From 1fcaf35515263192c1fbdd27dd3285ac325529b3 Mon Sep 17 00:00:00 2001 From: m7pr Date: Wed, 29 Jan 2025 16:31:47 +0100 Subject: [PATCH 1/6] switch to r-lib/actions/setup-r-dependencies@v2 --- .github/workflows/build-check-install.yaml | 10 +++++----- .github/workflows/pkgdown.yaml | 2 +- .github/workflows/revdepcheck.yaml | 4 ++-- .github/workflows/rhub.yaml | 4 ++-- .github/workflows/roxygen.yaml | 4 ++-- .github/workflows/test-coverage.yaml | 2 +- .github/workflows/validation.yaml | 2 +- 7 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml index 681b227f..f54902a2 100644 --- a/.github/workflows/build-check-install.yaml +++ b/.github/workflows/build-check-install.yaml @@ -146,28 +146,28 @@ on: default: "" skip-desc-branch: description: | - Passed to `insightsengineering/setup-r-dependencies`. + Passed to `r-lib/setup-r-dependencies`. Used only if deps-installation-method == 'setup-r-dependencies'. required: false type: boolean default: false skip-desc-dev: description: | - Passed to `insightsengineering/setup-r-dependencies`. + Passed to `r-lib/setup-r-dependencies`. Used only if deps-installation-method == 'setup-r-dependencies'. required: false type: boolean default: false repository-list: description: | - Passed to `insightsengineering/setup-r-dependencies`. + Passed to `r-lib/setup-r-dependencies`. Used only if deps-installation-method == 'setup-r-dependencies'. required: false type: string default: "PPM=PPM@latest" cache-version: description: | - Passed to `insightsengineering/setup-r-dependencies`. + Passed to `r-lib/setup-r-dependencies`. Used only if deps-installation-method == 'setup-r-dependencies'. required: false type: string @@ -441,7 +441,7 @@ jobs: if: >- env.deps_installation_method == 'setup-r-dependencies' && inputs.install-deps-from-package-repositories == '' - uses: insightsengineering/setup-r-dependencies@v1 + uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 3db00e17..b6405b2b 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -230,7 +230,7 @@ jobs: - name: Setup R dependencies 🎦 if: >- inputs.deps-installation-method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/revdepcheck.yaml b/.github/workflows/revdepcheck.yaml index ce163f51..ec4952c4 100644 --- a/.github/workflows/revdepcheck.yaml +++ b/.github/workflows/revdepcheck.yaml @@ -91,7 +91,7 @@ jobs: shell: bash - name: Install dependencies - uses: insightsengineering/setup-r-dependencies@v1 + uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: @@ -100,7 +100,7 @@ jobs: - name: revdepcheck 🔄 id: revdepcheck - uses: insightsengineering/r-revdepcheck-action@main + uses: r-lib/r-revdepcheck-action@main with: github-token: ${{ steps.github-token.outputs.token }} additional-env-vars: ${{ inputs.additional-env-vars }} diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml index 4a1240d6..e401b694 100644 --- a/.github/workflows/rhub.yaml +++ b/.github/workflows/rhub.yaml @@ -96,7 +96,7 @@ jobs: with: job-config: ${{ matrix.config.job-config }} - - uses: insightsengineering/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: @@ -149,7 +149,7 @@ jobs: with: job-config: ${{ matrix.config.job-config }} - - uses: insightsengineering/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml index 73562c59..97e130e8 100644 --- a/.github/workflows/roxygen.yaml +++ b/.github/workflows/roxygen.yaml @@ -51,7 +51,7 @@ on: default: staged-dependencies lookup-refs: description: | - Passed to insightsengineering/setup-r-dependencies. See its documentation. + Passed to r-lib/setup-r-dependencies. See its documentation. Used only if deps-installation-method == 'setup-r-dependencies'. required: false type: string @@ -152,7 +152,7 @@ jobs: - name: Setup R dependencies 🎦 if: >- env.deps_installation_method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index eaf6e138..2f8f8589 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -243,7 +243,7 @@ jobs: - name: Setup R dependencies 🎦 if: >- inputs.deps-installation-method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml index 961d4e39..a1396ff0 100644 --- a/.github/workflows/validation.yaml +++ b/.github/workflows/validation.yaml @@ -147,7 +147,7 @@ jobs: - name: Setup R dependencies 🎦 if: >- inputs.deps-installation-method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: From 41e9e644ff4bc7ff84d3e470660ae83c2c9a360b Mon Sep 17 00:00:00 2001 From: m7pr Date: Wed, 29 Jan 2025 16:54:34 +0100 Subject: [PATCH 2/6] remove inputs that do not exist in r-lib/actions/setup-r-dependncies nor in r-hub/actions/setup-deps --- .github/workflows/bioccheck.yaml | 8 +----- .github/workflows/build-check-install.yaml | 31 ++-------------------- .github/workflows/pkgdown.yaml | 6 ----- .github/workflows/rhub.yaml | 7 ----- .github/workflows/roxygen.yaml | 7 ----- .github/workflows/test-coverage.yaml | 6 ----- .github/workflows/validation.yaml | 6 ----- 7 files changed, 3 insertions(+), 68 deletions(-) diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml index dcccb144..05f2253d 100644 --- a/.github/workflows/bioccheck.yaml +++ b/.github/workflows/bioccheck.yaml @@ -61,12 +61,6 @@ on: required: false type: string default: staged-dependencies - lookup-refs: - description: | - List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'. - required: false - type: string - default: "" concurrency: group: bioccheck-${{ github.event.pull_request.number || github.ref }} @@ -158,7 +152,7 @@ jobs: - name: Setup R dependencies 🎦 if: >- inputs.deps-installation-method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml index f54902a2..ef810f6f 100644 --- a/.github/workflows/build-check-install.yaml +++ b/.github/workflows/build-check-install.yaml @@ -138,40 +138,13 @@ on: required: false type: string default: staged-dependencies - lookup-refs: - description: | - List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'. - required: false - type: string - default: "" - skip-desc-branch: - description: | - Passed to `r-lib/setup-r-dependencies`. - Used only if deps-installation-method == 'setup-r-dependencies'. - required: false - type: boolean - default: false - skip-desc-dev: - description: | - Passed to `r-lib/setup-r-dependencies`. - Used only if deps-installation-method == 'setup-r-dependencies'. - required: false - type: boolean - default: false - repository-list: - description: | - Passed to `r-lib/setup-r-dependencies`. - Used only if deps-installation-method == 'setup-r-dependencies'. - required: false - type: string - default: "PPM=PPM@latest" cache-version: description: | - Passed to `r-lib/setup-r-dependencies`. + Passed to `r-lib/actions/setup-r-dependencies`. Used only if deps-installation-method == 'setup-r-dependencies'. required: false type: string - default: "1" + default: 1 unit-test-report-brand: description: Image URL to use in unit test report for branding. If empty, the default xunit-viewer brand will be used. required: false diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index b6405b2b..562b005a 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -128,12 +128,6 @@ on: required: false type: string default: staged-dependencies - lookup-refs: - description: | - List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'. - required: false - type: string - default: "" concurrency: group: docs-${{ github.event.pull_request.number || github.ref }} diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml index e401b694..2ac5ddf5 100644 --- a/.github/workflows/rhub.yaml +++ b/.github/workflows/rhub.yaml @@ -40,13 +40,6 @@ on: gcc13, noSuggests, donttest - lookup-refs: - description: | - List of package references to be used for the feature branch. - Multiple entries in new lines or separated by commas. - required: false - default: "" - type: string concurrency: group: r-hub-${{ github.event.pull_request.number || github.ref }} diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml index 97e130e8..36067b8f 100644 --- a/.github/workflows/roxygen.yaml +++ b/.github/workflows/roxygen.yaml @@ -49,13 +49,6 @@ on: required: false type: string default: staged-dependencies - lookup-refs: - description: | - Passed to r-lib/setup-r-dependencies. See its documentation. - Used only if deps-installation-method == 'setup-r-dependencies'. - required: false - type: string - default: "" secrets: REPO_GITHUB_TOKEN: description: | diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 2f8f8589..5b31fc33 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -90,12 +90,6 @@ on: required: false type: string default: staged-dependencies - lookup-refs: - description: | - List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'. - required: false - type: string - default: "" secrets: REPO_GITHUB_TOKEN: description: | diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml index a1396ff0..84183b88 100644 --- a/.github/workflows/validation.yaml +++ b/.github/workflows/validation.yaml @@ -46,12 +46,6 @@ on: required: false type: string default: staged-dependencies - lookup-refs: - description: | - List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'. - required: false - type: string - default: "" secrets: REPO_GITHUB_TOKEN: description: | From b9096a7d7a21e18ad80a9ff2fea6e23ca3308517 Mon Sep 17 00:00:00 2001 From: m7pr Date: Thu, 30 Jan 2025 13:56:46 +0100 Subject: [PATCH 3/6] remove lookup-refs, skip-desc-branch, skip-desc-dev and repository-list --- .github/workflows/bioccheck.yaml | 1 - .github/workflows/build-check-install.yaml | 4 ---- .github/workflows/pkgdown.yaml | 1 - .github/workflows/revdepcheck.yaml | 3 --- .github/workflows/rhub.yaml | 2 -- .github/workflows/roxygen.yaml | 1 - .github/workflows/test-coverage.yaml | 1 - .github/workflows/validation.yaml | 1 - 8 files changed, 14 deletions(-) diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml index 05f2253d..b7eb88e9 100644 --- a/.github/workflows/bioccheck.yaml +++ b/.github/workflows/bioccheck.yaml @@ -156,7 +156,6 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - lookup-refs: ${{ inputs.lookup-refs }} repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} - name: Run BiocCheck ☣️ diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml index ef810f6f..b16aaff2 100644 --- a/.github/workflows/build-check-install.yaml +++ b/.github/workflows/build-check-install.yaml @@ -418,11 +418,7 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - lookup-refs: ${{ inputs.lookup-refs }} repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} - skip-desc-branch: ${{ inputs.skip-desc-branch }} - skip-desc-dev: ${{ inputs.skip-desc-dev }} - repository-list: ${{ inputs.repository-list }} cache-version: ${{ inputs.cache-version }} - name: Install dependencies from package repositories 🗄️ diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 562b005a..b809c5ec 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -228,7 +228,6 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - lookup-refs: ${{ inputs.lookup-refs }} repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} - name: Install R package 🚧 diff --git a/.github/workflows/revdepcheck.yaml b/.github/workflows/revdepcheck.yaml index ec4952c4..a9b50f04 100644 --- a/.github/workflows/revdepcheck.yaml +++ b/.github/workflows/revdepcheck.yaml @@ -94,9 +94,6 @@ jobs: uses: r-lib/actions/setup-r-dependencies@v2 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} - with: - lookup-refs: ${{ inputs.lookup-refs }} - skip-desc-branch: true - name: revdepcheck 🔄 id: revdepcheck diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml index 2ac5ddf5..70c574a5 100644 --- a/.github/workflows/rhub.yaml +++ b/.github/workflows/rhub.yaml @@ -93,7 +93,6 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - lookup-refs: ${{ inputs.lookup-refs }} skip-install: true restore-description: false install-quarto: "false" @@ -146,7 +145,6 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - lookup-refs: ${{ inputs.lookup-refs }} skip-install: true restore-description: false install-quarto: "false" diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml index 36067b8f..becbe189 100644 --- a/.github/workflows/roxygen.yaml +++ b/.github/workflows/roxygen.yaml @@ -149,7 +149,6 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - lookup-refs: ${{ inputs.lookup-refs }} repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} - name: Generate man pages 📄 diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 5b31fc33..74cfb409 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -241,7 +241,6 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - lookup-refs: ${{ inputs.lookup-refs }} repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} - name: Install R package 🚧 diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml index 84183b88..3f6da447 100644 --- a/.github/workflows/validation.yaml +++ b/.github/workflows/validation.yaml @@ -145,7 +145,6 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - lookup-refs: ${{ inputs.lookup-refs }} repository-path: ${{ env.package_subdirectory }} - name: Build report 🏗 From ba60dbe5b97126239f6613cfcc7efbf924ede1c1 Mon Sep 17 00:00:00 2001 From: Marcin <133694481+m7pr@users.noreply.github.com> Date: Fri, 31 Jan 2025 10:49:43 +0100 Subject: [PATCH 4/6] Update .github/workflows/revdepcheck.yaml Co-authored-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com> --- .github/workflows/revdepcheck.