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ci: upgrade to biocthis::use_bioc_github_action('devel')
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@sgibb
sgibb committed Apr 24, 2024
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157 changes: 92 additions & 65 deletions .github/workflows/check-bioc.yml
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Expand Up @@ -5,7 +5,7 @@
## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
##
## You can add this workflow to other packages using:
## > biocthis::use_bioc_github_action()
## > biocthis::use_bioc_github_action("devel", testthat = TRUE, pkgdown = TRUE)
##
## Using GitHub Actions exposes you to many details about how R packages are
## compiled and installed in several operating system.s
Expand Down Expand Up @@ -52,10 +52,10 @@ jobs:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
- { os: macOS-latest, r: '4.2', bioc: '3.16'}
- { os: windows-latest, r: '4.2', bioc: '3.16'}
## Check https://github.com/r-lib/actions/tree/v2/examples
- { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: 'devel', bioc: '3.19'}
- { os: windows-latest, r: 'devel', bioc: '3.19'}
## Check https://github.com/r-lib/actions/tree/master/examples
## for examples using the http-user-agent
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
Expand All @@ -76,10 +76,10 @@ jobs:
echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
## Most of these steps are the same as the ones in
## https://github.com/r-lib/actions/blob/v2/examples/check-standard.yaml
## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
## If they update their steps, we will also need to update ours.
- name: Checkout Repository
uses: actions/checkout@v2
uses: actions/checkout@v3

## R is already included in the Bioconductor docker images
- name: Setup R from r-lib
Expand All @@ -102,26 +102,26 @@ jobs:

- name: Restore R package cache
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.2-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-

- name: Cache R packages on Linux
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: /home/runner/work/_temp/Library
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.2-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-

- name: Install Linux system dependencies
if: runner.os == 'Linux'
run: |
sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
echo $sysreqs
sudo -s eval "$sysreqs"
# - name: Install Linux system dependencies
# if: runner.os == 'Linux'
# run: |
# sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
# echo $sysreqs
# sudo -s eval "$sysreqs"

- name: Install macOS system dependencies
if: matrix.config.os == 'macOS-latest'
Expand Down Expand Up @@ -169,35 +169,19 @@ jobs:
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Set the repos source depending on the OS
## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
## though based on https://bit.ly/bioc2021-package-binaries
## the Azure link will be the main one going forward.
gha_repos <- if(
.Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
) c(
"AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.16/bioc",
BiocManager::repositories()
) else BiocManager::repositories()
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
## Pass #1 at installing dependencies
## This pass uses AnVIL-powered fast binaries
## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
## The speed gains only apply to the docker builds.
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
continue-on-error: true
shell: Rscript {0}

- name: Install dependencies pass 2
run: |
## Pass #2 at installing dependencies
## This pass does not use AnVIL and will thus update any packages
## that have seen been updated in Bioconductor
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
shell: Rscript {0}
Expand All @@ -210,15 +194,15 @@ jobs:
shell: Rscript {0}

- name: Install covr
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("covr")
shell: Rscript {0}

- name: Install pkgdown
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("pkgdown")
remotes::install_github("r-lib/pkgdown")
shell: Rscript {0}

- name: Session info
Expand Down Expand Up @@ -266,46 +250,89 @@ jobs:
shell: Rscript {0}

- name: Test coverage
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
covr::codecov()
covr::codecov(coverage = covr::package_coverage(type = "all"))
shell: Rscript {0}

- name: Install package
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .

- name: Build and deploy pkgdown site
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
git config --local user.name "$GITHUB_ACTOR"
git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
shell: bash {0}
- name: Build pkgdown site
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
shell: Rscript {0}
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
## at least one locally before this will work. This creates the gh-pages
## branch (erasing anything you haven't version controlled!) and
## makes the git history recognizable by pkgdown.

- name: Install deploy dependencies
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
apt-get update && apt-get -y install rsync
- name: Deploy pkgdown site to GitHub pages 🚀
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
uses: JamesIves/github-pages-deploy-action@releases/v4
with:
clean: false
branch: gh-pages
folder: docs

- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-devel-r-4.2-results
name: ${{ runner.os }}-biocversion-devel-r-devel-results
path: check

## Note that DOCKER_PASSWORD is really a token for your dockerhub
## account, not your actual dockerhub account password.
## This comes from
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
## Check https://github.com/docker/build-push-action/tree/releases/v1
## for more details.
- uses: docker/build-push-action@v1
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "

## Code adapted from
## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
docker-build-and-push:
runs-on: ubuntu-latest
needs: build-check
steps:
- name: Checkout Repository
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: actions/checkout@v3

- name: Register repo name
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
id: reg_repo_name
run: |
echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
- name: Set up QEMU
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: docker/setup-qemu-action@v2

- name: Set up Docker Buildx
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: docker/setup-buildx-action@v2

- name: Login to Docker Hub
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: docker/login-action@v2
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
## account, not your actual dockerhub account password. You can get it
## from https://hub.docker.com/settings/security.
## Check https://github.com/docker/build-push-action/tree/v4.0.0
## for more details.
## Alternatively, try checking
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.

- name: Build and Push Docker
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
uses: docker/build-push-action@v4
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
repository: sgibb/cleaver
tag_with_ref: true
tag_with_sha: true
tags: latest
context: .
push: true
tags: >
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel

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