From 4cf3677220ed0236bbc0a011f37bf194cabad169 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 Jun 2026 08:15:58 +0000 Subject: [PATCH 1/2] build(deps): bump actions/checkout from 6 to 7 Bumps [actions/checkout](https://github.com/actions/checkout) from 6 to 7. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v6...v7) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ci.yaml | 4 ++-- .github/workflows/docs-ci.yaml | 2 +- .github/workflows/pathogen-repo-build.yaml | 14 +++++++------- .github/workflows/pathogen-repo-ci.yaml | 4 ++-- .github/workflows/sync-rtd-redirects.yaml | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index ffdb12a..b5e3013 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -19,7 +19,7 @@ jobs: - windows-latest runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - uses: ./actions/setup-nextstrain-cli - run: nextstrain version --verbose @@ -96,7 +96,7 @@ jobs: lint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - run: make check - run: ./devel/check-readme - uses: ./actions/shellcheck diff --git a/.github/workflows/docs-ci.yaml b/.github/workflows/docs-ci.yaml index bec120e..f2138b3 100644 --- a/.github/workflows/docs-ci.yaml +++ b/.github/workflows/docs-ci.yaml @@ -73,7 +73,7 @@ jobs: ~~ exit 1 - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 with: repository: ${{ inputs.repo }} diff --git a/.github/workflows/pathogen-repo-build.yaml b/.github/workflows/pathogen-repo-build.yaml index 140dfec..09936d1 100644 --- a/.github/workflows/pathogen-repo-build.yaml +++ b/.github/workflows/pathogen-repo-build.yaml @@ -250,14 +250,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout build repository - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ inputs.repo }} - # Need to run this after the build repo is cloned so that cloning the # build repo does not overwrite the .git dir and remove the extra support files # that we need from nextstrain/.github repo name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }}) - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ needs.workflow-context.outputs.repository }} ref: ${{ needs.workflow-context.outputs.sha }} @@ -379,7 +379,7 @@ jobs: # build repo does not overwrite the .git dir and remove the extra support files # that we need from nextstrain/.github repo name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }}) - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ needs.workflow-context.outputs.repository }} ref: ${{ needs.workflow-context.outputs.sha }} @@ -469,7 +469,7 @@ jobs: # build repo does not overwrite the .git dir and remove the extra support files # that we need from nextstrain/.github repo name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }}) - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ needs.workflow-context.outputs.repository }} ref: ${{ needs.workflow-context.outputs.sha }} @@ -560,7 +560,7 @@ jobs: # build repo does not overwrite the .git dir and remove the extra support files # that we need from nextstrain/.github repo name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }}) - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ needs.workflow-context.outputs.repository }} ref: ${{ needs.workflow-context.outputs.sha }} @@ -651,7 +651,7 @@ jobs: # build repo does not overwrite the .git dir and remove the extra support files # that we need from nextstrain/.github repo name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }}) - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ needs.workflow-context.outputs.repository }} ref: ${{ needs.workflow-context.outputs.sha }} @@ -752,7 +752,7 @@ jobs: # build repo does not overwrite the .git dir and remove the extra support files # that we need from nextstrain/.github repo name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }}) - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ needs.workflow-context.outputs.repository }} ref: ${{ needs.workflow-context.outputs.sha }} diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml index 5d8ebff..2ebe691 100644 --- a/.github/workflows/pathogen-repo-ci.yaml +++ b/.github/workflows/pathogen-repo-ci.yaml @@ -256,7 +256,7 @@ jobs: ' | tee -a "$GITHUB_ENV" - name: Checkout ${{ inputs.repo }} - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ inputs.repo }} ref: ${{ inputs.ref }} @@ -264,7 +264,7 @@ jobs: # build repo does not overwrite the .git dir and remove the extra support files # that we need from nextstrain/.github repo - name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }}) - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ needs.workflow-context.outputs.repository }} ref: ${{ needs.workflow-context.outputs.sha }} diff --git a/.github/workflows/sync-rtd-redirects.yaml b/.github/workflows/sync-rtd-redirects.yaml index 0ee7fc5..f962e0d 100644 --- a/.github/workflows/sync-rtd-redirects.yaml +++ b/.github/workflows/sync-rtd-redirects.yaml @@ -31,7 +31,7 @@ jobs: sync: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - uses: actions/setup-python@v6 - name: Upgrade Python toolchain From 408c5fedbb18b076a39acb0259ebb3dbecfecab7 Mon Sep 17 00:00:00 2001 From: Victor Lin Date: Tue, 23 Jun 2026 11:42:32 -0700 Subject: [PATCH 2/2] Update template files --- .github/workflows/pathogen-repo-build.yaml.in | 4 ++-- .github/workflows/pathogen-repo-ci.yaml.in | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pathogen-repo-build.yaml.in b/.github/workflows/pathogen-repo-build.yaml.in index 53cfc62..1c61b5e 100644 --- a/.github/workflows/pathogen-repo-build.yaml.in +++ b/.github/workflows/pathogen-repo-build.yaml.in @@ -211,7 +211,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout build repository - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ inputs.repo }} @@ -220,7 +220,7 @@ jobs: # that we need from nextstrain/.github repo - &checkout-workflow-support name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }}) - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ needs.workflow-context.outputs.repository }} ref: ${{ needs.workflow-context.outputs.sha }} diff --git a/.github/workflows/pathogen-repo-ci.yaml.in b/.github/workflows/pathogen-repo-ci.yaml.in index 46aff5e..6723d7d 100644 --- a/.github/workflows/pathogen-repo-ci.yaml.in +++ b/.github/workflows/pathogen-repo-ci.yaml.in @@ -231,7 +231,7 @@ jobs: | tee -a "$GITHUB_ENV" - name: Checkout ${{ inputs.repo }} - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ inputs.repo }} ref: ${{ inputs.ref }} @@ -240,7 +240,7 @@ jobs: # build repo does not overwrite the .git dir and remove the extra support files # that we need from nextstrain/.github repo - name: Checkout ${{ needs.workflow-context.outputs.repository }} (sha ${{ needs.workflow-context.outputs.sha }}) - uses: actions/checkout@v6 + uses: actions/checkout@v7 with: repository: ${{ needs.workflow-context.outputs.repository }} ref: ${{ needs.workflow-context.outputs.sha }}