Merge pull request #74 from computational-cell-analytics/software-upd… #42

	name: Build and Deploy Docs

	on:
	push:
	paths:
	- "doc/*.md" # Trigger on changes to any markdown file
	- "*/.py" # Optionally include changes in Python files
	branches:
	- main # Run the workflow only on pushes to the main branch
	workflow_dispatch:

	# security: restrict permissions for CI jobs.
	permissions:
	contents: read

	jobs:
	build:
	name: Build Documentation
	runs-on: ubuntu-latest

	steps:
	- name: Checkout Code
	uses: actions/checkout@v4

	- name: Set up Micromamba
	uses: mamba-org/setup-micromamba@v2
	with:
	micromamba-version: "latest" # Use the latest version of micromamba
	environment-file: .github/doc_env.yaml # Reference your environment.yml file
	init-shell: bash
	cache-environment: true
	post-cleanup: 'all'
	# cache: true # Cache the micromamba environment

	- name: Install package
	# shell: bash -l {0}
	run: pip install -e .

	- name: Generate Documentation
	shell: bash -l {0}
	run: pdoc synaptic_reconstruction -o doc/

	- name: Verify Documentation Output
	run: ls -la doc/

	- name: Upload Documentation Artifact
	uses: actions/upload-pages-artifact@v3
	with:
	# name: documentation
	path: doc/

	deploy:
	name: Deploy Documentation
	needs: build
	runs-on: ubuntu-latest
	permissions:
	pages: write
	id-token: write
	environment:
	name: github-pages
	url: ${{ steps.deployment.outputs.page_url }}
	steps:
	# - name: Download Documentation Artifact
	# uses: actions/download-artifact@v4
	# with:
	# name: documentation
	# path: .

	- name: Deploy to GiHub Pages
	uses: actions/deploy-pages@v4
	# with:
	# artifact_name: documentation

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