Skip to content

Commit

Permalink
Merge branch 'devel' into annot_from_TxDB
Browse files Browse the repository at this point in the history
  • Loading branch information
@charles-plessy
charles-plessy authored May 31, 2024
2 parents 23473df + be47c26 commit 5e7d906
Show file tree
Hide file tree
Showing 137 changed files with 10,155 additions and 3,206 deletions.
168 changes: 118 additions & 50 deletions .github/workflows/check-bioc.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@ env:
run_pkgdown: 'false'
has_RUnit: 'false'
cache-version: 'cache-v1'
run_docker: 'false'

jobs:
build-check:
Expand All @@ -51,9 +52,11 @@ jobs:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.0', bioc: '3.12', cont: "bioconductor/bioconductor_docker:RELEASE_3_12", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
- { os: macOS-latest, r: '4.0', bioc: '3.12'}
- { os: windows-latest, r: '4.0', bioc: '3.12'}
- { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: '4.4', bioc: '3.20'}
- { os: windows-latest, r: '4.4', bioc: '3.20'}
## 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
RSPM: ${{ matrix.config.rspm }}
Expand All @@ -76,48 +79,49 @@ jobs:
## 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
if: runner.os != 'Linux'
uses: r-lib/actions/setup-r@master
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}

## pandoc is already included in the Bioconductor docker images
- name: Setup pandoc from r-lib
if: runner.os != 'Linux'
uses: r-lib/actions/setup-pandoc@master
uses: r-lib/actions/setup-pandoc@v2

- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}

- name: Cache R packages
- 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-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-

- 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-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-

- 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 All @@ -133,8 +137,11 @@ jobs:
## For textshaping, required by ragg, and required by pkgdown
brew install harfbuzz fribidi
## Helps compile RCurl from source
brew uninstall curl
## For installing usethis's dependency gert
brew install libgit2
## Required for tcltk
brew install xquartz --cask
- name: Install Windows system dependencies
if: runner.os == 'Windows'
Expand All @@ -150,10 +157,10 @@ jobs:

- name: Set BiocVersion
run: |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
shell: Rscript {0}

- name: Install dependencies
- name: Install dependencies pass 1
run: |
## Try installing the package dependencies in steps. First the local
## dependencies, then any remaining dependencies to avoid the
Expand All @@ -162,23 +169,21 @@ jobs:
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79
remotes::install_github("ropensci/bibtex")
remotes::install_github("ropensci/RefManageR")
remotes::install_github("cboettig/knitcitations")
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
## Pass #1 at installing dependencies
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, 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
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)
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
BiocManager::install("BiocCheck")
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
shell: Rscript {0}

- name: Install BiocGenerics
Expand All @@ -189,15 +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 All @@ -210,10 +215,12 @@ jobs:
- name: Run CMD check
env:
_R_CHECK_CRAN_INCOMING_: false
DISPLAY: 99.0
run: |
options(crayon.enabled = TRUE)
rcmdcheck::rcmdcheck(
args = c("--no-build-vignettes", "--no-manual", "--timings"),
build_args = c("--no-manual", "--no-resave-data"),
args = c("--no-manual", "--no-vignettes", "--timings"),
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
error_on = "warning",
check_dir = "check"
)
Expand All @@ -231,6 +238,8 @@ jobs:
shell: Rscript {0}

- name: Run BiocCheck
env:
DISPLAY: 99.0
run: |
BiocCheck::BiocCheck(
dir('check', 'tar.gz$', full.names = TRUE),
Expand All @@ -241,30 +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: Deploy package
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
git config --local user.email "[email protected]"
git config --local user.name "GitHub Actions"
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-RELEASE_3_12-r-4.0-results
name: ${{ runner.os }}-biocversion-devel-r-4.4-results
path: check


## 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:
context: .
push: true
tags: >
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel
1 change: 1 addition & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,3 +3,4 @@
.RData
.Ruserdata
.httr-oauth
CAGEr.Rproj
Loading

0 comments on commit 5e7d906

Please sign in to comment.