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/revdepcheck.yaml b/.github/workflows/revdepcheck.yaml index a9b50f04..c31b5706 100644 --- a/.github/workflows/revdepcheck.yaml +++ b/.github/workflows/revdepcheck.yaml @@ -97,7 +97,7 @@ jobs: - name: revdepcheck 🔄 id: revdepcheck - uses: r-lib/r-revdepcheck-action@main + uses: insightsengineering/r-revdepcheck-action@main with: github-token: ${{ steps.github-token.outputs.token }} additional-env-vars: ${{ inputs.additional-env-vars }} From 1ed87bff9b3d477d9e0760566b6bddabaaa68cdb Mon Sep 17 00:00:00 2001 From: m7pr Date: Mon, 3 Feb 2025 14:23:24 +0100 Subject: [PATCH 5/6] change repository-path to working-directory --- .github/workflows/bioccheck.yaml | 2 +- .github/workflows/build-check-install.yaml | 2 +- .github/workflows/pkgdown.yaml | 2 +- .github/workflows/roxygen.yaml | 2 +- .github/workflows/test-coverage.yaml | 2 +- .github/workflows/validation.yaml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml index b7eb88e9..7e29d98d 100644 --- a/.github/workflows/bioccheck.yaml +++ b/.github/workflows/bioccheck.yaml @@ -156,7 +156,7 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} + working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} - name: Run BiocCheck ☣️ uses: insightsengineering/bioc-check-action@v1 diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml index b16aaff2..be37fb80 100644 --- a/.github/workflows/build-check-install.yaml +++ b/.github/workflows/build-check-install.yaml @@ -418,7 +418,7 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} + working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} cache-version: ${{ inputs.cache-version }} - name: Install dependencies from package repositories 🗄️ diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index b809c5ec..9fa35ed8 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -228,7 +228,7 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} + working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} - name: Install R package 🚧 run: | diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml index becbe189..725a5a84 100644 --- a/.github/workflows/roxygen.yaml +++ b/.github/workflows/roxygen.yaml @@ -149,7 +149,7 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} + working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} - name: Generate man pages 📄 run: | diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 74cfb409..9d430db7 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -241,7 +241,7 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} + working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} - name: Install R package 🚧 run: | diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml index 3f6da447..08a0e8ce 100644 --- a/.github/workflows/validation.yaml +++ b/.github/workflows/validation.yaml @@ -145,7 +145,7 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - repository-path: ${{ env.package_subdirectory }} + working-directory: ${{ env.package_subdirectory }} - name: Build report 🏗 uses: insightsengineering/thevalidatoR@v2 From 46627aa47c3cbe289d38672c58f72e31b8dda075 Mon Sep 17 00:00:00 2001 From: m7pr Date: Mon, 3 Feb 2025 14:25:22 +0100 Subject: [PATCH 6/6] remove skip-install and restore-description --- .github/workflows/rhub.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml index 70c574a5..52789e44 100644 --- a/.github/workflows/rhub.yaml +++ b/.github/workflows/rhub.yaml @@ -93,8 +93,6 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - skip-install: true - restore-description: false install-quarto: "false" - uses: r-hub/actions/setup-deps@v1 @@ -145,8 +143,6 @@ jobs: env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: - skip-install: true - restore-description: false install-quarto: "false" - uses: r-hub/actions/setup-deps@v1