docs(dev): document manual bioconda fork update #1937
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| # 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 |