Upgrade IQ-TREE to 2.3.5 with CMAPLE support #1384
Workflow file for this run
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| name: CI | |
| on: [push, pull_request, workflow_dispatch] | |
| # Prevent intermediate images from being used by another run. | |
| # Concurrency group is unique: | |
| # 1. to this workflow (github.workflow) | |
| # 2. per event ref (github.ref) | |
| # 3. per run on the default branch (github.run_id) | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ github.ref_type == 'branch' && github.ref_name == github.event.repository.default_branch && github.run_id }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: nextstrain/.github/actions/shellcheck@master | |
| # Build multi-platform builder and final images with caching from Docker Hub | |
| # and GitHub Container Registry; push to GitHub Container Registry. | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '>=3.8' | |
| - name: Set $CACHE_DATE | |
| run: echo "CACHE_DATE=$(date --utc +%Y%m%dT%H%M%SZ)" | tee -a "$GITHUB_ENV" | |
| - if: github.event_name != 'pull_request' && github.ref_type == 'branch' && github.ref_name == github.event.repository.default_branch | |
| name: Set $TAG (default branch) | |
| run: echo "TAG=build-$CACHE_DATE" | tee -a "$GITHUB_ENV" | |
| - if: env.TAG == '' | |
| name: Set $TAG (PRs, non-default branch) | |
| # From `man docker-image-tag`: The tag name must be valid ASCII and may | |
| # contain lowercase and uppercase letters, digits, underscores, periods | |
| # and hyphens. | |
| run: echo "TAG=branch-${GITHUB_REF_NAME//[^A-Za-z0-9._-]/-}" | tee -a "$GITHUB_ENV" | |
| - uses: docker/setup-qemu-action@v3 | |
| # GITHUB_TOKEN is unreliable¹ so use a token from nextstrain-bot. | |
| # ¹ https://github.com/docker/build-push-action/issues/463#issuecomment-939394233 | |
| - uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: nextstrain-bot | |
| password: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_MANAGE_PACKAGES }} | |
| - run: ./devel/build -p linux/amd64,linux/arm64 -r ghcr.io -t "$TAG" -l logs/ | |
| - if: always() | |
| name: Upload build logs as artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-logs | |
| path: logs/ | |
| - if: always() | |
| name: Summarize build logs for the GitHub Actions run summary page | |
| run: | | |
| for log in logs/*; do | |
| { | |
| echo "## $(basename "$log")" | |
| echo '' | |
| echo '```' | |
| ./devel/summarize-buildkit-output "$log" 2>&1 | |
| echo '```' | |
| echo '' | |
| } >> "$GITHUB_STEP_SUMMARY" | |
| done | |
| outputs: | |
| tag: ${{ env.TAG }} | |
| # Run tests with the final image from GitHub Container Registry. | |
| test: | |
| name: test (${{ matrix.platform }}) | |
| needs: build | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| platform: | |
| - linux/amd64 | |
| - linux/arm64 | |
| permissions: | |
| contents: read | |
| id-token: write | |
| steps: | |
| - uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: nextstrain-bot | |
| password: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_MANAGE_PACKAGES }} | |
| - uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-region: us-east-1 | |
| role-to-assume: arn:aws:iam::827581582529:role/GitHubActionsRoleNextstrainTmpBucket | |
| - run: aws sts get-caller-identity | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ~3 | |
| # The ubuntu-latest runner is linux/amd64 so anything else will | |
| # run with emulation, which is still better than nothing. | |
| - if: matrix.platform != 'linux/amd64' | |
| uses: docker/setup-qemu-action@v3 | |
| - uses: actions/checkout@v4 | |
| - run: pip install cram | |
| - run: make test | |
| env: | |
| IMAGE: ghcr.io/nextstrain/base:${{ needs.build.outputs.tag }} | |
| DOCKER_DEFAULT_PLATFORM: ${{ matrix.platform }} | |
| - uses: nextstrain/.github/actions/setup-nextstrain-cli@master | |
| - name: Run zika-tutorial | |
| run: | | |
| git clone https://github.com/nextstrain/zika-tutorial | |
| nextstrain build --image ghcr.io/nextstrain/base:${{ needs.build.outputs.tag }} zika-tutorial -F | |
| env: | |
| DOCKER_DEFAULT_PLATFORM: ${{ matrix.platform }} | |
| validate-platforms: | |
| name: Validate platforms | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/setup-qemu-action@v3 | |
| - uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: nextstrain-bot | |
| password: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_MANAGE_PACKAGES }} | |
| - name: Validate final images | |
| run: ./devel/validate-platforms -r ghcr.io -t ${{ needs.build.outputs.tag }} | |
| # "Push" (copy) the builder and final images from GitHub Container Registry to | |
| # Docker Hub, where they will persist. Do this regardless of test results. | |
| push-branch: | |
