docs: do not execute notebooks (#93) #121

Workflow file for this run

	# Workflow for deploying static content to GitHub Pages with PR previews
	name: Deploy Documentation
	on:
	# Runs on pushes targeting the default branch
	push:
	branches: ["main"]
	# Runs on pull requests for preview builds
	pull_request:
	branches: ["main"]
	# Allows you to run this workflow manually from the Actions tab
	workflow_dispatch:
	inputs:
	pr_number:
	description: 'PR number to build preview for (leave empty for current branch)'
	required: false
	type: string

	# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
	permissions:
	contents: write
	pages: write
	id-token: write
	pull-requests: write

	# Allow only one concurrent deployment per branch/PR
	concurrency:
	group: "pages-${{ github.ref }}"
	cancel-in-progress: false

	jobs:
	# Build job - runs for both main branch and PRs
	build:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Set up python
	uses: actions/setup-python@v4
	with:
	python-version: '3.12'

	- name: Install dependencies
	run: \|
	sudo apt install pandoc
	pip install -r requirements.txt
	pip install ipykernel rdkit cairosvg pymzml
	pip install .

	- name: Build Documentation
	run: sphinx-build -b html ./docs ./_build

	- name: Copy binder files
	run: cp -r ./.binder ./_build

	- name: Upload build artifacts
	uses: actions/upload-artifact@v4
	with:
	name: documentation-${{ github.sha }}
	path: _build/
	retention-days: 30

	# Deploy to main GitHub Pages (only for main branch)
	deploy-main:
	if: github.ref == 'refs/heads/main' && github.event_name == 'push'
	needs: build
	environment:
	name: github-pages
	url: ${{ steps.deployment.outputs.page_url }}
	runs-on: ubuntu-latest
	steps:
	- name: Download build artifacts
	uses: actions/download-artifact@v4
	with:
	name: documentation-${{ github.sha }}
	path: _build/

	- name: Setup Pages
	uses: actions/configure-pages@v5

	- name: Upload to GitHub Pages
	uses: actions/upload-pages-artifact@v3
	with:
	path: _build/

	- name: Deploy to GitHub Pages
	id: deployment
	uses: actions/deploy-pages@v4

	# Deploy PR preview using subdirectories in gh_pages
	deploy-preview:
	if: github.event_name == 'pull_request' \|\| (github.event_name == 'workflow_dispatch' && github.event.inputs.pr_number != '')
	needs: build
	runs-on: ubuntu-latest
	steps:
	- name: Checkout gh_pages branch
	uses: actions/checkout@v4
	with:
	ref: gh_pages
	token: ${{ secrets.GITHUB_TOKEN }}

	- name: Download build artifacts
	uses: actions/download-artifact@v4
	with:
	name: documentation-${{ github.sha }}
	path: _temp_build/

	- name: Get PR number
	id: pr_info
	run: \|
	if [ "${{ github.event_name }}" == "pull_request" ]; then
	echo "pr_number=${{ github.event.number }}" >> $GITHUB_OUTPUT
	else
	echo "pr_number=${{ github.event.inputs.pr_number }}" >> $GITHUB_OUTPUT
	fi

	- name: Deploy PR preview to subdirectory
	run: \|
	PR_NUMBER="${{ steps.pr_info.outputs.pr_number }}"
	PR_DIR="pr-${PR_NUMBER}"

	# Remove existing PR directory if it exists
	rm -rf "$PR_DIR"

	# Create PR directory and copy files
	mkdir -p "$PR_DIR"
	cp -r _temp_build/* "$PR_DIR/"

	# Clean up temp directory
	rm -rf _temp_build

	# Configure git
	git config user.name "github-actions[bot]"
	git config user.email "github-actions[bot]@users.noreply.github.com"

	# Add and commit changes
	git add "$PR_DIR"
	git commit -m "Deploy PR #${PR_NUMBER} preview [skip ci]" \|\| echo "No changes to commit"

	# Push to gh_pages
	git push origin gh_pages

	- name: Comment on PR with preview link
	if: github.event_name == 'pull_request' \|\| github.event.inputs.pr_number != ''
	uses: actions/github-script@v7
	with:
	script: \|
	const prNumber = "${{ steps.pr_info.outputs.pr_number }}";
	const repoOwner = context.repo.owner;
	const repoName = context.repo.repo;
	const previewUrl = `https://${repoOwner}.github.io/${repoName}/pr-${prNumber}/`;

	// Check if we already commented
	const comments = await github.rest.issues.listComments({
	owner: repoOwner,
	repo: repoName,
	issue_number: prNumber,
	});

	const botComment = comments.data.find(comment =>
	comment.user.login === 'github-actions[bot]' &&
	comment.body.includes('📖 Documentation Preview')
	);

	const commentBody = `📖 Documentation Preview

	The documentation for this PR has been built and is available at:
	🔗 [View Preview](${previewUrl})

	This preview will be updated automatically when you push new commits to this PR.

	---
	Preview built from commit: \`${context.sha.substring(0, 7)}\``;

	if (botComment) {
	// Update existing comment
	await github.rest.issues.updateComment({
	owner: repoOwner,
	repo: repoName,
	comment_id: botComment.id,
	body: commentBody
	});
	} else {
	// Create new comment
	await github.rest.issues.createComment({
	owner: repoOwner,
	repo: repoName,
	issue_number: prNumber,
	body: commentBody
	});
	}

	# Cleanup old PR preview branches
	cleanup-previews:
	if: github.event_name == 'pull_request' && github.event.action == 'closed'
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	token: ${{ secrets.GITHUB_TOKEN }}
	fetch-depth: 0

	- name: Delete PR preview directory
	run: \|
	PR_NUMBER="${{ github.event.number }}"
	PR_DIR="pr-${PR_NUMBER}"

	# Checkout gh_pages branch
	git checkout gh_pages

	# Remove PR directory if it exists
	if [ -d "$PR_DIR" ]; then
	rm -rf "$PR_DIR"
	git add "$PR_DIR"
	git commit -m "Remove PR #${PR_NUMBER} preview [skip ci]"
	git push origin gh_pages
	echo "Deleted preview directory: $PR_DIR"
	else
	echo "Preview directory $PR_DIR not found"
	fi

	- name: Comment cleanup notification
	uses: actions/github-script@v7
	with:
	script: \|
	const prNumber = context.payload.number;

	await github.rest.issues.createComment({
	owner: context.repo.owner,
	repo: context.repo.repo,
	issue_number: prNumber,
	body: `🧹 Preview Cleanup

	The documentation preview for this PR has been cleaned up and is no longer available.`
	});

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docs: do not execute notebooks (#93) #121

Workflow file

docs: do not execute notebooks (#93) #121

Uh oh!

Workflow file for this run