docs(presentations): add HRI-SSI user story deck #305

Workflow file for this run

	name: Deploy MkDocs site to GitHub Pages

	# Runs for:
	# - pushes to main: build -> commit generated files -> deploy
	# - PRs into main: build/validate only (no commits, no deploy)
	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]
	types: [opened, synchronize, reopened]

	# --------------------------------------------------------------------------------------
	# Default shell behavior for ALL `run:` steps (both jobs)
	#
	# Why this:
	# - GitHub's built-in `bash` already uses: `bash --noprofile --norc -eo pipefail {0}`
	# which is effectively "fail fast" for bash scripts.
	# - We add `-u` for extra safety: referencing unset variables becomes an error.
	# - `--noprofile --norc` prevents unexpected user-profile side effects.
	# - `pipefail` ensures a failing command inside a pipeline fails the step.
	# --------------------------------------------------------------------------------------
	defaults:
	run:
	shell: bash --noprofile --norc -euo pipefail {0}

	# Prevent overlapping runs on the same ref from stepping on each other (e.g., deploy pushes).
	# If you push multiple commits quickly, older runs for the same branch are canceled.
	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	# Default least-privilege; PRs only need read
	permissions:
	contents: read

	jobs:
	build:
	name: Build & validate (PRs and main)
	runs-on: ubuntu-latest
	steps:
	# --- Checkout repo files so we can build & run scripts ---
	- name: Checkout repository
	uses: actions/checkout@v6

	# --- Install Python with pip cache for faster subsequent runs ---
	- name: Set up Python 3.x with pip cache
	uses: actions/setup-python@v6
	with:
	python-version: "3.13"
	cache: pip
	cache-dependency-path: scripts/requirements-deploy.txt

	# --- Install all required Python packages for docs & tooling ---
	- name: Install Python dependencies
	run: pip install -r scripts/requirements-deploy.txt

	# --- Clean up repo-specific detritus before generating docs ---
	- name: Clean unwanted files
	run: python scripts/clean-unwanted-files.py

	# --- OWL post-processing (latest versioned pair): labels, synonyms, packages, stages, isDefinedBy, comment cleanup ---
	- name: OWL post-processing (labels, packages, maturity)
	run: python scripts/owl-postprocess.py

	# --- Ensure ontology metadata is present/updated (gUFO file) ---
	- name: Ensure metadata is added to gUFO file
	run: python scripts/insert-metadata.py

	# --- Promote newest versioned files into 'latest' folder ---
	- name: Move newest files from versioned to latest
	run: python scripts/move-latest.py

	# --- Copy ontology changelog into docs so it appears on the MkDocs site ---
	- name: Copy ontology changelog into docs
	run: \|
	mkdir -p docs/deliverables
	cp ontologies/changelog-ontology.md docs/deliverables/changelog-ontology.md

	# --- Ensure no stale PyLODE HTML / docs remain (forces regeneration) ---
	- name: Forces clean sync
	run: \|
	rm -f docs/deliverables/specification-ontology.html
	rm -f docs/method/specification-vocabulary.html
	rm -f docs/deliverables/documentation.md

	# --- Refresh images in docs from latest ontology assets ---
	# Robust variant:
	# - avoids glob failures when folders are empty or missing
	# - ensures destination exists before copy
	- name: Replace ontology images in docs with latest
	run: \|
	rm -rf docs/deliverables/assets/images
	mkdir -p docs/deliverables/assets/images
	cp -r ontologies/latest/images/. docs/deliverables/assets/images/

	# --- Generate OntoUML documentation (custom script) ---
	- name: Generate OntoUML documentation
	run: python scripts/docgen-ontouml.py

	# --- Generate PyLODE HTML specs for ontology and vocabulary ---
	- name: Generate PyLODE specifications
	run: python scripts/docgen-pylode.py

	# --- Convert SSSOM TSV to TTL (kept in repo + used in site) ---
	- name: Create TTL serialization of SSSOM TSV
	run: python scripts/sssom-tsv2ttl.py

