bactopia.github.io

Documentation for Bactopia, built with Docusaurus 3.

Prerequisites

• Node.js >= 18
• Conda environment bactopia-dev from the bactopia repo (provides Node.js, Python, and all shared dependencies)

# Create the environment (from the bactopia repo)cd /path/to/bactopia
conda env create -f environment.yml -n bactopia-dev
conda activate bactopia-dev

Development Setup

git clone git@github.com:bactopia/bactopia.github.io.git
cd bactopia.github.io
npm install
npm start

The dev server runs at http://0.0.0.0:8000 with hot reload.

Available Scripts

Script	Description
npm start	Start the dev server with hot reload
npm run build	Production build to build/
npm run serve	Serve the production build locally
npm run clear	Clear the Docusaurus cache
npm run typecheck	Run TypeScript type checking

Generating Docs from Bactopia Source

Most documentation under bactopia-tools/, bactopia-pipelines/, developers/, and impact/ is auto-generated from the bactopia source repo using Python scripts in bin/.

# Generate all docs (requires bactopia repo path)
make generate BACTOPIA_REPO=/path/to/bactopia

Individual targets are also available:

Target	Description
parse	Parse the bactopia repo into data/bactopia.json
generate-workflows	Generate tool and pipeline docs
generate-subworkflows	Generate subworkflow docs
generate-modules	Generate module docs
generate-citations	Generate citations page
generate-acknowledgements	Generate acknowledgements page
generate-enhancements	Generate enhancements page
parse-cli	Parse bactopia-py CLI into data/cli.json
generate-cli	Generate CLI reference docs
update-citations	Refresh data/citations.yml from source
clean-generated	Remove all generated files

By default, parse-cli uses the Python from bactopia-dev. Override with:

make parse-cli BACTOPIA_DEV_PYTHON=/path/to/python

Project Structure

docs/ Main Bactopia documentation
bactopia-tools/ Auto-generated tool docs
bactopia-pipelines/ Auto-generated pipeline docs
developers/ Developer guides, subworkflows, modules, CLI reference
impact/ Impact & outreach content
blog/ Blog posts
data/ JSON/YAML data files (citations, CLI, bactopia metadata)
src/ React components, custom CSS, pages
bin/ Python doc-generation scripts
templates/ Jinja2 templates for doc generation
static/ Static assets (images, logos)

Version Snapshots

The site uses 5 Docusaurus docs plugins, so native versioning (which only supports the default plugin) is not used. Instead, each release is preserved as a static build snapshot stored in an orphan git branch (snapshot/vX.Y.Z). The deploy workflow assembles active snapshots into the build output at deploy time.

• / -- always serves the current version
• /vX.Y.Z/ -- serves active version snapshots (with an announcement banner linking to latest)
• snapshots.json -- registry of all versions; the active flag controls which are included in the deploy
• Cloudflare Pages free plan has a 20,000 file limit; each snapshot uses ~2,000 files

Creating a snapshot (new Bactopia release)

1. Go to Actions > Create Version Snapshot and run the workflow
   • version: the version tag (e.g., v4.0.0)
   • bactopia_ref: the bactopia repo ref to build from (e.g., v4.0.0)
2. The workflow builds the site with a version banner, pushes an orphan branch snapshot/vX.Y.Z, and updates snapshots.json on master
3. The deploy workflow runs automatically, including the new snapshot

After creating the snapshot, update the version label in docusaurus.config.ts to the new version:

versions: {current: {label: 'v4.1.0',// update to new version
...
},},

Rebuilding a snapshot

Re-run the Create Version Snapshot workflow with the same version. The orphan branch is force-pushed with the new build.

Managing versions

make snapshot-list # show all versions and file budget
make snapshot-add VERSION=vX.Y.Z FILES=N # manually register a snapshot
make snapshot-deactivate VERSION=v2.1.0 # drop from active deploy
make snapshot-activate VERSION=v2.1.0 # restore to active deploy

Deactivated versions appear under "Archived Versions" in the dropdown, linking to the GitHub branch. Re-activate anytime with make snapshot-activate.

Deployment

The site is deployed to Cloudflare Pages via GitHub Actions. Pushes to master trigger the deploy workflow (.github/workflows/deploy.yml), which:

1. Generates docs from the bactopia source repo
2. Builds the Docusaurus site
3. Fetches active version snapshots from their orphan branches
4. Deploys the assembled output to Cloudflare Pages