cli

fix: dataset changelog url in update notification widget #1947

Workflow file for this run

	# Build CLI binaries and publish them to GitHub Releases
	name: cli

	on:
	push:
	branches: [ 'master', 'staging-cli', 'release-cli' ]

	pull_request:

	repository_dispatch:
	types: build

	workflow_dispatch:

	workflow_call:

	concurrency:
	group: cli-${{ github.workflow }}-${{ github.ref_type }}-${{ github.event.pull_request.number \|\| github.ref \|\| github.run_id }}
	cancel-in-progress: true

	defaults:
	run:
	shell: bash -euxo pipefail {0}

	env:
	GITHUB_REPOSITORY_URL: ${{ github.server_url }}/${{ github.repository }}
	VERBOSE: 1

	jobs:

	builder-docker-image:
	name: "Run 'builder-docker-image.yml' workflow"
	uses: ./.github/workflows/builder-docker-image.yml
	secrets: inherit
	concurrency:
	group: cli-builder-docker-image-workflow_call-${{ github.workflow }}-${{ github.ref_type }}-${{ github.event.pull_request.number \|\| github.ref \|\| github.run_id }}
	cancel-in-progress: true

	build-cli:
	name: "Build CLI (${{ matrix.arch }})"
	needs: [ builder-docker-image ]
	runs-on: ubuntu-22.04

	strategy:
	fail-fast: false
	matrix:
	arch:
	- aarch64-apple-darwin
	- aarch64-unknown-linux-gnu
	- aarch64-unknown-linux-musl
	- x86_64-apple-darwin
	- x86_64-pc-windows-gnu
	- x86_64-unknown-linux-gnu
	- x86_64-unknown-linux-musl

	steps:
	- name: "Set up Docker Buildx"
	uses: docker/setup-buildx-action@v3

	- name: "Free disk space"
	run: \|
	sudo swapoff -a \|\| true
	sudo rm -f /swapfile \|\| true

	sudo apt-get remove --yes --purge --verbose-versions '^dotnet-.' '^llvm-.' 'php.' '^mongodb-.' '^mysql-.*' azure-cli google-cloud-sdk hhvm google-chrome-stable firefox powershell mono-devel libgl1-mesa-dri \|\| true
	sudo apt-get autoremove --purge --verbose-versions --yes
	sudo apt-get clean
	sudo apt-get update

	sudo rm -rf /opt/ghc
	sudo rm -rf /usr/local/.ghcup
	sudo rm -rf /usr/local/graalvm
	sudo rm -rf /usr/local/lib/android
	sudo rm -rf /usr/local/lib/node_modules
	sudo rm -rf /usr/local/share/chromium
	sudo rm -rf /usr/local/share/powershell
	sudo rm -rf /usr/share/dotnet

	docker container stop $(docker ps -q) \|\| true
	docker rmi $(docker image ls -aq) \|\| true
	yes \| docker system prune -af --volumes \|\| true
	yes \| docker network prune -f \|\| true
	yes \| docker image prune -af \|\| true
	yes \| docker builder prune -af \|\| true
	yes \| docker buildx prune -af \|\| true

	- name: "Check disk space"
	run: \|
	echo ""

	df -Th \| awk 'NR == 1; NR > 1 {print $0 \| "sort -n"}'

	echo ""

	lsblk -o MOUNTPOINT,FSTYPE,FSSIZE,FSAVAIL,FSUSE%,TYPE,NAME,ROTA,SIZE,MODEL,UUID

	- name: "Setup environment (release)"
	if: endsWith(github.ref, '/release-cli')
	run: \|
	echo "DATA_FULL_DOMAIN=https://data.clades.nextstrain.org/v3" >> $GITHUB_ENV

	- name: "Setup environment (staging)"
	if: endsWith(github.ref, '/staging-cli')
	run: \|
	echo "DATA_FULL_DOMAIN=https://data.staging.clades.nextstrain.org/v3" >> $GITHUB_ENV

	- name: "Setup environment (master)"
	if: ${{ !endsWith(github.ref, '/staging-cli') && !endsWith(github.ref, '/release-cli') }}
	run: \|
	echo "DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3" >> $GITHUB_ENV

	- name: "Checkout code"
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	submodules: true

	- name: "Get docker build checksum"
	id: docker-build-checksum
	run: echo "checksum=$(./scripts/docker_build_checksum.sh)" >> $GITHUB_OUTPUT

