Add automatic detection of datasets #1013
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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: "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" >> $GITHUB_ENV | |
| - name: "Checkout code" | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: "Get docker build checksum" | |
| id: docker-build-checksum | |
| run: echo "checksum=$(./scripts/docker_build_checksum.sh)" >> $GITHUB_OUTPUT | |
| - name: "Setup cache for Docker buildx (${{ matrix.arch }})" | |
| uses: actions/cache@v3 | |
| 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-${{ runner.os }}- | |
| - name: "Setup cache for Rust and Cargo" | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| .cache/docker/.cargo | |
| .build/ | |
| key: cache-v1-cargo-${{ 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: "Prepare .env file" | |
| run: | | |
| cp .env.example .env | |
| sed -i -e "s|OSXCROSS_URL=http://example.com/osxcross/osxcross.tar.xz|OSXCROSS_URL=${{ secrets.OSXCROSS_URL }}|g" .env | |
| sed -i -e "s|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3|DATA_FULL_DOMAIN=${DATA_FULL_DOMAIN}|g" .env | |
| - name: "Login to Docker Hub" | |
| uses: docker/login-action@v2 | |
| 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@v3 | |
| with: | |
| name: out | |
| path: ./.out/* | |
| run-unit-tests: | |
| name: "Run unit tests" | |
| needs: [ builder-docker-image ] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: "Checkout code" | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: "Get docker build checksum" | |
| id: docker-build-checksum | |
| run: echo "checksum=$(./scripts/docker_build_checksum.sh)" >> $GITHUB_OUTPUT | |
| - name: "Setup cache for Docker buildx" | |
| uses: actions/cache@v3 | |
| with: | |
| path: .cache/docker/buildx | |
| key: cache-v1-buildx-unit-tests-${{ 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@v3 | |
| 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: "Checkout code" | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: "Get docker build checksum" | |
| id: docker-build-checksum | |
| run: echo "checksum=$(./scripts/docker_build_checksum.sh)" >> $GITHUB_OUTPUT | |
| - name: "Setup cache for Docker buildx" | |
| uses: actions/cache@v3 | |
| with: | |
| path: .cache/docker/buildx | |
| key: cache-v1-buildx-lints-${{ 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@v3 | |
| 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: "Checkout code" | |
| uses: actions/checkout@v3 | |
| 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@v3 | |
| with: | |
| name: "out" | |
| 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@v3 | |
| # with: | |
| # fetch-depth: 1 | |
| # submodules: true | |
| # | |
| # - name: "Download build artifacts" | |
| # uses: actions/download-artifact@v3 | |
| # 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: "Checkout code" | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: "Download build artifacts" | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: "out" | |
| 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 | |
| publish-to-github-releases: | |
| name: "Publish to GitHub Releases" | |
| needs: [ build-cli, run-unit-tests, run-lints, run-smoke-tests, run-linux-distros-test ] | |
| if: endsWith(github.ref, '/release-cli') | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: "Checkout code" | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: "Download build artifacts" | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: "out" | |
| 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 ] | |
| if: endsWith(github.ref, '/release-cli') | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: "Checkout code" | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: "Download build artifacts" | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: "out" | |
| 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@v2 | |
| 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 |