| if: startsWith(needs.build.outputs.tag, 'branch-') && github.event_name != 'pull_request' | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: nextstrain-bot | |
| password: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_MANAGE_PACKAGES }} | |
| - uses: docker/login-action@v3 | |
| with: | |
| registry: docker.io | |
| username: nextstrainbot | |
| password: ${{ secrets.DOCKER_TOKEN }} | |
| - name: Copy $TAG images to Docker Hub | |
| run: ./devel/copy-images -i ghcr.io -o docker.io -t ${{ needs.build.outputs.tag }} | |
| # "Push" (copy) the builder and final images from GitHub Container Registry to | |
| # Docker Hub, where they will persist. Only do this if tests pass. | |
| push-build: | |
| if: startsWith(needs.build.outputs.tag, 'build-') | |
| needs: [build, test, validate-platforms] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: nextstrain-bot | |
| password: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_MANAGE_PACKAGES }} | |
| - uses: docker/login-action@v3 | |
| with: | |
| registry: docker.io | |
| username: nextstrainbot | |
| password: ${{ secrets.DOCKER_TOKEN }} | |
| - name: Copy $TAG + latest images to Docker Hub | |
| run: | | |
| ./devel/copy-images -i ghcr.io -o docker.io -t ${{ needs.build.outputs.tag }} -l | |
| # Run pathogen repo CI builds with the final image | |
| # This is running pathogen-repo-ci@v0 for pathogen repos that do not conform | |
| # to the standard pathogen repo structure and is not expected to be updated. | |
| # Any new pathogen repos should be added to the job using the latest version | |
| # of the pathogen-repo-ci below. | |
| test-pathogen-repo-ci-v0: | |
| # Only one of push-{branch,build} runs for any given workflow run, and | |
| # we're ok with either of them. | |
| needs: [build, push-branch, push-build] | |
| if: |2 | |
| success() | |
| || needs.push-branch.result == 'success' | |
| || needs.push-build.result == 'success' | |
| strategy: | |
| matrix: | |
| include: | |
| - { pathogen: avian-flu, build-args: --configfile config/gisaid.yaml -pf test_target } | |
| - { pathogen: ebola } | |
| - { pathogen: lassa } | |
| - { pathogen: mumps } | |
| - { pathogen: ncov, build-args: all_regions -j 2 --profile nextstrain_profiles/nextstrain-ci } | |
| - { pathogen: rsv } | |
| - { pathogen: seasonal-flu, build-args: --configfile profiles/ci/builds.yaml -p } | |
| name: test-pathogen-repo-ci-v0 (${{ matrix.pathogen }}) | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@v0 | |
| with: | |
| repo: nextstrain/${{ matrix.pathogen }} | |
| build-args: ${{ matrix.build-args }} | |
| runtimes: | | |
| - docker | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: nextstrain/base:${{ needs.build.outputs.tag }} | |
| artifact-name: ${{ matrix.pathogen }}-outputs | |
| continue-on-error: true | |
| secrets: inherit | |
| # Run pathogen repo CI builds with the final image | |
| # This is running pathogen-repo-ci@master for pathogen repos that _do_ follow | |
| # standard pathogen repo structure and new pathogens should be added here | |
| # to be supported for future updates such as testing on multiple platforms. | |
| test-pathogen-repo-ci: | |
| # Only one of push-{branch,build} runs for any given workflow run, and | |
| # we're ok with either of them. | |
| needs: [build, push-branch, push-build] | |
| if: |2 | |
| success() | |
| || needs.push-branch.result == 'success' | |
| || needs.push-build.result == 'success' | |
| strategy: | |
| # XXX TODO: Test on multiple platforms via the matrix too, as above? | |
| matrix: | |
| pathogen: | |
| - dengue | |
| - measles | |
| - mpox | |
| - seasonal-cov | |
| - zika | |
| name: test-pathogen-repo-ci (${{ matrix.pathogen }}) | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master | |
| with: | |
| repo: nextstrain/${{ matrix.pathogen }} | |
| runtimes: | | |
| - docker | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: nextstrain/base:${{ needs.build.outputs.tag }} | |
| artifact-name: ${{ matrix.pathogen }}-outputs | |
| continue-on-error: true | |
| secrets: inherit | |
| # Delete the builder and final images from GitHub Container Registry. | |
| cleanup-registry: | |
| if: always() | |
| needs: [build, test, validate-platforms, push-branch, push-build] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/github-script@v7 | |
| with: | |
| github-token: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_MANAGE_PACKAGES }} | |
| script: | | |
| const script = require('./devel/delete-from-ghcr.js'); | |
| const tag = "${{ needs.build.outputs.tag }}"; | |
| const token = "${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_MANAGE_PACKAGES }}"; | |
| script({fetch, octokit: github, tag, token}); |