	- name: "Setup cache for Docker buildx (${{ matrix.arch }})"
	uses: actions/cache@v4
	with:
	path: .cache/docker/buildx
	key: cache-v1-buildx-${{ runner.os }}-${{ matrix.arch }}-${{ steps.docker-build-checksum.outputs.checksum }}
	restore-keys: \|
	cache-v1-buildx-${{ runner.os }}-${{ matrix.arch }}-${{ steps.docker-build-checksum.outputs.checksum }}
	cache-v1-buildx-${{ runner.os }}-${{ matrix.arch }}-
	cache-v1-buildx-${{ runner.os }}-${{ steps.docker-build-checksum.outputs.checksum }}
	cache-v1-buildx-${{ runner.os }}-

	- name: "Setup cache for Rust and Cargo"
	uses: actions/cache@v4
	with:
	path: \|
	.cache/docker/.cargo
	.build/
	key: cache-v1-cargo-${{ runner.os }}-${{ matrix.arch }}-${{ hashFiles('**/Cargo.lock') }}
	restore-keys: \|
	cache-v1-cargo-${{ runner.os }}-${{ matrix.arch }}-${{ hashFiles('**/Cargo.lock') }}
	cache-v1-cargo-${{ runner.os }}-${{ matrix.arch }}-
	cache-v1-cargo-${{ runner.os }}-

	- name: "Install deps"
	run: \|
	mkdir -p "${HOME}/bin"
	curl -fsSL "https://github.com/TomWright/dasel/releases/download/v1.24.3/dasel_linux_amd64" -o "${HOME}/bin/dasel" && chmod +x "${HOME}/bin/dasel"

	- name: "Prepare .env file"
	run: \|
	export PATH="${PATH}:${HOME}/bin"

	version=$(dasel select -p toml -s ".workspace.package.version" -f "Cargo.toml")
	if [[ "$version" =~ (rc\|beta\|alpha) ]]; then
	export DATA_FULL_DOMAIN="https://data.master.clades.nextstrain.org/v3"
	fi

	cp .env.example .env
	sed -i -e "s\|OSXCROSS_URL=http://example.com/osxcross/osxcross.tar.xz\|OSXCROSS_URL=${{ secrets.OSXCROSS_URL }}\|g" .env
	sed -i -e "s\|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3\|DATA_FULL_DOMAIN=${DATA_FULL_DOMAIN}\|g" .env

	- name: "Login to Docker Hub"
	uses: docker/login-action@v3
	with:
	registry: docker.io
	username: nextstrainbot
	password: ${{ secrets.DOCKER_TOKEN }}

	- name: "Build docker image (${{ matrix.arch }})"
	run: \|
	CROSS="${{ matrix.arch }}" ./docker/dev docker-image-build-push

	- name: "Build CLI (${{ matrix.arch }})"
	run: \|
	CROSS="${{ matrix.arch }}" ./docker/dev build-release

	- name: "Upload build artifacts (${{ matrix.arch }})"
	uses: actions/upload-artifact@v4
	with:
	name: out-${{ matrix.arch }}
	path: ./.out/*
	include-hidden-files: true


	run-unit-tests:
	name: "Run unit tests"
	needs: [ builder-docker-image ]
	runs-on: ubuntu-22.04

	steps:
	- name: "Set up Docker Buildx"
	uses: docker/setup-buildx-action@v3

	- name: "Checkout code"
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	submodules: true

	- name: "Get docker build checksum"
	id: docker-build-checksum
	run: echo "checksum=$(./scripts/docker_build_checksum.sh)" >> $GITHUB_OUTPUT

	- name: "Setup cache for Docker buildx"
	uses: actions/cache@v4
	with:
	path: .cache/docker/buildx
	key: cache-v1-buildx-unit-tests-${{ runner.os }}-${{ steps.docker-build-checksum.outputs.checksum }}
	restore-keys: \|
	cache-v1-buildx-unit-tests-${{ runner.os }}-${{ steps.docker-build-checksum.outputs.checksum }}
	cache-v1-buildx-unit-tests-${{ runner.os }}-

	- name: "Setup cache for Rust and Cargo"
	uses: actions/cache@v4
	with:
	path: \|
	.cache/docker/.cargo
	.build/
	key: cache-v1-cargo-unit-tests-${{ runner.os }}-${{ hashFiles('**/Cargo.lock') }}
	restore-keys: \|
	cache-v1-cargo-unit-tests-${{ runner.os }}-${{ hashFiles('**/Cargo.lock') }}
	cache-v1-cargo-unit-tests-${{ runner.os }}-

