Merge pull request #90 from nextstrain/update-ci-89 #494

	name: CI

	on:
	push:
	branches:
	- master
	pull_request:
	workflow_dispatch:

	jobs:
	test-setup-nextstrain-cli:
	name: test-setup-nextstrain-cli (os=${{ matrix.os }})
	strategy:
	fail-fast: false
	matrix:
	os:
	- ubuntu-latest
	- macos-latest
	- windows-latest
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v4
	- uses: ./actions/setup-nextstrain-cli
	- run: nextstrain version --verbose

	test-pathogen-repo-ci:
	uses: ./.github/workflows/pathogen-repo-ci.yaml
	with:
	repo: nextstrain/zika
	artifact-name: outputs-test-pathogen-repo-ci
	secrets: inherit

	test-pathogen-repo-ci-no-example-data:
	uses: ./.github/workflows/pathogen-repo-ci.yaml
	with:
	repo: nextstrain/zika-tutorial
	artifact-name: outputs-test-pathogen-repo-ci-no-example-data

	test-docs-ci-conda:
	uses: ./.github/workflows/docs-ci.yaml
	with:
	repo: nextstrain/docs.nextstrain.org
	docs-directory: .
	environment-file: conda.yml

	test-docs-ci-pip:
	uses: ./.github/workflows/docs-ci.yaml
	with:
	repo: nextstrain/augur
	docs-directory: docs/
	pip-install-target: .[dev]

	test-pathogen-repo-build:
	permissions:
	id-token: write
	strategy:
	matrix:
	runtime: [docker, conda, aws-batch]
	uses: ./.github/workflows/pathogen-repo-build.yaml
	with:
	repo: nextstrain/zika-tutorial
	runtime: ${{ matrix.runtime }}
	run: nextstrain build --env BOGUS_ENVVAR .
	artifact-name: build-output-${{ matrix.runtime }}
	env: \|
	BOGUS_ENVVAR: BOGUS_ENVVAR
	secrets: inherit

	lint:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- run: make check
	- run: ./devel/check-readme
	- uses: ./actions/shellcheck

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