cli.yml

# 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