From 6c24b99e98c699b63364ad1e6a8347bb838191d4 Mon Sep 17 00:00:00 2001 From: Franciszek Walkowiak Date: Thu, 8 Feb 2024 15:46:01 +0100 Subject: [PATCH 1/5] Update actions versions --- .github/workflows/bioccheck.yaml | 2 +- .github/workflows/build-check-install.yaml | 14 +++++++------- .github/workflows/grammar.yaml | 6 +++--- .github/workflows/pkgdown.yaml | 4 ++-- .github/workflows/roxygen.yaml | 2 +- .github/workflows/style.yaml | 2 +- .github/workflows/test-coverage.yaml | 8 ++++---- .github/workflows/validation.yaml | 4 ++-- .github/workflows/verdepcheck.yaml | 4 ++-- .github/workflows/version-bump.yaml | 4 ++-- .github/workflows/version.yaml | 2 +- 11 files changed, 26 insertions(+), 26 deletions(-) diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml index 4284a8e16..5b7a0b54e 100644 --- a/.github/workflows/bioccheck.yaml +++ b/.github/workflows/bioccheck.yaml @@ -108,7 +108,7 @@ jobs: path: ${{ github.event.repository.name }} - name: Restore SD cache ๐Ÿ’ฐ - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: sd-${{ runner.os }}-${{ github.event.repository.name }} path: ~/.staged.dependencies diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml index f451a8a4f..66aad2b3a 100644 --- a/.github/workflows/build-check-install.yaml +++ b/.github/workflows/build-check-install.yaml @@ -271,7 +271,7 @@ jobs: if: >- inputs.publish-unit-test-report-gh-pages == true && github.event_name != 'pull_request' - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: npm-${{ runner.os }}-${{ github.job }} restore-keys: | @@ -312,7 +312,7 @@ jobs: - name: Restore SD cache ๐Ÿ’ฐ if: inputs.install-deps-from-package-repositories == '' - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: sd-${{ runner.os }}-${{ github.event.repository.name }} path: ~/.staged.dependencies @@ -386,7 +386,7 @@ jobs: - name: Restore any additional caches ๐Ÿ“ฅ if: inputs.additional-caches != '' - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: "${{ inputs.additional-caches }}" key: additional-caches-${{ runner.os }} @@ -512,7 +512,7 @@ jobs: - name: Check whether JUnit XML report exists ๐Ÿšฆ id: check-junit-xml - uses: andstor/file-existence-action@v2 + uses: andstor/file-existence-action@v3 with: files: "${{ env.PKGNAME }}.Rcheck/tests/testthat/junit-result.xml" @@ -538,7 +538,7 @@ jobs: steps.check-junit-xml.outputs.files_exists == 'true' && inputs.publish-unit-test-report-gh-pages == true && github.event_name != 'pull_request' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: unit-test-report path: "index.html" @@ -661,7 +661,7 @@ jobs: env.junit_xml_comparison_result_method == 'artifact' && !github.event.pull_request.head.repo.fork && github.event_name == 'pull_request' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: path: output-artifact.md name: junit-xml-report-comparison @@ -754,7 +754,7 @@ jobs: - name: Upload package build โคด if: startsWith(github.ref, 'refs/tags/v') - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/${{ env.PKGBUILD }} name: ${{ env.PKGBUILD }} diff --git a/.github/workflows/grammar.yaml b/.github/workflows/grammar.yaml index 35ba48206..aa8403a38 100644 --- a/.github/workflows/grammar.yaml +++ b/.github/workflows/grammar.yaml @@ -43,7 +43,7 @@ jobs: uses: actions/checkout@v4 - name: Restore npm cache ๐Ÿ’ฐ - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: npm-${{ runner.os }}-${{ github.job }} restore-keys: | @@ -51,7 +51,7 @@ jobs: path: node_modules - name: Setup NodeJS โ˜Š - uses: actions/setup-node@v3 + uses: actions/setup-node@v4 id: npm-cache with: node-version: 20 @@ -122,7 +122,7 @@ jobs: - name: Check whether annotations exist ๐Ÿ’ญ id: check-annotations if: inputs.enable-annotations - uses: andstor/file-existence-action@v2 + uses: andstor/file-existence-action@v3 with: files: "annotations.json" diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 5480e3f31..e82b17820 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -173,7 +173,7 @@ jobs: path: ${{ github.event.repository.name }} - name: Restore SD cache ๐Ÿ’ฐ - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: sd-${{ runner.os }}-${{ github.event.repository.name }} path: ~/.staged.dependencies @@ -267,7 +267,7 @@ jobs: - name: Upload docs for review โฌ† if: github.event_name == 'pull_request' || startsWith(github.ref, 'refs/tags/v') - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: pkgdown.zip path: pkgdown.zip diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml index e89a8a9bc..64dfa02ff 100644 --- a/.github/workflows/roxygen.yaml +++ b/.github/workflows/roxygen.yaml @@ -94,7 +94,7 @@ jobs: path: ${{ github.event.repository.name }} - name: Restore SD cache ๐Ÿ’ฐ - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: sd-${{ runner.os }}-${{ github.event.repository.name }} path: ~/.staged.dependencies diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml index dd1a60296..cb3cb2d35 100644 --- a/.github/workflows/style.yaml +++ b/.github/workflows/style.yaml @@ -99,7 +99,7 @@ jobs: - name: Check file existence ๐Ÿค” id: check_files - uses: andstor/file-existence-action@v2 + uses: andstor/file-existence-action@v3 with: files: "/tmp/style-problems.R, /tmp/style-problems.txt" diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index f8f670441..0ea66585e 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -181,7 +181,7 @@ jobs: path: ${{ github.event.repository.name }} - name: Restore SD cache ๐Ÿ’ฐ - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: sd-${{ runner.os }}-${{ github.event.repository.name }} path: ~/.staged.dependencies @@ -257,7 +257,7 @@ jobs: - name: Check whether coverage reports exists ๐Ÿ’ญ id: check_coverage_reports - uses: andstor/file-existence-action@v2 + uses: andstor/file-existence-action@v3 with: files: >- ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage.xml, @@ -276,7 +276,7 @@ jobs: continue-on-error: true - name: Upload report ๐Ÿ”ผ - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-report path: | @@ -312,7 +312,7 @@ jobs: path: ${{ github.event.repository.name }} - name: Restore SD cache ๐Ÿ’ฐ - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: sd-${{ runner.os }}-${{ github.event.repository.name }} path: ~/.staged.dependencies diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml index ef13ec1b0..9b93814e5 100644 --- a/.github/workflows/validation.yaml +++ b/.github/workflows/validation.yaml @@ -84,7 +84,7 @@ jobs: shell: bash - name: Restore SD cache ๐Ÿ’ฐ - uses: actions/cache@v3 + uses: actions/cache@v4 with: key: sd-${{ runner.os }}-${{ github.event.repository.name }} path: ~/.staged.dependencies @@ -109,7 +109,7 @@ jobs: - name: Upload report for review โฌ† if: github.ref != 'refs/heads/main' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: validation_report.pdf path: validation_report.pdf diff --git a/.github/workflows/verdepcheck.yaml b/.github/workflows/verdepcheck.yaml index d4d56b3c8..b7102f9d1 100644 --- a/.github/workflows/verdepcheck.yaml +++ b/.github/workflows/verdepcheck.yaml @@ -92,14 +92,14 @@ jobs: - name: Upload lock file โคด๏ธ if: always() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: "lock-file-${{ env.strategy }}" path: pkg.lock - name: Upload output file โคด๏ธ if: always() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: "res-${{ env.strategy }}" path: res.RDS diff --git a/.github/workflows/version-bump.yaml b/.github/workflows/version-bump.yaml index 11faf3dc5..7c3d22fdd 100644 --- a/.github/workflows/version-bump.yaml +++ b/.github/workflows/version-bump.yaml @@ -100,7 +100,7 @@ jobs: - name: Check if a pre-commit config exists id: precommit-config-exists - uses: andstor/file-existence-action@v2 + uses: andstor/file-existence-action@v3 with: files: ".pre-commit-config.yaml" @@ -108,7 +108,7 @@ jobs: if: | inputs.disable-precommit-autoupdate != 'true' && steps.precommit-config-exists.outputs.files_exists == 'true' - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.12' diff --git a/.github/workflows/version.yaml b/.github/workflows/version.yaml index 27a6a11ee..2ea74f723 100644 --- a/.github/workflows/version.yaml +++ b/.github/workflows/version.yaml @@ -74,7 +74,7 @@ jobs: uses: actions/checkout@v4 - name: Set up Python ๐Ÿ - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.12' From ca5e369759b36be07becd35aa241a6c75b78a447 Mon Sep 17 00:00:00 2001 From: cicdguy <26552821+cicdguy@users.noreply.github.com> Date: Thu, 8 Feb 2024 08:52:26 -0600 Subject: [PATCH 2/5] Upgrade to Roxygen 7.3.1 Signed-off-by: cicdguy <26552821+cicdguy@users.noreply.github.com> --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 52ae6bd89..be06a7df1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,4 +28,4 @@ Encoding: UTF-8 Language: en-US LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.0 +RoxygenNote: 7.3.1 From 01ad528a8948ec5e8d70f6a0d4a97e8cb2b6ded2 Mon Sep 17 00:00:00 2001 From: Franciszek Walkowiak Date: Thu, 8 Feb 2024 15:52:33 +0100 Subject: [PATCH 3/5] Update --- .github/workflows/bioccheck.yaml | 2 +- .github/workflows/build-check-install.yaml | 2 +- DESCRIPTION | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml index 5b7a0b54e..cf5408fd1 100644 --- a/.github/workflows/bioccheck.yaml +++ b/.github/workflows/bioccheck.yaml @@ -93,7 +93,7 @@ jobs: uses: tj-actions/branch-names@v7 - name: Checkout repo (PR) ๐Ÿ›Ž - uses: actions/checkout@v3 + uses: actions/checkout@v4 if: github.event_name == 'pull_request' with: ref: ${{ steps.branch-name.outputs.head_ref_branch }} diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml index 66aad2b3a..ec7476cb3 100644 --- a/.github/workflows/build-check-install.yaml +++ b/.github/workflows/build-check-install.yaml @@ -564,7 +564,7 @@ jobs: - name: Fetch JUnit XML reports from ${{ env.junit_xml_storage }} โคต๏ธ if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true' - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: path: ${{ env.junit_xml_storage }} fetch-depth: 0 diff --git a/DESCRIPTION b/DESCRIPTION index 52ae6bd89..be06a7df1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,4 +28,4 @@ Encoding: UTF-8 Language: en-US LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.0 +RoxygenNote: 7.3.1 From c306d137bafb5e438a079cc12398639a1a1a9ba0 Mon Sep 17 00:00:00 2001 From: Franciszek Walkowiak Date: Thu, 8 Feb 2024 16:31:22 +0100 Subject: [PATCH 4/5] Empty From 1f913071254e0e27129f23266bd29d2c1020887c Mon Sep 17 00:00:00 2001 From: Franciszek Walkowiak Date: Thu, 8 Feb 2024 17:01:24 +0100 Subject: [PATCH 5/5] Empty