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switch to r-lib/actions/setup-r-dependencies@v2 #274

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1fcaf35
switch to r-lib/actions/setup-r-dependencies@v2
m7pr Jan 29, 2025
41e9e64
remove inputs that do not exist in r-lib/actions/setup-r-dependncies …
m7pr Jan 29, 2025
b9096a7
remove lookup-refs, skip-desc-branch, skip-desc-dev and repository-list
m7pr Jan 30, 2025
ba60dbe
Update .github/workflows/revdepcheck.yaml
m7pr Jan 31, 2025
1ed87bf
change repository-path to working-directory
m7pr Feb 3, 2025
d64903a
Merge branch 'rlib_setup_r_dependencies' of https://github.com/insigh…
m7pr Feb 3, 2025
46627aa
remove skip-install and restore-description
m7pr Feb 3, 2025
ba95801
Merge branch 'main' into rlib_setup_r_dependencies
m7pr Feb 3, 2025
b0b08e0
Merge branch 'main' into rlib_setup_r_dependencies
m7pr Feb 11, 2025
47dc57f
Merge branch 'main' into rlib_setup_r_dependencies
cicdguy May 25, 2025
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11 changes: 2 additions & 9 deletions .github/workflows/bioccheck.yaml
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Expand Up @@ -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 }}
Expand Down Expand Up @@ -158,12 +152,11 @@ jobs:
- name: Setup R dependencies 🎦
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Adding a comment, so it can not be merged.
It should not be merged before other packages are not suited for changes introduced in this PR.
Other packages are tracked in this card insightsengineering/nestdevs-tasks#103

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:
lookup-refs: ${{ inputs.lookup-refs }}
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
Expand Down
39 changes: 4 additions & 35 deletions .github/workflows/build-check-install.yaml
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Expand Up @@ -139,40 +139,13 @@ 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 `insightsengineering/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`.
Used only if deps-installation-method == 'setup-r-dependencies'.
required: false
type: boolean
default: false
repository-list:
description: |
Passed to `insightsengineering/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/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
Expand Down Expand Up @@ -442,15 +415,11 @@ 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:
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 }}
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
cache-version: ${{ inputs.cache-version }}

- name: Install dependencies from package repositories 🗄️
Expand Down
11 changes: 2 additions & 9 deletions .github/workflows/pkgdown.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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 }}
Expand Down Expand Up @@ -230,12 +224,11 @@ 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:
lookup-refs: ${{ inputs.lookup-refs }}
repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
needs: "website"

- name: Install R package 🚧
Expand Down
5 changes: 1 addition & 4 deletions .github/workflows/revdepcheck.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -91,12 +91,9 @@ 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:
lookup-refs: ${{ inputs.lookup-refs }}
skip-desc-branch: true

- name: revdepcheck 🔄
id: revdepcheck
Expand Down
17 changes: 2 additions & 15 deletions .github/workflows/rhub.yaml
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Expand Up @@ -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 }}
Expand Down Expand Up @@ -96,13 +89,10 @@ 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:
lookup-refs: ${{ inputs.lookup-refs }}
skip-install: true
restore-description: false
install-quarto: "false"

- uses: r-hub/actions/setup-deps@v1
Expand Down Expand Up @@ -149,13 +139,10 @@ 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:
lookup-refs: ${{ inputs.lookup-refs }}
skip-install: true
restore-description: false
install-quarto: "false"

- uses: r-hub/actions/setup-deps@v1
Expand Down
12 changes: 2 additions & 10 deletions .github/workflows/roxygen.yaml
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Expand Up @@ -49,13 +49,6 @@ on:
required: false
type: string
default: staged-dependencies
lookup-refs:
description: |
Passed to insightsengineering/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: |
Expand Down Expand Up @@ -152,12 +145,11 @@ 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:
lookup-refs: ${{ inputs.lookup-refs }}
repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

- name: Generate man pages 📄
run: |
Expand Down
11 changes: 2 additions & 9 deletions .github/workflows/test-coverage.yaml
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Expand Up @@ -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: |
Expand Down Expand Up @@ -243,12 +237,11 @@ 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:
lookup-refs: ${{ inputs.lookup-refs }}
repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

- name: Install R package 🚧
run: |
Expand Down
11 changes: 2 additions & 9 deletions .github/workflows/validation.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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: |
Expand Down Expand Up @@ -147,12 +141,11 @@ 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:
lookup-refs: ${{ inputs.lookup-refs }}
repository-path: ${{ env.package_subdirectory }}
working-directory: ${{ env.package_subdirectory }}

- name: Build report 🏗
uses: insightsengineering/thevalidatoR@v2
Expand Down