shpc update biocontainers #795

	name: shpc update biocontainers

	on:
	workflow_dispatch:
	schedule:
	# Temporary just to test more frequently
	- cron: 0 2 * * *

	jobs:
	auto-scan:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	fetch-depth: '0'

	- name: Create conda environment
	run: conda create --quiet -c conda-forge --name cache spython

	- name: Derive BioContainers List
	run: \|
	export PATH="/usr/share/miniconda/bin:$PATH"
	source activate cache
	pip install --break-system-packages -r .github/scripts/dev-requirements.txt
	python .github/scripts/get_biocontainers.py /tmp/biocontainers.txt
	head /tmp/biocontainers.txt

	# registry defaults to PWD, branch defaults to main
	# url_format_string defaults to shpc docs, this gets formatted to include the entry_name
	- name: Update Biocontainers
	uses: singularityhub/singularity-hpc/actions/cache-update@main
	with:
	token: ${{ secrets.GITHUB_TOKEN }}
	cache: https://github.com/singularityhub/shpc-registry-cache
	namespace: quay.io/biocontainers
	min-count-inclusion: 10
	max-count-inclusion: 1000
	additional-count-inclusion: 25
	url_format_string: "https://biocontainers.pro/tools/%s"
	pull_request: "${{ github.event_name != 'pull_request' }}"
	listing: /tmp/biocontainers.txt

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