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lambdamoses committed Nov 8, 2024
1 parent ed3a8dc commit 373bb1d
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14 changes: 8 additions & 6 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -22,9 +22,9 @@ jobs:
config:
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
#- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-latest, r: 'oldrel-1'}
#- {os: ubuntu-latest, r: 'oldrel-1'}

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
Expand All @@ -34,12 +34,14 @@ jobs:
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

- if: runner.os == 'macOS'
run: brew install apache-arrow fftw jpeg libtiff imagemagick

- uses: r-lib/actions/setup-r@v2
- name: Setup R and Bioconductor
uses: grimbough/bioc-actions/setup-bioc@v1
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
bioc-version: devel

- uses: r-lib/actions/setup-r-dependencies@v2
with:
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51 changes: 51 additions & 0 deletions .github/workflows/pkgdown.yaml
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@@ -0,0 +1,51 @@
# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]
release:
types: [published]
workflow_dispatch:

name: pkgdown.yaml

permissions: read-all

jobs:
pkgdown:
runs-on: ubuntu-latest
# Only restrict concurrency for non-PR jobs
concurrency:
group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
permissions:
contents: write
steps:
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

- name: Setup R and Bioconductor
uses: grimbough/bioc-actions/setup-bioc@v1
with:
bioc-version: devel

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::pkgdown, local::.
needs: website

- name: Build site
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
shell: Rscript {0}

- name: Deploy to GitHub pages 🚀
if: github.event_name != 'pull_request'
uses: JamesIves/[email protected]
with:
clean: false
branch: gh-pages
folder: docs
5 changes: 3 additions & 2 deletions .github/workflows/test-coverage.yaml
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Expand Up @@ -19,9 +19,10 @@ jobs:
steps:
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-r@v2
- name: Setup R and Bioconductor
uses: grimbough/bioc-actions/setup-bioc@v1
with:
use-public-rspm: true
bioc-version: devel

- uses: r-lib/actions/setup-r-dependencies@v2
with:
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -45,3 +45,4 @@ VignetteBuilder: knitr
Remotes:
Voyager=github::pachterlab/voyager@devel,
github::pachterlab/SpatialFeatureExperiment@devel
URL: https://pachterlab.github.io/alabaster.sfe/
2 changes: 1 addition & 1 deletion _pkgdown.yml
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@@ -1,4 +1,4 @@
url: ~
url: https://pachterlab.github.io/alabaster.sfe/
template:
bootstrap: 5

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