	# --- Include SSSOM TSV in built site (docs static assets) ---
	- name: Copy SSSOM TSV into docs assets
	run: \|
	mkdir -p docs/deliverables/assets
	cp mappings/health-ri-mappings.tsv docs/deliverables/assets/health-ri-mappings.tsv

	# --- Remove comments from public copy of TSV in docs assets ---
	- name: Strip commented lines from public TSV copy
	run: sed -i '/^#/d' docs/deliverables/assets/health-ri-mappings.tsv

	# --- Validate MkDocs config before full build (fast fail) ---
	- name: Validate MkDocs configuration
	run: mkdocs build --verbose --clean --site-dir /tmp/mkdocs-check

	# --- Build MkDocs site into ./site ---
	- name: Build MkDocs site
	run: mkdocs build

	# --- Check internal links (ignore ephemeral hash-like URLs) ---
	- name: Check links in built site
	run: \|
	linkchecker ./site \
	--no-status \
	--ignore-url="n[0-9a-f]{32,}"

	# --- Upload built site as artifact for deploy job ---
	- name: Upload built site artifact
	uses: actions/upload-artifact@v7
	with:
	name: site
	path: site
	retention-days: 7

	# --- Upload generated content that should be committed on main ---
	# This keeps the repo’s generated artifacts (ontologies, vocabulary, mappings, specs) up-to-date.
	- name: Upload generated content artifact (to commit on main)
	uses: actions/upload-artifact@v7
	with:
	name: generated
	path: \|
	ontologies/versioned/**
	ontologies/latest/**
	vocabulary/versioned/**
	vocabulary/latest/**
	mappings/**
	docs/deliverables/assets/health-ri-mappings.tsv
	docs/deliverables/specification-ontology.html
	docs/method/specification-vocabulary.html
	retention-days: 7

	deploy:
	name: Commit generated files & publish (main only)
	needs: build
	runs-on: ubuntu-latest

	# Only run on direct pushes to main (not PRs)
	if: github.event_name == 'push' && github.ref == 'refs/heads/main'

	# Needs write permission to commit and push changes
	permissions:
	contents: write

	steps:
	# --- Checkout the exact commit that triggered this workflow run ---
	- name: Checkout repository
	uses: actions/checkout@v6

	# --- Retrieve generated files produced by the build job ---
	- name: Download generated content artifact
	uses: actions/download-artifact@v8
	with:
	name: generated
	path: .

	# --- Retrieve the already-built site folder ---
	- name: Download built site artifact
	uses: actions/download-artifact@v8
	with:
	name: site
	path: ./site

	# --- Commit any changes from generation (idempotent) ---
	- name: Commit and push generated files (if there are changes)
	run: \|
	git config user.name "github-actions[bot]"
	git config user.email "github-actions[bot]@users.noreply.github.com"

	shopt -s globstar

	git add ontologies/versioned/ ontologies/latest/ \|\| true
	git add vocabulary/versioned/ vocabulary/latest/ \|\| true
	git add mappings/** \|\| true
	git add docs/deliverables/assets/health-ri-mappings.tsv \|\| true
	git add docs/deliverables/specification-ontology.html \|\| true
	git add docs/method/specification-vocabulary.html \|\| true

	# If nothing is staged, do nothing; otherwise commit + push.
	git diff --cached --quiet \|\| git commit -m "docs: update generated documentation and specifications"

	# Future-proof: push back to the branch that triggered the run (here: main).
	git push origin "HEAD:${GITHUB_REF_NAME}"

	# --- Publish the built site to GitHub Pages from ./site ---
	- name: Deploy to GitHub Pages
	uses: peaceiris/actions-gh-pages@v4
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	publish_dir: ./site

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docs(presentations): add HRI-SSI user story deck #305

Workflow file

docs(presentations): add HRI-SSI user story deck #305

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Workflow file for this run