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init-env.sh

Create project-local R, Python, and Julia environments.

The container ships the language runtimes and enough packages to render, but no project-local environment. init-env.sh, at the root of the repository, creates one for R, Python, Julia, or all three.

Nothing runs it for you: no configuration sets it as a postCreateCommand. Run it once, in your project directory, when you want lock files under version control.

Usage

./init-env.sh [--what/-w all|r|python|julia] [--force/-f] [--help/-h]

Option	Default	Description
--what, -w	all	Which environment to initialise: all, r, python, or julia.
--force, -f	off	Reinitialise even when the lock file already exists.
--help, -h		Print the usage message and exit.

Without --force, each environment is skipped when its marker file is already present: renv.lock for R, uv.lock for Python, and Project.toml for Julia. That makes the script safe to re-run, and safe to run on a repository that already has one of the three set up.

What each environment gets

Environment	Tool	Packages	Lock file
R	renv	rmarkdown, languageserver	renv.lock
Python	uv	jupyter, papermill	uv.lock
Julia	Pkg	IJulia	Project.toml

The package sets are fixed in the script. To use different ones, edit the calls at the bottom of init-env.sh, or add packages afterwards with renv::install(), uv add, and Pkg.add().

R

./init-env.sh --what r

Runs renv::init(bare = FALSE), installs rmarkdown and languageserver, then snapshots with type = "all" so every installed package is recorded.

If .Rprofile already sources renv/activate.R, the script removes that line first, so renv::init() starts from a clean state instead of failing against a half-configured project.

The R extension is configured with r.useRenvLibPath: true, so it picks up the project library as soon as it exists.

Python

./init-env.sh --what python

Runs uv init --no-package --vcs none --bare --no-readme --author-from none, creates a virtual environment in .venv, adds jupyter and papermill, and syncs.

Quarto finds .venv automatically when rendering from the project directory.

Julia

./init-env.sh --what julia

Activates the current directory as a Julia project, instantiates it, and adds IJulia so the Jupyter engine can run Julia cells.

Force a rebuild

./init-env.sh --what all --force

Recreates every environment from scratch, discarding the existing resolution. Use it after changing the package sets, or when a lock file no longer resolves.