	- name: "Prepare .env file"
	run: \|
	cp .env.example .env
	sed -i -e "s\|OSXCROSS_URL=http://example.com/osxcross/osxcross.tar.xz\|OSXCROSS_URL=${{ secrets.OSXCROSS_URL }}\|g" .env

	- name: "Run unit tests"
	run: \|
	./docker/dev test


	run-lints:
	name: "Run lints"
	needs: [ builder-docker-image ]
	runs-on: ubuntu-22.04

	steps:
	- name: "Set up Docker Buildx"
	uses: docker/setup-buildx-action@v3

	- name: "Checkout code"
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	submodules: true

	- name: "Get docker build checksum"
	id: docker-build-checksum
	run: echo "checksum=$(./scripts/docker_build_checksum.sh)" >> $GITHUB_OUTPUT

	- name: "Setup cache for Docker buildx"
	uses: actions/cache@v4
	with:
	path: .cache/docker/buildx
	key: cache-v1-buildx-lints-${{ runner.os }}-${{ steps.docker-build-checksum.outputs.checksum }}
	restore-keys: \|
	cache-v1-buildx-lints-${{ runner.os }}-${{ steps.docker-build-checksum.outputs.checksum }}
	cache-v1-buildx-lints-${{ runner.os }}-

	- name: "Setup cache for Rust and Cargo"
	uses: actions/cache@v4
	with:
	path: \|
	.cache/docker/.cargo
	.build/
	key: cache-v1-cargo-lints-${{ runner.os }}-${{ hashFiles('**/Cargo.lock') }}
	restore-keys: \|
	cache-v1-cargo-lints-${{ runner.os }}-${{ hashFiles('**/Cargo.lock') }}
	cache-v1-cargo-lints-${{ runner.os }}-

	- name: "Prepare .env file"
	run: \|
	cp .env.example .env
	sed -i -e "s\|OSXCROSS_URL=http://example.com/osxcross/osxcross.tar.xz\|OSXCROSS_URL=${{ secrets.OSXCROSS_URL }}\|g" .env

	- name: "Run lints"
	run: \|
	./docker/dev lint-ci


	run-smoke-tests:
	name: "Run smoke tests (linux)"
	needs: [ build-cli ]
	runs-on: ubuntu-22.04

	steps:
	- name: "Set up Docker Buildx"
	uses: docker/setup-buildx-action@v3

	- name: "Checkout code"
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	submodules: true

	- name: "Install dependencies"
	run: \|
	mkdir -p "${HOME}/bin"
	export PATH="${HOME}/bin:${PATH}"
	curl -fsSL "https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64" -o ${HOME}/bin/jq && chmod +x ${HOME}/bin/jq

	- name: "Download build artifacts"
	uses: actions/download-artifact@v4
	with:
	pattern: out-*
	merge-multiple: true
	path: ".out"

	- name: "Run smoke tests (linux)"
	run: \|
	chmod +x ./.out/*
	JOBS=2 ./tests/run-smoke-tests ./.out/nextclade-x86_64-unknown-linux-gnu

	# run-smoke-tests-mac:
	# name: "Run smoke tests (mac)"
	# needs: [ build-cli ]
	# runs-on: macos-latest
	#
	# steps:
	# - name: "Checkout code"
	# uses: actions/checkout@v4
	# with:
	# fetch-depth: 1
	# submodules: true
	#
	# - name: "Download build artifacts"
	# uses: actions/download-artifact@v4
	# with:
	# name: "out"
	# path: ".out"
	#
	# - name: "Run smoke tests (mac)"
	# run: \|
	# chmod +x ./.out/*
	# ./tests/run-smoke-tests ./.out/nextclade-x86_64-apple-darwin


	run-linux-distros-test:
	name: "Run Linux distros compatibility test"
	needs: [ build-cli ]
	runs-on: ubuntu-22.04

	steps:
	- name: "Set up Docker Buildx"
	uses: docker/setup-buildx-action@v3

	- name: "Checkout code"
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	submodules: true

	- name: "Download build artifacts"
	uses: actions/download-artifact@v4
	with:
	pattern: out-*
	merge-multiple: true
	path: ".out"

