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‎.github/workflows/check-bioc.yml‎

Lines changed: 21 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -40,8 +40,6 @@ env:
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has_RUnit: 'false'
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cache-version: 'cache-v1'
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run_docker: 'false'
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bioc_check: 'false'
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cmd_check: 'false'
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jobs:
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build-check:
@@ -54,9 +52,9 @@ jobs:
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fail-fast: false
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matrix:
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config:
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- { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
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- { os: macOS-latest, r: 'devel', bioc: '3.19'}
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- { os: windows-latest, r: 'devel', bioc: '3.19'}
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- { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
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- { os: macOS-latest, r: '4.4', bioc: '3.20'}
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- { os: windows-latest, r: '4.4', bioc: '3.20'}
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## Check https://github.com/r-lib/actions/tree/master/examples
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## for examples using the http-user-agent
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env:
@@ -107,16 +105,16 @@ jobs:
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uses: actions/cache@v3
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-
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- name: Cache R packages on Linux
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if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
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uses: actions/cache@v3
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with:
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path: /home/runner/work/_temp/Library
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-
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# - name: Install Linux system dependencies
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# if: runner.os == 'Linux'
@@ -185,7 +183,6 @@ jobs:
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run: |
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## Pass #2 at installing dependencies
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message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
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httr::set_config(httr::config(http_version = 0))
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remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
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shell: Rscript {0}
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@@ -197,13 +194,13 @@ jobs:
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shell: Rscript {0}
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- name: Install covr
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if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
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if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
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run: |
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remotes::install_cran("covr")
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shell: Rscript {0}
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- name: Install pkgdown
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if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: |
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remotes::install_github("r-lib/pkgdown")
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shell: Rscript {0}
@@ -216,7 +213,6 @@ jobs:
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shell: Rscript {0}
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- name: Run CMD check
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if: env.cmd_check == 'true'
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env:
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_R_CHECK_CRAN_INCOMING_: false
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DISPLAY: 99.0
@@ -242,7 +238,6 @@ jobs:
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shell: Rscript {0}
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- name: Run BiocCheck
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if: env.has_bioc_check == 'true'
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env:
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DISPLAY: 99.0
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run: |
@@ -255,17 +250,17 @@ jobs:
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shell: Rscript {0}
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- name: Test coverage
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if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
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if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
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run: |
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covr::codecov(coverage = covr::package_coverage(type = "all"))
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shell: Rscript {0}
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- name: Install package
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if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
259+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: R CMD INSTALL .
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- name: Build pkgdown site
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if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
@@ -274,12 +269,12 @@ jobs:
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## makes the git history recognizable by pkgdown.
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- name: Install deploy dependencies
277-
if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
272+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: |
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apt-get update && apt-get -y install rsync
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- name: Deploy pkgdown site to GitHub pages 🚀
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if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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uses: JamesIves/github-pages-deploy-action@releases/v4
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with:
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clean: false
@@ -290,7 +285,7 @@ jobs:
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if: failure()
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uses: actions/upload-artifact@master
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with:
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name: ${{ runner.os }}-biocversion-devel-r-devel-results
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name: ${{ runner.os }}-biocversion-devel-r-4.4-results
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path: check
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@@ -301,25 +296,25 @@ jobs:
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needs: build-check
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steps:
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- name: Checkout Repository
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/main'"
299+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: actions/checkout@v3
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307302
- name: Register repo name
308-
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/main'"
303+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
309304
id: reg_repo_name
310305
run: |
311306
echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
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313308
- name: Set up QEMU
314-
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/main'"
309+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: docker/setup-qemu-action@v2
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- name: Set up Docker Buildx
318-
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/main'"
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: docker/setup-buildx-action@v2
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- name: Login to Docker Hub
322-
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/main'"
317+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: docker/login-action@v2
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
@@ -333,7 +328,7 @@ jobs:
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## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
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335330
- name: Build and Push Docker
336-
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/main' && success()"
331+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
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uses: docker/build-push-action@v4
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with:
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context: .

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