From c9f9e724501642800bf30771b853b3ca68c764d8 Mon Sep 17 00:00:00 2001
From: Johannes Rainer <johannes.rainer@gmail.com>
Date: Fri, 20 Sep 2024 21:58:18 +0200
Subject: [PATCH] ci: update GHA

---
 .github/workflows/check-bioc.yml | 35 ++++++--------------------------
 1 file changed, 6 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 0f394c7..7080842 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -22,7 +22,8 @@
 
 on:
   push:
-  pull_request:
+    paths-ignore:
+      - 'README.md'
 
 name: R-CMD-check-bioc
 
@@ -53,8 +54,8 @@ jobs:
       matrix:
         config:
           - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.19'}
-          - { os: windows-latest, r: 'devel', bioc: '3.19'}
+          - { os: macOS-latest, r: '4.4', bioc: 'devel'}
+          - { os: windows-latest, r: '4.4', bioc: 'devel'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -123,31 +124,7 @@ jobs:
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
         run: |
-          ## Enable installing XML from source if needed
-          brew install libxml2
-          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
-
-          ## Required to install magick as noted at
-          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
-          brew install imagemagick@6
-
-          ## For textshaping, required by ragg, and required by pkgdown
-          brew install harfbuzz fribidi
-
-          ## For installing usethis's dependency gert
-          brew install libgit2
-
-          ## required for ncdf4 - can not use the homebrew one because that uses GCC
-          ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/
-          curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz
-          tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /
-          rm netcdf-4.7.4-darwin.17-x86_64.tar.gz
-          curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz
-          tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /
-          rm hdf5-1.12.0-darwin.17-x86_64.tar.gz
-          curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz
-          tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /
-          rm szip-2.1.1-darwin.17-x86_64.tar.gz
+        shell: Rscript {0}
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
@@ -264,7 +241,7 @@ jobs:
       - name: Test coverage
         if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
-          covr::codecov()
+          covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
         shell: Rscript {0}
 
       - name: Install package