Configuration Reference

Vaibify projects are configured through three files in the project root directory. This page documents every field and option.

vaibify.yml

The primary configuration file. All fields use camelCase keys in the YAML file; the Python dataclass uses Hungarian notation internally.

Top-Level Fields

YAML Key	Type	Default	Description
projectName	string	(required)	Docker container and image name
containerUser	string	researcher	Non-root user inside the container
pythonVersion	string	3.12	Python version to install
baseImage	string	ubuntu:24.04	Base Docker image
workspaceRoot	string	/workspace	Mount point for the workspace volume
packageManager	string	pip	Package manager: pip, conda, or mamba
networkIsolation	boolean	false	Disable outbound network access

List Fields

YAML Key	Element Type	Description
repositories	dict	Repository definitions (see below)
systemPackages	string	APT packages to install
pythonPackages	string	pip packages to install
condaPackages	string	conda/mamba packages to install
binaries	dict	Pre-built binaries to download
ports	dict	Ports to expose from the container
bindMounts	dict	Host directories to mount
secrets	dict	Secret references (see Security below)

Features Block

Nested under the features key:

YAML Key	Type	Default	Description
jupyter	boolean	false	Install JupyterLab
rLanguage	boolean	false	Install R and IRkernel
julia	boolean	false	Install Julia
database	boolean	false	Install PostgreSQL client
dvc	boolean	false	Install DVC for data versioning
latex	boolean	true	Install TeX Live
claude	boolean	false	Install Claude Code CLI
gpu	boolean	false	Enable NVIDIA GPU passthrough

Reproducibility Block

Nested under the reproducibility key:

YAML Key	Type	Default	Description
zenodoService	string	sandbox	sandbox or production
latexRoot	string	src/tex	Path to LaTeX source files
figuresRoot	string	src/tex/figures	Path to generated figures

Overleaf Sub-Block

Nested under reproducibility.overleaf:

YAML Key	Type	Default	Description
projectId	string	""	Overleaf project identifier
figureDirectory	string	figures	Target directory in Overleaf
pullPaths	list	[]	Paths to sync from Overleaf

Example

projectName: earth-water-study
containerUser: researcher
pythonVersion: "3.12"
baseImage: ubuntu:24.04
workspaceRoot: /workspace
packageManager: pip
networkIsolation: false

systemPackages:
  - gcc
  - make
  - git
  - curl

pythonPackages:
  - numpy
  - matplotlib
  - h5py

features:
  jupyter: true
  latex: true

reproducibility:
  zenodoService: sandbox
  latexRoot: src/tex
  figuresRoot: src/tex/figures

container.conf

A line-oriented file listing repositories to clone and install. Each non-comment line has four pipe-separated fields:

name|url|branch|install_method

Install Methods

Method	Action
c_and_pip	make opt then pip install -e . --no-deps
pip_no_deps	pip install -e . --no-deps
pip_editable	pip install -e .
scripts_only	Add to PYTHONPATH and PATH only
reference	Clone for reference, do not install

Example

mycode|git@github.com:user/mycode.git|main|pip_editable
data-utils|git@github.com:user/data-utils.git|develop|pip_no_deps

workflow.json

Defines the execution pipeline. See Pipelines for full documentation.

Security

Secrets are never stored in configuration files. The secrets field in vaibify.yml lists secret references (names), not values. At build time, Vaibify delegates to the host’s credential manager (e.g., gh auth, OS keychain) to resolve secrets. See the Reproducibility page for details on how secrets interact with published workflows.