the chat.
| Command | What it does |
|---|---|
codeflower-show FILE… |
opens files in a tab beside the chat (figures, tables, Markdown, HTML, reports) |
codeflower-doctor |
what this sandbox may use: the job’s CPUs, memory and end time, disk, GPUs, the network allowlist |
codeflower-inventory [PATHS] |
describes data folders: tables (CSV, Parquet), HDF5, AnnData, loom, 10x, Zarr, SQLite, zip |
codeflower-env-export |
records the installed environments |
codeflower-network [check HOST] |
in an isolated sandbox: what it may reach |
codeflower-sketch |
the icon gallery for scientific figures |
When the sandbox starts, it also writes a snapshot of its environment and an inventory of your input folders, which the agent reads first.