From 373bb1dcbd3253e65f7d2c6cab0512556fc28c6c Mon Sep 17 00:00:00 2001
From: Lambda Moses <dlu2@caltech.edu>
Date: Fri, 8 Nov 2024 00:38:01 -0500
Subject: [PATCH] Make the repo public, pachterlab/SpatialFeatureExperiment#50

---
 .github/workflows/R-CMD-check.yaml   | 14 ++++----
 .github/workflows/pkgdown.yaml       | 51 ++++++++++++++++++++++++++++
 .github/workflows/test-coverage.yaml |  5 +--
 DESCRIPTION                          |  1 +
 _pkgdown.yml                         |  2 +-
 5 files changed, 64 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/pkgdown.yaml

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index d46a617..bae3719 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -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 }}
@@ -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:
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..72b03a6
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -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/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 9882260..50e3c1e 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -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:
diff --git a/DESCRIPTION b/DESCRIPTION
index b096b4c..076ead9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -45,3 +45,4 @@ VignetteBuilder: knitr
 Remotes:
     Voyager=github::pachterlab/voyager@devel,
     github::pachterlab/SpatialFeatureExperiment@devel
+URL: https://pachterlab.github.io/alabaster.sfe/
diff --git a/_pkgdown.yml b/_pkgdown.yml
index d71acfb..cead546 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: ~
+url: https://pachterlab.github.io/alabaster.sfe/
 template:
   bootstrap: 5