From 48c1a0260d063f921359967054232eca0836053b Mon Sep 17 00:00:00 2001
From: Zewen Kelvin Tuong <z.tuong@uq.edu.au>
Date: Tue, 30 Apr 2024 13:47:59 +1000
Subject: [PATCH] remove testing on macos-latest because there's no
 blast/igblast available (#380)

* remove testing on macos-latest because there's no blast/igblast available

* update action

* fix R

* try and fix r and bioc
---
 .github/workflows/tests.yml        | 20 ++++++++++----------
 .github/workflows/tests_weekly.yml | 20 ++++++++++----------
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index eda32e8a0..965748c17 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -54,9 +54,9 @@ jobs:
           - { python-version: 3.9, os: ubuntu-latest }
           - { python-version: "3.10", os: ubuntu-latest }
           - { python-version: "3.11", os: ubuntu-latest }
-          - { python-version: 3.9, os: macos-latest }
-          - { python-version: "3.10", os: macos-latest }
-          - { python-version: "3.11", os: macos-latest }
+          - { python-version: 3.9, os: macos-13 }
+          - { python-version: "3.10", os: macos-13 }
+          - { python-version: "3.11", os: macos-13 }
           # disabled until it's fixed.
     runs-on: ${{ matrix.config.os }}
     env:
@@ -77,10 +77,15 @@ jobs:
           sudo apt-get update -y && sudo apt-get install -y zlib1g-dev libglpk-dev libgmp3-dev libxml2-dev libicu-dev libhdf5-serial-dev libcurl4-gnutls-dev
 
       - name: Install macOS system dependencies
-        if: matrix.config.os == 'macos-latest'
+        if: matrix.config.os == 'macos-13'
         run: |
           brew install cairo pkg-config autoconf automake libtool
 
+      - name: Setup R and Bioconductor
+        uses: grimbough/bioc-actions/setup-bioc@v1
+        with:
+          bioc-version: release
+
       - name: Cache conda
         uses: actions/cache@v3
         env:
@@ -92,7 +97,7 @@ jobs:
             hashFiles('environment.yml') }}
 
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-activate-base: true
           auto-update-conda: true
@@ -133,11 +138,6 @@ jobs:
           echo "biocversion=$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT
         shell: bash -l {0}
 
-      - name: Set up R
-        uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ steps.R.outputs.version}}
-
       - name: Cache ubuntu R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'"
         uses: actions/cache@v3
diff --git a/.github/workflows/tests_weekly.yml b/.github/workflows/tests_weekly.yml
index 9a5102368..dd2c4fab3 100644
--- a/.github/workflows/tests_weekly.yml
+++ b/.github/workflows/tests_weekly.yml
@@ -30,9 +30,9 @@ jobs:
           - { python-version: 3.9, os: ubuntu-latest }
           - { python-version: "3.10", os: ubuntu-latest }
           - { python-version: "3.11", os: ubuntu-latest }
-          - { python-version: 3.9, os: macos-latest }
-          - { python-version: "3.10", os: macos-latest }
-          - { python-version: "3.11", os: macos-latest }
+          - { python-version: 3.9, os: macos-13 }
+          - { python-version: "3.10", os: macos-13 }
+          - { python-version: "3.11", os: macos-13 }
           # disabled until it's fixed.
     runs-on: ${{ matrix.config.os }}
     env:
@@ -53,10 +53,15 @@ jobs:
           sudo apt-get update -y && sudo apt-get install -y zlib1g-dev libglpk-dev libgmp3-dev libxml2-dev libicu-dev libhdf5-serial-dev libcurl4-gnutls-dev
 
       - name: Install macOS system dependencies
-        if: matrix.config.os == 'macos-latest'
+        if: matrix.config.os == 'macos-13'
         run: |
           brew install cairo pkg-config autoconf automake libtool
 
+      - name: Setup R and Bioconductor
+        uses: grimbough/bioc-actions/setup-bioc@v1
+        with:
+          bioc-version: release
+
       - name: Cache conda
         uses: actions/cache@v3
         env:
@@ -68,7 +73,7 @@ jobs:
             hashFiles('environment.yml') }}
 
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-activate-base: true
           auto-update-conda: true
@@ -109,11 +114,6 @@ jobs:
           echo "biocversion=$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT
         shell: bash -l {0}
 
-      - name: Set up R
-        uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ steps.R.outputs.version}}
-
       - name: Cache ubuntu R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'"
         uses: actions/cache@v3