From fc68ca46999f1fa50862b4a1d43950033b65d2ac Mon Sep 17 00:00:00 2001 From: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Date: Thu, 7 Nov 2024 11:08:58 +0100 Subject: [PATCH 1/2] setup-r-deps: replace `github-token` param with `GITHUB_PAT` env var --- .github/workflows/bioccheck.yaml | 5 +++-- .github/workflows/build-check-install.yaml | 5 +++-- .github/workflows/pkgdown.yaml | 5 +++-- .github/workflows/revdepcheck.yaml | 5 +++-- .github/workflows/rhub.yaml | 10 ++++++---- .github/workflows/roxygen.yaml | 5 +++-- .github/workflows/test-coverage.yaml | 5 +++-- .github/workflows/validation.yaml | 5 +++-- 8 files changed, 27 insertions(+), 18 deletions(-) diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml index 0a59282a..a861388d 100644 --- a/.github/workflows/bioccheck.yaml +++ b/.github/workflows/bioccheck.yaml @@ -158,10 +158,11 @@ jobs: - name: Setup R dependencies 🎦 if: >- inputs.deps-installation-method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: insightsengineering/setup-r-dependencies@rm_param_github_token + env: + GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: lookup-refs: ${{ inputs.lookup-refs }} - github-token: ${{ steps.github-token.outputs.token }} 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 841b066a..8d5bec22 100644 --- a/.github/workflows/build-check-install.yaml +++ b/.github/workflows/build-check-install.yaml @@ -436,10 +436,11 @@ jobs: if: >- env.deps_installation_method == 'setup-r-dependencies' && inputs.install-deps-from-package-repositories == '' - uses: insightsengineering/setup-r-dependencies@v1 + uses: insightsengineering/setup-r-dependencies@rm_param_github_token + env: + GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: lookup-refs: ${{ inputs.lookup-refs }} - github-token: ${{ steps.github-token.outputs.token }} repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} skip-desc-branch: ${{ inputs.skip-desc-branch }} skip-desc-dev: ${{ inputs.skip-desc-dev }} diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 63952abb..b69ee7c5 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -230,10 +230,11 @@ jobs: - name: Setup R dependencies 🎦 if: >- inputs.deps-installation-method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: insightsengineering/setup-r-dependencies@rm_param_github_token + env: + GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: lookup-refs: ${{ inputs.lookup-refs }} - github-token: ${{ steps.github-token.outputs.token }} 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 4ac6f1a1..9648066b 100644 --- a/.github/workflows/revdepcheck.yaml +++ b/.github/workflows/revdepcheck.yaml @@ -91,11 +91,12 @@ jobs: shell: bash - name: Install dependencies - uses: insightsengineering/setup-r-dependencies@v1 + uses: insightsengineering/setup-r-dependencies@rm_param_github_token + env: + GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: lookup-refs: ${{ inputs.lookup-refs }} skip-desc-branch: true - github-token: ${{ steps.github-token.outputs.token }} - name: revdepcheck 🔄 id: revdepcheck diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml index be38ed51..8c7f3676 100644 --- a/.github/workflows/rhub.yaml +++ b/.github/workflows/rhub.yaml @@ -96,11 +96,12 @@ jobs: with: job-config: ${{ matrix.config.job-config }} - - uses: insightsengineering/setup-r-dependencies@v1 + - uses: insightsengineering/setup-r-dependencies@rm_param_github_token + env: + GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: lookup-refs: ${{ inputs.lookup-refs }} skip-install: true - github-token: ${{ steps.github-token.outputs.token }} restore-description: false install-quarto: "false" @@ -148,11 +149,12 @@ jobs: with: job-config: ${{ matrix.config.job-config }} - - uses: insightsengineering/setup-r-dependencies@v1 + - uses: insightsengineering/setup-r-dependencies@rm_param_github_token + env: + GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: lookup-refs: ${{ inputs.lookup-refs }} skip-install: true - github-token: ${{ steps.github-token.outputs.token }} restore-description: false install-quarto: "false" diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml index 56e22f8e..b5ff656e 100644 --- a/.github/workflows/roxygen.yaml +++ b/.github/workflows/roxygen.yaml @@ -152,10 +152,11 @@ jobs: - name: Setup R dependencies 🎦 if: >- env.deps_installation_method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: insightsengineering/setup-r-dependencies@rm_param_github_token + env: + GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: lookup-refs: ${{ inputs.lookup-refs }} - github-token: ${{ steps.github-token.outputs.token }} 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 24058269..c45cd833 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -243,10 +243,11 @@ jobs: - name: Setup R dependencies 🎦 if: >- inputs.deps-installation-method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: insightsengineering/setup-r-dependencies@rm_param_github_token + env: + GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: lookup-refs: ${{ inputs.lookup-refs }} - github-token: ${{ steps.github-token.outputs.token }} 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 f33b21a2..61023ee5 100644 --- a/.github/workflows/validation.yaml +++ b/.github/workflows/validation.yaml @@ -147,10 +147,11 @@ jobs: - name: Setup R dependencies 🎦 if: >- inputs.deps-installation-method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@v1 + uses: insightsengineering/setup-r-dependencies@rm_param_github_token + env: + GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: lookup-refs: ${{ inputs.lookup-refs }} - github-token: ${{ steps.github-token.outputs.token }} repository-path: ${{ env.package_subdirectory }} - name: Build report 🏗 From 9434b5309ecbefa25469b5c46d7b37e2c8bfbb32 Mon Sep 17 00:00:00 2001 From: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Date: Thu, 7 Nov 2024 11:25:20 +0100 Subject: [PATCH 2/2] Apply suggestions from code review Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com> --- .github/workflows/bioccheck.yaml | 2 +- .github/workflows/build-check-install.yaml | 2 +- .github/workflows/pkgdown.yaml | 2 +- .github/workflows/revdepcheck.yaml | 2 +- .github/workflows/rhub.yaml | 4 ++-- .github/workflows/roxygen.yaml | 2 +- .github/workflows/test-coverage.yaml | 2 +- .github/workflows/validation.yaml | 2 +- 8 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml index a861388d..dcccb144 100644 --- a/.github/workflows/bioccheck.yaml +++ b/.github/workflows/bioccheck.yaml @@ -158,7 +158,7 @@ jobs: - name: Setup R dependencies 🎦 if: >- inputs.deps-installation-method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@rm_param_github_token + uses: insightsengineering/setup-r-dependencies@v1 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 8d5bec22..7a20f432 100644 --- a/.github/workflows/build-check-install.yaml +++ b/.github/workflows/build-check-install.yaml @@ -436,7 +436,7 @@ jobs: if: >- env.deps_installation_method == 'setup-r-dependencies' && inputs.install-deps-from-package-repositories == '' - uses: insightsengineering/setup-r-dependencies@rm_param_github_token + uses: insightsengineering/setup-r-dependencies@v1 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index b69ee7c5..3db00e17 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@rm_param_github_token + uses: insightsengineering/setup-r-dependencies@v1 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/revdepcheck.yaml b/.github/workflows/revdepcheck.yaml index 9648066b..ce163f51 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@rm_param_github_token + uses: insightsengineering/setup-r-dependencies@v1 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml index 8c7f3676..4a1240d6 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@rm_param_github_token + - uses: insightsengineering/setup-r-dependencies@v1 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@rm_param_github_token + - uses: insightsengineering/setup-r-dependencies@v1 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml index b5ff656e..73562c59 100644 --- a/.github/workflows/roxygen.yaml +++ b/.github/workflows/roxygen.yaml @@ -152,7 +152,7 @@ jobs: - name: Setup R dependencies 🎦 if: >- env.deps_installation_method == 'setup-r-dependencies' - uses: insightsengineering/setup-r-dependencies@rm_param_github_token + uses: insightsengineering/setup-r-dependencies@v1 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index c45cd833..1c89bdf8 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@rm_param_github_token + uses: insightsengineering/setup-r-dependencies@v1 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml index 61023ee5..961d4e39 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@rm_param_github_token + uses: insightsengineering/setup-r-dependencies@v1 env: GITHUB_PAT: ${{ steps.github-token.outputs.token }} with: