BioVault Desktop

Repo structure

This repo is a kind of mono-repo for BioVault but uses Google's repo tool so the sub repos are still independent.

Workspace deps (repo tool)

• Source of truth: manifest.xml pins each dependency repo to a commit.
• Initialize/sync workspace: repo init -u <manifest-url> -m manifest.xml then repo sync
• Status across repos: repo status
• Branch all repos together: repo forall -c 'git checkout -B <branch>'
• Local helper: ./repo (tree view), ./repo --init, ./repo sync, ./repo pin, ./repo ssh

Layout + fallbacks

• Preferred layout is sibling repos at the repo root: biovault/, biovault-beaver/, bioscript/, syftbox/, syftbox-sdk/, syft-crypto-core/, sbenv/
• Scripts and Rust code accept overrides via env vars (examples): WORKSPACE_ROOT, BIOVAULT_DIR, BIOVAULT_BEAVER_DIR, SYFTBOX_DIR, SYFTBOX_SDK_DIR, SBENV_DIR
• Legacy fallback: if a dependency only exists under biovault/..., most scripts will detect and use it.

Nested repo (libsignal)

• The libsignal repo is checked out under syft-crypto-core/vendor/libsignal-protocol-syft
• It is pinned in manifest.xml to avoid submodule workflows.

Notes for CI

• Do not use submodules: recursive in actions/checkout.
• Use ./repo --init --https (forces HTTPS for CI) and ./repo sync for retries.

Dependency Order & Release Process

Dependency Graph

syft-crypto-core (foundational crypto)
    ↓
syftbox-sdk (depends on syft-crypto-protocol)
    ↓
biovault CLI (depends on syftbox-sdk)
    ↓
biovault-desktop/src-tauri (depends on biovault CLI + syftbox-sdk)

biovault-beaver (independent Python, but uses syftbox conventions)

Release Order

When making changes that span multiple repos, release in this order:

1. syft-crypto-core - Foundational crypto library

   • Contains syft-crypto-protocol crate
   • Must be released first if crypto changes

2. syftbox-sdk - Rust SDK for SyftBox

   • Depends on syft-crypto-protocol
   • Update version, release to crates.io

3. biovault (CLI) - BioVault CLI library

   • Depends on syftbox-sdk
   • Update Cargo.toml version references

4. biovault-desktop - Desktop application (this repo)

   • Depends on both biovault CLI and syftbox-sdk
   • Update Cargo.toml version references
   • Tag release triggers CI build

5. biovault-beaver - Python notebooks/workers

   • Independent but should be compatible
   • Release after desktop if notebooks change

Branching Workflow

# Check which repos have changes
./repo branch

# Create branch in all dirty repos
./repo branch feature/my-feature

# Commit in each repo
cd syftbox-sdk && git add -A && git commit -m "feat: add X"
cd ../biovault && git add -A && git commit -m "feat: use X"
cd .. && git add -A && git commit -m "feat: integrate X"

# Push all branches
./repo forall -c 'git push -u origin feature/my-feature'

# Create PRs, merge in dependency order, then release

Version Updates

When releasing, update versions in this order:

1. syft-crypto-core/protocol/Cargo.toml - bump version
2. syftbox-sdk/Cargo.toml - bump version, update syft-crypto-protocol dep
3. biovault/cli/Cargo.toml - bump version, update syftbox-sdk dep
4. src-tauri/Cargo.toml - bump version (auto-triggers release)
5. biovault-beaver/pyproject.toml - bump version if needed

Development Workflow

Linting & Testing

Each repo has a lint.sh script that runs all checks in parallel:

# Lint all dirty repos (parallel, quiet on success)
./repo lint

# Run fast unit tests in dirty repos (quiet on success)
./repo test
./repo test --force

# Or lint a single repo
./lint.sh                  # Auto-fix mode (default)
./lint.sh --check          # Read-only mode for CI
./lint.sh --test           # Also run tests
./lint.sh --check --test   # CI mode with tests

What Each lint.sh Does

Repo	Languages	Checks
biovault-desktop	Rust + JS/TS	cargo fmt + clippy + prettier + eslint
biovault	Rust	cargo fmt + clippy
syftbox-sdk	Rust	cargo fmt + clippy
syft-crypto-core	Rust	cargo fmt + clippy
biovault-beaver	Python	ruff format + ruff check + mypy + vulture

With --test: adds cargo test (Rust) or pytest (Python)

Before Committing

# Check which repos have changes and lint them
./repo lint

# If lint passes, create branches and commit
./repo branch feature/my-change
# ... commit in each repo ...