Make Ct 0 for positive control samples (#20) #5

	name: "Build & Deploy Documentation"
	on:
	push:
	branches:
	- main
	workflow_dispatch:

	jobs:
	docs:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: directly build sphinx
	run: \|
	pip install .
	pip install -r docs/requirements.txt
	sphinx-build docs/source ./docs/_build/html
	- uses: actions/upload-artifact@v1
	with:
	name: DocumentationHTML
	path: docs/_build/html
	- name: Commit documentation changes
	run: \|
	git clone https://github.com/BCCDC-PHL/auto-ncov.git --branch gh-pages --single-branch gh-pages
	cp -r docs/_build/html/* gh-pages/
	cd gh-pages
	touch .nojekyll
	git config --local user.email "[email protected]"
	git config --local user.name "GitHub Action"
	git add .
	git commit -m "Update documentation" -a \|\| true
	# The above command will fail if no changes were present, so we ignore
	# that.
	- name: Push changes
	uses: ad-m/github-push-action@master
	with:
	branch: gh-pages
	directory: gh-pages
	github_token: ${{ secrets.GITHUB_TOKEN }}

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