Changes to fix missing bibliography online. #238

	name: API docs / pdoc3

	# We should trigger this from an upload event. Note that pdoc requires us to import the
	# built code, so this is a building test as well as documentation deployment

	on:
	push:
	branches:
	- main # Occurs on protected branch through PR
	- development
	- Quick_Start_Docs

	workflow_dispatch:

	jobs:
	deploy:
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v3

	- name: Install Conda environment with Micromamba
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: ./.github/workflows/envs/build_uw_docs.yml
	cache-downloads: true
	cache-env: true

	# the following may be needed if conda-forge is out of date
	# - name: Add compatible petsc4py
	# shell: bash -l {0}
	# run: \|
	# export PETSC_DIR="/home/runner/micromamba-root/envs/uw3_docs"
	# pip3 install petsc4py==3.18 --upgrade

	- name: Build UW3
	shell: bash -l {0}
	run: \|
	export PETSC_DIR="/home/runner/micromamba-root/envs/uw3_docs"
	VERSION=`python3 setup.py --version`
	echo "UW - version " ${VERSION}

	python3 setup.py develop
	pip3 install -e .

	- name: Build docs with pdoc
	shell: bash -l {0}
	run: \|
	VERSION=`python3 setup.py --version`
	echo "VERSION=$(echo $VERSION)" >> $GITHUB_ENV
	# mkdir -p docs
	./build_api_docs.sh

	# There is an action to build the jupyter book to a different directory
	# and then they can be uploaded side by side

	- name: Deploy
	uses: peaceiris/actions-gh-pages@v3

	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	destination_dir: ${{ github.ref_name }}_api # The dest dir is identified by branch
	publish_dir: uw3_api_docs # /underworld3

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