	- name: "Test Linux distros compatibility"
	run: \|
	chmod +x ./.out/nextclade-x86_64-unknown-linux-gnu
	./tests/test-linux-distros ./.out/nextclade-x86_64-unknown-linux-gnu


	check-cli-docs:
	name: "Check that autogenerated CLI documentation is up-to-date"
	needs: [ build-cli ]
	runs-on: ubuntu-22.04

	steps:
	- name: "Checkout code"
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	submodules: true

	- name: "Download build artifacts"
	uses: actions/download-artifact@v4
	with:
	pattern: out-*
	merge-multiple: true
	path: ".out"

	- name: "Re-generate CLI docs"
	run: \|
	chmod +x ./.out/nextclade-x86_64-unknown-linux-gnu
	./scripts/update_cli_reference_docs ./.out/nextclade-x86_64-unknown-linux-gnu

	- name: "Check that the git diff is clean"
	run: \|
	git -c color.ui=always diff --exit-code 'docs/user/nextclade-cli/reference.md' \|\| (echo "Autogenerated CLI documentation is not up-to-date, please run './scripts/update_cli_reference_docs <path_to_nextclade>', then verify and commit the changes." >&2; exit 1)

	publish-to-github-releases:
	name: "Publish to GitHub Releases"
	needs: [ build-cli, run-unit-tests, run-lints, run-smoke-tests, run-linux-distros-test, check-cli-docs ]
	if: endsWith(github.ref, '/release-cli')
	runs-on: ubuntu-22.04

	steps:
	- name: "Checkout code"
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	submodules: true

	- name: "Download build artifacts"
	uses: actions/download-artifact@v4
	with:
	pattern: out-*
	merge-multiple: true
	path: ".out"

	- name: "Install deploy dependencies"
	run: \|
	mkdir -p "${HOME}/bin"
	curl -fsSL "https://github.com/cli/cli/releases/download/v2.10.1/gh_2.10.1_linux_amd64.tar.gz" \| tar xz -C "${HOME}/bin" --strip-components=2 gh_2.10.1_linux_amd64/bin/gh
	curl -fsSL "https://github.com/TomWright/dasel/releases/download/v1.24.3/dasel_linux_amd64" -o "${HOME}/bin/dasel" && chmod +x "${HOME}/bin/dasel"
	curl -fsSL "https://github.com/orhun/git-cliff/releases/download/v0.7.0/git-cliff-0.7.0-x86_64-unknown-linux-gnu.tar.gz" \| tar -C "${HOME}/bin" --strip-components=1 -xz "git-cliff-0.7.0/git-cliff"
	curl -fsSL "https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64" -o ${HOME}/bin/jq && chmod +x ${HOME}/bin/jq

	- name: "Publish build artifacts to GitHub releases"
	run: \|
	export PATH="${PATH}:${HOME}/bin"
	export GITHUB_TOKEN="${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_REPO }}"
	./scripts/publish_github \
	--artifacts_dir ".out" \
	--repo "${{ github.repository }}" \
	--git_sha "${{ github.sha }}"

	publish-to-docker-hub:
	name: "Publish to Docker Hub"
	needs: [ build-cli, run-unit-tests, run-lints, run-smoke-tests, run-linux-distros-test, check-cli-docs ]
	if: endsWith(github.ref, '/release-cli')
	runs-on: ubuntu-22.04

	steps:
	- name: "Checkout code"
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	submodules: true

	- name: "Download build artifacts"
	uses: actions/download-artifact@v4
	with:
	pattern: out-*
	merge-multiple: true
	path: ".out"

	- name: "Install deploy dependencies"
	run: \|
	mkdir -p "${HOME}/bin"
	curl -fsSL "https://github.com/TomWright/dasel/releases/download/v1.24.3/dasel_linux_amd64" -o "${HOME}/bin/dasel" && chmod +x "${HOME}/bin/dasel"

	- name: "Login to Docker Hub"
	uses: docker/login-action@v3
	with:
	registry: docker.io
	username: nextstrainbot
	password: ${{ secrets.DOCKER_TOKEN }}

	- name: "Build and publish Docker container images to Docker Hub"
	run: \|
	export PATH="${PATH}:${HOME}/bin"
	chmod +x ./.out/*
	./scripts/publish_docker --push

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fix: dataset changelog url in update notification widget #1947

Workflow file

fix: dataset changelog url in update notification widget #1947

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Workflow file for this run