From 0f464d1d6cdb9e38c861de23a21e93412b775f61 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 18 Nov 2024 11:14:45 -0600 Subject: [PATCH 1/3] ci(renovate): Add custom VERSION updates in GitHub actions https://docs.renovatebot.com/presets-customManagers/#custommanagersgithubactionsversions --- .github/renovate.json5 | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/.github/renovate.json5 b/.github/renovate.json5 index 46af7821e36..eacaed1524b 100644 --- a/.github/renovate.json5 +++ b/.github/renovate.json5 @@ -7,8 +7,24 @@ "prHeader": "## WARNING\n - [ ] I have made sure to update the singularity and conda images", "packageRules": [ { - "matchDatasources": ["conda", "pypi", "docker"], + "matchDatasources": [ + "conda", + "pypi", + "docker" + ], "automerge": false } - ] + ], + "customManagers": [ + { + "customType": "regex", + "fileMatch": [ + "(^|/)(workflow-templates|\\.(?:github|gitea|forgejo)/(?:workflows|actions))/.+\\.ya?ml$", + "(^|/)action\\.ya?ml$" + ], + "matchStrings": [ + "# renovate: datasource=(?[a-z-.]+?) depName=(?[^\\s]+?)(?: (?:lookupName|packageName)=(?[^\\s]+?))?(?: versioning=(?[^\\s]+?))?(?: extractVersion=(?[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VERSION\\s*:\\s*[\"']?(?.+?)[\"']?\\s" + ] + } + ] } From af432643db41bfb770798e1f26f580715c286cbd Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 18 Nov 2024 11:18:03 -0600 Subject: [PATCH 2/3] ci(#6664): Bump all Nextflow versions to 24.10.1 --- .github/workflows/gpu-tests.yml | 2 +- .github/workflows/nf-test.yml | 2 +- tests/config/nextflow.config | 2 +- tests/config/nf-test.config | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml index dfabddf07ca..41b633c9624 100644 --- a/.github/workflows/gpu-tests.yml +++ b/.github/workflows/gpu-tests.yml @@ -33,7 +33,7 @@ env: NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - NXF_VER: "24.04.4" + NXF_VER: "24.10.1" jobs: nf-test-gpu: diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 38ebea1eff9..41b31d638b2 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -30,7 +30,7 @@ env: NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - NXF_VER: "24.04.4" + NXF_VER: "24.10.1" jobs: nf-test: diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index c86fb134d75..f90c24c2bc8 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -43,5 +43,5 @@ conda { createTimeout = "120 min" } includeConfig 'test_data.config' manifest { - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=24.10.1' } diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config index 6a534a8f7c7..fa21cb2edd6 100644 --- a/tests/config/nf-test.config +++ b/tests/config/nf-test.config @@ -56,5 +56,5 @@ conda { createTimeout = "120 min" } includeConfig 'test_data.config' manifest { - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=24.10.1' } From c1a8c7e806b132b746a516b602e1587fd43f3854 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 18 Nov 2024 11:46:27 -0600 Subject: [PATCH 3/3] ci: Add renovate comments to version in actions --- .github/actions/nf-test-action/action.yml | 4 +++- .github/workflows/gpu-tests.yml | 6 ++++-- .github/workflows/lint.yml | 2 ++ .github/workflows/nf-test.yml | 6 ++++-- .github/workflows/pytest-workflow.yml | 4 ++++ .github/workflows/wave.yml | 18 +++++++++++------- 6 files changed, 28 insertions(+), 12 deletions(-) diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml index 5b87e1e3611..b45e04d467a 100644 --- a/.github/actions/nf-test-action/action.yml +++ b/.github/actions/nf-test-action/action.yml @@ -24,6 +24,8 @@ runs: - name: Setup Nextflow uses: nf-core/setup-nextflow@v2 + with: + version: "${{ env.NXF_VERSION }}" - name: Set up Python uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 @@ -33,7 +35,7 @@ runs: - name: Install nf-test uses: nf-core/setup-nf-test@v1 with: - version: "0.9.2" + version: "${{ env.NFTEST_VERSION }}" install-pdiff: true - name: Setup apptainer diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml index 41b633c9624..92188ed9702 100644 --- a/.github/workflows/gpu-tests.yml +++ b/.github/workflows/gpu-tests.yml @@ -29,11 +29,13 @@ concurrency: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - NFT_VER: "0.9.2" + # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver + NFTEST_VERSION: "0.9.2" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - NXF_VER: "24.10.1" + # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver + NXF_VERSION: "24.10.1" jobs: nf-test-gpu: diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 039e5069a7f..756894a27b0 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -28,6 +28,8 @@ env: NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver + NXF_VER: "24.10.1" jobs: pre-commit: diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 41b31d638b2..6eb3525404a 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -26,11 +26,13 @@ concurrency: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - NFT_VER: "0.9.2" + # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver + NFTEST_VERSION: "0.9.2" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - NXF_VER: "24.10.1" + # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver + NXF_VERSION: "24.10.1" jobs: nf-test: diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index a772dfc1db1..4d4a96d0f38 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -28,6 +28,8 @@ env: NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver + NXF_VERSION: "24.10.1" jobs: pytest-changes: @@ -263,6 +265,8 @@ jobs: - name: Setup Nextflow uses: nf-core/setup-nextflow@v2 + with: + version: ${{ env.NXF_VERSION }} - name: Setup apptainer if: matrix.profile == 'singularity' diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml index a86fd9bb10a..61d0d06a509 100644 --- a/.github/workflows/wave.yml +++ b/.github/workflows/wave.yml @@ -10,8 +10,12 @@ on: # TODO Skip testing CI if any changes to environment.yml env: - WAVE_VER: "1.5.0" - NFTEST_VER: "0.9.1" + # renovate: datasource=github-releases depName=seqeralabs/wave-cli versioning=semver + WAVE_VERSION: "1.5.0" + # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver + NFTEST_VERSION: "0.9.1" + # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver + NXF_VERSION: "24.10.1" jobs: generate-matrix: @@ -62,8 +66,8 @@ jobs: - name: Install wave-cli run: | - wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64 - sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave + wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64 + sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave chmod +x /usr/local/bin/wave - name: Build ${{ matrix.profile }} container @@ -98,8 +102,8 @@ jobs: - name: Install wave-cli run: | - wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64 - sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave + wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64 + sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave chmod +x /usr/local/bin/wave - name: Create a registry name @@ -139,7 +143,7 @@ jobs: # - uses: nf-core/setup-nf-test@v1 # with: - # version: ${{ env.NFTEST_VER }} + # version: ${{ env.NFTEST_VERSION }} # - name: Bump Snapshot Versions # env: